version 1.3.6

Dependency Updates

.gitignore

@@ -1,4 +1,6 @@
 */target/**
+# IntelliJ test run side-effects
+dependency-check-core/data/
 # Intellij project files
 *.iml
 *.ipr
@@ -7,8 +9,20 @@
 # Eclipse project files
 .classpath
 .project
+.settings
+maven-eclipse.xml
+.externalToolBuilders
+.pmd
 # Netbeans configuration
 nb-configuration.xml
 /target/
 #maven-shade-plugin generated pom
-dependency-reduced-pom.xml
+dependency-reduced-pom.xml
+#ruby Gemfile, etc. This is a java project, Gemfile is here to check site problem with Jekyll
+Gemfile
+Gemfile.lock
+_site/**
+#unknown as to why these are showing up... but need to be ignored.
+.LCKpom.xml~
+#coverity
+/cov-int/

LICENSE.txt

@@ -1,674 +1,202 @@
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README.md

@@ -1,3 +1,4 @@
+[![Build Status](https://dependency-check.ci.cloudbees.com/buildStatus/icon?job=dependency-check)](https://dependency-check.ci.cloudbees.com/job/dependency-check/)
 Dependency-Check
 ================
 
@@ -9,12 +10,14 @@ Current Releases
 -------------
 ### Jenkins Plugin
 
-For instructions on the use of the Jenkins plugin please see the [Jenkins dependency-check page](http://wiki.jenkins-ci.org/x/CwDgAQ).
+For instructions on the use of the Jenkins plugin please see the [OWASP Dependency-Check Plugin page](https://wiki.jenkins-ci.org/display/JENKINS/OWASP+Dependency-Check+Plugin).
 
 ### Command Line
 
-More detailed instructions can be found on the [dependency-check github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-cli/installation.html).
-The latest CLI can be downloaded from bintray's [dependency-check page](https://bintray.com/jeremy-long/owasp/dependency-check). 
+More detailed instructions can be found on the
+[dependency-check github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-cli/).
+The latest CLI can be downloaded from bintray's
+[dependency-check page](https://bintray.com/jeremy-long/owasp/dependency-check).
 
 On *nix
 ```
@@ -26,10 +29,16 @@ On Windows
 > bin/dependency-check.bat -h
 > bin/dependency-check.bat --app Testing --out . --scan [path to jar files to be scanned]
 ```
+On Mac with [Homebrew](http://brew.sh)
+```
+$ brew update && brew install dependency-check
+$ dependency-check -h
+$ dependency-check --app Testing --out . --scan [path to jar files to be scanned]
+```
 
 ### Maven Plugin
 
-More detailed instructions can be found on the [dependency-check-maven github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-maven/installation.html).
+More detailed instructions can be found on the [dependency-check-maven github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-maven).
 The plugin can be configured using the following:
 
 ```xml
@@ -40,7 +49,6 @@ The plugin can be configured using the following:
             <plugin>
               <groupId>org.owasp</groupId>
               <artifactId>dependency-check-maven</artifactId>
-              <version>1.0.2</version>
               <executions>
                   <execution>
                       <goals>
@@ -59,15 +67,19 @@ The plugin can be configured using the following:
 
 ### Ant Task
 
-For instructions on the use of the Ant Task, please see the [dependency-check-ant github page](http://jeremylong.github.io/DependencyCheck/dependency-check-maven/installation.html).
+For instructions on the use of the Ant Task, please see the [dependency-check-ant github page](http://jeremylong.github.io/DependencyCheck/dependency-check-ant).
 
 Development Usage
 -------------
 The following instructions outline how to compile and use the current snapshot. While every intention is to maintain a stable snapshot it is recommended
 that the release versions listed above be used.
 
-Note, currently the install goal may take a long time to execute the integration tests. However, if this takes more then 30 minutes it is likely that the
-download of data from the NVD is having an issue. This issue is still being researched and a solution should be published soon.
+The repository has some large files due to test resources. The team has tried to cleanup the history as much as possible.
+However, it is recommended that you perform a shallow clone to save yourself time:
+
+```bash
+git clone --depth 1 git@github.com:jeremylong/DependencyCheck.git
+```
 
 On *nix
 ```
@@ -82,7 +94,7 @@ On Windows
 > dependency-check-cli/target/release/bin/dependency-check.bat --app Testing --out . --scan ./src/test/resources
 ```
 
-Then load the resulting 'DependencyCheck-Report.html' into your favourite browser.
+Then load the resulting 'DependencyCheck-Report.html' into your favorite browser.
 
 Mailing List
 ------------
@@ -96,9 +108,9 @@ Archive: [google group](https://groups.google.com/forum/#!forum/dependency-check
 Copyright & License
 -
 
-Dependency-Check is Copyright (c) 2012-2013 Jeremy Long. All Rights Reserved.
+Dependency-Check is Copyright (c) 2012-2016 Jeremy Long. All Rights Reserved.
 
-Permission to modify and redistribute is granted under the terms of the GPLv3 license. See the [LICENSE.txt] [GPLv3] file for the full license.
+Permission to modify and redistribute is granted under the terms of the Apache 2.0 license. See the [LICENSE.txt](https://raw.githubusercontent.com/jeremylong/DependencyCheck/master/LICENSE.txt) file for the full license.
 
 Dependency-Check makes use of several other open source libraries. Please see the [NOTICE.txt] [notices] file for more information.
 
@@ -106,5 +118,4 @@ Dependency-Check makes use of several other open source libraries. Please see th
   [wiki]: https://github.com/jeremylong/DependencyCheck/wiki
   [subscribe]: mailto:dependency-check+subscribe@googlegroups.com
   [post]: mailto:dependency-check@googlegroups.com
-  [GPLv3]: https://github.com/jeremylong/DependencyCheck/blob/master/LICENSE.txt
-  [notices]: https://github.com/jeremylong/DependencyCheck/blob/master/NOTICES.txt
+  [notices]: https://github.com/jeremylong/DependencyCheck/blob/master/NOTICE.txt

dependency-check-ant/LICENSE.txt

@@ -1,674 +1,202 @@
-                    GNU GENERAL PUBLIC LICENSE 
-                       Version 3, 29 June 2007
-
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- Everyone is permitted to copy and distribute verbatim copies
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-
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-
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-your programs, too.
-
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-price.  Our General Public Licenses are designed to make sure that you
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-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
-free programs, and that you know you can do these things.
-
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+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

dependency-check-ant/NOTICE.txt

@@ -1,9 +1,6 @@
------------------------------
----begin dependency-check----
------------------------------
-dependency-check
+OWASP dependency-check
 
-Copyright (c) 2012-2013 Jeremy Long. All Rights Reserved.
+Copyright (c) 2012-2015 Jeremy Long. All Rights Reserved.
 
 The licenses for the software listed below can be found in the META-INF/licenses/[dependency name].
 
@@ -19,11 +16,3 @@ An original copy of the license agreement can be found at: http://www.h2database
 This product includes data from the Common Weakness Enumeration (CWE): http://cwe.mitre.org/
 
 This product downloads and utilizes data from the National Vulnerability Database hosted by NIST: http://nvd.nist.gov/download.cfm
-
------------------------------
----end dependency-check------
------------------------------
-
-Notices below are from dependent libraries and have been included via maven-shade-plugin.
-
------------------------------

dependency-check-ant/README.md

@@ -6,7 +6,7 @@ performed are a "best effort" and as such, there could be false positives as wel
 vulnerabilities in 3rd party components is a well-known problem and is currently documented in the 2013 OWASP
 Top 10 as [A9 - Using Components with Known Vulnerabilities](https://www.owasp.org/index.php/Top_10_2013-A9-Using_Components_with_Known_Vulnerabilities).
 
-Documentation and links to production binary releases can be found on the [github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-ant/installation.html).
+Documentation and links to production binary releases can be found on the [github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-ant/index.html).
 
 Mailing List
 ------------
@@ -18,8 +18,8 @@ Post: [dependency-check@googlegroups.com](mailto:dependency-check@googlegroups.c
 Copyright & License
 -------------------
 
-Dependency-Check is Copyright (c) 2012-2013 Jeremy Long. All Rights Reserved.
+Dependency-Check is Copyright (c) 2012-2014 Jeremy Long. All Rights Reserved.
 
-Permission to modify and redistribute is granted under the terms of the GPLv3 license. See the [LICENSE.txt](https://github.com/jeremylong/DependencyCheck/dependency-check-ant/blob/master/LICENSE.txt) file for the full license.
+Permission to modify and redistribute is granted under the terms of the Apache 2.0 license. See the [LICENSE.txt](https://raw.githubusercontent.com/jeremylong/DependencyCheck/master/LICENSE.txt) file for the full license.
 
-Dependency-Check-Ant makes use of other open source libraries. Please see the [NOTICE.txt](https://github.com/jeremylong/DependencyCheck/dependency-check-ant/blob/master/NOTICES.txt) file for more information.
+Dependency-Check-Ant makes use of other open source libraries. Please see the [NOTICE.txt](https://raw.githubusercontent.com/jeremylong/DependencyCheck/master/dependency-check-ant/NOTICE.txt) file for more information.

dependency-check-ant/config/checkstyle-checks.xml

@@ -1,223 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE module PUBLIC
-          "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
-          "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
-
-<module name="Checker">
-  <!--
-      If you set the basedir property below, then all reported file
-      names will be relative to the specified directory. See
-      http://checkstyle.sourceforge.net/5.x/config.html#Checker
-
-      <property name="basedir" value="${basedir}"/>
-  -->
-
-  <property name="severity" value="error"/>
-
-  <module name="SuppressionFilter">
-    <property name="file" value="${checkstyle.suppressions.file}"/>
-  </module>
-
-  <module name="JavadocPackage">
-    <property name="allowLegacy" value="false"/>
-  </module>
-
-  <module name="Translation">
-    <property name="severity" value="warning"/>
-  </module>
-
-  <module name="FileTabCharacter">
-    <property name="eachLine" value="false"/>
-  </module>
-
-  <module name="FileLength">
-    <property name="fileExtensions" value="java"/>
-  </module>
-
-  <module name="NewlineAtEndOfFile">
-  <property name="fileExtensions" value="java"/>
-  <property name="lineSeparator" value="lf"/>
-  </module>
-
-  <module name="RegexpHeader">
-    <property name="headerFile" value="${checkstyle.header.file}"/>
-    <property name="fileExtensions" value="java"/>
-    <property name="id" value="header"/>
-  </module>
-
-  <module name="RegexpSingleline">
-    <property name="format" value="\s+$"/>
-    <property name="minimum" value="0"/>
-    <property name="maximum" value="0"/>
-  </module>
-
-  <module name="TreeWalker">
-    <property name="tabWidth" value="4"/>
-
-    <module name="AvoidStarImport"/>
-    <module name="ConstantName"/>
-    <module name="EmptyBlock"/>
-    <module name="EmptyForIteratorPad"/>
-    <module name="EqualsHashCode"/>
-    <module name="OneStatementPerLine"/>
-
-    <!-- module name="IllegalCatch"/ -->
-    <!--module name="ImportControl">
-      <property name="file" value="${checkstyle.importcontrol.file}"/>
-    </module-->
-    <module name="IllegalImport"/>
-    <module name="IllegalInstantiation"/>
-    <module name="IllegalThrows"/>
-    <module name="InnerAssignment"/>
-    <module name="JavadocType">
-      <property name="authorFormat" value="\S"/>
-    </module>
-    <module name="JavadocMethod">
-      <property name="allowUndeclaredRTE" value="true"/>
-      <property name="allowThrowsTagsForSubclasses" value="true"/>
-      <property name="allowMissingPropertyJavadoc" value="true"/>
-    </module>
-    <module name="JavadocVariable"/>
-    <module name="JavadocStyle">
-      <property name="scope" value="public"/>
-    </module>
-
-    <module name="LeftCurly">
-      <property name="option" value="eol"/>
-      <property name="tokens" value="CLASS_DEF"/>
-      <property name="tokens" value="CTOR_DEF"/>
-      <property name="tokens" value="INTERFACE_DEF"/>
-      <property name="tokens" value="METHOD_DEF"/>
-      <property name="tokens" value="LITERAL_CATCH"/>
-      <property name="tokens" value="LITERAL_DO"/>
-      <property name="tokens" value="LITERAL_ELSE"/>
-      <property name="tokens" value="LITERAL_FINALLY"/>
-      <property name="tokens" value="LITERAL_FOR"/>
-      <property name="tokens" value="LITERAL_IF"/>
-      <property name="tokens" value="LITERAL_SWITCH"/>
-      <property name="tokens" value="LITERAL_SYNCHRONIZED"/>
-      <property name="tokens" value="LITERAL_TRY"/>
-      <property name="tokens" value="LITERAL_WHILE"/>
-    </module>
-
-    <module name="OuterTypeNumber"/>
-    <module name="LineLength">
-      <property name="ignorePattern" value="^ *\* *[^ ]+$"/>
-    <property name="max" value="150"/>
-    </module>
-
-    <module name="MethodCount">
-      <property name="maxTotal" value="40"/>
-    </module>
-
-    <module name="LocalFinalVariableName"/>
-    <module name="LocalVariableName"/>
-    <module name="MemberName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="MethodLength">
-        <property name="max" value="160"/>
-        <property name="countEmpty" value="false"/>
-    </module>
-    <module name="MethodName"/>
-    <module name="MethodParamPad"/>
-    <module name="ModifierOrder"/>
-    <module name="NeedBraces"/>
-    <module name="NoWhitespaceAfter">
-      <property name="tokens" value="ARRAY_INIT"/>
-      <property name="tokens" value="BNOT"/>
-      <property name="tokens" value="DEC"/>
-      <property name="tokens" value="DOT"/>
-      <property name="tokens" value="INC"/>
-      <property name="tokens" value="LNOT"/>
-      <property name="tokens" value="UNARY_MINUS"/>
-      <property name="tokens" value="UNARY_PLUS"/>
-    </module>
-
-    <module name="NoWhitespaceBefore"/>
-    <module name="NoWhitespaceBefore">
-      <property name="tokens" value="DOT"/>
-      <property name="allowLineBreaks" value="true"/>
-    </module>
-
-    <module name="OperatorWrap"/>
-    <module name="OperatorWrap">
-      <property name="tokens" value="ASSIGN"/>
-      <property name="tokens" value="DIV_ASSIGN"/>
-      <property name="tokens" value="PLUS_ASSIGN"/>
-      <property name="tokens" value="MINUS_ASSIGN"/>
-      <property name="tokens" value="STAR_ASSIGN"/>
-      <property name="tokens" value="MOD_ASSIGN"/>
-      <property name="tokens" value="SR_ASSIGN"/>
-      <property name="tokens" value="BSR_ASSIGN"/>
-      <property name="tokens" value="SL_ASSIGN"/>
-      <property name="tokens" value="BXOR_ASSIGN"/>
-      <property name="tokens" value="BOR_ASSIGN"/>
-      <property name="tokens" value="BAND_ASSIGN"/>
-      <property name="option" value="eol"/>
-    </module>
-    <module name="PackageName"/>
-    <module name="ParameterName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="ParameterNumber">
-      <property name="id" value="paramNum"/>
-    </module>
-    <module name="ParenPad"/>
-    <module name="TypecastParenPad"/>
-    <module name="RedundantImport"/>
-    <module name="RedundantModifier"/>
-    <module name="RightCurly">
-      <property name="option" value="same"/>
-    </module>
-    <module name="SimplifyBooleanExpression"/>
-    <module name="SimplifyBooleanReturn"/>
-    <module name="StaticVariableName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="TypeName"/>
-    <module name="UnusedImports"/>
-    <module name="UpperEll"/>
-    <module name="VisibilityModifier"/>
-    <module name="WhitespaceAfter"/>
-    <module name="WhitespaceAround"/>
-    <module name="GenericWhitespace"/>
-    <module name="FinalClass"/>
-    <module name="MissingSwitchDefault"/>
-    <!--module name="MagicNumber"/-->
-    <!--module name="Indentation">
-      <property name="basicOffset" value="4"/>
-      <property name="braceAdjustment" value="0"/>
-      <property name="caseIndent" value="0"/>
-    </module-->
-    <module name="ArrayTrailingComma"/>
-    <module name="FinalLocalVariable"/>
-    <module name="EqualsAvoidNull"/>
-    <module name="ParameterAssignment"/>
-
-    <!-- Generates quite a few errors -->
-    <module name="CyclomaticComplexity">
-      <property name="severity" value="ignore"/>
-    </module>
-
-    <module name="NestedForDepth">
-      <property name="max" value="2"/>
-    </module>
-    <module name="NestedIfDepth">
-      <property name="max" value="4"/>
-    </module>
-    <module name="NestedTryDepth">
-        <property name="max" value="2"/>
-    </module>
-    <!--module name="ExplicitInitialization"/-->
-    <module name="AnnotationUseStyle"/>
-    <module name="MissingDeprecated"/>
-    <module name="MissingOverride">
-      <property name="javaFiveCompatibility" value="true"/>
-    </module>
-    <module name="PackageAnnotation"/>
-    <module name="SuppressWarnings"/>
-    <module name="OuterTypeFilename"/>
-    <module name="HideUtilityClassConstructor"/>
-  </module>
-</module>

dependency-check-ant/config/checkstyle-header.txt

@@ -1,19 +0,0 @@
-^/\*\s*$
-^ \* This file is part of dependency-check-ant\.\s*$
-^ \*\s*$
-^ \* Dependency-check-ant is free software\: you can redistribute it and/or modify it\s*$
-^ \* under the terms of the GNU General Public License as published by the Free\s*$
-^ \* Software Foundation, either version 3 of the License, or \(at your option\) any\s*$
-^ \* later version\.
-^ \*\s*$
-^ \* Dependency-check-ant is distributed in the hope that it will be useful, but\s*$
-^ \* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or\s*$
-^ \* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more\s*$
-^ \* details\.\s*$
-^ \*\s*$
-^ \* You should have received a copy of the GNU General Public License along with\s*$
-^ \* dependency-check-ant\. If not, see http://www.gnu.org/licenses/\.\s*$
-^ \*\s*$
-^ \* Copyright \(c\) 2013 (Jeremy Long|Steve Springett)\. All Rights Reserved\.\s*$
-^ \*/\s*$
-^package

dependency-check-ant/config/checkstyle-suppressions.xml

@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-
-<!DOCTYPE suppressions PUBLIC
-     "-//Puppy Crawl//DTD Suppressions 1.0//EN"
-     "http://www.puppycrawl.com/dtds/suppressions_1_0.dtd">
-
-<suppressions>
-    <suppress checks=".*" files=".*[\\/]package-info\.java" />
-</suppressions>

dependency-check-ant/pom.xml

@@ -1,35 +1,33 @@
 <!--
 This file is part of dependency-check-ant.
 
-Dependency-check-ant is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-Dependency-check is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-You should have received a copy of the GNU General Public License
-along with dependency-check-ant.  If not, see <http://www.gnu.org/licenses />.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
 Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
 -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.0.5</version>
+        <version>1.3.6</version>
     </parent>
 
     <artifactId>dependency-check-ant</artifactId>
     <packaging>jar</packaging>
 
     <name>Dependency-Check Ant Task</name>
-    <description>Dependency-check is a utility that attempts to detect publicly disclosed vulnerabilities contained within project dependencies. It does this by determining if there is a Common Platform Enumeration (CPE) identifier for a given dependency. If found, it will generate a report linking to the associated CVE entries.</description>
+    <description>dependency-check-ant is an Ant Task that uses dependency-check-core to detect publicly disclosed vulnerabilities associated with the project's dependencies. The task will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.</description>
     <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
     <distributionManagement>
         <site>
@@ -70,7 +68,6 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-resources-plugin</artifactId>
-                <version>2.6</version>
                 <configuration>
                     <escapeWindowsPaths>false</escapeWindowsPaths>
                 </configuration>
@@ -195,50 +192,40 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-shade-plugin</artifactId>
-                <version>2.1</version>
+                <artifactId>maven-jar-plugin</artifactId>
                 <configuration>
-                    <transformers>
-                        <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
-                        <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
-                            <resource>META-INF/NOTICE.txt</resource>
-                        </transformer>
-                        <transformer implementation="org.apache.maven.plugins.shade.resource.DontIncludeResourceTransformer">
-                            <resource>META-INF/NOTICE</resource>
-                        </transformer>
-                        <transformer implementation="org.apache.maven.plugins.shade.resource.DontIncludeResourceTransformer">
-                            <resource>META-INF/LICENSE</resource>
-                        </transformer>
-                    </transformers>
+                    <archive>
+                        <manifest>
+                            <addClasspath>true</addClasspath>
+                            <classpathPrefix>lib/</classpathPrefix>
+                        </manifest>
+                    </archive>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <configuration>
+                    <attach>false</attach> <!-- don't install/deploy this archive -->
                 </configuration>
                 <executions>
                     <execution>
+                        <id>create-distribution</id>
                         <phase>package</phase>
                         <goals>
-                            <goal>shade</goal>
+                            <goal>single</goal>
                         </goals>
+                        <configuration>
+                            <descriptors>
+                                <descriptor>src/main/assembly/release.xml</descriptor>
+                            </descriptors>
+                        </configuration>
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <version>2.4</version>
-                <configuration>
-                    <archive>
-                        <manifest>
-                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
-                        </manifest>
-                    </archive>
-                    <excludes>
-                        <exclude>**/checkstyle*</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>cobertura-maven-plugin</artifactId>
-                <version>2.5.2</version>
                 <configuration>
                     <check>
                         <branchRate>85</branchRate>
@@ -268,14 +255,9 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>2.14</version>
                 <configuration>
+                    <argLine>-Dfile.encoding=UTF-8</argLine>
                     <systemProperties>
-                        <property>
-                            <name>net.sourceforge.cobertura.datafile</name>
-                            <value>${project.build.directory}/cobertura/cobertura.ser</value>
-                            <workingDirectory>target</workingDirectory>
-                        </property>
                         <property>
                             <name>data.directory</name>
                             <value>${project.build.directory}/dependency-check-data</value>
@@ -283,154 +265,55 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
                     </systemProperties>
                 </configuration>
             </plugin>
+        </plugins>
+    </build>
+    <reporting>
+        <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <version>2.3.2</version>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                <version>${reporting.checkstyle-plugin.version}</version>
                 <configuration>
-                    <showDeprecation>false</showDeprecation>
+                    <enableRulesSummary>false</enableRulesSummary>
+                    <enableFilesSummary>false</enableFilesSummary>
+                    <configLocation>${basedir}/../src/main/config/checkstyle-checks.xml</configLocation>
+                    <headerLocation>${basedir}/../src/main/config/checkstyle-header.txt</headerLocation>
+                    <suppressionsLocation>${basedir}/../src/main/config/checkstyle-suppressions.xml</suppressionsLocation>
+                    <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
                 </configuration>
             </plugin>
-
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-site-plugin</artifactId>
-                <version>3.3</version>
-                <dependencies>
-                    <dependency>
-                        <groupId>org.apache.maven.doxia</groupId>
-                        <artifactId>doxia-module-markdown</artifactId>
-                        <version>1.4</version>
-                    </dependency>
-                </dependencies>
+                <artifactId>maven-pmd-plugin</artifactId>
+                <version>${reporting.pmd-plugin.version}</version>
                 <configuration>
-                    <skipDeploy>true</skipDeploy>
-                    <reportPlugins>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-project-info-reports-plugin</artifactId>
-                            <version>2.6</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>index</report>
-                                        <report>summary</report>
-                                        <report>license</report>
-                                        <report>help</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-javadoc-plugin</artifactId>
-                            <version>2.9</version>
-                            <reportSets>
-                                <reportSet>
-                                    <id>default</id>
-                                    <reports>
-                                        <report>javadoc</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>versions-maven-plugin</artifactId>
-                            <version>2.0</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>dependency-updates-report</report>
-                                        <report>plugin-updates-report</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-jxr-plugin</artifactId>
-                            <version>2.3</version>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>cobertura-maven-plugin</artifactId>
-                            <version>2.5.2</version>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-surefire-report-plugin</artifactId>
-                            <version>2.14</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>report-only</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>taglist-maven-plugin</artifactId>
-                            <version>2.4</version>
-                            <configuration>
-                                <tagListOptions>
-                                    <tagClasses>
-                                        <tagClass>
-                                            <displayName>Todo Work</displayName>
-                                            <tags>
-                                                <tag>
-                                                    <matchString>todo</matchString>
-                                                    <matchType>ignoreCase</matchType>
-                                                </tag>
-                                                <tag>
-                                                    <matchString>FIXME</matchString>
-                                                    <matchType>exact</matchType>
-                                                </tag>
-                                            </tags>
-                                        </tagClass>
-                                    </tagClasses>
-                                </tagListOptions>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-checkstyle-plugin</artifactId>
-                            <version>2.10</version>
-                            <configuration>
-                                <enableRulesSummary>false</enableRulesSummary>
-                                <configLocation>${basedir}/config/checkstyle-checks.xml</configLocation>
-                                <headerLocation>${basedir}/config/checkstyle-header.txt</headerLocation>
-                                <suppressionsLocation>${basedir}/config/checkstyle-suppressions.xml</suppressionsLocation>
-                                <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-pmd-plugin</artifactId>
-                            <version>3.0.1</version>
-                            <configuration>
-                                <targetJdk>1.6</targetJdk>
-                                <linkXref>true</linkXref>
-                                <sourceEncoding>utf-8</sourceEncoding>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>findbugs-maven-plugin</artifactId>
-                            <version>2.5.2</version>
-                        </plugin>
-                    </reportPlugins>
+                    <targetJdk>1.6</targetJdk>
+                    <linkXref>true</linkXref>
+                    <sourceEncoding>utf-8</sourceEncoding>
+                    <excludes>
+                        <exclude>**/generated/*.java</exclude>
+                    </excludes>
+                    <rulesets>
+                        <ruleset>../src/main/config/dcrules.xml</ruleset>
+                        <ruleset>/rulesets/java/basic.xml</ruleset>
+                        <ruleset>/rulesets/java/imports.xml</ruleset>
+                        <ruleset>/rulesets/java/unusedcode.xml</ruleset>
+                    </rulesets>
                 </configuration>
             </plugin>
         </plugins>
-    </build>
+    </reporting>
     <dependencies>
         <dependency>
             <groupId>org.owasp</groupId>
             <artifactId>dependency-check-core</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.owasp</groupId>
             <artifactId>dependency-check-core</artifactId>
@@ -441,12 +324,11 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
         <dependency>
             <groupId>org.apache.ant</groupId>
             <artifactId>ant</artifactId>
-            <version>1.9.1</version>
+            <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.ant</groupId>
             <artifactId>ant-testutil</artifactId>
-            <version>1.9.1</version>
             <scope>test</scope>
         </dependency>
     </dependencies>

dependency-check-ant/src/main/assembly/release.xml

@@ -12,18 +12,25 @@
         <format>zip</format>
     </formats>
     <includeBaseDirectory>false</includeBaseDirectory>
-    <fileSets>
+    <!--fileSets>
         <fileSet>
-            <outputDirectory>/</outputDirectory>
+            <outputDirectory>dependency-check</outputDirectory>
             <directory>${project.build.directory}</directory>
             <includes>
                 <include>dependency-check*.jar</include>
             </includes>
         </fileSet>
-    </fileSets>
+    </fileSets-->
+    <files>
+        <file>
+            <source>${project.build.directory}/${project.artifactId}-${project.version}.jar</source>
+            <outputDirectory>dependency-check-ant</outputDirectory>
+            <destName>dependency-check-ant.jar</destName>
+        </file>
+    </files>
     <dependencySets>
         <dependencySet>
-            <outputDirectory>/lib</outputDirectory>
+            <outputDirectory>dependency-check-ant/lib</outputDirectory>
             <scope>runtime</scope>
         </dependencySet>
     </dependencySets>

dependency-check-ant/src/main/java/org/owasp/dependencycheck/ant/logging/AntLoggerAdapter.java

@@ -0,0 +1,273 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 The OWASP Foundation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.ant.logging;
+
+import org.apache.tools.ant.Project;
+import org.apache.tools.ant.Task;
+import org.slf4j.helpers.FormattingTuple;
+import org.slf4j.helpers.MarkerIgnoringBase;
+import org.slf4j.helpers.MessageFormatter;
+
+/**
+ * An instance of {@link org.slf4j.Logger} which simply calls the log method on the delegate Ant task.
+ *
+ * @author colezlaw
+ */
+public class AntLoggerAdapter extends MarkerIgnoringBase {
+
+    /**
+     * A reference to the Ant task used for logging.
+     */
+    private Task task;
+
+    /**
+     * Constructs an Ant Logger Adapter.
+     *
+     * @param task the Ant Task to use for logging
+     */
+    public AntLoggerAdapter(Task task) {
+        super();
+        this.task = task;
+    }
+
+    /**
+     * Sets the current Ant task to use for logging.
+     *
+     * @param task the Ant task to use for logging
+     */
+    public void setTask(Task task) {
+        this.task = task;
+    }
+
+    @Override
+    public boolean isTraceEnabled() {
+        // Might be a more efficient way to do this, but Ant doesn't enable or disable
+        // various levels globally - it just fires things at registered Listeners.
+        return true;
+    }
+
+    @Override
+    public void trace(String msg) {
+        if (task != null) {
+            task.log(msg, Project.MSG_VERBOSE);
+        }
+    }
+
+    @Override
+    public void trace(String format, Object arg) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg);
+            task.log(tp.getMessage(), Project.MSG_VERBOSE);
+        }
+    }
+
+    @Override
+    public void trace(String format, Object arg1, Object arg2) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg1, arg2);
+            task.log(tp.getMessage(), Project.MSG_VERBOSE);
+        }
+    }
+
+    @Override
+    public void trace(String format, Object... arguments) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arguments);
+            task.log(tp.getMessage(), Project.MSG_VERBOSE);
+        }
+    }
+
+    @Override
+    public void trace(String msg, Throwable t) {
+        if (task != null) {
+            task.log(msg, t, Project.MSG_VERBOSE);
+        }
+    }
+
+    @Override
+    public boolean isDebugEnabled() {
+        return true;
+    }
+
+    @Override
+    public void debug(String msg) {
+        if (task != null) {
+            task.log(msg, Project.MSG_DEBUG);
+        }
+    }
+
+    @Override
+    public void debug(String format, Object arg) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg);
+            task.log(tp.getMessage(), Project.MSG_DEBUG);
+        }
+    }
+
+    @Override
+    public void debug(String format, Object arg1, Object arg2) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg1, arg2);
+            task.log(tp.getMessage(), Project.MSG_DEBUG);
+        }
+    }
+
+    @Override
+    public void debug(String format, Object... arguments) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arguments);
+            task.log(tp.getMessage(), Project.MSG_DEBUG);
+        }
+    }
+
+    @Override
+    public void debug(String msg, Throwable t) {
+        if (task != null) {
+            task.log(msg, t, Project.MSG_DEBUG);
+        }
+    }
+
+    @Override
+    public boolean isInfoEnabled() {
+        return true;
+    }
+
+    @Override
+    public void info(String msg) {
+        if (task != null) {
+            task.log(msg, Project.MSG_INFO);
+        }
+    }
+
+    @Override
+    public void info(String format, Object arg) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg);
+            task.log(tp.getMessage(), Project.MSG_INFO);
+        }
+    }
+
+    @Override
+    public void info(String format, Object arg1, Object arg2) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg1, arg2);
+            task.log(tp.getMessage(), Project.MSG_INFO);
+        }
+    }
+
+    @Override
+    public void info(String format, Object... arguments) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arguments);
+            task.log(tp.getMessage(), Project.MSG_INFO);
+        }
+    }
+
+    @Override
+    public void info(String msg, Throwable t) {
+        if (task != null) {
+            task.log(msg, t, Project.MSG_INFO);
+        }
+    }
+
+    @Override
+    public boolean isWarnEnabled() {
+        return true;
+    }
+
+    @Override
+    public void warn(String msg) {
+        if (task != null) {
+            task.log(msg, Project.MSG_WARN);
+        }
+    }
+
+    @Override
+    public void warn(String format, Object arg) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg);
+            task.log(tp.getMessage(), Project.MSG_WARN);
+        }
+    }
+
+    @Override
+    public void warn(String format, Object... arguments) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arguments);
+            task.log(tp.getMessage(), Project.MSG_WARN);
+        }
+    }
+
+    @Override
+    public void warn(String format, Object arg1, Object arg2) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg1, arg2);
+            task.log(tp.getMessage(), Project.MSG_WARN);
+        }
+    }
+
+    @Override
+    public void warn(String msg, Throwable t) {
+        if (task != null) {
+            task.log(msg, t, Project.MSG_WARN);
+        }
+    }
+
+    @Override
+    public boolean isErrorEnabled() {
+        return true;
+    }
+
+    @Override
+    public void error(String msg) {
+        if (task != null) {
+            task.log(msg, Project.MSG_ERR);
+        }
+    }
+
+    @Override
+    public void error(String format, Object arg) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg);
+            task.log(tp.getMessage(), Project.MSG_ERR);
+        }
+    }
+
+    @Override
+    public void error(String format, Object arg1, Object arg2) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arg1, arg2);
+            task.log(tp.getMessage(), Project.MSG_ERR);
+        }
+    }
+
+    @Override
+    public void error(String format, Object... arguments) {
+        if (task != null) {
+            final FormattingTuple tp = MessageFormatter.format(format, arguments);
+            task.log(tp.getMessage(), Project.MSG_ERR);
+        }
+    }
+
+    @Override
+    public void error(String msg, Throwable t) {
+        if (task != null) {
+            task.log(msg, t, Project.MSG_ERR);
+        }
+    }
+}

dependency-check-ant/src/main/java/org/owasp/dependencycheck/ant/logging/AntLoggerFactory.java

@@ -0,0 +1,56 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 The OWASP Foundation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.ant.logging;
+
+import org.apache.tools.ant.Task;
+import org.slf4j.ILoggerFactory;
+import org.slf4j.Logger;
+
+/**
+ * An implementation of {@link org.slf4j.ILoggerFactory} which always returns {@link AntLoggerAdapter} instances.
+ *
+ * @author colezlaw
+ */
+public class AntLoggerFactory implements ILoggerFactory {
+
+    /**
+     * A reference to the Ant logger Adapter.
+     */
+    private final AntLoggerAdapter antLoggerAdapter;
+
+    /**
+     * Constructs a new Ant Logger Factory.
+     *
+     * @param task the Ant task to use for logging
+     */
+    public AntLoggerFactory(Task task) {
+        super();
+        this.antLoggerAdapter = new AntLoggerAdapter(task);
+    }
+
+    /**
+     * Returns the Ant logger adapter.
+     *
+     * @param name ignored in this implementation
+     * @return the Ant logger adapter
+     */
+    @Override
+    public Logger getLogger(String name) {
+        return antLoggerAdapter;
+    }
+}

dependency-check-ant/src/main/java/org/owasp/dependencycheck/ant/logging/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * This package includes the Ant task definitions.
+ */
+package org.owasp.dependencycheck.ant.logging;

dependency-check-ant/src/main/java/org/owasp/dependencycheck/taskdefs/Check.java

@@ -0,0 +1,966 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.taskdefs;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import org.apache.tools.ant.BuildException;
+import org.apache.tools.ant.Project;
+import org.apache.tools.ant.types.EnumeratedAttribute;
+import org.apache.tools.ant.types.Reference;
+import org.apache.tools.ant.types.Resource;
+import org.apache.tools.ant.types.ResourceCollection;
+import org.apache.tools.ant.types.resources.FileProvider;
+import org.apache.tools.ant.types.resources.Resources;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Identifier;
+import org.owasp.dependencycheck.dependency.Vulnerability;
+import org.owasp.dependencycheck.reporting.ReportGenerator;
+import org.owasp.dependencycheck.reporting.ReportGenerator.Format;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.impl.StaticLoggerBinder;
+
+/**
+ * An Ant task definition to execute dependency-check during an Ant build.
+ *
+ * @author Jeremy Long
+ */
+public class Check extends Update {
+
+    /**
+     * System specific new line character.
+     */
+    private static final String NEW_LINE = System.getProperty("line.separator", "\n").intern();
+
+    /**
+     * Construct a new DependencyCheckTask.
+     */
+    public Check() {
+        super();
+        // Call this before Dependency Check Core starts logging anything - this way, all SLF4J messages from
+        // core end up coming through this tasks logger
+        StaticLoggerBinder.getSingleton().setTask(this);
+    }
+    //The following code was copied Apache Ant PathConvert
+    //BEGIN COPY from org.apache.tools.ant.taskdefs.PathConvert
+    /**
+     * Path to be converted
+     */
+    private Resources path = null;
+    /**
+     * Reference to path/fileset to convert
+     */
+    private Reference refid = null;
+
+    /**
+     * Add an arbitrary ResourceCollection.
+     *
+     * @param rc the ResourceCollection to add.
+     * @since Ant 1.7
+     */
+    public void add(ResourceCollection rc) {
+        if (isReference()) {
+            throw new BuildException("Nested elements are not allowed when using the refid attribute.");
+        }
+        getPath().add(rc);
+    }
+
+    /**
+     * Returns the path. If the path has not been initialized yet, this class is synchronized, and will instantiate the path
+     * object.
+     *
+     * @return the path
+     */
+    private synchronized Resources getPath() {
+        if (path == null) {
+            path = new Resources(getProject());
+            path.setCache(true);
+        }
+        return path;
+    }
+
+    /**
+     * Learn whether the refid attribute of this element been set.
+     *
+     * @return true if refid is valid.
+     */
+    public boolean isReference() {
+        return refid != null;
+    }
+
+    /**
+     * Add a reference to a Path, FileSet, DirSet, or FileList defined elsewhere.
+     *
+     * @param r the reference to a path, fileset, dirset or filelist.
+     */
+    public void setRefid(Reference r) {
+        if (path != null) {
+            throw new BuildException("Nested elements are not allowed when using the refid attribute.");
+        }
+        refid = r;
+    }
+
+    /**
+     * If this is a reference, this method will add the referenced resource collection to the collection of paths.
+     *
+     * @throws BuildException if the reference is not to a resource collection
+     */
+    private void dealWithReferences() throws BuildException {
+        if (isReference()) {
+            final Object o = refid.getReferencedObject(getProject());
+            if (!(o instanceof ResourceCollection)) {
+                throw new BuildException("refid '" + refid.getRefId()
+                        + "' does not refer to a resource collection.");
+            }
+            getPath().add((ResourceCollection) o);
+        }
+    }
+    // END COPY from org.apache.tools.ant.taskdefs
+    /**
+     * The application name for the report.
+     *
+     * @deprecated use projectName instead.
+     */
+    @Deprecated
+    private String applicationName = null;
+
+    /**
+     * Get the value of applicationName.
+     *
+     * @return the value of applicationName
+     *
+     * @deprecated use projectName instead.
+     */
+    @Deprecated
+    public String getApplicationName() {
+        return applicationName;
+    }
+
+    /**
+     * Set the value of applicationName.
+     *
+     * @param applicationName new value of applicationName
+     * @deprecated use projectName instead.
+     */
+    @Deprecated
+    public void setApplicationName(String applicationName) {
+        this.applicationName = applicationName;
+    }
+    /**
+     * The name of the project being analyzed.
+     */
+    private String projectName = "dependency-check";
+
+    /**
+     * Get the value of projectName.
+     *
+     * @return the value of projectName
+     */
+    public String getProjectName() {
+        if (applicationName != null) {
+            log("Configuration 'applicationName' has been deprecated, please use 'projectName' instead", Project.MSG_WARN);
+            if ("dependency-check".equals(projectName)) {
+                projectName = applicationName;
+            }
+        }
+        return projectName;
+    }
+
+    /**
+     * Set the value of projectName.
+     *
+     * @param projectName new value of projectName
+     */
+    public void setProjectName(String projectName) {
+        this.projectName = projectName;
+    }
+
+    /**
+     * Specifies the destination directory for the generated Dependency-Check report.
+     */
+    private String reportOutputDirectory = ".";
+
+    /**
+     * Get the value of reportOutputDirectory.
+     *
+     * @return the value of reportOutputDirectory
+     */
+    public String getReportOutputDirectory() {
+        return reportOutputDirectory;
+    }
+
+    /**
+     * Set the value of reportOutputDirectory.
+     *
+     * @param reportOutputDirectory new value of reportOutputDirectory
+     */
+    public void setReportOutputDirectory(String reportOutputDirectory) {
+        this.reportOutputDirectory = reportOutputDirectory;
+    }
+    /**
+     * Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11 which
+     * means since the CVSS scores are 0-10, by default the build will never fail and the CVSS score is set to 11. The valid range
+     * for the fail build on CVSS is 0 to 11, where anything above 10 will not cause the build to fail.
+     */
+    private float failBuildOnCVSS = 11;
+
+    /**
+     * Get the value of failBuildOnCVSS.
+     *
+     * @return the value of failBuildOnCVSS
+     */
+    public float getFailBuildOnCVSS() {
+        return failBuildOnCVSS;
+    }
+
+    /**
+     * Set the value of failBuildOnCVSS.
+     *
+     * @param failBuildOnCVSS new value of failBuildOnCVSS
+     */
+    public void setFailBuildOnCVSS(float failBuildOnCVSS) {
+        this.failBuildOnCVSS = failBuildOnCVSS;
+    }
+    /**
+     * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to false. Default
+     * is true.
+     */
+    private Boolean autoUpdate;
+
+    /**
+     * Get the value of autoUpdate.
+     *
+     * @return the value of autoUpdate
+     */
+    public Boolean isAutoUpdate() {
+        return autoUpdate;
+    }
+
+    /**
+     * Set the value of autoUpdate.
+     *
+     * @param autoUpdate new value of autoUpdate
+     */
+    public void setAutoUpdate(Boolean autoUpdate) {
+        this.autoUpdate = autoUpdate;
+    }
+    /**
+     * Whether only the update phase should be executed.
+     *
+     * @deprecated Use the update task instead
+     */
+    @Deprecated
+    private boolean updateOnly = false;
+
+    /**
+     * Get the value of updateOnly.
+     *
+     * @return the value of updateOnly
+     * @deprecated Use the update task instead
+     */
+    @Deprecated
+    public boolean isUpdateOnly() {
+        return updateOnly;
+    }
+
+    /**
+     * Set the value of updateOnly.
+     *
+     * @param updateOnly new value of updateOnly
+     * @deprecated Use the update task instead
+     */
+    @Deprecated
+    public void setUpdateOnly(boolean updateOnly) {
+        this.updateOnly = updateOnly;
+    }
+
+    /**
+     * The report format to be generated (HTML, XML, VULN, ALL). Default is HTML.
+     */
+    private String reportFormat = "HTML";
+
+    /**
+     * Get the value of reportFormat.
+     *
+     * @return the value of reportFormat
+     */
+    public String getReportFormat() {
+        return reportFormat;
+    }
+
+    /**
+     * Set the value of reportFormat.
+     *
+     * @param reportFormat new value of reportFormat
+     */
+    public void setReportFormat(ReportFormats reportFormat) {
+        this.reportFormat = reportFormat.getValue();
+    }
+    /**
+     * The path to the suppression file.
+     */
+    private String suppressionFile;
+
+    /**
+     * Get the value of suppressionFile.
+     *
+     * @return the value of suppressionFile
+     */
+    public String getSuppressionFile() {
+        return suppressionFile;
+    }
+
+    /**
+     * Set the value of suppressionFile.
+     *
+     * @param suppressionFile new value of suppressionFile
+     */
+    public void setSuppressionFile(String suppressionFile) {
+        this.suppressionFile = suppressionFile;
+    }
+    /**
+     * flag indicating whether or not to show a summary of findings.
+     */
+    private boolean showSummary = true;
+
+    /**
+     * Get the value of showSummary.
+     *
+     * @return the value of showSummary
+     */
+    public boolean isShowSummary() {
+        return showSummary;
+    }
+
+    /**
+     * Set the value of showSummary.
+     *
+     * @param showSummary new value of showSummary
+     */
+    public void setShowSummary(boolean showSummary) {
+        this.showSummary = showSummary;
+    }
+
+    /**
+     * Whether or not the Jar Analyzer is enabled.
+     */
+    private Boolean jarAnalyzerEnabled;
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public Boolean isJarAnalyzerEnabled() {
+        return jarAnalyzerEnabled;
+    }
+
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param jarAnalyzerEnabled the value of the new setting
+     */
+    public void setJarAnalyzerEnabled(Boolean jarAnalyzerEnabled) {
+        this.jarAnalyzerEnabled = jarAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the Archive Analyzer is enabled.
+     */
+    private Boolean archiveAnalyzerEnabled;
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public Boolean isArchiveAnalyzerEnabled() {
+        return archiveAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the .NET Assembly Analyzer is enabled.
+     */
+    private Boolean assemblyAnalyzerEnabled;
+
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param archiveAnalyzerEnabled the value of the new setting
+     */
+    public void setArchiveAnalyzerEnabled(Boolean archiveAnalyzerEnabled) {
+        this.archiveAnalyzerEnabled = archiveAnalyzerEnabled;
+    }
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public Boolean isAssemblyAnalyzerEnabled() {
+        return assemblyAnalyzerEnabled;
+    }
+
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param assemblyAnalyzerEnabled the value of the new setting
+     */
+    public void setAssemblyAnalyzerEnabled(Boolean assemblyAnalyzerEnabled) {
+        this.assemblyAnalyzerEnabled = assemblyAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the .NET Nuspec Analyzer is enabled.
+     */
+    private Boolean nuspecAnalyzerEnabled;
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public Boolean isNuspecAnalyzerEnabled() {
+        return nuspecAnalyzerEnabled;
+    }
+
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param nuspecAnalyzerEnabled the value of the new setting
+     */
+    public void setNuspecAnalyzerEnabled(Boolean nuspecAnalyzerEnabled) {
+        this.nuspecAnalyzerEnabled = nuspecAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the PHP Composer Analyzer is enabled.
+     */
+    private Boolean composerAnalyzerEnabled;
+
+    /**
+     * Get the value of composerAnalyzerEnabled.
+     *
+     * @return the value of composerAnalyzerEnabled
+     */
+    public Boolean isComposerAnalyzerEnabled() {
+        return composerAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of composerAnalyzerEnabled.
+     *
+     * @param composerAnalyzerEnabled new value of composerAnalyzerEnabled
+     */
+    public void setComposerAnalyzerEnabled(Boolean composerAnalyzerEnabled) {
+        this.composerAnalyzerEnabled = composerAnalyzerEnabled;
+    }
+    /**
+     * Whether the autoconf analyzer should be enabled.
+     */
+    private Boolean autoconfAnalyzerEnabled;
+
+    /**
+     * Get the value of autoconfAnalyzerEnabled.
+     *
+     * @return the value of autoconfAnalyzerEnabled
+     */
+    public Boolean isAutoconfAnalyzerEnabled() {
+        return autoconfAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of autoconfAnalyzerEnabled.
+     *
+     * @param autoconfAnalyzerEnabled new value of autoconfAnalyzerEnabled
+     */
+    public void setAutoconfAnalyzerEnabled(Boolean autoconfAnalyzerEnabled) {
+        this.autoconfAnalyzerEnabled = autoconfAnalyzerEnabled;
+    }
+    /**
+     * Whether the CMake analyzer should be enabled.
+     */
+    private Boolean cmakeAnalyzerEnabled;
+
+    /**
+     * Get the value of cmakeAnalyzerEnabled.
+     *
+     * @return the value of cmakeAnalyzerEnabled
+     */
+    public Boolean isCMakeAnalyzerEnabled() {
+        return cmakeAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of cmakeAnalyzerEnabled.
+     *
+     * @param cmakeAnalyzerEnabled new value of cmakeAnalyzerEnabled
+     */
+    public void setCMakeAnalyzerEnabled(Boolean cmakeAnalyzerEnabled) {
+        this.cmakeAnalyzerEnabled = cmakeAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the openssl analyzer is enabled.
+     */
+    private Boolean opensslAnalyzerEnabled;
+
+    /**
+     * Get the value of opensslAnalyzerEnabled.
+     *
+     * @return the value of opensslAnalyzerEnabled
+     */
+    public Boolean isOpensslAnalyzerEnabled() {
+        return opensslAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of opensslAnalyzerEnabled.
+     *
+     * @param opensslAnalyzerEnabled new value of opensslAnalyzerEnabled
+     */
+    public void setOpensslAnalyzerEnabled(Boolean opensslAnalyzerEnabled) {
+        this.opensslAnalyzerEnabled = opensslAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the Node.js Analyzer is enabled.
+     */
+    private Boolean nodeAnalyzerEnabled;
+
+    /**
+     * Get the value of nodeAnalyzerEnabled.
+     *
+     * @return the value of nodeAnalyzerEnabled
+     */
+    public Boolean isNodeAnalyzerEnabled() {
+        return nodeAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of nodeAnalyzerEnabled.
+     *
+     * @param nodeAnalyzerEnabled new value of nodeAnalyzerEnabled
+     */
+    public void setNodeAnalyzerEnabled(Boolean nodeAnalyzerEnabled) {
+        this.nodeAnalyzerEnabled = nodeAnalyzerEnabled;
+    }
+    /**
+     * Whether the ruby gemspec analyzer should be enabled.
+     */
+    private Boolean rubygemsAnalyzerEnabled;
+
+    /**
+     * Get the value of rubygemsAnalyzerEnabled.
+     *
+     * @return the value of rubygemsAnalyzerEnabled
+     */
+    public Boolean isRubygemsAnalyzerEnabled() {
+        return rubygemsAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of rubygemsAnalyzerEnabled.
+     *
+     * @param rubygemsAnalyzerEnabled new value of rubygemsAnalyzerEnabled
+     */
+    public void setRubygemsAnalyzerEnabled(Boolean rubygemsAnalyzerEnabled) {
+        this.rubygemsAnalyzerEnabled = rubygemsAnalyzerEnabled;
+    }
+    /**
+     * Whether the python package analyzer should be enabled.
+     */
+    private Boolean pyPackageAnalyzerEnabled;
+
+    /**
+     * Get the value of pyPackageAnalyzerEnabled.
+     *
+     * @return the value of pyPackageAnalyzerEnabled
+     */
+    public Boolean isPyPackageAnalyzerEnabled() {
+        return pyPackageAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of pyPackageAnalyzerEnabled.
+     *
+     * @param pyPackageAnalyzerEnabled new value of pyPackageAnalyzerEnabled
+     */
+    public void setPyPackageAnalyzerEnabled(Boolean pyPackageAnalyzerEnabled) {
+        this.pyPackageAnalyzerEnabled = pyPackageAnalyzerEnabled;
+    }
+
+    /**
+     * Whether the python distribution analyzer should be enabled.
+     */
+    private Boolean pyDistributionAnalyzerEnabled;
+
+    /**
+     * Get the value of pyDistributionAnalyzerEnabled.
+     *
+     * @return the value of pyDistributionAnalyzerEnabled
+     */
+    public Boolean isPyDistributionAnalyzerEnabled() {
+        return pyDistributionAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of pyDistributionAnalyzerEnabled.
+     *
+     * @param pyDistributionAnalyzerEnabled new value of pyDistributionAnalyzerEnabled
+     */
+    public void setPyDistributionAnalyzerEnabled(Boolean pyDistributionAnalyzerEnabled) {
+        this.pyDistributionAnalyzerEnabled = pyDistributionAnalyzerEnabled;
+    }
+
+    /**
+     * Whether or not the central analyzer is enabled.
+     */
+    private Boolean centralAnalyzerEnabled;
+
+    /**
+     * Get the value of centralAnalyzerEnabled.
+     *
+     * @return the value of centralAnalyzerEnabled
+     */
+    public Boolean isCentralAnalyzerEnabled() {
+        return centralAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of centralAnalyzerEnabled.
+     *
+     * @param centralAnalyzerEnabled new value of centralAnalyzerEnabled
+     */
+    public void setCentralAnalyzerEnabled(Boolean centralAnalyzerEnabled) {
+        this.centralAnalyzerEnabled = centralAnalyzerEnabled;
+    }
+
+    /**
+     * Whether or not the nexus analyzer is enabled.
+     */
+    private Boolean nexusAnalyzerEnabled;
+
+    /**
+     * Get the value of nexusAnalyzerEnabled.
+     *
+     * @return the value of nexusAnalyzerEnabled
+     */
+    public Boolean isNexusAnalyzerEnabled() {
+        return nexusAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of nexusAnalyzerEnabled.
+     *
+     * @param nexusAnalyzerEnabled new value of nexusAnalyzerEnabled
+     */
+    public void setNexusAnalyzerEnabled(Boolean nexusAnalyzerEnabled) {
+        this.nexusAnalyzerEnabled = nexusAnalyzerEnabled;
+    }
+
+    /**
+     * The URL of a Nexus server's REST API end point (http://domain/nexus/service/local).
+     */
+    private String nexusUrl;
+
+    /**
+     * Get the value of nexusUrl.
+     *
+     * @return the value of nexusUrl
+     */
+    public String getNexusUrl() {
+        return nexusUrl;
+    }
+
+    /**
+     * Set the value of nexusUrl.
+     *
+     * @param nexusUrl new value of nexusUrl
+     */
+    public void setNexusUrl(String nexusUrl) {
+        this.nexusUrl = nexusUrl;
+    }
+    /**
+     * Whether or not the defined proxy should be used when connecting to Nexus.
+     */
+    private Boolean nexusUsesProxy;
+
+    /**
+     * Get the value of nexusUsesProxy.
+     *
+     * @return the value of nexusUsesProxy
+     */
+    public Boolean isNexusUsesProxy() {
+        return nexusUsesProxy;
+    }
+
+    /**
+     * Set the value of nexusUsesProxy.
+     *
+     * @param nexusUsesProxy new value of nexusUsesProxy
+     */
+    public void setNexusUsesProxy(Boolean nexusUsesProxy) {
+        this.nexusUsesProxy = nexusUsesProxy;
+    }
+
+    /**
+     * Additional ZIP File extensions to add analyze. This should be a comma-separated list of file extensions to treat like ZIP
+     * files.
+     */
+    private String zipExtensions;
+
+    /**
+     * Get the value of zipExtensions.
+     *
+     * @return the value of zipExtensions
+     */
+    public String getZipExtensions() {
+        return zipExtensions;
+    }
+
+    /**
+     * Set the value of zipExtensions.
+     *
+     * @param zipExtensions new value of zipExtensions
+     */
+    public void setZipExtensions(String zipExtensions) {
+        this.zipExtensions = zipExtensions;
+    }
+
+    /**
+     * The path to Mono for .NET assembly analysis on non-windows systems.
+     */
+    private String pathToMono;
+
+    /**
+     * Get the value of pathToMono.
+     *
+     * @return the value of pathToMono
+     */
+    public String getPathToMono() {
+        return pathToMono;
+    }
+
+    /**
+     * Set the value of pathToMono.
+     *
+     * @param pathToMono new value of pathToMono
+     */
+    public void setPathToMono(String pathToMono) {
+        this.pathToMono = pathToMono;
+    }
+
+    @Override
+    public void execute() throws BuildException {
+        dealWithReferences();
+        validateConfiguration();
+        populateSettings();
+        Engine engine = null;
+        try {
+            engine = new Engine(Check.class.getClassLoader());
+            if (isUpdateOnly()) {
+                log("Deprecated 'UpdateOnly' property set; please use the UpdateTask instead", Project.MSG_WARN);
+                engine.doUpdates();
+            } else {
+                try {
+                    for (Resource resource : path) {
+                        final FileProvider provider = resource.as(FileProvider.class);
+                        if (provider != null) {
+                            final File file = provider.getFile();
+                            if (file != null && file.exists()) {
+                                engine.scan(file);
+                            }
+                        }
+                    }
+
+                    engine.analyzeDependencies();
+                    DatabaseProperties prop = null;
+                    CveDB cve = null;
+                    try {
+                        cve = new CveDB();
+                        cve.open();
+                        prop = cve.getDatabaseProperties();
+                    } catch (DatabaseException ex) {
+                        log("Unable to retrieve DB Properties", ex, Project.MSG_DEBUG);
+                    } finally {
+                        if (cve != null) {
+                            cve.close();
+                        }
+                    }
+                    final ReportGenerator reporter = new ReportGenerator(getProjectName(), engine.getDependencies(), engine.getAnalyzers(), prop);
+                    reporter.generateReports(reportOutputDirectory, reportFormat);
+
+                    if (this.failBuildOnCVSS <= 10) {
+                        checkForFailure(engine.getDependencies());
+                    }
+                    if (this.showSummary) {
+                        showSummary(engine.getDependencies());
+                    }
+                } catch (IOException ex) {
+                    log("Unable to generate dependency-check report", ex, Project.MSG_DEBUG);
+                    throw new BuildException("Unable to generate dependency-check report", ex);
+                } catch (Exception ex) {
+                    log("An exception occurred; unable to continue task", ex, Project.MSG_DEBUG);
+                    throw new BuildException("An exception occurred; unable to continue task", ex);
+                }
+            }
+        } catch (DatabaseException ex) {
+            log("Unable to connect to the dependency-check database; analysis has stopped", ex, Project.MSG_ERR);
+        } finally {
+            Settings.cleanup(true);
+            if (engine != null) {
+                engine.cleanup();
+            }
+        }
+    }
+
+    /**
+     * Validate the configuration to ensure the parameters have been properly configured/initialized.
+     *
+     * @throws BuildException if the task was not configured correctly.
+     */
+    private void validateConfiguration() throws BuildException {
+        if (path == null) {
+            throw new BuildException("No project dependencies have been defined to analyze.");
+        }
+        if (failBuildOnCVSS < 0 || failBuildOnCVSS > 11) {
+            throw new BuildException("Invalid configuration, failBuildOnCVSS must be between 0 and 11.");
+        }
+    }
+
+    /**
+     * Takes the properties supplied and updates the dependency-check settings. Additionally, this sets the system properties
+     * required to change the proxy server, port, and connection timeout.
+     *
+     * @throws BuildException thrown when an invalid setting is configured.
+     */
+    @Override
+    protected void populateSettings() throws BuildException {
+        super.populateSettings();
+        Settings.setBooleanIfNotNull(Settings.KEYS.AUTO_UPDATE, autoUpdate);
+        Settings.setStringIfNotEmpty(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_JAR_ENABLED, jarAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED, pyDistributionAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED, pyPackageAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED, rubygemsAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_OPENSSL_ENABLED, opensslAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_CMAKE_ENABLED, cmakeAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_AUTOCONF_ENABLED, autoconfAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED, composerAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED, nodeAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, nuspecAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, centralAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, archiveAnalyzerEnabled);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, assemblyAnalyzerEnabled);
+        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY, nexusUsesProxy);
+        Settings.setStringIfNotEmpty(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
+        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+    }
+
+    /**
+     * Checks to see if a vulnerability has been identified with a CVSS score that is above the threshold set in the
+     * configuration.
+     *
+     * @param dependencies the list of dependency objects
+     * @throws BuildException thrown if a CVSS score is found that is higher then the threshold set
+     */
+    private void checkForFailure(List<Dependency> dependencies) throws BuildException {
+        final StringBuilder ids = new StringBuilder();
+        for (Dependency d : dependencies) {
+            for (Vulnerability v : d.getVulnerabilities()) {
+                if (v.getCvssScore() >= failBuildOnCVSS) {
+                    if (ids.length() == 0) {
+                        ids.append(v.getName());
+                    } else {
+                        ids.append(", ").append(v.getName());
+                    }
+                }
+            }
+        }
+        if (ids.length() > 0) {
+            final String msg = String.format("%n%nDependency-Check Failure:%n"
+                    + "One or more dependencies were identified with vulnerabilities that have a CVSS score greater then '%.1f': %s%n"
+                    + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
+            throw new BuildException(msg);
+        }
+    }
+
+    /**
+     * Generates a warning message listing a summary of dependencies and their associated CPE and CVE entries.
+     *
+     * @param dependencies a list of dependency objects
+     */
+    private void showSummary(List<Dependency> dependencies) {
+        final StringBuilder summary = new StringBuilder();
+        for (Dependency d : dependencies) {
+            boolean firstEntry = true;
+            final StringBuilder ids = new StringBuilder();
+            for (Vulnerability v : d.getVulnerabilities()) {
+                if (firstEntry) {
+                    firstEntry = false;
+                } else {
+                    ids.append(", ");
+                }
+                ids.append(v.getName());
+            }
+            if (ids.length() > 0) {
+                summary.append(d.getFileName()).append(" (");
+                firstEntry = true;
+                for (Identifier id : d.getIdentifiers()) {
+                    if (firstEntry) {
+                        firstEntry = false;
+                    } else {
+                        summary.append(", ");
+                    }
+                    summary.append(id.getValue());
+                }
+                summary.append(") : ").append(ids).append(NEW_LINE);
+            }
+        }
+        if (summary.length() > 0) {
+            final String msg = String.format("%n%n"
+                    + "One or more dependencies were identified with known vulnerabilities:%n%n%s"
+                    + "%n%nSee the dependency-check report for more details.%n%n", summary.toString());
+            log(msg, Project.MSG_WARN);
+        }
+    }
+
+    /**
+     * An enumeration of supported report formats: "ALL", "HTML", "XML", "VULN", etc..
+     */
+    public static class ReportFormats extends EnumeratedAttribute {
+
+        /**
+         * Returns the list of values for the report format.
+         *
+         * @return the list of values for the report format
+         */
+        @Override
+        public String[] getValues() {
+            int i = 0;
+            final Format[] formats = Format.values();
+            final String[] values = new String[formats.length];
+            for (Format format : formats) {
+                values[i++] = format.name();
+            }
+            return values;
+        }
+    }
+}

dependency-check-ant/src/main/java/org/owasp/dependencycheck/taskdefs/DependencyCheckTask.java

@@ -1,571 +0,0 @@
-/*
- * This file is part of dependency-check-ant.
- *
- * Dependency-check-ant is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Dependency-check-ant is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
- *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-ant. If not, see http://www.gnu.org/licenses/.
- *
- * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
- */
-package org.owasp.dependencycheck.taskdefs;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import org.apache.tools.ant.BuildException;
-import org.apache.tools.ant.Task;
-import org.apache.tools.ant.types.EnumeratedAttribute;
-import org.apache.tools.ant.types.Reference;
-import org.apache.tools.ant.types.Resource;
-import org.apache.tools.ant.types.ResourceCollection;
-import org.apache.tools.ant.types.resources.FileProvider;
-import org.apache.tools.ant.types.resources.Resources;
-import org.owasp.dependencycheck.Engine;
-import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.dependency.Vulnerability;
-import org.owasp.dependencycheck.reporting.ReportGenerator;
-import org.owasp.dependencycheck.reporting.ReportGenerator.Format;
-import org.owasp.dependencycheck.utils.LogUtils;
-import org.owasp.dependencycheck.utils.Settings;
-
-/**
- * An Ant task definition to execute dependency-check during an Ant build.
- *
- * @author Jeremy Long (jeremy.long@owasp.org)
- */
-public class DependencyCheckTask extends Task {
-
-    /**
-     * The properties file location.
-     */
-    private static final String PROPERTIES_FILE = "task.properties";
-    /**
-     * Name of the logging properties file.
-     */
-    private static final String LOG_PROPERTIES_FILE = "log.properties";
-
-    /**
-     * Construct a new DependencyCheckTask.
-     */
-    public DependencyCheckTask() {
-        super();
-    }
-    //The following code was copied Apache Ant PathConvert
-    //BEGIN COPY from org.apache.tools.ant.taskdefs.PathConvert
-    /**
-     * Path to be converted
-     */
-    private Resources path = null;
-    /**
-     * Reference to path/fileset to convert
-     */
-    private Reference refid = null;
-
-    /**
-     * Add an arbitrary ResourceCollection.
-     *
-     * @param rc the ResourceCollection to add.
-     * @since Ant 1.7
-     */
-    public void add(ResourceCollection rc) {
-        if (isReference()) {
-            throw new BuildException("Nested elements are not allowed when using the refid attribute.");
-        }
-        getPath().add(rc);
-    }
-
-    /**
-     * Returns the path. If the path has not been initialized yet, this class is
-     * synchronized, and will instantiate the path object.
-     *
-     * @return the path
-     */
-    private synchronized Resources getPath() {
-        if (path == null) {
-            path = new Resources(getProject());
-            path.setCache(true);
-        }
-        return path;
-    }
-
-    /**
-     * Learn whether the refid attribute of this element been set.
-     *
-     * @return true if refid is valid.
-     */
-    public boolean isReference() {
-        return refid != null;
-    }
-
-    /**
-     * Add a reference to a Path, FileSet, DirSet, or FileList defined
-     * elsewhere.
-     *
-     * @param r the reference to a path, fileset, dirset or filelist.
-     */
-    public void setRefid(Reference r) {
-        if (path != null) {
-            throw new BuildException("Nested elements are not allowed when using the refid attribute.");
-        }
-        refid = r;
-    }
-
-    /**
-     * If this is a reference, this method will add the referenced resource
-     * collection to the collection of paths.
-     *
-     * @throws BuildException if the reference is not to a resource collection
-     */
-    private void dealWithReferences() throws BuildException {
-        if (isReference()) {
-            final Object o = refid.getReferencedObject(getProject());
-            if (!(o instanceof ResourceCollection)) {
-                throw new BuildException("refid '" + refid.getRefId()
-                        + "' does not refer to a resource collection.");
-            }
-            getPath().add((ResourceCollection) o);
-        }
-    }
-    // END COPY from org.apache.tools.ant.taskdefs
-    /**
-     * The application name for the report.
-     */
-    private String applicationName = "Dependency-Check";
-
-    /**
-     * Get the value of applicationName.
-     *
-     * @return the value of applicationName
-     */
-    public String getApplicationName() {
-        return applicationName;
-    }
-
-    /**
-     * Set the value of applicationName.
-     *
-     * @param applicationName new value of applicationName
-     */
-    public void setApplicationName(String applicationName) {
-        this.applicationName = applicationName;
-    }
-    /**
-     * The location of the data directory that contains
-     */
-    private String dataDirectory = null;
-
-    /**
-     * Get the value of dataDirectory.
-     *
-     * @return the value of dataDirectory
-     */
-    public String getDataDirectory() {
-        return dataDirectory;
-    }
-
-    /**
-     * Set the value of dataDirectory.
-     *
-     * @param dataDirectory new value of dataDirectory
-     */
-    public void setDataDirectory(String dataDirectory) {
-        this.dataDirectory = dataDirectory;
-    }
-    /**
-     * Specifies the destination directory for the generated Dependency-Check
-     * report.
-     */
-    private String reportOutputDirectory = ".";
-
-    /**
-     * Get the value of reportOutputDirectory.
-     *
-     * @return the value of reportOutputDirectory
-     */
-    public String getReportOutputDirectory() {
-        return reportOutputDirectory;
-    }
-
-    /**
-     * Set the value of reportOutputDirectory.
-     *
-     * @param reportOutputDirectory new value of reportOutputDirectory
-     */
-    public void setReportOutputDirectory(String reportOutputDirectory) {
-        this.reportOutputDirectory = reportOutputDirectory;
-    }
-    /**
-     * Specifies if the build should be failed if a CVSS score above a specified
-     * level is identified. The default is 11 which means since the CVSS scores
-     * are 0-10, by default the build will never fail and the CVSS score is set
-     * to 11. The valid range for the fail build on CVSS is 0 to 11, where
-     * anything above 10 will not cause the build to fail.
-     */
-    private float failBuildOnCVSS = 11;
-
-    /**
-     * Get the value of failBuildOnCVSS.
-     *
-     * @return the value of failBuildOnCVSS
-     */
-    public float getFailBuildOnCVSS() {
-        return failBuildOnCVSS;
-    }
-
-    /**
-     * Set the value of failBuildOnCVSS.
-     *
-     * @param failBuildOnCVSS new value of failBuildOnCVSS
-     */
-    public void setFailBuildOnCVSS(float failBuildOnCVSS) {
-        this.failBuildOnCVSS = failBuildOnCVSS;
-    }
-    /**
-     * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not
-     * recommended that this be turned to false. Default is true.
-     */
-    private boolean autoUpdate = true;
-
-    /**
-     * Get the value of autoUpdate.
-     *
-     * @return the value of autoUpdate
-     */
-    public boolean isAutoUpdate() {
-        return autoUpdate;
-    }
-
-    /**
-     * Set the value of autoUpdate.
-     *
-     * @param autoUpdate new value of autoUpdate
-     */
-    public void setAutoUpdate(boolean autoUpdate) {
-        this.autoUpdate = autoUpdate;
-    }
-    /**
-     * The report format to be generated (HTML, XML, VULN, ALL). This
-     * configuration option has no affect if using this within the Site plugin
-     * unless the externalReport is set to true. Default is HTML.
-     */
-    private String reportFormat = "HTML";
-
-    /**
-     * Get the value of reportFormat.
-     *
-     * @return the value of reportFormat
-     */
-    public String getReportFormat() {
-        return reportFormat;
-    }
-
-    /**
-     * Set the value of reportFormat.
-     *
-     * @param reportFormat new value of reportFormat
-     */
-    public void setReportFormat(ReportFormats reportFormat) {
-        this.reportFormat = reportFormat.getValue();
-    }
-    /**
-     * The Proxy URL.
-     */
-    private String proxyUrl;
-
-    /**
-     * Get the value of proxyUrl.
-     *
-     * @return the value of proxyUrl
-     */
-    public String getProxyUrl() {
-        return proxyUrl;
-    }
-
-    /**
-     * Set the value of proxyUrl.
-     *
-     * @param proxyUrl new value of proxyUrl
-     */
-    public void setProxyUrl(String proxyUrl) {
-        this.proxyUrl = proxyUrl;
-    }
-    /**
-     * The Proxy Port.
-     */
-    private String proxyPort;
-
-    /**
-     * Get the value of proxyPort.
-     *
-     * @return the value of proxyPort
-     */
-    public String getProxyPort() {
-        return proxyPort;
-    }
-
-    /**
-     * Set the value of proxyPort.
-     *
-     * @param proxyPort new value of proxyPort
-     */
-    public void setProxyPort(String proxyPort) {
-        this.proxyPort = proxyPort;
-    }
-
-    /**
-     * The Proxy username.
-     */
-    private String proxyUsername;
-
-    /**
-     * Get the value of proxyUsername.
-     *
-     * @return the value of proxyUsername
-     */
-    public String getProxyUsername() {
-        return proxyUsername;
-    }
-
-    /**
-     * Set the value of proxyUsername.
-     *
-     * @param proxyUsername new value of proxyUsername
-     */
-    public void setProxyUsername(String proxyUsername) {
-        this.proxyUsername = proxyUsername;
-    }
-
-    /**
-     * The Proxy password.
-     */
-    private String proxyPassword;
-
-    /**
-     * Get the value of proxyPassword.
-     *
-     * @return the value of proxyPassword
-     */
-    public String getProxyPassword() {
-        return proxyPassword;
-    }
-
-    /**
-     * Set the value of proxyPassword.
-     *
-     * @param proxyPassword new value of proxyPassword
-     */
-    public void setProxyPassword(String proxyPassword) {
-        this.proxyPassword = proxyPassword;
-    }
-
-    /**
-     * The Connection Timeout.
-     */
-    private String connectionTimeout;
-
-    /**
-     * Get the value of connectionTimeout.
-     *
-     * @return the value of connectionTimeout
-     */
-    public String getConnectionTimeout() {
-        return connectionTimeout;
-    }
-
-    /**
-     * Set the value of connectionTimeout.
-     *
-     * @param connectionTimeout new value of connectionTimeout
-     */
-    public void setConnectionTimeout(String connectionTimeout) {
-        this.connectionTimeout = connectionTimeout;
-    }
-    /**
-     * The file path used for verbose logging.
-     */
-    private String logFile = null;
-
-    /**
-     * Get the value of logFile.
-     *
-     * @return the value of logFile
-     */
-    public String getLogFile() {
-        return logFile;
-    }
-
-    /**
-     * Set the value of logFile.
-     *
-     * @param logFile new value of logFile
-     */
-    public void setLogFile(String logFile) {
-        this.logFile = logFile;
-    }
-
-    @Override
-    public void execute() throws BuildException {
-        final InputStream in = DependencyCheckTask.class.getClassLoader().getResourceAsStream(LOG_PROPERTIES_FILE);
-        LogUtils.prepareLogger(in, logFile);
-
-        dealWithReferences();
-        validateConfiguration();
-        populateSettings();
-
-        final Engine engine = new Engine();
-        for (Resource resource : path) {
-            final FileProvider provider = resource.as(FileProvider.class);
-            if (provider != null) {
-                final File file = provider.getFile();
-                if (file != null && file.exists()) {
-                    engine.scan(file);
-                }
-            }
-        }
-        try {
-            engine.analyzeDependencies();
-            final ReportGenerator reporter = new ReportGenerator(applicationName, engine.getDependencies(), engine.getAnalyzers());
-            reporter.generateReports(reportOutputDirectory, reportFormat);
-
-            if (this.failBuildOnCVSS <= 10) {
-                checkForFailure(engine.getDependencies());
-            }
-        } catch (IOException ex) {
-            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE, null, ex);
-            throw new BuildException("Unable to generate dependency-check report", ex);
-        } catch (Exception ex) {
-            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.SEVERE, null, ex);
-            throw new BuildException("An exception occured; unable to continue task", ex);
-        }
-    }
-
-    /**
-     * Validate the configuration to ensure the parameters have been properly
-     * configured/initialized.
-     *
-     * @throws BuildException if the task was not configured correctly.
-     */
-    private void validateConfiguration() throws BuildException {
-        if (path == null) {
-            throw new BuildException("No project dependencies have been defined to analyze.");
-        }
-        if (failBuildOnCVSS < 0 || failBuildOnCVSS > 11) {
-            throw new BuildException("Invalid configuration, failBuildOnCVSS must be between 0 and 11.");
-        }
-    }
-
-    /**
-     * Takes the properties supplied and updates the dependency-check settings.
-     * Additionally, this sets the system properties required to change the
-     * proxy url, port, and connection timeout.
-     */
-    private void populateSettings() {
-        InputStream taskProperties = null;
-        try {
-            taskProperties = this.getClass().getClassLoader().getResourceAsStream(PROPERTIES_FILE);
-            Settings.mergeProperties(taskProperties);
-        } catch (IOException ex) {
-            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.WARNING, "Unable to load the dependency-check ant task.properties file.");
-            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE, null, ex);
-        } finally {
-            if (taskProperties != null) {
-                try {
-                    taskProperties.close();
-                } catch (IOException ex) {
-                    Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINEST, null, ex);
-                }
-            }
-        }
-        if (dataDirectory != null) {
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
-        } else {
-            final File jarPath = new File(DependencyCheckTask.class.getProtectionDomain().getCodeSource().getLocation().getPath());
-            final File base = jarPath.getParentFile();
-            final String sub = Settings.getString(Settings.KEYS.DATA_DIRECTORY);
-            final File dataDir = new File(base, sub);
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
-        }
-
-        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
-
-        if (proxyUrl != null && !proxyUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
-        }
-        if (proxyPort != null && !proxyPort.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);
-        }
-        if (proxyUsername != null && !proxyUsername.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_USERNAME, proxyUsername);
-        }
-        if (proxyPassword != null && !proxyPassword.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PASSWORD, proxyPassword);
-        }
-        if (connectionTimeout != null && !connectionTimeout.isEmpty()) {
-            Settings.setString(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
-        }
-    }
-
-    /**
-     * Checks to see if a vulnerability has been identified with a CVSS score
-     * that is above the threshold set in the configuration.
-     *
-     * @param dependencies the list of dependency objects
-     * @throws BuildException thrown if a CVSS score is found that is higher
-     * then the threshold set
-     */
-    private void checkForFailure(List<Dependency> dependencies) throws BuildException {
-        final StringBuilder ids = new StringBuilder();
-        for (Dependency d : dependencies) {
-            for (Vulnerability v : d.getVulnerabilities()) {
-                if (v.getCvssScore() >= failBuildOnCVSS) {
-                    if (ids.length() == 0) {
-                        ids.append(v.getName());
-                    } else {
-                        ids.append(", ").append(v.getName());
-                    }
-                }
-            }
-        }
-        if (ids.length() > 0) {
-            final String msg = String.format("%n%nDependency-Check Failure:%n"
-                    + "One or more dependencies were identified with vulnerabilities that have a CVSS score greater then '%.1f': %s%n"
-                    + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
-            throw new BuildException(msg);
-        }
-    }
-
-    /**
-     * An enumeration of supported report formats: "ALL", "HTML", "XML", "VULN",
-     * etc..
-     */
-    public static class ReportFormats extends EnumeratedAttribute {
-
-        /**
-         * Returns the list of values for the report format.
-         *
-         * @return the list of values for the report format
-         */
-        @Override
-        public String[] getValues() {
-            int i = 0;
-            final Format[] formats = Format.values();
-            final String[] values = new String[formats.length];
-            for (Format format : formats) {
-                values[i++] = format.name();
-            }
-            return values;
-        }
-    }
-}

dependency-check-ant/src/main/java/org/owasp/dependencycheck/taskdefs/Purge.java

@@ -0,0 +1,127 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.taskdefs;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import org.apache.tools.ant.BuildException;
+import org.apache.tools.ant.Project;
+import org.apache.tools.ant.Task;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.impl.StaticLoggerBinder;
+
+/**
+ * An Ant task definition to execute dependency-check during an Ant build.
+ *
+ * @author Jeremy Long
+ */
+public class Purge extends Task {
+
+    /**
+     * The properties file location.
+     */
+    private static final String PROPERTIES_FILE = "task.properties";
+
+    /**
+     * Construct a new DependencyCheckTask.
+     */
+    public Purge() {
+        super();
+        // Call this before Dependency Check Core starts logging anything - this way, all SLF4J messages from
+        // core end up coming through this tasks logger
+        StaticLoggerBinder.getSingleton().setTask(this);
+    }
+
+    /**
+     * The location of the data directory that contains
+     */
+    private String dataDirectory = null;
+
+    /**
+     * Get the value of dataDirectory.
+     *
+     * @return the value of dataDirectory
+     */
+    public String getDataDirectory() {
+        return dataDirectory;
+    }
+
+    /**
+     * Set the value of dataDirectory.
+     *
+     * @param dataDirectory new value of dataDirectory
+     */
+    public void setDataDirectory(String dataDirectory) {
+        this.dataDirectory = dataDirectory;
+    }
+
+    @Override
+    public void execute() throws BuildException {
+        populateSettings();
+        File db;
+        try {
+            db = new File(Settings.getDataDirectory(), "dc.h2.db");
+            if (db.exists()) {
+                if (db.delete()) {
+                    log("Database file purged; local copy of the NVD has been removed", Project.MSG_INFO);
+                } else {
+                    log(String.format("Unable to delete '%s'; please delete the file manually", db.getAbsolutePath()), Project.MSG_ERR);
+                }
+            } else {
+                log(String.format("Unable to purge database; the database file does not exists: %s", db.getAbsolutePath()), Project.MSG_ERR);
+            }
+        } catch (IOException ex) {
+            log("Unable to delete the database", Project.MSG_ERR);
+        } finally {
+            Settings.cleanup(true);
+        }
+    }
+
+    /**
+     * Takes the properties supplied and updates the dependency-check settings. Additionally, this sets the system properties
+     * required to change the proxy server, port, and connection timeout.
+     */
+    protected void populateSettings() {
+        Settings.initialize();
+        InputStream taskProperties = null;
+        try {
+            taskProperties = this.getClass().getClassLoader().getResourceAsStream(PROPERTIES_FILE);
+            Settings.mergeProperties(taskProperties);
+        } catch (IOException ex) {
+            log("Unable to load the dependency-check ant task.properties file.", ex, Project.MSG_WARN);
+        } finally {
+            if (taskProperties != null) {
+                try {
+                    taskProperties.close();
+                } catch (IOException ex) {
+                    log("", ex, Project.MSG_DEBUG);
+                }
+            }
+        }
+        if (dataDirectory != null) {
+            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
+        } else {
+            final File jarPath = new File(Purge.class.getProtectionDomain().getCodeSource().getLocation().getPath());
+            final File base = jarPath.getParentFile();
+            final String sub = Settings.getString(Settings.KEYS.DATA_DIRECTORY);
+            final File dataDir = new File(base, sub);
+            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
+        }
+    }
+}

dependency-check-ant/src/main/java/org/owasp/dependencycheck/taskdefs/Update.java

@@ -0,0 +1,437 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.taskdefs;
+
+import org.apache.tools.ant.BuildException;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.impl.StaticLoggerBinder;
+
+/**
+ * An Ant task definition to execute dependency-check update. This will download the latest data from the National Vulnerability
+ * Database (NVD) and store a copy in the local database.
+ *
+ * @author Jeremy Long
+ */
+public class Update extends Purge {
+
+    /**
+     * Construct a new UpdateTask.
+     */
+    public Update() {
+        super();
+        // Call this before Dependency Check Core starts logging anything - this way, all SLF4J messages from
+        // core end up coming through this tasks logger
+        StaticLoggerBinder.getSingleton().setTask(this);
+    }
+
+    /**
+     * The Proxy Server.
+     */
+    private String proxyServer;
+
+    /**
+     * Get the value of proxyServer.
+     *
+     * @return the value of proxyServer
+     */
+    public String getProxyServer() {
+        return proxyServer;
+    }
+
+    /**
+     * Set the value of proxyServer.
+     *
+     * @param server new value of proxyServer
+     */
+    public void setProxyServer(String server) {
+        this.proxyServer = server;
+    }
+
+    /**
+     * The Proxy Port.
+     */
+    private String proxyPort;
+
+    /**
+     * Get the value of proxyPort.
+     *
+     * @return the value of proxyPort
+     */
+    public String getProxyPort() {
+        return proxyPort;
+    }
+
+    /**
+     * Set the value of proxyPort.
+     *
+     * @param proxyPort new value of proxyPort
+     */
+    public void setProxyPort(String proxyPort) {
+        this.proxyPort = proxyPort;
+    }
+    /**
+     * The Proxy username.
+     */
+    private String proxyUsername;
+
+    /**
+     * Get the value of proxyUsername.
+     *
+     * @return the value of proxyUsername
+     */
+    public String getProxyUsername() {
+        return proxyUsername;
+    }
+
+    /**
+     * Set the value of proxyUsername.
+     *
+     * @param proxyUsername new value of proxyUsername
+     */
+    public void setProxyUsername(String proxyUsername) {
+        this.proxyUsername = proxyUsername;
+    }
+    /**
+     * The Proxy password.
+     */
+    private String proxyPassword;
+
+    /**
+     * Get the value of proxyPassword.
+     *
+     * @return the value of proxyPassword
+     */
+    public String getProxyPassword() {
+        return proxyPassword;
+    }
+
+    /**
+     * Set the value of proxyPassword.
+     *
+     * @param proxyPassword new value of proxyPassword
+     */
+    public void setProxyPassword(String proxyPassword) {
+        this.proxyPassword = proxyPassword;
+    }
+    /**
+     * The Connection Timeout.
+     */
+    private String connectionTimeout;
+
+    /**
+     * Get the value of connectionTimeout.
+     *
+     * @return the value of connectionTimeout
+     */
+    public String getConnectionTimeout() {
+        return connectionTimeout;
+    }
+
+    /**
+     * Set the value of connectionTimeout.
+     *
+     * @param connectionTimeout new value of connectionTimeout
+     */
+    public void setConnectionTimeout(String connectionTimeout) {
+        this.connectionTimeout = connectionTimeout;
+    }
+    /**
+     * The database driver name; such as org.h2.Driver.
+     */
+    private String databaseDriverName;
+
+    /**
+     * Get the value of databaseDriverName.
+     *
+     * @return the value of databaseDriverName
+     */
+    public String getDatabaseDriverName() {
+        return databaseDriverName;
+    }
+
+    /**
+     * Set the value of databaseDriverName.
+     *
+     * @param databaseDriverName new value of databaseDriverName
+     */
+    public void setDatabaseDriverName(String databaseDriverName) {
+        this.databaseDriverName = databaseDriverName;
+    }
+
+    /**
+     * The path to the database driver JAR file if it is not on the class path.
+     */
+    private String databaseDriverPath;
+
+    /**
+     * Get the value of databaseDriverPath.
+     *
+     * @return the value of databaseDriverPath
+     */
+    public String getDatabaseDriverPath() {
+        return databaseDriverPath;
+    }
+
+    /**
+     * Set the value of databaseDriverPath.
+     *
+     * @param databaseDriverPath new value of databaseDriverPath
+     */
+    public void setDatabaseDriverPath(String databaseDriverPath) {
+        this.databaseDriverPath = databaseDriverPath;
+    }
+    /**
+     * The database connection string.
+     */
+    private String connectionString;
+
+    /**
+     * Get the value of connectionString.
+     *
+     * @return the value of connectionString
+     */
+    public String getConnectionString() {
+        return connectionString;
+    }
+
+    /**
+     * Set the value of connectionString.
+     *
+     * @param connectionString new value of connectionString
+     */
+    public void setConnectionString(String connectionString) {
+        this.connectionString = connectionString;
+    }
+    /**
+     * The user name for connecting to the database.
+     */
+    private String databaseUser;
+
+    /**
+     * Get the value of databaseUser.
+     *
+     * @return the value of databaseUser
+     */
+    public String getDatabaseUser() {
+        return databaseUser;
+    }
+
+    /**
+     * Set the value of databaseUser.
+     *
+     * @param databaseUser new value of databaseUser
+     */
+    public void setDatabaseUser(String databaseUser) {
+        this.databaseUser = databaseUser;
+    }
+
+    /**
+     * The password to use when connecting to the database.
+     */
+    private String databasePassword;
+
+    /**
+     * Get the value of databasePassword.
+     *
+     * @return the value of databasePassword
+     */
+    public String getDatabasePassword() {
+        return databasePassword;
+    }
+
+    /**
+     * Set the value of databasePassword.
+     *
+     * @param databasePassword new value of databasePassword
+     */
+    public void setDatabasePassword(String databasePassword) {
+        this.databasePassword = databasePassword;
+    }
+
+    /**
+     * The url for the modified NVD CVE (1.2 schema).
+     */
+    private String cveUrl12Modified;
+
+    /**
+     * Get the value of cveUrl12Modified.
+     *
+     * @return the value of cveUrl12Modified
+     */
+    public String getCveUrl12Modified() {
+        return cveUrl12Modified;
+    }
+
+    /**
+     * Set the value of cveUrl12Modified.
+     *
+     * @param cveUrl12Modified new value of cveUrl12Modified
+     */
+    public void setCveUrl12Modified(String cveUrl12Modified) {
+        this.cveUrl12Modified = cveUrl12Modified;
+    }
+
+    /**
+     * The url for the modified NVD CVE (2.0 schema).
+     */
+    private String cveUrl20Modified;
+
+    /**
+     * Get the value of cveUrl20Modified.
+     *
+     * @return the value of cveUrl20Modified
+     */
+    public String getCveUrl20Modified() {
+        return cveUrl20Modified;
+    }
+
+    /**
+     * Set the value of cveUrl20Modified.
+     *
+     * @param cveUrl20Modified new value of cveUrl20Modified
+     */
+    public void setCveUrl20Modified(String cveUrl20Modified) {
+        this.cveUrl20Modified = cveUrl20Modified;
+    }
+
+    /**
+     * Base Data Mirror URL for CVE 1.2.
+     */
+    private String cveUrl12Base;
+
+    /**
+     * Get the value of cveUrl12Base.
+     *
+     * @return the value of cveUrl12Base
+     */
+    public String getCveUrl12Base() {
+        return cveUrl12Base;
+    }
+
+    /**
+     * Set the value of cveUrl12Base.
+     *
+     * @param cveUrl12Base new value of cveUrl12Base
+     */
+    public void setCveUrl12Base(String cveUrl12Base) {
+        this.cveUrl12Base = cveUrl12Base;
+    }
+
+    /**
+     * Data Mirror URL for CVE 2.0.
+     */
+    private String cveUrl20Base;
+
+    /**
+     * Get the value of cveUrl20Base.
+     *
+     * @return the value of cveUrl20Base
+     */
+    public String getCveUrl20Base() {
+        return cveUrl20Base;
+    }
+
+    /**
+     * Set the value of cveUrl20Base.
+     *
+     * @param cveUrl20Base new value of cveUrl20Base
+     */
+    public void setCveUrl20Base(String cveUrl20Base) {
+        this.cveUrl20Base = cveUrl20Base;
+    }
+
+    /**
+     * The number of hours to wait before re-checking for updates.
+     */
+    private Integer cveValidForHours;
+
+    /**
+     * Get the value of cveValidForHours.
+     *
+     * @return the value of cveValidForHours
+     */
+    public Integer getCveValidForHours() {
+        return cveValidForHours;
+    }
+
+    /**
+     * Set the value of cveValidForHours.
+     *
+     * @param cveValidForHours new value of cveValidForHours
+     */
+    public void setCveValidForHours(Integer cveValidForHours) {
+        this.cveValidForHours = cveValidForHours;
+    }
+
+    /**
+     * Executes the update by initializing the settings, downloads the NVD XML data, and then processes the data storing it in the
+     * local database.
+     *
+     * @throws BuildException thrown if a connection to the local database cannot be made.
+     */
+    @Override
+    public void execute() throws BuildException {
+        populateSettings();
+        Engine engine = null;
+        try {
+            engine = new Engine(Update.class.getClassLoader());
+            engine.doUpdates();
+        } catch (DatabaseException ex) {
+            throw new BuildException("Unable to connect to the dependency-check database; unable to update the NVD data", ex);
+        } finally {
+            Settings.cleanup(true);
+            if (engine != null) {
+                engine.cleanup();
+            }
+        }
+    }
+
+    /**
+     * Takes the properties supplied and updates the dependency-check settings. Additionally, this sets the system properties
+     * required to change the proxy server, port, and connection timeout.
+     *
+     * @throws BuildException thrown when an invalid setting is configured.
+     */
+    @Override
+    protected void populateSettings() throws BuildException {
+        super.populateSettings();
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_SERVER, proxyServer);
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_PORT, proxyPort);
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_USERNAME, proxyUsername);
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_PASSWORD, proxyPassword);
+        Settings.setStringIfNotEmpty(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_USER, databaseUser);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_PASSWORD, databasePassword);
+        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
+        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
+        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
+        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
+        if (cveValidForHours != null) {
+            if (cveValidForHours >= 0) {
+                Settings.setInt(Settings.KEYS.CVE_CHECK_VALID_FOR_HOURS, cveValidForHours);
+            } else {
+                throw new BuildException("Invalid setting: `cpeValidForHours` must be 0 or greater");
+            }
+        }
+    }
+}

dependency-check-ant/src/main/java/org/owasp/dependencycheck/taskdefs/package-info.java

@@ -1,11 +1,4 @@
 /**
- * <html>
- * <head>
- * <title>org.owasp.dependencycheck.taskdefs</title>
- * </head>
- * <body>
- * This package includes the Ant task definitions.
- * </body>
- * </html>
+ * This package includes the a slf4j logging implementation that wraps the Ant logger.
  */
 package org.owasp.dependencycheck.taskdefs;

dependency-check-ant/src/main/java/org/slf4j/impl/StaticLoggerBinder.java

@@ -0,0 +1,103 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 The OWASP Foundation. All Rights Reserved.
+ */
+package org.slf4j.impl;
+
+import org.apache.tools.ant.Task;
+import org.owasp.dependencycheck.ant.logging.AntLoggerFactory;
+import org.slf4j.ILoggerFactory;
+import org.slf4j.spi.LoggerFactoryBinder;
+
+/**
+ * The binding of org.slf4j.LoggerFactory class with an actual instance of org.slf4j.ILoggerFactory is performed using information
+ * returned by this class.
+ *
+ * @author colezlaw
+ */
+public class StaticLoggerBinder implements LoggerFactoryBinder {
+
+    /**
+     * The unique instance of this class
+     *
+     */
+    private static final StaticLoggerBinder SINGLETON = new StaticLoggerBinder();
+
+    /**
+     * Return the singleton of this class.
+     *
+     * @return the StaticLoggerBinder singleton
+     */
+    public static final StaticLoggerBinder getSingleton() {
+        return SINGLETON;
+    }
+
+    /**
+     * Ant tasks have the log method we actually want to call. So we hang onto the task as a delegate
+     */
+    private Task task = null;
+
+    /**
+     * Set the Task which will this is to log through.
+     *
+     * @param task the task through which to log
+     */
+    public void setTask(Task task) {
+        this.task = task;
+        loggerFactory = new AntLoggerFactory(task);
+    }
+
+    /**
+     * Declare the version of the SLF4J API this implementation is compiled against. The value of this filed is usually modified
+     * with each release.
+     */
+    // to avoid constant folding by the compiler, this field must *not* be final
+    public static String REQUESTED_API_VERSION = "1.7.12"; // final
+
+    private static final String LOGGER_FACTORY_CLASS = AntLoggerFactory.class.getName();
+
+    /**
+     * The ILoggerFactory instance returned by the {@link #getLoggerFactory} method should always be the smae object
+     */
+    private ILoggerFactory loggerFactory;
+
+    /**
+     * Constructs a new static logger binder.
+     */
+    private StaticLoggerBinder() {
+        loggerFactory = new AntLoggerFactory(task);
+    }
+
+    /**
+     * Returns the logger factory.
+     *
+     * @return the logger factory
+     */
+    @Override
+    public ILoggerFactory getLoggerFactory() {
+        return loggerFactory;
+    }
+
+    /**
+     * Returns the logger factory class string.
+     *
+     * @return the logger factory class string
+     */
+    @Override
+    public String getLoggerFactoryClassStr() {
+        return LOGGER_FACTORY_CLASS;
+    }
+}

dependency-check-ant/src/main/java/org/slf4j/impl/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * This package contains the static binder for the slf4j-ant logger.
+ */
+package org.slf4j.impl;

dependency-check-ant/src/main/resources/dependency-check-taskdefs.properties

@@ -0,0 +1,3 @@
+dependency-check=org.owasp.dependencycheck.taskdefs.Check
+dependency-check-purge=org.owasp.dependencycheck.taskdefs.Purge
+dependency-check-update=org.owasp.dependencycheck.taskdefs.Update

dependency-check-ant/src/main/resources/log.properties

@@ -1,23 +0,0 @@
-handlers=java.util.logging.ConsoleHandler, java.util.logging.FileHandler
-
-# logging levels
-# FINEST, FINER, FINE, CONFIG, INFO, WARNING and SEVERE.
-
-# Configure the ConsoleHandler.
-java.util.logging.ConsoleHandler.level=INFO
-
-#org.owasp.dependencycheck.data.nvdcve.xml
-
-# Configure the FileHandler.
-#java.util.logging.FileHandler.formatter=java.util.logging.SimpleFormatter
-#java.util.logging.FileHandler.level=FINEST
-
-# The following special tokens can be used in the pattern property
-# which specifies the location and name of the log file.
-#   / - standard path separator
-#   %t - system temporary directory
-#   %h - value of the user.home system property
-#   %g - generation number for rotating logs
-#   %u - unique number to avoid conflicts
-# FileHandler writes to %h/demo0.log by default.
-#java.util.logging.FileHandler.pattern=./target/dependency-check.log

dependency-check-ant/src/main/resources/task.properties

@@ -1,2 +1,2 @@
 # the path to the data directory
-data.directory=dependency-check-data
+data.directory=data/3.0

dependency-check-ant/src/main/resources/taskdefs.properties

@@ -1,3 +0,0 @@
-# define custom tasks here
-
-dependencycheck=org.owasp.dependencycheck.taskdefs.DependencyCheckTask

dependency-check-ant/src/site/markdown/config-purge.md

@@ -0,0 +1,19 @@
+Configuration
+====================
+The dependency-check-purge task deletes the local copy of the NVD. This task
+should rarely be used, if ever. This is included as a convenience method in
+the rare circumstance that the local H2 database because corrupt.
+
+```xml
+<target name="dependency-check-purge" description="Dependency-Check purge">
+    <dependency-check-purge />
+</target>
+```
+
+Configuration: dependency-check-purge Task
+--------------------
+The following properties can be set on the dependency-check-purge task.
+
+Property              | Description                                                    | Default Value
+----------------------|----------------------------------------------------------------|------------------
+dataDirectory         | Data directory that is used to store the local copy of the NVD | data

dependency-check-ant/src/site/markdown/config-update.md

@@ -0,0 +1,44 @@
+Configuration
+====================
+The dependency-check-update task downloads and updates the local copy of the NVD.
+There are several reasons that one may want to use this task; primarily, creating
+an update that will be run only once a day or once every few days (but not greater
+then 7 days) and then use the `autoUpdate="false"` setting on individual
+dependency-check scans. See [Internet Access Required](https://jeremylong.github.io/DependencyCheck/data/index.html)
+for more information on why this task would be used.
+
+```xml
+<target name="dependency-check-update" description="Dependency-Check Update">
+    <dependency-check-update />
+</target>
+```
+
+Configuration: dependency-check-update Task
+--------------------
+The following properties can be set on the dependency-check task.
+
+Property              | Description                        | Default Value
+----------------------|------------------------------------|------------------
+proxyServer           | The Proxy Server.                  | &nbsp;
+proxyPort             | The Proxy Port.                    | &nbsp;
+proxyUsername         | Defines the proxy user name.       | &nbsp;
+proxyPassword         | Defines the proxy password.        | &nbsp;
+connectionTimeout     | The URL Connection Timeout.        | &nbsp;
+
+Advanced Configuration
+====================
+The following properties can be configured in the plugin. However, they are less frequently changed. One exception
+may be the cvedUrl properties, which can be used to host a mirror of the NVD within an enterprise environment.
+
+Property             | Description                                                                                           | Default Value
+---------------------|-------------------------------------------------------------------------------------------------------|------------------
+cveUrl12Modified     | URL for the modified CVE 1.2.                                                                         | https://nvd.nist.gov/download/nvdcve-Modified.xml.gz
+cveUrl20Modified     | URL for the modified CVE 2.0.                                                                         | https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-Modified.xml.gz
+cveUrl12Base         | Base URL for each year's CVE 1.2, the %d will be replaced with the year.                              | https://nvd.nist.gov/download/nvdcve-%d.xml.gz
+cveUrl20Base         | Base URL for each year's CVE 2.0, the %d will be replaced with the year.                              | https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml.gz
+dataDirectory        | Data directory that is used to store the local copy of the NVD. This should generally not be changed. | data
+databaseDriverName   | The name of the database driver. Example: org.h2.Driver.                                              | &nbsp;
+databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path.           | &nbsp;
+connectionString     | The connection string used to connect to the database.                                                | &nbsp;
+databaseUser         | The username used when connecting to the database.                                                    | &nbsp;
+databasePassword     | The password used when connecting to the database.                                                    | &nbsp;

dependency-check-ant/src/site/markdown/configuration.md

@@ -1,5 +1,11 @@
 Configuration
 ====================
+Once dependency-check-ant has been [installed](index.html) the defined tasks can be used.
+
+* dependency-check - the primary task used to check the project dependencies. Configuration options are below.
+* dependency-check-purge - deletes the local copy of the NVD; this should rarely be used (if ever). See the [purge configuration](config-purge.html) for more information.
+* dependency-check-update - downloads and updates the local copy of the NVD. See the [update configuration](config-update.html) for more information.
+
 To configure the dependency-check task you can add it to a target and include a
 file based [resource collection](http://ant.apache.org/manual/Types/resources.html#collection)
 such as a [FileSet](http://ant.apache.org/manual/Types/fileset.html), [DirSet](http://ant.apache.org/manual/Types/dirset.html),
@@ -8,7 +14,7 @@ the project's dependencies.
 
 ```xml
 <target name="dependency-check" description="Dependency-Check Analysis">
-    <dependency-check applicationname="Hello World"
+    <dependency-check projectname="Hello World"
                       reportoutputdirectory="${basedir}"
                       reportformat="ALL">
 
@@ -18,21 +24,69 @@ the project's dependencies.
     </dependency-check>
 </target>
 ```
-The following table lists the configurable properties:
 
-Property              | Description | Requirement
-----------------------|-------------|---------
-ApplicationName       | The name of the application to use in the generated report. | Required
-ReportFormat          | The format of the report to be generated. Allowed values are: HTML, XML, VULN, or ALL. The default value is HTML.| Optional
-ReportOutputDirectory | The directory where dependency-check will store data used for analysis. Defaults to the current working directory. | Optional
-FailBuildOn           | If set and a CVE is found that is greater then the specified value the build will fail. The default value is 11 which means that the build will not fail. Valid values are 0-11. | Optional
-AutoUpdate            | If set to false the NVD CVE data is not automatically updated. Setting this to false could result in false negatives. However, this may be required in some environments. The default value is true. | Optional
-DataDirectory         | The directory where dependency-check will store data used for analysis. Defaults to a folder called, called 'dependency-check-data', that is in the same directory as the dependency-check-ant jar file was installed in. *It is not recommended to change this.* | Optional
-LogFile               | The file path to write verbose logging information. | Optional
-ProxyUrl              | Defines the proxy used to connect to the Internet. | Optional
-ProxyPort             | Defines the port for the proxy. | Optional
-ProxyUsername         | Defines the proxy user name. | Optional
-ProxyPassword         | Defines the proxy password. | Optional
-ConnectionTimeout     | The connection timeout used when downloading data files from the Internet. | Optional
+Configuration: dependency-check Task
+--------------------
+The following properties can be set on the dependency-check-update task.
 
+Property              | Description                                                                                                                                                                                        | Default Value
+----------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------
+autoUpdate            | Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to false.                                                                                 | true
+cveValidForHours      | Sets the number of hours to wait before checking for new updates from the NVD                                                                                                                      | 4
+failBuildOnCVSS       | Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11 which means since the CVSS scores are 0-10, by default the build will never fail. | 11
+projectName           | The name of the project being scanned.                                                                                                                                                             | Dependency-Check
+reportFormat          | The report format to be generated (HTML, XML, VULN, ALL). This configuration option has no affect if using this within the Site plugin unless the externalReport is set to true.                   | HTML
+reportOutputDirectory | The location to write the report(s). Note, this is not used if generating the report as part of a `mvn site` build                                                                                 | 'target'
+suppressionFile       | The file path to the XML suppression file \- used to suppress [false positives](../general/suppression.html)                                                                                       | &nbsp;
+proxyServer           | The Proxy Server.                                                                                                                                                                                  | &nbsp;
+proxyPort             | The Proxy Port.                                                                                                                                                                                    | &nbsp;
+proxyUsername         | Defines the proxy user name.                                                                                                                                                                       | &nbsp;
+proxyPassword         | Defines the proxy password.                                                                                                                                                                        | &nbsp;
+connectionTimeout     | The URL Connection Timeout.                                                                                                                                                                        | &nbsp;
 
+Analyzer Configuration
+====================
+The following properties are used to configure the various file type analyzers.
+These properties can be used to turn off specific analyzers if it is not needed.
+Note, that specific analyzers will automatically disable themselves if no file
+types that they support are detected - so specifically disabling them may not
+be needed.
+
+Property                      | Description                                                               | Default Value
+------------------------------|---------------------------------------------------------------------------|------------------
+archiveAnalyzerEnabled        | Sets whether the Archive Analyzer will be used.                           | true
+zipExtensions                 | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. | &nbsp;
+jarAnalyzer                   | Sets whether the Jar Analyzer will be used.                               | true
+centralAnalyzerEnabled        | Sets whether the Central Analyzer will be used. **Disabling this analyzer is not recommended as it could lead to false negatives (e.g. libraries that have vulnerabilities may not be reported correctly).** If this analyzer is being disabled there is a good chance you also want to disable the Nexus Analyzer (see below).                                  | true
+nexusAnalyzerEnabled          | Sets whether Nexus Analyzer will be used. This analyzer is superceded by the Central Analyzer; however, you can configure this to run against a Nexus Pro installation. | true
+nexusUrl                      | Defines the Nexus web service endpoint (example http://domain.enterprise/nexus/service/local/). If not set the Nexus Analyzer will be disabled. | &nbsp;
+nexusUsesProxy                | Whether or not the defined proxy should be used when connecting to Nexus. | true
+pyDistributionAnalyzerEnabled | Sets whether the Python Distribution Analyzer will be used.               | true
+pyPackageAnalyzerEnabled      | Sets whether the Python Package Analyzer will be used.                    | true
+rubygemsAnalyzerEnabled       | Sets whether the Ruby Gemspec Analyzer will be used.                      | true
+opensslAnalyzerEnabled        | Sets whether or not the openssl Analyzer should be used.                  | true
+cmakeAnalyzerEnabled          | Sets whether or not the CMake Analyzer should be used.                    | true
+autoconfAnalyzerEnabled       | Sets whether or not the autoconf Analyzer should be used.                 | true
+composerAnalyzerEnabled       | Sets whether or not the PHP Composer Lock File Analyzer should be used.   | true
+nodeAnalyzerEnabled           | Sets whether or not the Node.js Analyzer should be used.                  | true
+nuspecAnalyzerEnabled         | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.          | true
+assemblyAnalyzerEnabled       | Sets whether or not the .NET Assembly Analyzer should be used.            | true
+pathToMono                    | The path to Mono for .NET assembly analysis on non-windows systems.       | &nbsp;
+
+Advanced Configuration
+====================
+The following properties can be configured in the plugin. However, they are less frequently changed. One exception
+may be the cvedUrl properties, which can be used to host a mirror of the NVD within an enterprise environment.
+
+Property             | Description                                                              | Default Value
+---------------------|--------------------------------------------------------------------------|------------------
+cveUrl12Modified     | URL for the modified CVE 1.2.                                            | http://nvd.nist.gov/download/nvdcve-modified.xml
+cveUrl20Modified     | URL for the modified CVE 2.0.                                            | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+cveUrl12Base         | Base URL for each year's CVE 1.2, the %d will be replaced with the year. | http://nvd.nist.gov/download/nvdcve-%d.xml
+cveUrl20Base         | Base URL for each year's CVE 2.0, the %d will be replaced with the year. | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+dataDirectory        | Data directory that is used to store the local copy of the NVD. This should generally not be changed. | data
+databaseDriverName   | The name of the database driver. Example: org.h2.Driver.                                    | &nbsp;
+databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path. | &nbsp;
+connectionString     | The connection string used to connect to the database.                                      | &nbsp;
+databaseUser         | The username used when connecting to the database.                                          | &nbsp;
+databasePassword     | The password used when connecting to the database.                                          | &nbsp;

dependency-check-ant/src/site/markdown/index.md.vm

@@ -0,0 +1,35 @@
+About
+====================
+OWASP dependency-check-ant is an Ant Task that uses dependency-check-core to detect publicly
+disclosed vulnerabilities associated with the project's dependencies. The task will
+generate a report listing the dependency, any identified Common Platform Enumeration (CPE)
+identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.
+
+Installation
+====================
+1. Download dependency-check-ant from [bintray here](http://dl.bintray.com/jeremy-long/owasp/dependency-check-ant-${project.version}-release.zip).
+2. Unzip the archive
+3. Add the taskdef to your build.xml:
+
+    ```xml
+    <!-- Set the value to the installation directory's path -->
+    <property name="dependency-check.home" value="C:/tools/dependency-check-ant"/>
+    <path id="dependency-check.path">
+       <pathelement location="${dependency-check.home}/dependency-check-ant.jar"/>
+    </path>
+       <taskdef resource="dependency-check-taskdefs.properties">
+       <classpath refid="dependency-check.path" />
+    </taskdef>
+    ```
+4. Use the defined taskdefs:
+    * [dependency-check](configuration.html) - the primary task used to check the project dependencies.
+    * [dependency-check-purge](config-purge.html) - deletes the local copy of the NVD; this should rarely be used (if ever).
+    * [dependency-check-update](config-update.html) - downloads and updates the local copy of the NVD.
+
+
+It is important to understand that the first time this task is executed it may
+take 10 minutes or more as it downloads and processes the data from the National
+Vulnerability Database (NVD) hosted by NIST: https://nvd.nist.gov
+
+After the first batch download, as long as the task is executed at least once every
+seven days the update will only take a few seconds.

dependency-check-ant/src/site/markdown/installation.md.vm

@@ -1,13 +0,0 @@
-Installation
-====================
-Download dependency-check-ant from [bintray here](http://dl.bintray.com/jeremy-long/owasp/dependency-check-ant-${project.version}.jar).
-To install dependency-check-ant place the dependency-check-ant-${project.version}.jar into
-the lib directory of your Ant instalation directory. Once installed you can add
-the taskdef to you build.xml and add the task to a new or existing target.
-
-It is important to understand that the first time this task is executed it may
-take 20 minutes or more as it downloads and processes the data from the National
-Vulnerability Database (NVD) hosted by NIST: https://nvd.nist.gov
-
-After the first batch download, as long as the task is executed at least once every
-seven days the update will only take a few seconds.

dependency-check-ant/src/site/markdown/usage.md

@@ -1,25 +0,0 @@
-Usage
-====================
-First, add the dependency-check-ant taskdef to your build.xml:
-
-```xml
-<taskdef name="dependency-check" classname="org.owasp.dependencycheck.taskdefs.DependencyCheckTask"/>
-```
-
-Next, add the task to a target of your choosing:
-
-```xml
-<target name="dependency-check" description="Dependency-Check Analysis">
-    <dependency-check applicationname="Hello World"
-                      autoupdate="true"
-                      reportoutputdirectory="${basedir}"
-                      reportformat="HTML">
-
-        <fileset dir="lib">
-            <include name="**/*.jar"/>
-        </fileset>
-    </dependency-check>
-</target>
-```
-
-See the [configuration guide](configuration.html) for more information.

dependency-check-ant/src/site/site.xml

@@ -2,35 +2,34 @@
 <!--
 This file is part of dependency-check-ant.
 
-Dependency-check-ant is free software: you can redistribute it and/or modify it
-under the terms of the GNU General Public License as published by the Free
-Software Foundation, either version 3 of the License, or (at your option) any
-later version.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-Dependency-check-ant is distributed in the hope that it will be useful, but
-WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
-details.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-You should have received a copy of the GNU General Public License along with
-dependency-check-ant. If not, see http://www.gnu.org/licenses/.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
 Copyright (c) 2013 Jeremy Long. All Rights Reserved.
 -->
 <project name="dependency-check-ant">
     <bannerLeft>
-        <name>dependency-check-ant</name>
+        <name>OWASP dependency-check-ant</name>
+        <alt>OWASP dependency-check-ant</alt>
+        <src>./images/dc-ant.svg</src>
     </bannerLeft>
     <body>
         <breadcrumbs>
             <item name="dependency-check" href="../index.html"/>
         </breadcrumbs>
         <menu name="Getting Started">
-            <item name="Installation" href="installation.html"/>
-            <item name="Usage" href="usage.html"/>
+            <item name="Installation" href="index.html"/>
             <item name="Configuration" href="configuration.html"/>
         </menu>
-        <menu ref="Project Documentation" />
         <menu ref="reports" />
     </body>
 </project>

dependency-check-ant/src/test/java/org/owasp/dependencycheck/taskdefs/DependencyCheckTaskTest.java

@@ -1,63 +1,62 @@
 /*
  * This file is part of dependency-check-ant.
  *
- * Dependency-check-ant is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-ant is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-ant. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck.taskdefs;
 
 import java.io.File;
-import static junit.framework.TestCase.assertTrue;
+
+import org.apache.tools.ant.BuildException;
+import org.apache.tools.ant.BuildFileRule;
 import org.junit.After;
-import org.junit.AfterClass;
 import org.junit.Before;
-import org.junit.BeforeClass;
+import org.junit.Rule;
 import org.junit.Test;
-import org.apache.tools.ant.BuildFileTest;
-import org.owasp.dependencycheck.data.nvdcve.BaseDBTestCase;
+import org.junit.rules.ExpectedException;
+import org.owasp.dependencycheck.BaseDBTestCase;
+import org.owasp.dependencycheck.utils.Settings;
+
+import static org.junit.Assert.assertTrue;
+
 
 /**
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
-public class DependencyCheckTaskTest extends BuildFileTest {
+public class DependencyCheckTaskTest {
 
-    public DependencyCheckTaskTest() {
-    }
+    @Rule
+    public BuildFileRule buildFileRule = new BuildFileRule();
 
-    @BeforeClass
-    public static void setUpClass() {
-    }
-
-    @AfterClass
-    public static void tearDownClass() {
-    }
+    @Rule
+    public ExpectedException expectedException = ExpectedException.none();
 
     @Before
-    @Override
     public void setUp() throws Exception {
+        Settings.initialize();
         BaseDBTestCase.ensureDBExists();
         final String buildFile = this.getClass().getClassLoader().getResource("build.xml").getPath();
-        configureProject(buildFile);
+        buildFileRule.configureProject(buildFile);
     }
 
     @After
-    @Override
     public void tearDown() {
         //no cleanup...
         //executeTarget("cleanup");
+        Settings.cleanup(true);
     }
 
     /**
@@ -65,13 +64,13 @@ public class DependencyCheckTaskTest extends BuildFileTest {
      */
     @Test
     public void testAddFileSet() throws Exception {
-        File report = new File("target/DependencyCheck-Report.html");
+        File report = new File("target/dependency-check-report.html");
         if (report.exists()) {
             if (!report.delete()) {
                 throw new Exception("Unable to delete 'target/DependencyCheck-Report.html' prior to test.");
             }
         }
-        executeTarget("test.fileset");
+        buildFileRule.executeTarget("test.fileset");
 
         assertTrue("DependencyCheck report was not generated", report.exists());
 
@@ -84,13 +83,13 @@ public class DependencyCheckTaskTest extends BuildFileTest {
      */
     @Test
     public void testAddFileList() throws Exception {
-        File report = new File("target/DependencyCheck-Report.xml");
+        File report = new File("target/dependency-check-report.xml");
         if (report.exists()) {
             if (!report.delete()) {
                 throw new Exception("Unable to delete 'target/DependencyCheck-Report.xml' prior to test.");
             }
         }
-        executeTarget("test.filelist");
+        buildFileRule.executeTarget("test.filelist");
 
         assertTrue("DependencyCheck report was not generated", report.exists());
     }
@@ -102,13 +101,13 @@ public class DependencyCheckTaskTest extends BuildFileTest {
      */
     @Test
     public void testAddDirSet() throws Exception {
-        File report = new File("target/DependencyCheck-Vulnerability.html");
+        File report = new File("target/dependency-check-vulnerability.html");
         if (report.exists()) {
             if (!report.delete()) {
                 throw new Exception("Unable to delete 'target/DependencyCheck-Vulnerability.html' prior to test.");
             }
         }
-        executeTarget("test.dirset");
+        buildFileRule.executeTarget("test.dirset");
         assertTrue("DependencyCheck report was not generated", report.exists());
     }
 
@@ -117,7 +116,7 @@ public class DependencyCheckTaskTest extends BuildFileTest {
      */
     @Test
     public void testGetFailBuildOnCVSS() {
-        expectBuildException("failCVSS", "asdfasdfscore");
-        System.out.println(this.getOutput());
+        expectedException.expect(BuildException.class);
+        buildFileRule.executeTarget("failCVSS");
     }
 }

dependency-check-ant/src/test/resources/build.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project name="Dependency-Check Test Build" default="test.fileset" basedir=".">
 
-    <taskdef name="dependency-check" classname="org.owasp.dependencycheck.taskdefs.DependencyCheckTask" />
+    <taskdef name="dependency-check" classname="org.owasp.dependencycheck.taskdefs.Check" />
 
     <target name="test.fileset">
         <dependency-check

dependency-check-cli/LICENSE.txt

@@ -1,674 +1,202 @@
-                    GNU GENERAL PUBLIC LICENSE 
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-                            Preamble
-
-  The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
-  The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works.  By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users.  We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors.  You can apply it to
-your programs, too.
-
-  When we speak of free software, we are referring to freedom, not
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
-free programs, and that you know you can do these things.
-
-  To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights.  Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
-
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must pass on to the recipients the same
-freedoms that you received.  You must make sure that they, too, receive
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-know their rights.
-
-  Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
-giving you legal permission to copy, distribute and/or modify it.
-
-  For the developers' and authors' protection, the GPL clearly explains
-that there is no warranty for this free software.  For both users' and
-authors' sake, the GPL requires that modified versions be marked as
-changed, so that their problems will not be attributed erroneously to
-authors of previous versions.
-
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dependency-check-cli/README.md

@@ -5,7 +5,7 @@ performed are a "best effort" and as such, there could be false positives as wel
 vulnerabilities in 3rd party components is a well-known problem and is currently documented in the 2013 OWASP
 Top 10 as [A9 - Using Components with Known Vulnerabilities](https://www.owasp.org/index.php/Top_10_2013-A9-Using_Components_with_Known_Vulnerabilities).
 
-Documentation and links to production binary releases can be found on the [github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-cli/installation.html).
+Documentation and links to production binary releases can be found on the [github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-cli/index.html).
 
 Mailing List
 ------------
@@ -17,8 +17,8 @@ Post: [dependency-check@googlegroups.com](mailto:dependency-check@googlegroups.c
 Copyright & License
 ------------
 
-Dependency-Check is Copyright (c) 2012-2013 Jeremy Long. All Rights Reserved.
+Dependency-Check is Copyright (c) 2012-2014 Jeremy Long. All Rights Reserved.
 
-Permission to modify and redistribute is granted under the terms of the GPLv3 license. See the [LICENSE.txt](https://github.com/jeremylong/DependencyCheck/dependency-check-cli/blob/master/LICENSE.txt) file for the full license.
+Permission to modify and redistribute is granted under the terms of the Apache 2.0 license. See the [LICENSE.txt](https://raw.githubusercontent.com/jeremylong/DependencyCheck/master/LICENSE.txt) file for the full license.
 
-Dependency-Check Command Line makes use of other open source libraries. Please see the [NOTICE.txt](https://github.com/jeremylong/DependencyCheck/dependency-check-cli/blob/master/NOTICES.txt) file for more information.
+Dependency-Check Command Line makes use of other open source libraries. Please see the [NOTICE.txt](https://raw.githubusercontent.com/jeremylong/DependencyCheck/master/dependency-check-cli/NOTICE.txt) file for more information.

dependency-check-cli/config/checkstyle-checks.xml

@@ -1,223 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE module PUBLIC
-          "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
-          "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
-
-<module name="Checker">
-  <!--
-      If you set the basedir property below, then all reported file
-      names will be relative to the specified directory. See
-      http://checkstyle.sourceforge.net/5.x/config.html#Checker
-
-      <property name="basedir" value="${basedir}"/>
-  -->
-
-  <property name="severity" value="error"/>
-
-  <module name="SuppressionFilter">
-    <property name="file" value="${checkstyle.suppressions.file}"/>
-  </module>
-
-  <module name="JavadocPackage">
-    <property name="allowLegacy" value="false"/>
-  </module>
-
-  <module name="Translation">
-    <property name="severity" value="warning"/>
-  </module>
-
-  <module name="FileTabCharacter">
-    <property name="eachLine" value="false"/>
-  </module>
-
-  <module name="FileLength">
-    <property name="fileExtensions" value="java"/>
-  </module>
-
-  <module name="NewlineAtEndOfFile">
-  <property name="fileExtensions" value="java"/>
-  <property name="lineSeparator" value="lf"/>
-  </module>
-
-  <module name="RegexpHeader">
-    <property name="headerFile" value="${checkstyle.header.file}"/>
-    <property name="fileExtensions" value="java"/>
-    <property name="id" value="header"/>
-  </module>
-
-  <module name="RegexpSingleline">
-    <property name="format" value="\s+$"/>
-    <property name="minimum" value="0"/>
-    <property name="maximum" value="0"/>
-  </module>
-
-  <module name="TreeWalker">
-    <property name="tabWidth" value="4"/>
-
-    <module name="AvoidStarImport"/>
-    <module name="ConstantName"/>
-    <module name="EmptyBlock"/>
-    <module name="EmptyForIteratorPad"/>
-    <module name="EqualsHashCode"/>
-    <module name="OneStatementPerLine"/>
-
-    <!-- module name="IllegalCatch"/ -->
-    <!--module name="ImportControl">
-      <property name="file" value="${checkstyle.importcontrol.file}"/>
-    </module-->
-    <module name="IllegalImport"/>
-    <module name="IllegalInstantiation"/>
-    <module name="IllegalThrows"/>
-    <module name="InnerAssignment"/>
-    <module name="JavadocType">
-      <property name="authorFormat" value="\S"/>
-    </module>
-    <module name="JavadocMethod">
-      <property name="allowUndeclaredRTE" value="true"/>
-      <property name="allowThrowsTagsForSubclasses" value="true"/>
-      <property name="allowMissingPropertyJavadoc" value="true"/>
-    </module>
-    <module name="JavadocVariable"/>
-    <module name="JavadocStyle">
-      <property name="scope" value="public"/>
-    </module>
-
-    <module name="LeftCurly">
-      <property name="option" value="eol"/>
-      <property name="tokens" value="CLASS_DEF"/>
-      <property name="tokens" value="CTOR_DEF"/>
-      <property name="tokens" value="INTERFACE_DEF"/>
-      <property name="tokens" value="METHOD_DEF"/>
-      <property name="tokens" value="LITERAL_CATCH"/>
-      <property name="tokens" value="LITERAL_DO"/>
-      <property name="tokens" value="LITERAL_ELSE"/>
-      <property name="tokens" value="LITERAL_FINALLY"/>
-      <property name="tokens" value="LITERAL_FOR"/>
-      <property name="tokens" value="LITERAL_IF"/>
-      <property name="tokens" value="LITERAL_SWITCH"/>
-      <property name="tokens" value="LITERAL_SYNCHRONIZED"/>
-      <property name="tokens" value="LITERAL_TRY"/>
-      <property name="tokens" value="LITERAL_WHILE"/>
-    </module>
-
-    <module name="OuterTypeNumber"/>
-    <module name="LineLength">
-      <property name="ignorePattern" value="^ *\* *[^ ]+$"/>
-    <property name="max" value="150"/>
-    </module>
-
-    <module name="MethodCount">
-      <property name="maxTotal" value="40"/>
-    </module>
-
-    <module name="LocalFinalVariableName"/>
-    <module name="LocalVariableName"/>
-    <module name="MemberName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="MethodLength">
-        <property name="max" value="160"/>
-        <property name="countEmpty" value="false"/>
-    </module>
-    <module name="MethodName"/>
-    <module name="MethodParamPad"/>
-    <module name="ModifierOrder"/>
-    <module name="NeedBraces"/>
-    <module name="NoWhitespaceAfter">
-      <property name="tokens" value="ARRAY_INIT"/>
-      <property name="tokens" value="BNOT"/>
-      <property name="tokens" value="DEC"/>
-      <property name="tokens" value="DOT"/>
-      <property name="tokens" value="INC"/>
-      <property name="tokens" value="LNOT"/>
-      <property name="tokens" value="UNARY_MINUS"/>
-      <property name="tokens" value="UNARY_PLUS"/>
-    </module>
-
-    <module name="NoWhitespaceBefore"/>
-    <module name="NoWhitespaceBefore">
-      <property name="tokens" value="DOT"/>
-      <property name="allowLineBreaks" value="true"/>
-    </module>
-
-    <module name="OperatorWrap"/>
-    <module name="OperatorWrap">
-      <property name="tokens" value="ASSIGN"/>
-      <property name="tokens" value="DIV_ASSIGN"/>
-      <property name="tokens" value="PLUS_ASSIGN"/>
-      <property name="tokens" value="MINUS_ASSIGN"/>
-      <property name="tokens" value="STAR_ASSIGN"/>
-      <property name="tokens" value="MOD_ASSIGN"/>
-      <property name="tokens" value="SR_ASSIGN"/>
-      <property name="tokens" value="BSR_ASSIGN"/>
-      <property name="tokens" value="SL_ASSIGN"/>
-      <property name="tokens" value="BXOR_ASSIGN"/>
-      <property name="tokens" value="BOR_ASSIGN"/>
-      <property name="tokens" value="BAND_ASSIGN"/>
-      <property name="option" value="eol"/>
-    </module>
-    <module name="PackageName"/>
-    <module name="ParameterName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="ParameterNumber">
-      <property name="id" value="paramNum"/>
-    </module>
-    <module name="ParenPad"/>
-    <module name="TypecastParenPad"/>
-    <module name="RedundantImport"/>
-    <module name="RedundantModifier"/>
-    <module name="RightCurly">
-      <property name="option" value="same"/>
-    </module>
-    <module name="SimplifyBooleanExpression"/>
-    <module name="SimplifyBooleanReturn"/>
-    <module name="StaticVariableName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="TypeName"/>
-    <module name="UnusedImports"/>
-    <module name="UpperEll"/>
-    <module name="VisibilityModifier"/>
-    <module name="WhitespaceAfter"/>
-    <module name="WhitespaceAround"/>
-    <module name="GenericWhitespace"/>
-    <module name="FinalClass"/>
-    <module name="MissingSwitchDefault"/>
-    <!--module name="MagicNumber"/-->
-    <!--module name="Indentation">
-      <property name="basicOffset" value="4"/>
-      <property name="braceAdjustment" value="0"/>
-      <property name="caseIndent" value="0"/>
-    </module-->
-    <module name="ArrayTrailingComma"/>
-    <module name="FinalLocalVariable"/>
-    <module name="EqualsAvoidNull"/>
-    <module name="ParameterAssignment"/>
-
-    <!-- Generates quite a few errors -->
-    <module name="CyclomaticComplexity">
-      <property name="severity" value="ignore"/>
-    </module>
-
-    <module name="NestedForDepth">
-      <property name="max" value="2"/>
-    </module>
-    <module name="NestedIfDepth">
-      <property name="max" value="4"/>
-    </module>
-    <module name="NestedTryDepth">
-        <property name="max" value="2"/>
-    </module>
-    <!--module name="ExplicitInitialization"/-->
-    <module name="AnnotationUseStyle"/>
-    <module name="MissingDeprecated"/>
-    <module name="MissingOverride">
-      <property name="javaFiveCompatibility" value="true"/>
-    </module>
-    <module name="PackageAnnotation"/>
-    <module name="SuppressWarnings"/>
-    <module name="OuterTypeFilename"/>
-    <module name="HideUtilityClassConstructor"/>
-  </module>
-</module>

dependency-check-cli/config/checkstyle-header.txt

@@ -1,19 +0,0 @@
-^/\*\s*$
-^ \* This file is part of dependency-check-cli\.\s*$
-^ \*\s*$
-^ \* Dependency-check-cli is free software\: you can redistribute it and/or modify it\s*$
-^ \* under the terms of the GNU General Public License as published by the Free\s*$
-^ \* Software Foundation, either version 3 of the License, or \(at your option\) any\s*$
-^ \* later version\.
-^ \*\s*$
-^ \* Dependency-check-cli is distributed in the hope that it will be useful, but\s*$
-^ \* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or\s*$
-^ \* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more\s*$
-^ \* details\.\s*$
-^ \*\s*$
-^ \* You should have received a copy of the GNU General Public License along with\s*$
-^ \* dependency-check-cli\. If not, see http://www.gnu.org/licenses/\.\s*$
-^ \*\s*$
-^ \* Copyright \(c\) 201[23] (Jeremy Long|Steve Springett)\. All Rights Reserved\.\s*$
-^ \*/\s*$
-^package

dependency-check-cli/config/checkstyle-suppressions.xml

@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-
-<!DOCTYPE suppressions PUBLIC
-     "-//Puppy Crawl//DTD Suppressions 1.0//EN"
-     "http://www.puppycrawl.com/dtds/suppressions_1_0.dtd">
-
-<suppressions>
-    <suppress checks=".*" files=".*[\\/]package-info\.java" />
-</suppressions>

dependency-check-cli/pom.xml

@@ -1,35 +1,33 @@
 <!--
 This file is part of Dependency-Check.
 
-Dependency-Check is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-Dependency-Check is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-You should have received a copy of the GNU General Public License
-along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
 Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
 -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.0.5</version>
+        <version>1.3.6</version>
     </parent>
 
     <artifactId>dependency-check-cli</artifactId>
     <packaging>jar</packaging>
 
     <name>Dependency-Check Command Line</name>
-    <description>Dependency-Check-Maven is a Maven Plugin that attempts to detect publicly disclosed vulnerabilities contained within project dependencies. It does this by determining if there is a Common Platform Enumeration (CPE) identifier for a given dependency. If found, it will generate a report linking to the associated CVE entries.</description>
+    <description>dependency-check-cli is an command line tool that uses dependency-check-core to detect publicly disclosed vulnerabilities associated with the scanned project dependencies. The tool will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.</description>
     <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
     <distributionManagement>
         <site>
@@ -46,6 +44,7 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                 <directory>src/main/resources</directory>
                 <includes>
                     <include>**/*.properties</include>
+                    <include>logback.xml</include>
                 </includes>
                 <filtering>true</filtering>
             </resource>
@@ -62,24 +61,21 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>2.4</version>
                 <configuration>
                     <archive>
                         <manifest>
                             <mainClass>org.owasp.dependencycheck.App</mainClass>
-                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
                         </manifest>
                     </archive>
-                    <excludes>
-                        <exclude>**/checkstyle*</exclude>
-                    </excludes>
                 </configuration>
             </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>cobertura-maven-plugin</artifactId>
-                <version>2.5.2</version>
                 <configuration>
+                    <!--instrumentation>
+                        <ignoreTrivial>true</ignoreTrivial>
+                    </instrumentation-->
                     <check>
                         <branchRate>85</branchRate>
                         <lineRate>85</lineRate>
@@ -113,14 +109,9 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>2.14</version>
                 <configuration>
+                    <argLine>-Dfile.encoding=UTF-8</argLine>
                     <systemProperties>
-                        <property>
-                            <name>net.sourceforge.cobertura.datafile</name>
-                            <value>${project.build.directory}/cobertura/cobertura.ser</value>
-                            <workingDirectory>target</workingDirectory>
-                        </property>
                         <property>
                             <name>cpe</name>
                             <value>data/cpe</value>
@@ -134,157 +125,14 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                     </systemProperties>
                 </configuration>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <version>2.3.2</version>
-                <configuration>
-                    <showDeprecation>false</showDeprecation>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-site-plugin</artifactId>
-                <version>3.3</version>
-                <dependencies>
-                    <dependency>
-                        <groupId>org.apache.maven.doxia</groupId>
-                        <artifactId>doxia-module-markdown</artifactId>
-                        <version>1.4</version>
-                    </dependency>
-                </dependencies>
-                <configuration>
-                    <skipDeploy>true</skipDeploy>
-                    <reportPlugins>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-project-info-reports-plugin</artifactId>
-                            <version>2.6</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>index</report>
-                                        <report>summary</report>
-                                        <report>license</report>
-                                        <report>help</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-javadoc-plugin</artifactId>
-                            <version>2.9</version>
-                            <reportSets>
-                                <reportSet>
-                                    <id>default</id>
-                                    <reports>
-                                        <report>javadoc</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>versions-maven-plugin</artifactId>
-                            <version>2.0</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>dependency-updates-report</report>
-                                        <report>plugin-updates-report</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-jxr-plugin</artifactId>
-                            <version>2.3</version>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>cobertura-maven-plugin</artifactId>
-                            <version>2.5.2</version>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-surefire-report-plugin</artifactId>
-                            <version>2.14</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>report-only</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>taglist-maven-plugin</artifactId>
-                            <version>2.4</version>
-                            <configuration>
-                                <tagListOptions>
-                                    <tagClasses>
-                                        <tagClass>
-                                            <displayName>Todo Work</displayName>
-                                            <tags>
-                                                <tag>
-                                                    <matchString>todo</matchString>
-                                                    <matchType>ignoreCase</matchType>
-                                                </tag>
-                                                <tag>
-                                                    <matchString>FIXME</matchString>
-                                                    <matchType>exact</matchType>
-                                                </tag>
-                                            </tags>
-                                        </tagClass>
-                                    </tagClasses>
-                                </tagListOptions>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-checkstyle-plugin</artifactId>
-                            <version>2.10</version>
-                            <configuration>
-                                <enableRulesSummary>false</enableRulesSummary>
-                                <configLocation>${basedir}/config/checkstyle-checks.xml</configLocation>
-                                <headerLocation>${basedir}/config/checkstyle-header.txt</headerLocation>
-                                <suppressionsLocation>${basedir}/config/checkstyle-suppressions.xml</suppressionsLocation>
-                                <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-pmd-plugin</artifactId>
-                            <version>3.0.1</version>
-                            <configuration>
-                                <targetJdk>1.6</targetJdk>
-                                <linkXref>true</linkXref>
-                                <sourceEncoding>utf-8</sourceEncoding>
-                                <excludes>
-                                    <exclude>**/generated/*.java</exclude>
-                                </excludes>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>findbugs-maven-plugin</artifactId>
-                            <version>2.5.2</version>
-                        </plugin>
-                    </reportPlugins>
-                </configuration>
-            </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>appassembler-maven-plugin</artifactId>
-                <version>1.4</version>
                 <configuration>
                     <programs>
                         <program>
                             <mainClass>org.owasp.dependencycheck.App</mainClass>
-                            <name>dependency-check</name>
+                            <id>dependency-check</id>
                         </program>
                     </programs>
                     <assembleDirectory>${project.build.directory}/release</assembleDirectory>
@@ -325,16 +173,78 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
             </plugin>
         </plugins>
     </build>
+    <reporting>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                <version>${reporting.checkstyle-plugin.version}</version>
+                <configuration>
+                    <enableRulesSummary>false</enableRulesSummary>
+                    <enableFilesSummary>false</enableFilesSummary>
+                    <configLocation>${basedir}/../src/main/config/checkstyle-checks.xml</configLocation>
+                    <headerLocation>${basedir}/../src/main/config/checkstyle-header.txt</headerLocation>
+                    <suppressionsLocation>${basedir}/../src/main/config/checkstyle-suppressions.xml</suppressionsLocation>
+                    <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-pmd-plugin</artifactId>
+                <version>${reporting.pmd-plugin.version}</version>
+                <configuration>
+                    <targetJdk>1.6</targetJdk>
+                    <linkXref>true</linkXref>
+                    <sourceEncoding>utf-8</sourceEncoding>
+                    <excludes>
+                        <exclude>**/generated/*.java</exclude>
+                    </excludes>
+                    <rulesets>
+                        <ruleset>../src/main/config/dcrules.xml</ruleset>
+                        <ruleset>/rulesets/java/basic.xml</ruleset>
+                        <ruleset>/rulesets/java/imports.xml</ruleset>
+                        <ruleset>/rulesets/java/unusedcode.xml</ruleset>
+                    </rulesets>
+                </configuration>
+            </plugin>
+        </plugins>
+    </reporting>
     <dependencies>
         <dependency>
             <groupId>commons-cli</groupId>
             <artifactId>commons-cli</artifactId>
-            <version>1.2</version>
         </dependency>
         <dependency>
             <groupId>org.owasp</groupId>
             <artifactId>dependency-check-core</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.ant</groupId>
+            <artifactId>ant</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.apache.ant</groupId>
+                    <artifactId>ant-launcher</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
     </dependencies>
 </project>

dependency-check-cli/src/main/assembly/license.txt

@@ -1,11 +1,11 @@
 
 Copyright (c) 2012-2013 Jeremy Long.  All rights reserved.
 
-Licensed under the GPL License, Version 3; you may not use this work
-except in compliance with the License. You may obtain a copy of the
-License in the LICENSE.txt file, or at:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-http://www.gnu.org/licenses/gpl-3.0.txt
+    http://www.apache.org/licenses/LICENSE-2.0
 
 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,

dependency-check-cli/src/main/assembly/release.xml

@@ -2,11 +2,8 @@
 <assembly
     xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="
-    http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
-      http://maven.apache.org/xsd/assembly-1.1.2.xsd
-  "
->
+    xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
+      http://maven.apache.org/xsd/assembly-1.1.2.xsd">
     <id>release</id>
     <formats>
         <format>zip</format>
@@ -14,25 +11,41 @@
     <includeBaseDirectory>false</includeBaseDirectory>
     <fileSets>
         <fileSet>
-            <outputDirectory>/</outputDirectory>
-            <directory>${project.build.directory}/release</directory>
+            <outputDirectory>dependency-check/bin</outputDirectory>
+            <directory>${project.build.directory}/release/bin</directory>
+            <includes>
+                <include>*.sh</include>
+            </includes>
+            <fileMode>0755</fileMode>
         </fileSet>
         <fileSet>
+            <outputDirectory>dependency-check/bin</outputDirectory>
+            <directory>${project.build.directory}/release/bin</directory>
+            <includes>
+                <include>*.bat</include>
+            </includes>
+        </fileSet>
+        <fileSet>
+            <outputDirectory>dependency-check/repo</outputDirectory>
+            <directory>${project.build.directory}/release/repo</directory>
+        </fileSet>
+        <fileSet>
+            <outputDirectory>dependency-check</outputDirectory>
             <includes>
                 <include>LICENSE*</include>
                 <include>NOTICE*</include>
             </includes>
         </fileSet>
         <fileSet>
-            <outputDirectory>licenses</outputDirectory>
+            <outputDirectory>dependency-check/licenses</outputDirectory>
             <directory>${basedir}/src/main/resources/META-INF/licenses</directory>
         </fileSet>
         <fileSet>
-            <outputDirectory>licenses</outputDirectory>
+            <outputDirectory>dependency-check/licenses</outputDirectory>
             <directory>${basedir}/../dependency-check-core/src/main/resources/META-INF/licenses</directory>
         </fileSet>
         <fileSet>
-            <outputDirectory>/</outputDirectory>
+            <outputDirectory>dependency-check</outputDirectory>
             <directory>${basedir}</directory>
             <includes>
                 <include>README.md</include>

dependency-check-cli/src/main/java/org/owasp/dependencycheck/App.java

@@ -1,65 +1,55 @@
 /*
  * This file is part of dependency-check-cli.
  *
- * Dependency-check-cli is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-cli is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-cli. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck;
 
+import ch.qos.logback.classic.LoggerContext;
+import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
-import java.util.logging.Level;
-import java.util.logging.Logger;
+import java.util.Set;
 import org.apache.commons.cli.ParseException;
-import org.owasp.dependencycheck.reporting.ReportGenerator;
+import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.cli.CliParser;
-import org.owasp.dependencycheck.utils.LogUtils;
+import org.apache.tools.ant.DirectoryScanner;
+import org.owasp.dependencycheck.reporting.ReportGenerator;
 import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import ch.qos.logback.core.FileAppender;
+import org.slf4j.impl.StaticLoggerBinder;
 
-/*
- * This file is part of App.
- *
- * App is free software: you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any later
- * version.
- *
- * App is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with
- * App. If not, see http://www.gnu.org/licenses/.
- *
- * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
- */
 /**
  * The command line interface for the DependencyCheck application.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class App {
 
     /**
-     * The location of the log properties configuration file.
+     * The logger.
      */
-    private static final String LOG_PROPERTIES_FILE = "log.properties";
+    private static final Logger LOGGER = LoggerFactory.getLogger(App.class);
 
     /**
      * The main method for the application.
@@ -67,8 +57,13 @@ public class App {
      * @param args the command line arguments
      */
     public static void main(String[] args) {
-        final App app = new App();
-        app.run(args);
+        try {
+            Settings.initialize();
+            final App app = new App();
+            app.run(args);
+        } finally {
+            Settings.cleanup(true);
+        }
     }
 
     /**
@@ -77,8 +72,8 @@ public class App {
      * @param args the command line arguments
      */
     public void run(String[] args) {
-
         final CliParser cli = new CliParser();
+
         try {
             cli.parse(args);
         } catch (FileNotFoundException ex) {
@@ -91,81 +86,216 @@ public class App {
             return;
         }
 
-        final InputStream in = App.class.getClassLoader().getResourceAsStream(LOG_PROPERTIES_FILE);
-        LogUtils.prepareLogger(in, cli.getVerboseLog());
+        if (cli.getVerboseLog() != null) {
+            prepareLogger(cli.getVerboseLog());
+        }
 
-        if (cli.isGetVersion()) {
+        if (cli.isPurge()) {
+            if (cli.getConnectionString() != null) {
+                LOGGER.error("Unable to purge the database when using a non-default connection string");
+            } else {
+                populateSettings(cli);
+                File db;
+                try {
+                    db = new File(Settings.getDataDirectory(), "dc.h2.db");
+                    if (db.exists()) {
+                        if (db.delete()) {
+                            LOGGER.info("Database file purged; local copy of the NVD has been removed");
+                        } else {
+                            LOGGER.error("Unable to delete '{}'; please delete the file manually", db.getAbsolutePath());
+                        }
+                    } else {
+                        LOGGER.error("Unable to purge database; the database file does not exists: {}", db.getAbsolutePath());
+                    }
+                } catch (IOException ex) {
+                    LOGGER.error("Unable to delete the database");
+                }
+            }
+        } else if (cli.isGetVersion()) {
             cli.printVersionInfo();
+        } else if (cli.isUpdateOnly()) {
+            populateSettings(cli);
+            runUpdateOnly();
         } else if (cli.isRunScan()) {
-            updateSettings(cli.isAutoUpdate(), cli.getConnectionTimeout(), cli.getProxyUrl(),
-                    cli.getProxyPort(), cli.getProxyUsername(), cli.getProxyPassword(),
-                    cli.getDataDirectory(), cli.getPropertiesFile());
-            runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getApplicationName(), cli.getScanFiles());
+            populateSettings(cli);
+            try {
+                runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getProjectName(), cli.getScanFiles(),
+                        cli.getExcludeList(), cli.getSymLinkDepth());
+            } catch (InvalidScanPathException ex) {
+                LOGGER.error("An invalid scan path was detected; unable to scan '//*' paths");
+            }
         } else {
             cli.printHelp();
         }
     }
 
     /**
-     * Scans the specified directories and writes the dependency reports to the
-     * reportDirectory.
+     * Scans the specified directories and writes the dependency reports to the reportDirectory.
      *
-     * @param reportDirectory the path to the directory where the reports will
-     * be written
+     * @param reportDirectory the path to the directory where the reports will be written
      * @param outputFormat the output format of the report
      * @param applicationName the application name for the report
      * @param files the files/directories to scan
+     * @param excludes the patterns for files/directories to exclude
+     * @param symLinkDepth the depth that symbolic links will be followed
+     *
+     * @throws InvalidScanPathException thrown if the path to scan starts with "//"
      */
-    private void runScan(String reportDirectory, String outputFormat, String applicationName, String[] files) {
-        final Engine scanner = new Engine();
-
-        for (String file : files) {
-            scanner.scan(file);
-        }
-
-        scanner.analyzeDependencies();
-        final List<Dependency> dependencies = scanner.getDependencies();
-
-        final ReportGenerator report = new ReportGenerator(applicationName, dependencies, scanner.getAnalyzers());
+    private void runScan(String reportDirectory, String outputFormat, String applicationName, String[] files,
+            String[] excludes, int symLinkDepth) throws InvalidScanPathException {
+        Engine engine = null;
         try {
-            report.generateReports(reportDirectory, outputFormat);
-        } catch (IOException ex) {
-            Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an IO error while attempting to generate the report.");
-            Logger.getLogger(App.class.getName()).log(Level.INFO, null, ex);
-        } catch (Exception ex) {
-            Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an error while attempting to generate the report.");
-            Logger.getLogger(App.class.getName()).log(Level.INFO, null, ex);
+            engine = new Engine();
+            final List<String> antStylePaths = new ArrayList<String>();
+            for (String file : files) {
+                final String antPath = ensureCanonicalPath(file);
+                antStylePaths.add(antPath);
+            }
+
+            final Set<File> paths = new HashSet<File>();
+            for (String file : antStylePaths) {
+                LOGGER.debug("Scanning {}", file);
+                final DirectoryScanner scanner = new DirectoryScanner();
+                String include = file.replace('\\', '/');
+                File baseDir;
+
+                if (include.startsWith("//")) {
+                    throw new InvalidScanPathException("Unable to scan paths specified by //");
+                } else {
+                    final int pos = getLastFileSeparator(include);
+                    final String tmpBase = include.substring(0, pos);
+                    final String tmpInclude = include.substring(pos + 1);
+                    if (tmpInclude.indexOf('*') >= 0 || tmpInclude.indexOf('?') >= 0
+                            || (new File(include)).isFile()) {
+                        baseDir = new File(tmpBase);
+                        include = tmpInclude;
+                    } else {
+                        baseDir = new File(tmpBase, tmpInclude);
+                        include = "**/*";
+                    }
+                }
+                //LOGGER.debug("baseDir: {}", baseDir);
+                //LOGGER.debug("include: {}", include);
+                scanner.setBasedir(baseDir);
+                final String[] includes = {include};
+                scanner.setIncludes(includes);
+                scanner.setMaxLevelsOfSymlinks(symLinkDepth);
+                if (symLinkDepth <= 0) {
+                    scanner.setFollowSymlinks(false);
+                }
+                if (excludes != null && excludes.length > 0) {
+                    scanner.addExcludes(excludes);
+                }
+                scanner.scan();
+                if (scanner.getIncludedFilesCount() > 0) {
+                    for (String s : scanner.getIncludedFiles()) {
+                        final File f = new File(baseDir, s);
+                        LOGGER.debug("Found file {}", f.toString());
+                        paths.add(f);
+                    }
+                }
+            }
+            engine.scan(paths);
+
+            engine.analyzeDependencies();
+            final List<Dependency> dependencies = engine.getDependencies();
+            DatabaseProperties prop = null;
+            CveDB cve = null;
+            try {
+                cve = new CveDB();
+                cve.open();
+                prop = cve.getDatabaseProperties();
+            } catch (DatabaseException ex) {
+                LOGGER.debug("Unable to retrieve DB Properties", ex);
+            } finally {
+                if (cve != null) {
+                    cve.close();
+                }
+            }
+            final ReportGenerator report = new ReportGenerator(applicationName, dependencies, engine.getAnalyzers(), prop);
+            try {
+                report.generateReports(reportDirectory, outputFormat);
+            } catch (IOException ex) {
+                LOGGER.error("There was an IO error while attempting to generate the report.");
+                LOGGER.debug("", ex);
+            } catch (Throwable ex) {
+                LOGGER.error("There was an error while attempting to generate the report.");
+                LOGGER.debug("", ex);
+            }
+        } catch (DatabaseException ex) {
+            LOGGER.error("Unable to connect to the dependency-check database; analysis has stopped");
+            LOGGER.debug("", ex);
+        } finally {
+            if (engine != null) {
+                engine.cleanup();
+            }
+        }
+    }
+
+    /**
+     * Only executes the update phase of dependency-check.
+     */
+    private void runUpdateOnly() {
+        Engine engine = null;
+        try {
+            engine = new Engine();
+            engine.doUpdates();
+        } catch (DatabaseException ex) {
+            LOGGER.error("Unable to connect to the dependency-check database; analysis has stopped");
+            LOGGER.debug("", ex);
+        } finally {
+            if (engine != null) {
+                engine.cleanup();
+            }
         }
     }
 
     /**
      * Updates the global Settings.
      *
-     * @param autoUpdate whether or not to update cached web data sources
-     * @param connectionTimeout the timeout to use when downloading resources
-     * (null or blank will use default)
-     * @param proxyUrl the proxy url (null or blank means no proxy will be used)
-     * @param proxyPort the proxy port (null or blank means no port will be
-     * used)
-     * @param dataDirectory the directory to store/retrieve persistent data from
-     * @param propertiesFile the properties file to utilize
+     * @param cli a reference to the CLI Parser that contains the command line arguments used to set the corresponding settings in
+     * the core engine.
      */
-    private void updateSettings(boolean autoUpdate, String connectionTimeout, String proxyUrl, String proxyPort,
-                                String proxyUser, String proxyPass, String dataDirectory, File propertiesFile) {
+    private void populateSettings(CliParser cli) {
+
+        final boolean autoUpdate = cli.isAutoUpdate();
+        final String connectionTimeout = cli.getConnectionTimeout();
+        final String proxyServer = cli.getProxyServer();
+        final String proxyPort = cli.getProxyPort();
+        final String proxyUser = cli.getProxyUsername();
+        final String proxyPass = cli.getProxyPassword();
+        final String dataDirectory = cli.getDataDirectory();
+        final File propertiesFile = cli.getPropertiesFile();
+        final String suppressionFile = cli.getSuppressionFile();
+        final String nexusUrl = cli.getNexusUrl();
+        final String databaseDriverName = cli.getDatabaseDriverName();
+        final String databaseDriverPath = cli.getDatabaseDriverPath();
+        final String connectionString = cli.getConnectionString();
+        final String databaseUser = cli.getDatabaseUser();
+        final String databasePassword = cli.getDatabasePassword();
+        final String additionalZipExtensions = cli.getAdditionalZipExtensions();
+        final String pathToMono = cli.getPathToMono();
+        final String cveMod12 = cli.getModifiedCve12Url();
+        final String cveMod20 = cli.getModifiedCve20Url();
+        final String cveBase12 = cli.getBaseCve12Url();
+        final String cveBase20 = cli.getBaseCve20Url();
+        final Integer cveValidForHours = cli.getCveValidForHours();
 
         if (propertiesFile != null) {
             try {
                 Settings.mergeProperties(propertiesFile);
             } catch (FileNotFoundException ex) {
-                final String msg = String.format("Unable to load properties file '%s'", propertiesFile.getPath());
-                Logger.getLogger(App.class.getName()).log(Level.SEVERE, msg);
-                Logger.getLogger(App.class.getName()).log(Level.FINE, null, ex);
+                LOGGER.error("Unable to load properties file '{}'", propertiesFile.getPath());
+                LOGGER.debug("", ex);
             } catch (IOException ex) {
-                final String msg = String.format("Unable to find properties file '%s'", propertiesFile.getPath());
-                Logger.getLogger(App.class.getName()).log(Level.SEVERE, msg);
-                Logger.getLogger(App.class.getName()).log(Level.FINE, null, ex);
+                LOGGER.error("Unable to find properties file '{}'", propertiesFile.getPath());
+                LOGGER.debug("", ex);
             }
         }
+        // We have to wait until we've merged the properties before attempting to set whether we use
+        // the proxy for Nexus since it could be disabled in the properties, but not explicitly stated
+        // on the command line
+        final boolean nexusUsesProxy = cli.isNexusUsesProxy();
         if (dataDirectory != null) {
             Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
         } else if (System.getProperty("basedir") != null) {
@@ -179,20 +309,134 @@ public class App {
             Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
         }
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
-        if (proxyUrl != null && !proxyUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_SERVER, proxyServer);
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_PORT, proxyPort);
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_USERNAME, proxyUser);
+        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_PASSWORD, proxyPass);
+        Settings.setStringIfNotEmpty(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
+        Settings.setStringIfNotEmpty(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
+        Settings.setIntIfNotNull(Settings.KEYS.CVE_CHECK_VALID_FOR_HOURS, cveValidForHours);
+
+        //File Type Analyzer Settings
+        Settings.setBoolean(Settings.KEYS.ANALYZER_JAR_ENABLED, !cli.isJarDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, !cli.isArchiveDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED, !cli.isPythonDistributionDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED, !cli.isPythonPackageDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_AUTOCONF_ENABLED, !cli.isAutoconfDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_CMAKE_ENABLED, !cli.isCmakeDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, !cli.isNuspecDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, !cli.isAssemblyDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_ENABLED, !cli.isBundleAuditDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_OPENSSL_ENABLED, !cli.isOpenSSLDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED, !cli.isComposerDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED, !cli.isNodeJsDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED, !cli.isRubyGemspecDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, !cli.isCentralDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, !cli.isNexusDisabled());
+
+        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_PATH, cli.getPathToBundleAudit());
+        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY, nexusUsesProxy);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_USER, databaseUser);
+        Settings.setStringIfNotEmpty(Settings.KEYS.DB_PASSWORD, databasePassword);
+        Settings.setStringIfNotEmpty(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, additionalZipExtensions);
+        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+        if (cveBase12 != null && !cveBase12.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, cveBase12);
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveBase20);
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveMod12);
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, cveMod20);
         }
-        if (proxyPort != null && !proxyPort.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);
+    }
+
+    /**
+     * Creates a file appender and adds it to logback.
+     *
+     * @param verboseLog the path to the verbose log file
+     */
+    private void prepareLogger(String verboseLog) {
+        final StaticLoggerBinder loggerBinder = StaticLoggerBinder.getSingleton();
+        final LoggerContext context = (LoggerContext) loggerBinder.getLoggerFactory();
+
+        final PatternLayoutEncoder encoder = new PatternLayoutEncoder();
+        encoder.setPattern("%d %C:%L%n%-5level - %msg%n");
+        encoder.setContext(context);
+        encoder.start();
+        final FileAppender fa = new FileAppender();
+        fa.setAppend(true);
+        fa.setEncoder(encoder);
+        fa.setContext(context);
+        fa.setFile(verboseLog);
+        final File f = new File(verboseLog);
+        String name = f.getName();
+        final int i = name.lastIndexOf('.');
+        if (i > 1) {
+            name = name.substring(0, i);
         }
-        if (proxyUser != null && !proxyUser.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_USERNAME, proxyUser);
+        fa.setName(name);
+        fa.start();
+        final ch.qos.logback.classic.Logger rootLogger = context.getLogger(ch.qos.logback.classic.Logger.ROOT_LOGGER_NAME);
+        rootLogger.addAppender(fa);
+    }
+
+    /**
+     * Takes a path and resolves it to be a canonical &amp; absolute path. The caveats are that this method will take an Ant style
+     * file selector path (../someDir/**\/*.jar) and convert it to an absolute/canonical path (at least to the left of the first *
+     * or ?).
+     *
+     * @param path the path to canonicalize
+     * @return the canonical path
+     */
+    protected String ensureCanonicalPath(String path) {
+        String basePath = null;
+        String wildCards = null;
+        final String file = path.replace('\\', '/');
+        if (file.contains("*") || file.contains("?")) {
+
+            int pos = getLastFileSeparator(file);
+            if (pos < 0) {
+                return file;
+            }
+            pos += 1;
+            basePath = file.substring(0, pos);
+            wildCards = file.substring(pos);
+        } else {
+            basePath = file;
         }
-        if (proxyPass != null && !proxyPass.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PASSWORD, proxyPass);
+
+        File f = new File(basePath);
+        try {
+            f = f.getCanonicalFile();
+            if (wildCards != null) {
+                f = new File(f, wildCards);
+            }
+        } catch (IOException ex) {
+            LOGGER.warn("Invalid path '{}' was provided.", path);
+            LOGGER.debug("Invalid path provided", ex);
         }
-        if (connectionTimeout != null && !connectionTimeout.isEmpty()) {
-            Settings.setString(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
+        return f.getAbsolutePath().replace('\\', '/');
+    }
+
+    /**
+     * Returns the position of the last file separator.
+     *
+     * @param file a file path
+     * @return the position of the last file separator
+     */
+    private int getLastFileSeparator(String file) {
+        if (file.contains("*") || file.contains("?")) {
+            int p1 = file.indexOf('*');
+            int p2 = file.indexOf('?');
+            p1 = p1 > 0 ? p1 : file.length();
+            p2 = p2 > 0 ? p2 : file.length();
+            int pos = p1 < p2 ? p1 : p2;
+            pos = file.lastIndexOf('/', pos);
+            return pos;
+        } else {
+            return file.lastIndexOf('/');
         }
     }
 }

dependency-check-cli/src/main/java/org/owasp/dependencycheck/InvalidScanPathException.java

@@ -0,0 +1,66 @@
+/*
+ * This file is part of dependency-check-cli.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck;
+
+/**
+ * Thrown if an invalid path is encountered.
+ *
+ * @author Jeremy Long
+ */
+public class InvalidScanPathException extends Exception {
+
+    /**
+     * The serial version UID for serialization.
+     */
+    private static final long serialVersionUID = 1L;
+
+    /**
+     * Creates a new InvalidScanPathException.
+     */
+    public InvalidScanPathException() {
+        super();
+    }
+
+    /**
+     * Creates a new InvalidScanPathException.
+     *
+     * @param msg a message for the exception
+     */
+    public InvalidScanPathException(String msg) {
+        super(msg);
+    }
+
+    /**
+     * Creates a new InvalidScanPathException.
+     *
+     * @param ex the cause of the exception
+     */
+    public InvalidScanPathException(Throwable ex) {
+        super(ex);
+    }
+
+    /**
+     * Creates a new InvalidScanPathException.
+     *
+     * @param msg a message for the exception
+     * @param ex the cause of the exception
+     */
+    public InvalidScanPathException(String msg, Throwable ex) {
+        super(msg, ex);
+    }
+}

dependency-check-cli/src/main/java/org/owasp/dependencycheck/cli/CliParser.java

@@ -1,553 +0,0 @@
-/*
- * This file is part of dependency-check-cli.
- *
- * Dependency-check-cli is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Dependency-check-cli is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
- *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-cli. If not, see http://www.gnu.org/licenses/.
- *
- * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
- */
-package org.owasp.dependencycheck.cli;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.OptionGroup;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.owasp.dependencycheck.reporting.ReportGenerator.Format;
-import org.owasp.dependencycheck.utils.Settings;
-
-/**
- * A utility to parse command line arguments for the DependencyCheck.
- *
- * @author Jeremy Long (jeremy.long@owasp.org)
- */
-public final class CliParser {
-
-    /**
-     * The command line.
-     */
-    private CommandLine line;
-    /**
-     * The options for the command line parser.
-     */
-    private final Options options = createCommandLineOptions();
-    /**
-     * Indicates whether the arguments are valid.
-     */
-    private boolean isValid = true;
-
-    /**
-     * Parses the arguments passed in and captures the results for later use.
-     *
-     * @param args the command line arguments
-     * @throws FileNotFoundException is thrown when a 'file' argument does not
-     * point to a file that exists.
-     * @throws ParseException is thrown when a Parse Exception occurs.
-     */
-    public void parse(String[] args) throws FileNotFoundException, ParseException {
-        line = parseArgs(args);
-
-        if (line != null) {
-            validateArgs();
-        }
-    }
-
-    /**
-     * Parses the command line arguments.
-     *
-     * @param args the command line arguments
-     * @return the results of parsing the command line arguments
-     * @throws ParseException if the arguments are invalid
-     */
-    private CommandLine parseArgs(String[] args) throws ParseException {
-        final CommandLineParser parser = new PosixParser();
-        return parser.parse(options, args);
-    }
-
-    /**
-     * Validates that the command line arguments are valid.
-     *
-     * @throws FileNotFoundException if there is a file specified by either the
-     * SCAN or CPE command line arguments that does not exist.
-     * @throws ParseException is thrown if there is an exception parsing the
-     * command line.
-     */
-    private void validateArgs() throws FileNotFoundException, ParseException {
-        if (isRunScan()) {
-            validatePathExists(getScanFiles(), "scan");
-            validatePathExists(getReportDirectory(), "out");
-            if (!line.hasOption(ArgumentName.APP_NAME)) {
-                throw new ParseException("Missing 'app' argument; the scan cannot be run without the an application name.");
-            }
-            if (line.hasOption(ArgumentName.OUTPUT_FORMAT)) {
-                final String format = line.getOptionValue(ArgumentName.OUTPUT_FORMAT);
-                try {
-                    Format.valueOf(format);
-                } catch (IllegalArgumentException ex) {
-                    final String msg = String.format("An invalid 'format' of '%s' was specified. Supported output formats are XML, HTML, VULN, or ALL", format);
-                    throw new ParseException(msg);
-                }
-            }
-        }
-    }
-
-    /**
-     * Validates whether or not the path(s) points at a file that exists; if the
-     * path(s) does not point to an existing file a FileNotFoundException is
-     * thrown.
-     *
-     * @param paths the paths to validate if they exists
-     * @param optType the option being validated (e.g. scan, out, etc.)
-     * @throws FileNotFoundException is thrown if one of the paths being
-     * validated does not exist.
-     */
-    private void validatePathExists(String[] paths, String optType) throws FileNotFoundException {
-        for (String path : paths) {
-            validatePathExists(path, optType);
-        }
-    }
-
-    /**
-     * Validates whether or not the path points at a file that exists; if the
-     * path does not point to an existing file a FileNotFoundException is
-     * thrown.
-     *
-     * @param path the paths to validate if they exists
-     * @param optType the option being validated (e.g. scan, out, etc.)
-     * @throws FileNotFoundException is thrown if the path being validated does
-     * not exist.
-     */
-    private void validatePathExists(String path, String optType) throws FileNotFoundException {
-        final File f = new File(path);
-        if (!f.exists()) {
-            isValid = false;
-            final String msg = String.format("Invalid '%s' argument: '%s'", optType, path);
-            throw new FileNotFoundException(msg);
-        }
-    }
-
-    /**
-     * Generates an Options collection that is used to parse the command line
-     * and to display the help message.
-     *
-     * @return the command line options used for parsing the command line
-     */
-    @SuppressWarnings("static-access")
-    private Options createCommandLineOptions() {
-        final Option help = new Option(ArgumentName.HELP_SHORT, ArgumentName.HELP, false,
-                "Print this message.");
-
-        final Option version = new Option(ArgumentName.VERSION_SHORT, ArgumentName.VERSION,
-                false, "Print the version information.");
-
-        final Option noUpdate = new Option(ArgumentName.DISABLE_AUTO_UPDATE_SHORT, ArgumentName.DISABLE_AUTO_UPDATE,
-                false, "Disables the automatic updating of the CPE data.");
-
-        final Option appName = OptionBuilder.withArgName("name").hasArg().withLongOpt(ArgumentName.APP_NAME)
-                .withDescription("The name of the application being scanned. This is a required argument.")
-                .create(ArgumentName.APP_NAME_SHORT);
-
-        final Option connectionTimeout = OptionBuilder.withArgName("timeout").hasArg().withLongOpt(ArgumentName.CONNECTION_TIMEOUT)
-                .withDescription("The connection timeout (in milliseconds) to use when downloading resources.")
-                .create(ArgumentName.CONNECTION_TIMEOUT_SHORT);
-
-        final Option proxyUrl = OptionBuilder.withArgName("url").hasArg().withLongOpt(ArgumentName.PROXY_URL)
-                .withDescription("The proxy url to use when downloading resources.")
-                .create(ArgumentName.PROXY_URL_SHORT);
-
-        final Option proxyPort = OptionBuilder.withArgName("port").hasArg().withLongOpt(ArgumentName.PROXY_PORT)
-                .withDescription("The proxy port to use when downloading resources.")
-                .create(ArgumentName.PROXY_PORT_SHORT);
-
-        final Option proxyUsername = OptionBuilder.withArgName("user").hasArg().withLongOpt(ArgumentName.PROXY_USERNAME)
-                .withDescription("The proxy username to use when downloading resources.")
-                .create(ArgumentName.PROXY_USERNAME_SHORT);
-
-        final Option proxyPassword = OptionBuilder.withArgName("pass").hasArg().withLongOpt(ArgumentName.PROXY_PASSWORD)
-                .withDescription("The proxy password to use when downloading resources.")
-                .create(ArgumentName.PROXY_PASSWORD_SHORT);
-
-        final Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.SCAN)
-                .withDescription("The path to scan - this option can be specified multiple times.")
-                .create(ArgumentName.SCAN_SHORT);
-
-        final Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP)
-                .withDescription("A property file to load.")
-                .create(ArgumentName.PROP_SHORT);
-
-        final Option data = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.DATA_DIRECTORY)
-                .withDescription("The location of the data directory used to store persistent data. This option should generally not be set.")
-                .create(ArgumentName.DATA_DIRECTORY_SHORT);
-
-        final Option out = OptionBuilder.withArgName("folder").hasArg().withLongOpt(ArgumentName.OUT)
-                .withDescription("The folder to write reports to. This defaults to the current directory.")
-                .create(ArgumentName.OUT_SHORT);
-
-        final Option outputFormat = OptionBuilder.withArgName("format").hasArg().withLongOpt(ArgumentName.OUTPUT_FORMAT)
-                .withDescription("The output format to write to (XML, HTML, VULN, ALL). The default is HTML.")
-                .create(ArgumentName.OUTPUT_FORMAT_SHORT);
-
-        final Option verboseLog = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.VERBOSE_LOG)
-                .withDescription("The file path to write verbose logging information.")
-                .create(ArgumentName.VERBOSE_LOG_SHORT);
-
-        final OptionGroup og = new OptionGroup();
-        og.addOption(path);
-
-        final Options opts = new Options();
-        opts.addOptionGroup(og);
-        opts.addOption(out);
-        opts.addOption(outputFormat);
-        opts.addOption(appName);
-        opts.addOption(version);
-        opts.addOption(help);
-        opts.addOption(noUpdate);
-        opts.addOption(props);
-        opts.addOption(data);
-        opts.addOption(verboseLog);
-        opts.addOption(proxyPort);
-        opts.addOption(proxyUrl);
-        opts.addOption(proxyUsername);
-        opts.addOption(proxyPassword);
-        opts.addOption(connectionTimeout);
-
-        return opts;
-    }
-
-    /**
-     * Determines if the 'version' command line argument was passed in.
-     *
-     * @return whether or not the 'version' command line argument was passed in
-     */
-    public boolean isGetVersion() {
-        return (line != null) && line.hasOption(ArgumentName.VERSION);
-    }
-
-    /**
-     * Determines if the 'help' command line argument was passed in.
-     *
-     * @return whether or not the 'help' command line argument was passed in
-     */
-    public boolean isGetHelp() {
-        return (line != null) && line.hasOption(ArgumentName.HELP);
-    }
-
-    /**
-     * Determines if the 'scan' command line argument was passed in.
-     *
-     * @return whether or not the 'scan' command line argument was passed in
-     */
-    public boolean isRunScan() {
-        return (line != null) && isValid && line.hasOption(ArgumentName.SCAN);
-    }
-
-    /**
-     * Displays the command line help message to the standard output.
-     */
-    public void printHelp() {
-        final HelpFormatter formatter = new HelpFormatter();
-        final String nl = System.getProperty("line.separator");
-
-        formatter.printHelp(Settings.getString("application.name", "DependencyCheck"),
-                nl + Settings.getString("application.name", "DependencyCheck")
-                + " can be used to identify if there are any known CVE vulnerabilities in libraries utilized by an application. "
-                + Settings.getString("application.name", "DependencyCheck")
-                + " will automatically update required data from the Internet, such as the CVE and CPE data files from nvd.nist.gov." + nl + nl,
-                options,
-                "",
-                true);
-    }
-
-    /**
-     * Retrieves the file command line parameter(s) specified for the 'scan'
-     * argument.
-     *
-     * @return the file paths specified on the command line for scan
-     */
-    public String[] getScanFiles() {
-        return line.getOptionValues(ArgumentName.SCAN);
-    }
-
-    /**
-     * Returns the directory to write the reports to specified on the command
-     * line.
-     *
-     * @return the path to the reports directory.
-     */
-    public String getReportDirectory() {
-        return line.getOptionValue(ArgumentName.OUT, ".");
-    }
-
-    /**
-     * Returns the output format specified on the command line. Defaults to HTML
-     * if no format was specified.
-     *
-     * @return the output format name.
-     */
-    public String getReportFormat() {
-        return line.getOptionValue(ArgumentName.OUTPUT_FORMAT, "HTML");
-    }
-
-    /**
-     * Returns the application name specified on the command line.
-     *
-     * @return the application name.
-     */
-    public String getApplicationName() {
-        return line.getOptionValue(ArgumentName.APP_NAME);
-    }
-
-    /**
-     * Returns the connection timeout.
-     *
-     * @return the connection timeout
-     */
-    public String getConnectionTimeout() {
-        return line.getOptionValue(ArgumentName.CONNECTION_TIMEOUT);
-    }
-
-    /**
-     * Returns the proxy url.
-     *
-     * @return the proxy url
-     */
-    public String getProxyUrl() {
-        return line.getOptionValue(ArgumentName.PROXY_URL);
-    }
-
-    /**
-     * Returns the proxy port.
-     *
-     * @return the proxy port
-     */
-    public String getProxyPort() {
-        return line.getOptionValue(ArgumentName.PROXY_PORT);
-    }
-
-    /**
-     * Returns the proxy username.
-     *
-     * @return the proxy username
-     */
-    public String getProxyUsername() {
-        return line.getOptionValue(ArgumentName.PROXY_USERNAME);
-    }
-
-    /**
-     * Returns the proxy password.
-     *
-     * @return the proxy password
-     */
-    public String getProxyPassword() {
-        return line.getOptionValue(ArgumentName.PROXY_PASSWORD);
-    }
-
-    /**
-     * Get the value of dataDirectory.
-     *
-     * @return the value of dataDirectory
-     */
-    public String getDataDirectory() {
-        return line.getOptionValue(ArgumentName.DATA_DIRECTORY);
-    }
-
-    /**
-     * Returns the properties file specified on the command line.
-     *
-     * @return the properties file specified on the command line
-     */
-    public File getPropertiesFile() {
-        final String path = line.getOptionValue(ArgumentName.PROP);
-        if (path != null) {
-            return new File(path);
-        }
-        return null;
-    }
-
-    /**
-     * Returns the path to the verbose log file.
-     *
-     * @return the path to the verbose log file
-     */
-    public String getVerboseLog() {
-        return line.getOptionValue(ArgumentName.VERBOSE_LOG);
-    }
-
-    /**
-     * <p>Prints the manifest information to standard output.</p>
-     * <ul><li>Implementation-Title: ${pom.name}</li>
-     * <li>Implementation-Version: ${pom.version}</li></ul>
-     */
-    public void printVersionInfo() {
-        final String version = String.format("%s version %s",
-                Settings.getString("application.name", "DependencyCheck"),
-                Settings.getString("application.version", "Unknown"));
-        System.out.println(version);
-    }
-
-    /**
-     * Checks if the auto update feature has been disabled. If it has been
-     * disabled via the command line this will return false.
-     *
-     * @return if auto-update is allowed.
-     */
-    public boolean isAutoUpdate() {
-        return (line == null) || !line.hasOption(ArgumentName.DISABLE_AUTO_UPDATE);
-    }
-
-    /**
-     * A collection of static final strings that represent the possible command
-     * line arguments.
-     */
-    public static class ArgumentName {
-
-        /**
-         * The long CLI argument name specifying the directory/file to scan.
-         */
-        public static final String SCAN = "scan";
-        /**
-         * The short CLI argument name specifying the directory/file to scan.
-         */
-        public static final String SCAN_SHORT = "s";
-        /**
-         * The long CLI argument name specifying that the CPE/CVE/etc. data
-         * should not be automatically updated.
-         */
-        public static final String DISABLE_AUTO_UPDATE = "noupdate";
-        /**
-         * The short CLI argument name specifying that the CPE/CVE/etc. data
-         * should not be automatically updated.
-         */
-        public static final String DISABLE_AUTO_UPDATE_SHORT = "n";
-        /**
-         * The long CLI argument name specifying the directory to write the
-         * reports to.
-         */
-        public static final String OUT = "out";
-        /**
-         * The short CLI argument name specifying the directory to write the
-         * reports to.
-         */
-        public static final String OUT_SHORT = "o";
-        /**
-         * The long CLI argument name specifying the output format to write the
-         * reports to.
-         */
-        public static final String OUTPUT_FORMAT = "format";
-        /**
-         * The short CLI argument name specifying the output format to write the
-         * reports to.
-         */
-        public static final String OUTPUT_FORMAT_SHORT = "f";
-        /**
-         * The long CLI argument name specifying the name of the application to
-         * be scanned.
-         */
-        public static final String APP_NAME = "app";
-        /**
-         * The short CLI argument name specifying the name of the application to
-         * be scanned.
-         */
-        public static final String APP_NAME_SHORT = "a";
-        /**
-         * The long CLI argument name asking for help.
-         */
-        public static final String HELP = "help";
-        /**
-         * The short CLI argument name asking for help.
-         */
-        public static final String HELP_SHORT = "h";
-        /**
-         * The long CLI argument name asking for the version.
-         */
-        public static final String VERSION_SHORT = "v";
-        /**
-         * The short CLI argument name asking for the version.
-         */
-        public static final String VERSION = "version";
-        /**
-         * The short CLI argument name indicating the proxy port.
-         */
-        public static final String PROXY_PORT_SHORT = "p";
-        /**
-         * The CLI argument name indicating the proxy port.
-         */
-        public static final String PROXY_PORT = "proxyport";
-        /**
-         * The short CLI argument name indicating the proxy url.
-         */
-        public static final String PROXY_URL_SHORT = "u";
-        /**
-         * The CLI argument name indicating the proxy url.
-         */
-        public static final String PROXY_URL = "proxyurl";
-        /**
-         * The short CLI argument name indicating the proxy username.
-         */
-        public static final String PROXY_USERNAME_SHORT = "pu";
-        /**
-         * The CLI argument name indicating the proxy username.
-         */
-        public static final String PROXY_USERNAME = "proxyuser";
-        /**
-         * The short CLI argument name indicating the proxy password.
-         */
-        public static final String PROXY_PASSWORD_SHORT = "pp";
-        /**
-         * The CLI argument name indicating the proxy password.
-         */
-        public static final String PROXY_PASSWORD = "proxypass";
-        /**
-         * The short CLI argument name indicating the connection timeout.
-         */
-        public static final String CONNECTION_TIMEOUT_SHORT = "c";
-        /**
-         * The CLI argument name indicating the connection timeout.
-         */
-        public static final String CONNECTION_TIMEOUT = "connectiontimeout";
-        /**
-         * The short CLI argument name for setting the location of an additional
-         * properties file.
-         */
-        public static final String PROP_SHORT = "p";
-        /**
-         * The CLI argument name for setting the location of an additional
-         * properties file.
-         */
-        public static final String PROP = "propertyfile";
-        /**
-         * The CLI argument name for setting the location of the data directory.
-         */
-        public static final String DATA_DIRECTORY = "data";
-        /**
-         * The short CLI argument name for setting the location of the data
-         * directory.
-         */
-        public static final String DATA_DIRECTORY_SHORT = "d";
-        /**
-         * The CLI argument name for setting the location of the data directory.
-         */
-        public static final String VERBOSE_LOG = "log";
-        /**
-         * The short CLI argument name for setting the location of the data
-         * directory.
-         */
-        public static final String VERBOSE_LOG_SHORT = "l";
-    }
-}

dependency-check-cli/src/main/java/org/owasp/dependencycheck/cli/package-info.java

@@ -1,12 +0,0 @@
-/**
- * <html>
- * <head>
- * <title>org.owasp.dependencycheck.cli</title>
- * </head>
- * <body>
- * Includes utility classes such as the CLI Parser,
- * </body>
- * </html>
-*/
-
-package org.owasp.dependencycheck.cli;

dependency-check-cli/src/main/java/org/owasp/dependencycheck/package-info.java

@@ -1,12 +1,4 @@
 /**
- * <html>
- * <head>
- * <title>org.owasp.dependencycheck</title>
- * </head>
- * <body>
  * Includes the main entry point for the DependencyChecker.
- * </body>
- * </html>
-*/
-
+ */
 package org.owasp.dependencycheck;

dependency-check-cli/src/main/resources/log.properties

@@ -1,22 +0,0 @@
-handlers=java.util.logging.ConsoleHandler
-#, java.util.logging.FileHandler
-
-# logging levels
-# FINEST, FINER, FINE, CONFIG, INFO, WARNING and SEVERE.
-
-# Configure the ConsoleHandler.
-java.util.logging.ConsoleHandler.level=INFO
-
-# Configure the FileHandler.
-java.util.logging.FileHandler.formatter=java.util.logging.SimpleFormatter
-java.util.logging.FileHandler.level=FINE
-
-# The following special tokens can be used in the pattern property
-# which specifies the location and name of the log file.
-#   / - standard path separator
-#   %t - system temporary directory
-#   %h - value of the user.home system property
-#   %g - generation number for rotating logs
-#   %u - unique number to avoid conflicts
-# FileHandler writes to %h/demo0.log by default.
-java.util.logging.FileHandler.pattern=./dependency-check.log

dependency-check-cli/src/main/resources/logback.xml

@@ -0,0 +1,16 @@
+<configuration>
+    <contextName>dependency-check</contextName>
+    <!-- Logging configuration -->
+    <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
+        <Target>System.out</Target>
+        <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+            <level>INFO</level>
+        </filter>
+        <encoder>
+            <pattern>[%level] %msg%n</pattern>
+        </encoder>
+    </appender>
+    <root level="DEBUG">
+        <appender-ref ref="console"/>
+    </root>
+</configuration>

dependency-check-cli/src/site/markdown/arguments.md

@@ -0,0 +1,64 @@
+Command Line Arguments
+======================
+
+The following table lists the command line arguments:
+
+Short  | Argument Name   | Parameter       | Description | Requirement
+-------|-----------------------|-----------------|-------------|------------
+       | \-\-project           | \<name\>        | The name of the project being scanned. | Required
+ \-s   | \-\-scan              | \<path\>        | The path to scan \- this option can be specified multiple times. It is also possible to specify Ant style paths (e.g. directory/**/*.jar). | Required
+       | \-\-exclude           | \<pattern\>     | The path patterns to exclude from the scan \- this option can be specified multiple times. This accepts Ant style path patterns (e.g. **/exclude/**). | Optional
+       | \-\-symLink           | \<depth\>       | The depth that symbolic links will be followed; the default is 0 meaning symbolic links will not be followed. | Optional
+ \-o   | \-\-out               | \<path\>        | The folder to write reports to. This defaults to the current directory. If the format is not set to ALL one could specify a specific file name. | Optional
+ \-f   | \-\-format            | \<format\>      | The output format to write to (XML, HTML, VULN, ALL). The default is HTML. | Required
+ \-l   | \-\-log               | \<file\>        | The file path to write verbose logging information. | Optional
+ \-n   | \-\-noupdate          |                 | Disables the automatic updating of the CPE data. | Optional
+       | \-\-suppression       | \<file\>        | The file path to the suppression XML file; used to suppress [false positives](../general/suppression.html). | Optional
+ \-h   | \-\-help              |                 | Print the help message. | Optional
+       | \-\-advancedHelp      |                 | Print the advanced help message. | Optional
+ \-v   | \-\-version           |                 | Print the version information. | Optional
+       | \-\-cveValidForHours  | \<hours\>       | The number of hours to wait before checking for new updates from the NVD. The default is 4 hours. | Optional
+
+
+Advanced Options
+================
+Short  | Argument&nbsp;Name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; | Parameter | Description                                     | Default&nbsp;Value
+-------|-----------------------|-----------------|----------------------------------------------------------------------------------|-------------------
+       | \-\-cveUrl12Modified  | \<url\>         | URL for the modified CVE 1.2                                                     | https://nvd.nist.gov/download/nvdcve-Modified.xml.gz
+       | \-\-cveUrl20Modified  | \<url\>         | URL for the modified CVE 2.0                                                     | https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-Modified.xml.gz
+       | \-\-cveUrl12Base      | \<url\>         | Base URL for each year's CVE 1.2, the %d will be replaced with the year          | https://nvd.nist.gov/download/nvdcve-%d.xml.gz
+       | \-\-cveUrl20Base      | \<url\>         | Base URL for each year's CVE 2.0, the %d will be replaced with the year          | https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml.gz
+ \-P   | \-\-propertyfile      | \<file\>        | Specifies a file that contains properties to use instead of applicaion defaults. | &nbsp;
+       | \-\-updateonly        |                 | If set only the update phase of dependency-check will be executed; no scan will be executed and no report will be generated. | &nbsp;
+       | \-\-disablePyDist     |                 | Sets whether the Python Distribution Analyzer will be used.                      | false
+       | \-\-disablePyPkg      |                 | Sets whether the Python Package Analyzer will be used.                           | false
+       | \-\-disableNodeJS     |                 | Sets whether the Node.js Package Analyzer will be used.                          | false
+       | \-\-disableRubygems   |                 | Sets whether the Ruby Gemspec Analyzer will be used.                             | false
+       | \-\-disableBundleAudit |               | Sets whether the Ruby Bundler Audit Analyzer will be used.                             | false
+       | \-\-disableAutoconf   |                 | Sets whether the Autoconf Analyzer will be used.                                 | false
+       | \-\-disableOpenSSL    |                 | Sets whether the OpenSSL Analyzer will be used.                                  | false
+       | \-\-disableCmake      |                 | Sets whether the Cmake Analyzer will be disabled.                                | false
+       | \-\-disableArchive    |                 | Sets whether the Archive Analyzer will be disabled.                              | false
+       | \-\-zipExtensions     | \<strings\>     | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. | &nbsp;
+       | \-\-disableJar        |                 | Sets whether the Jar Analyzer will be disabled.                                  | false
+       | \-\-disableComposer   |                 | Sets whether the PHP Composer Lock File Analyzer will be disabled.               | false
+       | \-\-disableCentral    |                 | Sets whether the Central Analyzer will be used. **Disabling this analyzer is not recommended as it could lead to false negatives (e.g. libraries that have vulnerabilities may not be reported correctly).** If this analyzer is being disabled there is a good chance you also want to disable the Nexus Analyzer. | false
+       | \-\-disableNexus      |                 | Sets whether the Nexus Analyzer will be used. Note, this has been superceded by the Central Analyzer. However, you can configure the Nexus URL to utilize an internally hosted Nexus Pro server. | false
+       | \-\-nexus             | \<url\>         | The url to the Nexus Server's web service end point (example: http://domain.enterprise/nexus/service/local/). If not set the Nexus Analyzer will be disabled. | &nbsp;
+       | \-\-nexusUsesProxy    | \<true\|false\> | Whether or not the defined proxy should be used when connecting to Nexus.        | true
+       | \-\-disableNuspec     |                 | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.                 | false
+       | \-\-disableAssembly   |                 | Sets whether or not the .NET Assembly Analyzer should be used.                   | false
+       | \-\-mono              | \<path\>        | The path to Mono for .NET Assembly analysis on non-windows systems.              | &nbsp;
+       | \-\-bundleAudit       |                 | The path to the bundle-audit executable. | &nbsp;
+       | \-\-proxyserver       | \<server\>      | The proxy server to use when downloading resources.                              | &nbsp;
+       | \-\-proxyport         | \<port\>        | The proxy port to use when downloading resources.                                | &nbsp;
+       | \-\-connectiontimeout | \<timeout\>     | The connection timeout (in milliseconds) to use when downloading resources.      | &nbsp;
+       | \-\-proxypass         | \<pass\>        | The proxy password to use when downloading resources.                            | &nbsp;
+       | \-\-proxyuser         | \<user\>        | The proxy username to use when downloading resources.                            | &nbsp;
+       | \-\-connectionString  | \<connStr\>     | The connection string to the database.                                           | &nbsp;
+       | \-\-dbDriverName      | \<driver\>      | The database driver name.                                                        | &nbsp;
+       | \-\-dbDriverPath      | \<path\>        | The path to the database driver; note, this does not need to be set unless the JAR is outside of the class path. | &nbsp;
+       | \-\-dbPassword        | \<password\>    | The password for connecting to the database.                                     | &nbsp;
+       | \-\-dbUser            | \<user\>        | The username used to connect to the database.                                    | &nbsp;
+ \-d   | \-\-data              | \<path\>        | The location of the data directory used to store persistent data. This option should generally not be set. | &nbsp;
+       | \-\-purge             |                 | Delete the local copy of the NVD. This is used to force a refresh of the data.   | &nbsp;

dependency-check-cli/src/site/markdown/index.md.vm

@@ -0,0 +1,39 @@
+About
+====================
+OWASP dependency-check-cli is an command line tool that uses dependency-check-core to detect
+publicly disclosed vulnerabilities associated with the scanned project dependencies. The tool
+will generate a report listing the dependency, any identified Common Platform Enumeration (CPE)
+identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.
+
+Installation & Usage
+====================
+Download the dependency-check command line tool [here](http://dl.bintray.com/jeremy-long/owasp/dependency-check-${project.version}-release.zip).
+Extract the zip file to a location on your computer and put the 'bin' directory into the
+path environment variable. On \*nix systems you will likely need to make the shell
+script executable:
+
+    $ chmod +777 dependency-check.sh
+
+#set( $H = '#' )
+
+$H$H$H Homebrew
+    $ brew install dependency-check
+
+This puts an executable `dependency-check` script in the `/bin` directory of
+your homebrew installation.
+
+To scan a folder on the system you can run:
+
+$H$H$H Windows
+    dependency-check.bat --project "My App Name" --scan "c:\java\application\lib"
+
+$H$H$H *nix
+    dependency-check.sh --project "My App Name" --scan "/java/application/lib"
+
+To view the command line arguments, see the <a href="arguments.html">arguments page</a>, or you can run:
+
+$H$H$H Windows
+    dependency-check.bat --help
+
+$H$H$H *nix
+    dependency-check.sh --help

dependency-check-cli/src/site/markdown/installation.md.vm

@@ -1,16 +0,0 @@
-Installation & Usage
---------------------
-Downlod the dependency-check command line tool [here](http://dl.bintray.com/jeremy-long/owasp/dependency-check-${project.version}-release.zip).
-Extract the zip file to a location on your computer and put the 'bin' directory into the
-path environment variable. On \*nix systems you will likely need to make the shell
-script executable:
-
-    $ chmod +777 dependency-check.sh
-
-To scan a folder on the system you can run:
-
-### Windows
-    dependency-check.bat --app "My App Name" --scan "c:\java\application\lib"
-
-### \*nix
-    dependency-check.sh --app "My App Name" --scan "/java/application/lib"

dependency-check-cli/src/site/site.xml

@@ -2,33 +2,34 @@
 <!--
 This file is part of dependency-check-cli.
 
-Dependency-check-cli is free software: you can redistribute it and/or modify it
-under the terms of the GNU General Public License as published by the Free
-Software Foundation, either version 3 of the License, or (at your option) any
-later version.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-Dependency-check-cli is distributed in the hope that it will be useful, but
-WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
-FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
-details.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-You should have received a copy of the GNU General Public License along with
-dependency-check-cli. If not, see http://www.gnu.org/licenses/.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
 Copyright (c) 2013 Jeremy Long. All Rights Reserved.
 -->
 <project name="dependency-check-cli">
     <bannerLeft>
-        <name>dependency-check-cli</name>
+        <name>OWASP dependency-check-cli</name>
+        <alt>OWASP dependency-check-cli</alt>
+        <src>./images/dc-cli.svg</src>
     </bannerLeft>
     <body>
         <breadcrumbs>
             <item name="dependency-check" href="../index.html"/>
         </breadcrumbs>
         <menu name="Getting Started">
-            <item name="Installation" href="installation.html"/>
+            <item name="Installation" href="index.html"/>
+            <item name="Configuration" href="arguments.html"/>
         </menu>
-        <menu ref="Project Documentation" />
         <menu ref="reports" />
     </body>
 </project>

dependency-check-cli/src/test/java/org/owasp/dependencycheck/AppTest.java

@@ -0,0 +1,75 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 The OWASP Foundatio. All Rights Reserved.
+ */
+package org.owasp.dependencycheck;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+/**
+ *
+ * @author jeremy
+ */
+public class AppTest {
+
+    public AppTest() {
+    }
+
+    @BeforeClass
+    public static void setUpClass() {
+    }
+
+    @AfterClass
+    public static void tearDownClass() {
+    }
+
+    @Before
+    public void setUp() {
+    }
+
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * Test of ensureCanonicalPath method, of class App.
+     */
+    @Test
+    public void testEnsureCanonicalPath() {
+        String file = "../*.jar";
+        App instance = new App();
+        String result = instance.ensureCanonicalPath(file);
+        assertFalse(result.contains(".."));
+        assertTrue(result.endsWith("*.jar"));
+    }
+
+    /**
+     * Test of ensureCanonicalPath method, of class App.
+     */
+    @Test
+    public void testEnsureCanonicalPath2() {
+        String file = "../some/skip/../path/file.txt";
+        App instance = new App();
+        String expResult = "/some/path/file.txt";
+        String result = instance.ensureCanonicalPath(file);
+        assertTrue("result=" + result, result.endsWith(expResult));
+    }
+}

dependency-check-cli/src/test/java/org/owasp/dependencycheck/CliParserTest.java

@@ -1,24 +1,23 @@
 /*
  * This file is part of Dependency-Check.
  *
- * Dependency-Check is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-Check is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * Dependency-Check. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
-package org.owasp.dependencycheck.cli;
+package org.owasp.dependencycheck;
 
-import org.owasp.dependencycheck.cli.CliParser;
+import org.owasp.dependencycheck.CliParser;
 import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -31,19 +30,22 @@ import org.junit.Assert;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class CliParserTest {
 
     @BeforeClass
     public static void setUpClass() throws Exception {
+        Settings.initialize();
     }
 
     @AfterClass
     public static void tearDownClass() throws Exception {
+        Settings.cleanup(true);
     }
 
     @Before

dependency-check-core/LICENSE.txt

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
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+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
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+      direction or management of such entity, whether by contract or
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+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
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+          include a readable copy of the attribution notices contained
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+          of the NOTICE file are for informational purposes only and
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+          notices within Derivative Works that You distribute, alongside
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+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
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+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
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+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
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+      result of this License or out of the use or inability to use the
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+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
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+      on Your own behalf and on Your sole responsibility, not on behalf
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+
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+
+      To apply the Apache License to your work, attach the following
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+   you may not use this file except in compliance with the License.
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+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
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+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

dependency-check-core/NOTICE.txt

@@ -0,0 +1,18 @@
+dependency-check
+
+Copyright (c) 2012-2013 Jeremy Long. All Rights Reserved.
+
+The licenses for the software listed below can be found in the META-INF/licenses/[dependency name].
+
+This product includes software developed by The Apache Software Foundation (http://www.apache.org/).
+
+This product includes software developed by Jquery.com (http://jquery.com/).
+
+This product includes software developed by Jonathan Hedley (jsoup.org)
+
+This software contains unmodified binary redistributions for H2 database engine (http://www.h2database.com/), which is dual licensed and available under a modified version of the MPL 1.1 (Mozilla Public License) or under the (unmodified) EPL 1.0 (Eclipse Public License).
+An original copy of the license agreement can be found at: http://www.h2database.com/html/license.html
+
+This product includes data from the Common Weakness Enumeration (CWE): http://cwe.mitre.org/
+
+This product downloads and utilizes data from the National Vulnerability Database hosted by NIST: http://nvd.nist.gov/download.cfm

dependency-check-core/README.md

@@ -0,0 +1,28 @@
+Dependency-Check-Core
+================
+
+Dependency-Check-Core is the main engine used by all of the other modules to do the analysis and reporting.
+
+Mailing List
+------------
+
+Subscribe: [dependency-check+subscribe@googlegroups.com] [subscribe]
+
+Post: [dependency-check@googlegroups.com] [post]
+
+Archive: [google group](https://groups.google.com/forum/#!forum/dependency-check)
+
+Copyright & License
+------------
+
+Dependency-Check is Copyright (c) 2012-2014 Jeremy Long. All Rights Reserved.
+
+Permission to modify and redistribute is granted under the terms of the Apache 2.0 license. See the [LICENSE.txt](https://raw.githubusercontent.com/jeremylong/DependencyCheck/master/LICENSE.txt) file for the full license.
+
+Dependency-Check makes use of several other open source libraries. Please see the [NOTICE.txt] [notices] file for more information.
+
+
+  [wiki]: https://github.com/jeremylong/DependencyCheck/wiki
+  [subscribe]: mailto:dependency-check+subscribe@googlegroups.com
+  [post]: mailto:dependency-check@googlegroups.com
+  [notices]: https://raw.githubusercontent.com/jeremylong/DependencyCheck/master/NOTICE.txt

dependency-check-core/config/checkstyle-checks.xml

@@ -1,223 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE module PUBLIC
-          "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
-          "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
-
-<module name="Checker">
-  <!--
-      If you set the basedir property below, then all reported file
-      names will be relative to the specified directory. See
-      http://checkstyle.sourceforge.net/5.x/config.html#Checker
-
-      <property name="basedir" value="${basedir}"/>
-  -->
-
-  <property name="severity" value="error"/>
-
-  <module name="SuppressionFilter">
-    <property name="file" value="${checkstyle.suppressions.file}"/>
-  </module>
-
-  <module name="JavadocPackage">
-    <property name="allowLegacy" value="false"/>
-  </module>
-
-  <module name="Translation">
-    <property name="severity" value="warning"/>
-  </module>
-
-  <module name="FileTabCharacter">
-    <property name="eachLine" value="false"/>
-  </module>
-
-  <module name="FileLength">
-    <property name="fileExtensions" value="java"/>
-  </module>
-
-  <module name="NewlineAtEndOfFile">
-  <property name="fileExtensions" value="java"/>
-  <property name="lineSeparator" value="lf"/>
-  </module>
-
-  <module name="RegexpHeader">
-    <property name="headerFile" value="${checkstyle.header.file}"/>
-    <property name="fileExtensions" value="java"/>
-    <property name="id" value="header"/>
-  </module>
-
-  <module name="RegexpSingleline">
-    <property name="format" value="\s+$"/>
-    <property name="minimum" value="0"/>
-    <property name="maximum" value="0"/>
-  </module>
-
-  <module name="TreeWalker">
-    <property name="tabWidth" value="4"/>
-
-    <module name="AvoidStarImport"/>
-    <module name="ConstantName"/>
-    <module name="EmptyBlock"/>
-    <module name="EmptyForIteratorPad"/>
-    <module name="EqualsHashCode"/>
-    <module name="OneStatementPerLine"/>
-
-    <!-- module name="IllegalCatch"/ -->
-    <!--module name="ImportControl">
-      <property name="file" value="${checkstyle.importcontrol.file}"/>
-    </module-->
-    <module name="IllegalImport"/>
-    <module name="IllegalInstantiation"/>
-    <module name="IllegalThrows"/>
-    <module name="InnerAssignment"/>
-    <module name="JavadocType">
-      <property name="authorFormat" value="\S"/>
-    </module>
-    <module name="JavadocMethod">
-      <property name="allowUndeclaredRTE" value="true"/>
-      <property name="allowThrowsTagsForSubclasses" value="true"/>
-      <property name="allowMissingPropertyJavadoc" value="true"/>
-    </module>
-    <module name="JavadocVariable"/>
-    <module name="JavadocStyle">
-      <property name="scope" value="public"/>
-    </module>
-
-    <module name="LeftCurly">
-      <property name="option" value="eol"/>
-      <property name="tokens" value="CLASS_DEF"/>
-      <property name="tokens" value="CTOR_DEF"/>
-      <property name="tokens" value="INTERFACE_DEF"/>
-      <property name="tokens" value="METHOD_DEF"/>
-      <property name="tokens" value="LITERAL_CATCH"/>
-      <property name="tokens" value="LITERAL_DO"/>
-      <property name="tokens" value="LITERAL_ELSE"/>
-      <property name="tokens" value="LITERAL_FINALLY"/>
-      <property name="tokens" value="LITERAL_FOR"/>
-      <property name="tokens" value="LITERAL_IF"/>
-      <property name="tokens" value="LITERAL_SWITCH"/>
-      <property name="tokens" value="LITERAL_SYNCHRONIZED"/>
-      <property name="tokens" value="LITERAL_TRY"/>
-      <property name="tokens" value="LITERAL_WHILE"/>
-    </module>
-
-    <module name="OuterTypeNumber"/>
-    <module name="LineLength">
-      <property name="ignorePattern" value="^ *\* *[^ ]+$"/>
-    <property name="max" value="150"/>
-    </module>
-
-    <module name="MethodCount">
-      <property name="maxTotal" value="40"/>
-    </module>
-
-    <module name="LocalFinalVariableName"/>
-    <module name="LocalVariableName"/>
-    <module name="MemberName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="MethodLength">
-        <property name="max" value="160"/>
-        <property name="countEmpty" value="false"/>
-    </module>
-    <module name="MethodName"/>
-    <module name="MethodParamPad"/>
-    <module name="ModifierOrder"/>
-    <module name="NeedBraces"/>
-    <module name="NoWhitespaceAfter">
-      <property name="tokens" value="ARRAY_INIT"/>
-      <property name="tokens" value="BNOT"/>
-      <property name="tokens" value="DEC"/>
-      <property name="tokens" value="DOT"/>
-      <property name="tokens" value="INC"/>
-      <property name="tokens" value="LNOT"/>
-      <property name="tokens" value="UNARY_MINUS"/>
-      <property name="tokens" value="UNARY_PLUS"/>
-    </module>
-
-    <module name="NoWhitespaceBefore"/>
-    <module name="NoWhitespaceBefore">
-      <property name="tokens" value="DOT"/>
-      <property name="allowLineBreaks" value="true"/>
-    </module>
-
-    <module name="OperatorWrap"/>
-    <module name="OperatorWrap">
-      <property name="tokens" value="ASSIGN"/>
-      <property name="tokens" value="DIV_ASSIGN"/>
-      <property name="tokens" value="PLUS_ASSIGN"/>
-      <property name="tokens" value="MINUS_ASSIGN"/>
-      <property name="tokens" value="STAR_ASSIGN"/>
-      <property name="tokens" value="MOD_ASSIGN"/>
-      <property name="tokens" value="SR_ASSIGN"/>
-      <property name="tokens" value="BSR_ASSIGN"/>
-      <property name="tokens" value="SL_ASSIGN"/>
-      <property name="tokens" value="BXOR_ASSIGN"/>
-      <property name="tokens" value="BOR_ASSIGN"/>
-      <property name="tokens" value="BAND_ASSIGN"/>
-      <property name="option" value="eol"/>
-    </module>
-    <module name="PackageName"/>
-    <module name="ParameterName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="ParameterNumber">
-      <property name="id" value="paramNum"/>
-    </module>
-    <module name="ParenPad"/>
-    <module name="TypecastParenPad"/>
-    <module name="RedundantImport"/>
-    <module name="RedundantModifier"/>
-    <module name="RightCurly">
-      <property name="option" value="same"/>
-    </module>
-    <module name="SimplifyBooleanExpression"/>
-    <module name="SimplifyBooleanReturn"/>
-    <module name="StaticVariableName">
-      <property name="format" value="^[a-z][a-zA-Z0-9]*$"/>
-    </module>
-    <module name="TypeName"/>
-    <module name="UnusedImports"/>
-    <module name="UpperEll"/>
-    <module name="VisibilityModifier"/>
-    <module name="WhitespaceAfter"/>
-    <module name="WhitespaceAround"/>
-    <module name="GenericWhitespace"/>
-    <module name="FinalClass"/>
-    <module name="MissingSwitchDefault"/>
-    <!--module name="MagicNumber"/-->
-    <!--module name="Indentation">
-      <property name="basicOffset" value="4"/>
-      <property name="braceAdjustment" value="0"/>
-      <property name="caseIndent" value="0"/>
-    </module-->
-    <module name="ArrayTrailingComma"/>
-    <module name="FinalLocalVariable"/>
-    <module name="EqualsAvoidNull"/>
-    <module name="ParameterAssignment"/>
-
-    <!-- Generates quite a few errors -->
-    <module name="CyclomaticComplexity">
-      <property name="severity" value="ignore"/>
-    </module>
-
-    <module name="NestedForDepth">
-      <property name="max" value="2"/>
-    </module>
-    <module name="NestedIfDepth">
-      <property name="max" value="4"/>
-    </module>
-    <module name="NestedTryDepth">
-        <property name="max" value="2"/>
-    </module>
-    <!--module name="ExplicitInitialization"/-->
-    <module name="AnnotationUseStyle"/>
-    <module name="MissingDeprecated"/>
-    <module name="MissingOverride">
-      <property name="javaFiveCompatibility" value="true"/>
-    </module>
-    <module name="PackageAnnotation"/>
-    <module name="SuppressWarnings"/>
-    <module name="OuterTypeFilename"/>
-    <module name="HideUtilityClassConstructor"/>
-  </module>
-</module>

dependency-check-core/config/checkstyle-header.txt

@@ -1,19 +0,0 @@
-^/\*\s*$
-^ \* This file is part of dependency-check-core\.\s*$
-^ \*\s*$
-^ \* Dependency-check-core is free software\: you can redistribute it and/or modify it\s*$
-^ \* under the terms of the GNU General Public License as published by the Free\s*$
-^ \* Software Foundation, either version 3 of the License, or \(at your option\) any\s*$
-^ \* later version\.
-^ \*\s*$
-^ \* Dependency-check-core is distributed in the hope that it will be useful, but\s*$
-^ \* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or\s*$
-^ \* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more\s*$
-^ \* details\.\s*$
-^ \*\s*$
-^ \* You should have received a copy of the GNU General Public License along with\s*$
-^ \* dependency-check-core\. If not, see http://www.gnu.org/licenses/\.\s*$
-^ \*\s*$
-^ \* Copyright \(c\) 201[23] (Jeremy Long|Steve Springett)\. All Rights Reserved\.\s*$
-^ \*/\s*$
-^package

dependency-check-core/config/checkstyle-suppressions.xml

@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-
-<!DOCTYPE suppressions PUBLIC
-     "-//Puppy Crawl//DTD Suppressions 1.0//EN"
-     "http://www.puppycrawl.com/dtds/suppressions_1_0.dtd">
-
-<suppressions>
-    <suppress checks=".*" files=".*[\\/]package-info\.java" />
-    <suppress checks=".*" files=".*org[\\/]owasp[\\/]dependencycheck[\\/]utils[\\/]Filter.java" />
-    <suppress checks=".*" files=".*org[\\/]owasp[\\/]dependencycheck[\\/]utils[\\/]Checksum.java" />
-    <suppress checks=".*" files=".*[\\/]generated[\\/].*.java" />
-</suppressions>

dependency-check-core/pom.xml

@@ -1,34 +1,33 @@
 <!--
-Copyright (c) 2012 - Jeremy Long
+This file is part of dependency-check-core.
 
-This file is part of Dependency-Check.
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-Dependency-Check is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-Dependency-Check is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
-You should have received a copy of the GNU General Public License
-along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
+Copyright (c) 2012 Jeremy Long. All Rights Reserved.
 -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.0.5</version>
+        <version>1.3.6</version>
     </parent>
 
     <artifactId>dependency-check-core</artifactId>
     <packaging>jar</packaging>
 
     <name>Dependency-Check Core</name>
+    <description>dependency-check-core is the engine and reporting tool used to identify and report if there are any known, publicly disclosed vulnerabilities in the scanned project's dependencies. The engine extracts meta-data from the dependencies and uses this to do fuzzy key-word matching against the Common Platfrom Enumeration (CPE), if any CPE identifiers are found the associated Common Vulnerability and Exposure (CVE) entries are added to the generated report.</description>
     <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
     <distributionManagement>
         <site>
@@ -71,12 +70,22 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
             </resource>
         </resources>
         <testResources>
+            <testResource>
+                <directory>src/test/resources</directory>
+                <includes>
+                    <include>**/*.properties</include>
+                </includes>
+                <filtering>true</filtering>
+            </testResource>
             <testResource>
                 <directory>${basedir}/../src/test/resources</directory>
                 <filtering>false</filtering>
             </testResource>
             <testResource>
                 <directory>${basedir}/src/test/resources</directory>
+                <excludes>
+                    <exclude>**/mysql-connector-java-5.1.27-bin.jar</exclude>
+                </excludes>
                 <filtering>false</filtering>
             </testResource>
         </testResources>
@@ -84,7 +93,6 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>
-                <version>2.8</version>
                 <executions>
                     <execution>
                         <phase>generate-resources</phase>
@@ -93,7 +101,7 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
                         </goals>
                         <configuration>
                             <outputDirectory>${project.build.directory}/test-classes</outputDirectory>
-                            <includeScope>provided</includeScope>
+                            <includeScope>test</includeScope>
                         </configuration>
                     </execution>
                 </executions>
@@ -101,40 +109,27 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>2.4</version>
                 <executions>
-                    <execution>
-                        <id>jar</id>
-                        <phase>package</phase>
-                        <goals>
-                            <goal>jar</goal>
-                        </goals>
-                    </execution>
                     <execution>
                         <id>test-jar</id>
                         <phase>package</phase>
                         <goals>
                             <goal>test-jar</goal>
                         </goals>
+                        <configuration>
+                            <includes>
+                                <include>**/*.class</include>
+                            </includes>
+                        </configuration>
                     </execution>
                 </executions>
-                <configuration>
-                    <archive>
-                        <manifest>
-                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
-                        </manifest>
-                    </archive>
-                    <excludes>
-                        <exclude>**/checkstyle*</exclude>
-                    </excludes>
-                </configuration>
             </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>cobertura-maven-plugin</artifactId>
-                <version>2.5.2</version>
                 <configuration>
                     <instrumentation>
+                        <!--ignoreTrivial>true</ignoreTrivial-->
                         <ignores>
                             <ignore>.*\$KEYS\.class</ignore>
                             <ignore>.*\$Element\.class</ignore>
@@ -182,14 +177,9 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
-                <version>2.14</version>
                 <configuration>
+                    <argLine>-Dfile.encoding=UTF-8</argLine>
                     <systemProperties>
-                        <property>
-                            <name>net.sourceforge.cobertura.datafile</name>
-                            <value>${project.build.directory}/cobertura/cobertura.ser</value>
-                            <workingDirectory>target</workingDirectory>
-                        </property>
                         <property>
                             <name>data.directory</name>
                             <value>${project.build.directory}/data</value>
@@ -201,347 +191,216 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
                     </systemProperties>
                     <excludes>
                         <exclude>**/*IntegrationTest.java</exclude>
+                        <exclude>**/*MySQLTest.java</exclude>
                     </excludes>
                 </configuration>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
-                <version>2.14</version>
                 <configuration>
                     <systemProperties>
                         <property>
                             <name>data.directory</name>
                             <value>${project.build.directory}/data</value>
                         </property>
+                        <property>
+                            <name>temp.directory</name>
+                            <value>${project.build.directory}/temp</value>
+                        </property>
                     </systemProperties>
-                    <includes>
-                        <include>**/*IntegrationTest.java</include>
-                    </includes>
-                </configuration>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>integration-test</goal>
-                            <goal>verify</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-site-plugin</artifactId>
-                <version>3.3</version>
-                <dependencies>
-                    <dependency>
-                        <groupId>org.apache.maven.doxia</groupId>
-                        <artifactId>doxia-module-markdown</artifactId>
-                        <version>1.4</version>
-                    </dependency>
-                </dependencies>
-                <configuration>
-                    <skipDeploy>true</skipDeploy>
-                    <reportPlugins>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-project-info-reports-plugin</artifactId>
-                            <version>2.6</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>index</report>
-                                        <report>summary</report>
-                                        <report>license</report>
-                                        <report>help</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-javadoc-plugin</artifactId>
-                            <version>2.9</version>
-                            <reportSets>
-                                <reportSet>
-                                    <id>default</id>
-                                    <reports>
-                                        <report>javadoc</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>versions-maven-plugin</artifactId>
-                            <version>2.0</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>dependency-updates-report</report>
-                                        <report>plugin-updates-report</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-jxr-plugin</artifactId>
-                            <version>2.3</version>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>cobertura-maven-plugin</artifactId>
-                            <version>2.5.2</version>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-surefire-report-plugin</artifactId>
-                            <version>2.14</version>
-                            <reportSets>
-                                <reportSet>
-                                    <reports>
-                                        <report>report-only</report>
-                                    </reports>
-                                </reportSet>
-                                <reportSet>
-                                    <id>integration-tests</id>
-                                    <reports>
-                                        <report>report-only</report>
-                                        <report>failsafe-report-only</report>
-                                    </reports>
-                                </reportSet>
-                            </reportSets>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>taglist-maven-plugin</artifactId>
-                            <version>2.4</version>
-                            <configuration>
-                                <tagListOptions>
-                                    <tagClasses>
-                                        <tagClass>
-                                            <displayName>Todo Work</displayName>
-                                            <tags>
-                                                <tag>
-                                                    <matchString>todo</matchString>
-                                                    <matchType>ignoreCase</matchType>
-                                                </tag>
-                                                <tag>
-                                                    <matchString>FIXME</matchString>
-                                                    <matchType>exact</matchType>
-                                                </tag>
-                                            </tags>
-                                        </tagClass>
-                                    </tagClasses>
-                                </tagListOptions>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-checkstyle-plugin</artifactId>
-                            <version>2.10</version>
-                            <configuration>
-                                <enableRulesSummary>false</enableRulesSummary>
-                                <configLocation>${basedir}/config/checkstyle-checks.xml</configLocation>
-                                <headerLocation>${basedir}/config/checkstyle-header.txt</headerLocation>
-                                <suppressionsLocation>${basedir}/config/checkstyle-suppressions.xml</suppressionsLocation>
-                                <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-pmd-plugin</artifactId>
-                            <version>3.0.1</version>
-                            <configuration>
-                                <targetJdk>1.6</targetJdk>
-                                <linkXref>true</linkXref>
-                                <sourceEncoding>utf-8</sourceEncoding>
-                                <excludes>
-                                    <exclude>**/generated/*.java</exclude>
-                                </excludes>
-                            </configuration>
-                        </plugin>
-                        <plugin>
-                            <groupId>org.codehaus.mojo</groupId>
-                            <artifactId>findbugs-maven-plugin</artifactId>
-                            <version>2.5.2</version>
-                        </plugin>
-                    </reportPlugins>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <version>2.3.2</version>
-                <configuration>
-                    <showDeprecation>false</showDeprecation>
                 </configuration>
             </plugin>
         </plugins>
     </build>
+    <reporting>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-report-plugin</artifactId>
+                <reportSets>
+                    <reportSet>
+                        <id>integration-tests</id>
+                        <reports>
+                            <report>report-only</report>
+                            <report>failsafe-report-only</report>
+                        </reports>
+                    </reportSet>
+                </reportSets>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                <version>${reporting.checkstyle-plugin.version}</version>
+                <configuration>
+                    <enableRulesSummary>false</enableRulesSummary>
+                    <enableFilesSummary>false</enableFilesSummary>
+                    <configLocation>${basedir}/../src/main/config/checkstyle-checks.xml</configLocation>
+                    <headerLocation>${basedir}/../src/main/config/checkstyle-header.txt</headerLocation>
+                    <suppressionsLocation>${basedir}/../src/main/config/checkstyle-suppressions.xml</suppressionsLocation>
+                    <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-pmd-plugin</artifactId>
+                <version>${reporting.pmd-plugin.version}</version>
+                <configuration>
+                    <targetJdk>1.6</targetJdk>
+                    <linkXref>true</linkXref>
+                    <sourceEncoding>utf-8</sourceEncoding>
+                    <excludes>
+                        <exclude>**/generated/*.java</exclude>
+                    </excludes>
+                    <rulesets>
+                        <ruleset>../src/main/config/dcrules.xml</ruleset>
+                        <ruleset>/rulesets/java/basic.xml</ruleset>
+                        <ruleset>/rulesets/java/imports.xml</ruleset>
+                        <ruleset>/rulesets/java/unusedcode.xml</ruleset>
+                    </rulesets>
+                </configuration>
+            </plugin>
+        </plugins>
+    </reporting>
     <dependencies>
-        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-test-framework</artifactId>
-            <version>4.3.1</version>
-            <scope>test</scope>
-        </dependency>
+        <!-- Note, to stay compatible with Jenkins installations only JARs compiled to 1.6 can be used -->
         <dependency>
             <groupId>com.google.code.findbugs</groupId>
             <artifactId>annotations</artifactId>
-            <version>2.0.1</version>
             <optional>true</optional>
         </dependency>
         <dependency>
-            <groupId>commons-cli</groupId>
-            <artifactId>commons-cli</artifactId>
-            <version>1.2</version>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <!-- Set this to test so that each project that uses this has to have its own implementation of SLF4J -->
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+            <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-            <version>2.4</version>
-        </dependency>
-        <dependency>
-            <groupId>commons-lang</groupId>
-            <artifactId>commons-lang</artifactId>
-            <version>2.5</version>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.parent.version}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-            <version>4.3.1</version>
+            <artifactId>lucene-test-framework</artifactId>
+            <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-analyzers-common</artifactId>
-            <version>4.3.1</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-queryparser</artifactId>
-            <version>4.3.1</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.velocity</groupId>
-            <artifactId>velocity</artifactId>
-            <version>1.7</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.velocity</groupId>
-            <artifactId>velocity-tools</artifactId>
-            <version>2.0</version>
-            <!-- very limited use of the velocity-tools, not all of the dependencies are needed-->
-            <exclusions>
-                <exclusion>
-                    <groupId>commons-chain</groupId>
-                    <artifactId>commons-chain</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>javax.servlet</groupId>
-                    <artifactId>servlet-api</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>commons-validator</groupId>
-                    <artifactId>commons-validator</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>dom4j</groupId>
-                    <artifactId>dom4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>sslext</groupId>
-                    <artifactId>sslext</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.struts</groupId>
-                    <artifactId>struts-core</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>antlr</groupId>
-                    <artifactId>antlr</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.struts</groupId>
-                    <artifactId>struts-taglib</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.struts</groupId>
-                    <artifactId>struts-tiles</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>com.h2database</groupId>
-            <artifactId>h2</artifactId>
-            <version>1.3.172</version>
-        </dependency>
-        <dependency>
-            <groupId>org.jsoup</groupId>
-            <artifactId>jsoup</artifactId>
-            <version>1.7.2</version>
-            <type>jar</type>
+            <groupId>org.jmockit</groupId>
+            <artifactId>jmockit</artifactId>
+            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-compress</artifactId>
-            <version>1.5</version>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-analyzers-common</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-queryparser</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.velocity</groupId>
+            <artifactId>velocity</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.h2database</groupId>
+            <artifactId>h2</artifactId>
+            <scope>runtime</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish</groupId>
+            <artifactId>javax.json</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.jsoup</groupId>
+            <artifactId>jsoup</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.sun.mail</groupId>
+            <artifactId>mailapi</artifactId>
         </dependency>
         <!-- The following dependencies are only used during testing -->
         <dependency>
             <groupId>org.apache.maven.scm</groupId>
             <artifactId>maven-scm-provider-cvsexe</artifactId>
             <version>1.8.1</version>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-webmvc</artifactId>
             <version>2.5.5</version>
-            <scope>provided</scope>
+            <scope>test</scope>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.security</groupId>
+            <artifactId>spring-security-web</artifactId>
+            <version>3.0.0.RELEASE</version>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>com.hazelcast</groupId>
             <artifactId>hazelcast</artifactId>
             <version>2.5</version>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>net.sf.ehcache</groupId>
             <artifactId>ehcache-core</artifactId>
             <version>2.2.0</version>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.struts</groupId>
             <artifactId>struts2-core</artifactId>
             <version>2.1.2</version>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.mortbay.jetty</groupId>
             <artifactId>jetty</artifactId>
             <version>6.1.0</version>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.axis2</groupId>
             <artifactId>axis2-spring</artifactId>
             <version>1.4.1</version>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.axis2</groupId>
             <artifactId>axis2-adb</artifactId>
             <version>1.4.1</version>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
@@ -549,7 +408,7 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
             <artifactId>daytrader-ear</artifactId>
             <version>2.1.7</version>
             <type>ear</type>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
@@ -557,7 +416,7 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
             <artifactId>war</artifactId>
             <version>4.0</version>
             <type>war</type>
-            <scope>provided</scope>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
         <dependency>
@@ -565,8 +424,313 @@ along with Dependency-Check.  If not, see <http://www.gnu.org/licenses />.
             <artifactId>dojo-war</artifactId>
             <version>1.3.0</version>
             <type>war</type>
-            <scope>provided</scope>
+            <scope>test</scope>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.openjpa</groupId>
+            <artifactId>openjpa</artifactId>
+            <version>2.0.1</version>
+            <scope>test</scope>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>com.google.inject</groupId>
+            <artifactId>guice</artifactId>
+            <version>3.0</version>
+            <scope>test</scope>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.retry</groupId>
+            <artifactId>spring-retry</artifactId>
+            <version>1.1.0.RELEASE</version>
+            <scope>test</scope>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>uk.ltd.getahead</groupId>
+            <artifactId>dwr</artifactId>
+            <version>1.1.1</version>
+            <scope>test</scope>
+            <optional>true</optional>
+        </dependency>
+        <dependency>
+            <groupId>xalan</groupId>
+            <artifactId>xalan</artifactId>
+            <version>2.7.0</version>
+            <scope>test</scope>
             <optional>true</optional>
         </dependency>
     </dependencies>
+    <profiles>
+        <profile>
+            <id>MySQL-IntegrationTest</id>
+            <activation>
+                <property>
+                    <name>mysql</name>
+                </property>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-surefire-plugin</artifactId>
+                        <configuration>
+                            <skip>true</skip>
+                        </configuration>
+                    </plugin>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-failsafe-plugin</artifactId>
+                        <configuration>
+                            <systemProperties>
+                                <property>
+                                    <name>data.driver_path</name>
+                                    <value>${driver_path}</value>
+                                </property>
+                                <property>
+                                    <name>data.driver_name</name>
+                                    <value>${driver_name}</value>
+                                </property>
+                                <property>
+                                    <name>data.connection_string</name>
+                                    <value>${connection_string}</value>
+                                </property>
+                            </systemProperties>
+                            <includes>
+                                <include>**/*MySQLTest.java</include>
+                            </includes>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <goals>
+                                    <goal>integration-test</goal>
+                                    <goal>verify</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <profile>
+            <id>Postgresql-IntegrationTest</id>
+            <activation>
+                <property>
+                    <name>postgresql</name>
+                </property>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>org.postgresql</groupId>
+                    <artifactId>postgresql</artifactId>
+                    <version>9.4-1204-jdbc42</version>
+                </dependency>
+            </dependencies>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-surefire-plugin</artifactId>
+                        <configuration>
+                            <skip>true</skip>
+                        </configuration>
+                    </plugin>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-failsafe-plugin</artifactId>
+                        <configuration>
+                            <systemProperties>
+                                <property>
+                                    <name>data.driver_path</name>
+                                    <value>${driver_path}</value>
+                                </property>
+                                <property>
+                                    <name>data.driver_name</name>
+                                    <value>${driver_name}</value>
+                                </property>
+                                <property>
+                                    <name>data.connection_string</name>
+                                    <value>${connection_string}</value>
+                                </property>
+                            </systemProperties>
+                            <includes>
+                                <include>**/*MySQLTest.java</include>
+                            </includes>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <goals>
+                                    <goal>integration-test</goal>
+                                    <goal>verify</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <profile>
+            <!-- The following profile adds additional
+            dependencies that are only used during testing.
+            Additionally, these are only added when using "allTests" to
+            make the build slightly faster in most cases. -->
+            <id>False Positive Tests</id>
+            <activation>
+                <property>
+                    <name>allTests</name>
+                </property>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>org.apache.xmlgraphics</groupId>
+                    <artifactId>batik-util</artifactId>
+                    <version>1.7</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.thoughtworks.xstream</groupId>
+                    <artifactId>xstream</artifactId>
+                    <version>1.4.2</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.apache.ws.security</groupId>
+                    <artifactId>wss4j</artifactId>
+                    <version>1.5.7</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.ganyo</groupId>
+                    <artifactId>gcm-server</artifactId>
+                    <version>1.0.2</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.python</groupId>
+                    <artifactId>jython-standalone</artifactId>
+                    <version>2.7-b1</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.jruby</groupId>
+                    <artifactId>jruby-complete</artifactId>
+                    <version>1.7.4</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.jruby</groupId>
+                    <artifactId>jruby</artifactId>
+                    <version>1.6.3</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.glassfish.jersey.core</groupId>
+                    <artifactId>jersey-client</artifactId>
+                    <version>2.12</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.sun.jersey</groupId>
+                    <artifactId>jersey-client</artifactId>
+                    <version>1.11.1</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.sun.faces</groupId>
+                    <artifactId>jsf-impl</artifactId>
+                    <version>2.2.8-02</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.google.inject</groupId>
+                    <artifactId>guice</artifactId>
+                    <version>3.0</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.opensaml</groupId>
+                    <artifactId>xmltooling</artifactId>
+                    <version>1.4.1</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.springframework</groupId>
+                    <artifactId>spring-webmvc</artifactId>
+                    <version>3.2.12.RELEASE</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.google.code.gson</groupId>
+                    <artifactId>gson</artifactId>
+                    <version>2.3.1</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.google.gerrit</groupId>
+                    <artifactId>gerrit-extension-api</artifactId>
+                    <version>2.11</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.google.apis</groupId>
+                    <artifactId>google-api-services-sqladmin</artifactId>
+                    <version>v1beta4-rev5-1.20.0</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.google.gwt.google-apis</groupId>
+                    <artifactId>gwt-gears</artifactId>
+                    <version>1.2.1</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.mozilla</groupId>
+                    <artifactId>rhino</artifactId>
+                    <version>1.7.6</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.microsoft.windowsazure</groupId>
+                    <artifactId>microsoft-azure-api-media</artifactId>
+                    <version>0.5.0</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.microsoft.windowsazure</groupId>
+                    <artifactId>microsoft-azure-api-management-sql</artifactId>
+                    <version>0.5.0</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.microsoft.bingads</groupId>
+                    <artifactId>microsoft.bingads</artifactId>
+                    <version>9.3.4</version>
+                    <scope>test</scope>
+                    <optional>true</optional>
+                </dependency>
+            </dependencies>
+        </profile>
+    </profiles>
 </project>

dependency-check-core/src/main/java/org/owasp/dependencycheck/Engine.java

@@ -1,121 +1,137 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck;
 
-import java.util.EnumMap;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import org.owasp.dependencycheck.analyzer.AnalysisException;
 import org.owasp.dependencycheck.analyzer.AnalysisPhase;
 import org.owasp.dependencycheck.analyzer.Analyzer;
 import org.owasp.dependencycheck.analyzer.AnalyzerService;
-import org.owasp.dependencycheck.data.CachedWebDataSource;
-import org.owasp.dependencycheck.data.NoDataException;
-import org.owasp.dependencycheck.data.UpdateException;
-import org.owasp.dependencycheck.data.UpdateService;
-import org.owasp.dependencycheck.data.cpe.CpeIndexReader;
+import org.owasp.dependencycheck.analyzer.FileTypeAnalyzer;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.data.nvdcve.ConnectionFactory;
+import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.update.CachedWebDataSource;
+import org.owasp.dependencycheck.data.update.UpdateService;
+import org.owasp.dependencycheck.data.update.exception.UpdateException;
 import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.utils.FileUtils;
+import org.owasp.dependencycheck.exception.NoDataException;
 import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.EnumMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 /**
- * Scans files, directories, etc. for Dependencies. Analyzers are loaded and
- * used to process the files found by the scan, if a file is encountered and an
- * Analyzer is associated with the file type then the file is turned into a
- * dependency.
+ * Scans files, directories, etc. for Dependencies. Analyzers are loaded and used to process the files found by the scan, if a
+ * file is encountered and an Analyzer is associated with the file type then the file is turned into a dependency.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
-public class Engine {
+public class Engine implements FileFilter {
 
     /**
      * The list of dependencies.
      */
-    private final List<Dependency> dependencies = new ArrayList<Dependency>();
+    private List<Dependency> dependencies = new ArrayList<Dependency>();
     /**
      * A Map of analyzers grouped by Analysis phase.
      */
-    private final EnumMap<AnalysisPhase, List<Analyzer>> analyzers =
-            new EnumMap<AnalysisPhase, List<Analyzer>>(AnalysisPhase.class);
+    private Map<AnalysisPhase, List<Analyzer>> analyzers = new EnumMap<AnalysisPhase, List<Analyzer>>(AnalysisPhase.class);
+
     /**
-     * A set of extensions supported by the analyzers.
+     * A Map of analyzers grouped by Analysis phase.
      */
-    private final Set<String> extensions = new HashSet<String>();
+    private Set<FileTypeAnalyzer> fileTypeAnalyzers = new HashSet<FileTypeAnalyzer>();
+
+    /**
+     * The ClassLoader to use when dynamically loading Analyzer and Update services.
+     */
+    private ClassLoader serviceClassLoader = Thread.currentThread().getContextClassLoader();
+    /**
+     * The Logger for use throughout the class.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(Engine.class);
 
     /**
      * Creates a new Engine.
+     *
+     * @throws DatabaseException thrown if there is an error connecting to the database
      */
-    public Engine() {
-        boolean autoUpdate = true;
-        try {
-            autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
-        } catch (InvalidSettingException ex) {
-            Logger.getLogger(Engine.class.getName()).log(Level.FINE, "Invalid setting for auto-update; using true.");
-        }
-        if (autoUpdate) {
-            doUpdates();
-        }
-        loadAnalyzers();
+    public Engine() throws DatabaseException {
+        initializeEngine();
     }
 
     /**
      * Creates a new Engine.
      *
-     * @param autoUpdate indicates whether or not data should be updated from
-     * the Internet
-     * @deprecated This function should no longer be used; the autoupdate flag
-     * should be set using:
-     * <code>Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, value);</code>
+     * @param serviceClassLoader a reference the class loader being used
+     * @throws DatabaseException thrown if there is an error connecting to the database
      */
-    @Deprecated
-    public Engine(boolean autoUpdate) {
-        if (autoUpdate) {
-            doUpdates();
-        }
+    public Engine(ClassLoader serviceClassLoader) throws DatabaseException {
+        this.serviceClassLoader = serviceClassLoader;
+        initializeEngine();
+    }
+
+    /**
+     * Creates a new Engine using the specified classloader to dynamically load Analyzer and Update services.
+     *
+     * @throws DatabaseException thrown if there is an error connecting to the database
+     */
+    protected final void initializeEngine() throws DatabaseException {
+        ConnectionFactory.initialize();
         loadAnalyzers();
     }
 
     /**
-     * Loads the analyzers specified in the configuration file (or system
-     * properties).
+     * Properly cleans up resources allocated during analysis.
+     */
+    public void cleanup() {
+        ConnectionFactory.cleanup();
+    }
+
+    /**
+     * Loads the analyzers specified in the configuration file (or system properties).
      */
     private void loadAnalyzers() {
-
+        if (!analyzers.isEmpty()) {
+            return;
+        }
         for (AnalysisPhase phase : AnalysisPhase.values()) {
             analyzers.put(phase, new ArrayList<Analyzer>());
         }
 
-        final AnalyzerService service = AnalyzerService.getInstance();
+        final AnalyzerService service = new AnalyzerService(serviceClassLoader);
         final Iterator<Analyzer> iterator = service.getAnalyzers();
         while (iterator.hasNext()) {
             final Analyzer a = iterator.next();
             analyzers.get(a.getAnalysisPhase()).add(a);
-            if (a.getSupportedExtensions() != null) {
-                extensions.addAll(a.getSupportedExtensions());
+            if (a instanceof FileTypeAnalyzer) {
+                this.fileTypeAnalyzers.add((FileTypeAnalyzer) a);
             }
         }
     }
@@ -140,242 +156,292 @@ public class Engine {
     }
 
     /**
-     * Scans an array of files or directories. If a directory is specified, it
-     * will be scanned recursively. Any dependencies identified are added to the
-     * dependency collection.
+     * Sets the dependencies.
      *
-     * @since v0.3.2.5
-     *
-     * @param paths an array of paths to files or directories to be analyzed.
+     * @param dependencies the dependencies
      */
-    public void scan(String[] paths) {
+    public void setDependencies(List<Dependency> dependencies) {
+        this.dependencies = dependencies;
+    }
+
+    /**
+     * Scans an array of files or directories. If a directory is specified, it will be scanned recursively. Any dependencies
+     * identified are added to the dependency collection.
+     *
+     * @param paths an array of paths to files or directories to be analyzed
+     * @return the list of dependencies scanned
+     * @since v0.3.2.5
+     */
+    public List<Dependency> scan(String[] paths) {
+        final List<Dependency> deps = new ArrayList<Dependency>();
         for (String path : paths) {
-            final File file = new File(path);
-            scan(file);
-        }
-    }
-
-    /**
-     * Scans a given file or directory. If a directory is specified, it will be
-     * scanned recursively. Any dependencies identified are added to the
-     * dependency collection.
-     *
-     * @param path the path to a file or directory to be analyzed.
-     */
-    public void scan(String path) {
-        final File file = new File(path);
-        scan(file);
-    }
-
-    /**
-     * Scans an array of files or directories. If a directory is specified, it
-     * will be scanned recursively. Any dependencies identified are added to the
-     * dependency collection.
-     *
-     * @since v0.3.2.5
-     *
-     * @param files an array of paths to files or directories to be analyzed.
-     */
-    public void scan(File[] files) {
-        for (File file : files) {
-            scan(file);
-        }
-    }
-
-    /**
-     * Scans a list of files or directories. If a directory is specified, it
-     * will be scanned recursively. Any dependencies identified are added to the
-     * dependency collection.
-     *
-     * @since v0.3.2.5
-     *
-     * @param files a set of paths to files or directories to be analyzed.
-     */
-    public void scan(Set<File> files) {
-        for (File file : files) {
-            scan(file);
-        }
-    }
-
-    /**
-     * Scans a list of files or directories. If a directory is specified, it
-     * will be scanned recursively. Any dependencies identified are added to the
-     * dependency collection.
-     *
-     * @since v0.3.2.5
-     *
-     * @param files a set of paths to files or directories to be analyzed.
-     */
-    public void scan(List<File> files) {
-        for (File file : files) {
-            scan(file);
-        }
-    }
-
-    /**
-     * Scans a given file or directory. If a directory is specified, it will be
-     * scanned recursively. Any dependencies identified are added to the
-     * dependency collection.
-     *
-     * @since v0.3.2.4
-     *
-     * @param file the path to a file or directory to be analyzed.
-     */
-    public void scan(File file) {
-        if (file.exists()) {
-            if (file.isDirectory()) {
-                scanDirectory(file);
-            } else {
-                scanFile(file);
+            final List<Dependency> d = scan(path);
+            if (d != null) {
+                deps.addAll(d);
             }
         }
+        return deps;
     }
 
     /**
-     * Recursively scans files and directories. Any dependencies identified are
-     * added to the dependency collection.
+     * Scans a given file or directory. If a directory is specified, it will be scanned recursively. Any dependencies identified
+     * are added to the dependency collection.
      *
-     * @param dir the directory to scan.
+     * @param path the path to a file or directory to be analyzed
+     * @return the list of dependencies scanned
      */
-    protected void scanDirectory(File dir) {
-        final File[] files = dir.listFiles();
-        if (files != null) {
-            for (File f : files) {
-                if (f.isDirectory()) {
-                    scanDirectory(f);
-                } else {
-                    scanFile(f);
+    public List<Dependency> scan(String path) {
+        final File file = new File(path);
+        return scan(file);
+    }
+
+    /**
+     * Scans an array of files or directories. If a directory is specified, it will be scanned recursively. Any dependencies
+     * identified are added to the dependency collection.
+     *
+     * @param files an array of paths to files or directories to be analyzed.
+     * @return the list of dependencies
+     * @since v0.3.2.5
+     */
+    public List<Dependency> scan(File[] files) {
+        final List<Dependency> deps = new ArrayList<Dependency>();
+        for (File file : files) {
+            final List<Dependency> d = scan(file);
+            if (d != null) {
+                deps.addAll(d);
+            }
+        }
+        return deps;
+    }
+
+    /**
+     * Scans a collection of files or directories. If a directory is specified, it will be scanned recursively. Any dependencies
+     * identified are added to the dependency collection.
+     *
+     * @param files a set of paths to files or directories to be analyzed
+     * @return the list of dependencies scanned
+     * @since v0.3.2.5
+     */
+    public List<Dependency> scan(Collection<File> files) {
+        final List<Dependency> deps = new ArrayList<Dependency>();
+        for (File file : files) {
+            final List<Dependency> d = scan(file);
+            if (d != null) {
+                deps.addAll(d);
+            }
+        }
+        return deps;
+    }
+
+    /**
+     * Scans a given file or directory. If a directory is specified, it will be scanned recursively. Any dependencies identified
+     * are added to the dependency collection.
+     *
+     * @param file the path to a file or directory to be analyzed
+     * @return the list of dependencies scanned
+     * @since v0.3.2.4
+     */
+    public List<Dependency> scan(File file) {
+        if (file.exists()) {
+            if (file.isDirectory()) {
+                return scanDirectory(file);
+            } else {
+                final Dependency d = scanFile(file);
+                if (d != null) {
+                    final List<Dependency> deps = new ArrayList<Dependency>();
+                    deps.add(d);
+                    return deps;
                 }
             }
         }
+        return null;
     }
 
     /**
-     * Scans a specified file. If a dependency is identified it is added to the
-     * dependency collection.
+     * Recursively scans files and directories. Any dependencies identified are added to the dependency collection.
      *
-     * @param file The file to scan.
+     * @param dir the directory to scan
+     * @return the list of Dependency objects scanned
      */
-    protected void scanFile(File file) {
-        if (!file.isFile()) {
-            final String msg = String.format("Path passed to scanFile(File) is not a file: %s. Skipping the file.", file.toString());
-            Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
-            return;
+    protected List<Dependency> scanDirectory(File dir) {
+        final File[] files = dir.listFiles();
+        final List<Dependency> deps = new ArrayList<Dependency>();
+        if (files != null) {
+            for (File f : files) {
+                if (f.isDirectory()) {
+                    final List<Dependency> d = scanDirectory(f);
+                    if (d != null) {
+                        deps.addAll(d);
+                    }
+                } else {
+                    final Dependency d = scanFile(f);
+                    deps.add(d);
+                }
+            }
         }
-        final String fileName = file.getName();
-        final String extension = FileUtils.getFileExtension(fileName);
-        if (extension != null) {
-            if (extensions.contains(extension)) {
-                final Dependency dependency = new Dependency(file);
+        return deps;
+    }
+
+    /**
+     * Scans a specified file. If a dependency is identified it is added to the dependency collection.
+     *
+     * @param file The file to scan
+     * @return the scanned dependency
+     */
+    protected Dependency scanFile(File file) {
+        Dependency dependency = null;
+        if (file.isFile()) {
+            if (accept(file)) {
+                dependency = new Dependency(file);
                 dependencies.add(dependency);
             }
         } else {
-            final String msg = String.format("No file extension found on file '%s'. The file was not analyzed.",
-                    file.toString());
-            Logger.getLogger(Engine.class.getName()).log(Level.FINEST, msg);
+            LOGGER.debug("Path passed to scanFile(File) is not a file: {}. Skipping the file.", file);
         }
+        return dependency;
     }
 
     /**
-     * Runs the analyzers against all of the dependencies.
+     * Runs the analyzers against all of the dependencies. Since the mutable dependencies list is exposed via
+     * {@link #getDependencies()}, this method iterates over a copy of the dependencies list. Thus, the potential for
+     * {@link java.util.ConcurrentModificationException}s is avoided, and analyzers may safely add or remove entries from the
+     * dependencies list.
      */
     public void analyzeDependencies() {
+        boolean autoUpdate = true;
+        try {
+            autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
+        } catch (InvalidSettingException ex) {
+            LOGGER.debug("Invalid setting for auto-update; using true.");
+        }
+        if (autoUpdate) {
+            doUpdates();
+        }
+
         //need to ensure that data exists
         try {
             ensureDataExists();
         } catch (NoDataException ex) {
-            final String msg = String.format("%n%n%s%n%nUnable to continue dependency-check analysis.", ex.getMessage());
-            Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, msg);
-            Logger.getLogger(Engine.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.error("{}\n\nUnable to continue dependency-check analysis.", ex.getMessage());
+            LOGGER.debug("", ex);
             return;
+        } catch (DatabaseException ex) {
+            LOGGER.error("{}\n\nUnable to continue dependency-check analysis.", ex.getMessage());
+            LOGGER.debug("", ex);
+            return;
+
         }
 
-        //phase one initialize
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
-            final List<Analyzer> analyzerList = analyzers.get(phase);
-            for (Analyzer a : analyzerList) {
-                try {
-                    final String msg = String.format("Initializing %s", a.getName());
-                    Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
-                    a.initialize();
-                } catch (Exception ex) {
-                    final String msg = String.format("Exception occurred initializing %s.", a.getName());
-                    Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, msg);
-                    Logger.getLogger(Engine.class.getName()).log(Level.INFO, null, ex);
-                    try {
-                        a.close();
-                    } catch (Exception ex1) {
-                        Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex1);
-                    }
-                }
-            }
-        }
+        LOGGER.debug("\n----------------------------------------------------\nBEGIN ANALYSIS\n----------------------------------------------------");
+        LOGGER.info("Analysis Starting");
+        final long analysisStart = System.currentTimeMillis();
 
         // analysis phases
         for (AnalysisPhase phase : AnalysisPhase.values()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
 
             for (Analyzer a : analyzerList) {
+                a = initializeAnalyzer(a);
+
                 /* need to create a copy of the collection because some of the
                  * analyzers may modify it. This prevents ConcurrentModificationExceptions.
                  * This is okay for adds/deletes because it happens per analyzer.
                  */
-                final String msg = String.format("Begin Analyzer '%s'", a.getName());
-                Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
-                final Set<Dependency> dependencySet = new HashSet<Dependency>();
-                dependencySet.addAll(dependencies);
+                LOGGER.debug("Begin Analyzer '{}'", a.getName());
+                final Set<Dependency> dependencySet = new HashSet<Dependency>(dependencies);
                 for (Dependency d : dependencySet) {
-                    final String msgFile = String.format("Begin Analysis of '%s'", d.getActualFilePath());
-                    Logger.getLogger(Engine.class.getName()).log(Level.FINE, msgFile);
-                    if (a.supportsExtension(d.getFileExtension())) {
+                    boolean shouldAnalyze = true;
+                    if (a instanceof FileTypeAnalyzer) {
+                        final FileTypeAnalyzer fAnalyzer = (FileTypeAnalyzer) a;
+                        shouldAnalyze = fAnalyzer.accept(d.getActualFile());
+                    }
+                    if (shouldAnalyze) {
+                        LOGGER.debug("Begin Analysis of '{}'", d.getActualFilePath());
                         try {
                             a.analyze(d, this);
                         } catch (AnalysisException ex) {
-                            d.addAnalysisException(ex);
+                            LOGGER.warn("An error occurred while analyzing '{}'.", d.getActualFilePath());
+                            LOGGER.debug("", ex);
+                        } catch (Throwable ex) {
+                            //final AnalysisException ax = new AnalysisException(axMsg, ex);
+                            LOGGER.warn("An unexpected error occurred during analysis of '{}'", d.getActualFilePath());
+                            LOGGER.debug("", ex);
                         }
                     }
                 }
             }
         }
-
-        //close/cleanup
         for (AnalysisPhase phase : AnalysisPhase.values()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
+
             for (Analyzer a : analyzerList) {
-                final String msg = String.format("Closing Analyzer '%s'", a.getName());
-                Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
-                try {
-                    a.close();
-                } catch (Exception ex) {
-                    Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex);
-                }
+                closeAnalyzer(a);
             }
         }
+
+        LOGGER.debug("\n----------------------------------------------------\nEND ANALYSIS\n----------------------------------------------------");
+        LOGGER.info("Analysis Complete ({} ms)", System.currentTimeMillis() - analysisStart);
+    }
+
+    /**
+     * Initializes the given analyzer.
+     *
+     * @param analyzer the analyzer to initialize
+     * @return the initialized analyzer
+     */
+    protected Analyzer initializeAnalyzer(Analyzer analyzer) {
+        try {
+            LOGGER.debug("Initializing {}", analyzer.getName());
+            analyzer.initialize();
+        } catch (Throwable ex) {
+            LOGGER.error("Exception occurred initializing {}.", analyzer.getName());
+            LOGGER.debug("", ex);
+            try {
+                analyzer.close();
+            } catch (Throwable ex1) {
+                LOGGER.trace("", ex1);
+            }
+        }
+        return analyzer;
+    }
+
+    /**
+     * Closes the given analyzer.
+     *
+     * @param analyzer the analyzer to close
+     */
+    protected void closeAnalyzer(Analyzer analyzer) {
+        LOGGER.debug("Closing Analyzer '{}'", analyzer.getName());
+        try {
+            analyzer.close();
+        } catch (Throwable ex) {
+            LOGGER.trace("", ex);
+        }
     }
 
     /**
-     * Cycles through the cached web data sources and calls update on all of
-     * them.
+     * Cycles through the cached web data sources and calls update on all of them.
      */
-    private void doUpdates() {
-        final UpdateService service = UpdateService.getInstance();
+    public void doUpdates() {
+        LOGGER.info("Checking for updates");
+        final long updateStart = System.currentTimeMillis();
+        final UpdateService service = new UpdateService(serviceClassLoader);
         final Iterator<CachedWebDataSource> iterator = service.getDataSources();
         while (iterator.hasNext()) {
             final CachedWebDataSource source = iterator.next();
             try {
                 source.update();
             } catch (UpdateException ex) {
-                Logger.getLogger(Engine.class.getName()).log(Level.WARNING,
+                LOGGER.warn(
                         "Unable to update Cached Web DataSource, using local data instead. Results may not include recent vulnerabilities.");
-                Logger.getLogger(Engine.class.getName()).log(Level.FINE,
-                        String.format("Unable to update details for %s", source.getClass().getName()), ex);
+                LOGGER.debug("Unable to update details for {}", source.getClass().getName(), ex);
             }
         }
+        LOGGER.info("Check for updates complete ({} ms)", System.currentTimeMillis() - updateStart);
     }
 
     /**
-     * Returns a full list of all of the analyzers. This is useful for reporting
-     * which analyzers where used.
+     * Returns a full list of all of the analyzers. This is useful for reporting which analyzers where used.
      *
      * @return a list of Analyzers
      */
@@ -391,55 +457,49 @@ public class Engine {
     /**
      * Checks all analyzers to see if an extension is supported.
      *
-     * @param ext a file extension
-     * @return true or false depending on whether or not the file extension is
-     * supported
+     * @param file a file extension
+     * @return true or false depending on whether or not the file extension is supported
      */
-    public boolean supportsExtension(String ext) {
-        if (ext == null) {
+    @Override
+    public boolean accept(File file) {
+        if (file == null) {
             return false;
         }
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
-            final List<Analyzer> analyzerList = analyzers.get(phase);
-            for (Analyzer a : analyzerList) {
-                if (a.getSupportedExtensions() != null && a.supportsExtension(ext)) {
-                    return true;
-                }
-            }
+        boolean scan = false;
+        for (FileTypeAnalyzer a : this.fileTypeAnalyzers) {
+            /* note, we can't break early on this loop as the analyzers need to know if
+             they have files to work on prior to initialization */
+            scan |= a.accept(file);
         }
-        return false;
+        return scan;
     }
 
     /**
-     * Checks the CPE Index to ensure documents exists. If none exist a
-     * NoDataException is thrown.
+     * Returns the set of file type analyzers.
+     *
+     * @return the set of file type analyzers
+     */
+    public Set<FileTypeAnalyzer> getFileTypeAnalyzers() {
+        return this.fileTypeAnalyzers;
+    }
+
+    /**
+     * Checks the CPE Index to ensure documents exists. If none exist a NoDataException is thrown.
      *
      * @throws NoDataException thrown if no data exists in the CPE Index
+     * @throws DatabaseException thrown if there is an exception opening the database
      */
-    private void ensureDataExists() throws NoDataException {
-        CpeIndexReader cpe = null;
-        boolean noDataExists = false;
+    private void ensureDataExists() throws NoDataException, DatabaseException {
+        final CveDB cve = new CveDB();
         try {
-            cpe = new CpeIndexReader();
-            cpe.open();
-            if (cpe.numDocs() <= 0) {
-                noDataExists = true;
+            cve.open();
+            if (!cve.dataExists()) {
+                throw new NoDataException("No documents exist");
             }
-        } catch (IOException ex) {
-            noDataExists = true;
-        } catch (NullPointerException ex) {
-            noDataExists = true;
+        } catch (DatabaseException ex) {
+            throw new NoDataException(ex.getMessage(), ex);
         } finally {
-            if (cpe != null) {
-                cpe.close();
-            }
-        }
-        if (noDataExists) {
-            throw new NoDataException("No data exists in the data store. Please check that you are able to connect "
-                    + "to the Internet and re-run dependency-check. If the problem persists determine whether you need "
-                    + "to set a proxy url and port.\\n\\nIf you are unable to solve this problem please contact the mailing "
-                    + "list for help: dependency-check@googlegroups.com");
-
+            cve.close();
         }
     }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/agent/package-info.java

@@ -0,0 +1,6 @@
+/**
+ * The agent package holds an agent API that can be used by other applications that have information about dependencies; but would
+ * rather implement something in their code directly rather then spawn a process to run the entire dependency-check engine. This
+ * basically provides programmatic access to running a scan.
+ */
+package org.owasp.dependencycheck.agent;

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/AbstractAnalyzer.java

@@ -1,51 +1,28 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
-
 /**
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public abstract class AbstractAnalyzer implements Analyzer {
 
-    /**
-     * Utility method to help in the creation of the extensions set. This
-     * constructs a new Set that can be used in a final static
-     * declaration.<br/><br/>
-     *
-     * This implementation was copied from
-     * http://stackoverflow.com/questions/2041778/initialize-java-hashset-values-by-construction
-     *
-     * @param strings a list of strings to add to the set.
-     * @return a Set of strings.
-     */
-    protected static Set<String> newHashSet(String... strings) {
-        final Set<String> set = new HashSet<String>();
-
-        Collections.addAll(set, strings);
-        return set;
-    }
-
     /**
      * The initialize method does nothing for this Analyzer.
      *

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/AbstractFileTypeAnalyzer.java

@@ -0,0 +1,221 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * The base FileTypeAnalyzer that all analyzers that have specific file types they analyze should extend.
+ *
+ * @author Jeremy Long
+ */
+public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implements FileTypeAnalyzer {
+
+    //<editor-fold defaultstate="collapsed" desc="Constructor">
+    /**
+     * Base constructor that all children must call. This checks the configuration to determine if the analyzer is enabled.
+     */
+    public AbstractFileTypeAnalyzer() {
+        reset();
+    }
+//</editor-fold>
+
+    //<editor-fold defaultstate="collapsed" desc="Field definitions">
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AbstractFileTypeAnalyzer.class);
+    /**
+     * Whether the file type analyzer detected any files it needs to analyze.
+     */
+    private boolean filesMatched = false;
+
+    /**
+     * Get the value of filesMatched. A flag indicating whether the scan included any file types this analyzer supports.
+     *
+     * @return the value of filesMatched
+     */
+    protected boolean isFilesMatched() {
+        return filesMatched;
+    }
+
+    /**
+     * Set the value of filesMatched. A flag indicating whether the scan included any file types this analyzer supports.
+     *
+     * @param filesMatched new value of filesMatched
+     */
+    protected void setFilesMatched(boolean filesMatched) {
+        this.filesMatched = filesMatched;
+    }
+
+    /**
+     * A flag indicating whether or not the analyzer is enabled.
+     */
+    private boolean enabled = true;
+
+    /**
+     * Get the value of enabled.
+     *
+     * @return the value of enabled
+     */
+    public boolean isEnabled() {
+        return enabled;
+    }
+
+    /**
+     * Set the value of enabled.
+     *
+     * @param enabled new value of enabled
+     */
+    public void setEnabled(boolean enabled) {
+        this.enabled = enabled;
+    }
+//</editor-fold>
+
+    //<editor-fold defaultstate="collapsed" desc="Abstract methods children must implement">
+    /**
+     * <p>
+     * Returns the {@link java.io.FileFilter} used to determine which files are to be analyzed. An example would be an analyzer
+     * that inspected Java jar files. Implementors may use {@link org.owasp.dependencycheck.utils.FileFilterBuilder}.</p>
+     * <p>
+     * If the analyzer returns null it will not cause additional files to be analyzed, but will be executed against every file
+     * loaded.</p>
+     *
+     * @return the file filter used to determine which files are to be analyzed
+     */
+    protected abstract FileFilter getFileFilter();
+
+    /**
+     * Initializes the file type analyzer.
+     *
+     * @throws Exception thrown if there is an exception during initialization
+     */
+    protected abstract void initializeFileTypeAnalyzer() throws Exception;
+
+    /**
+     * Analyzes a given dependency. If the dependency is an archive, such as a WAR or EAR, the contents are extracted, scanned,
+     * and added to the list of dependencies within the engine.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine scanning
+     * @throws AnalysisException thrown if there is an analysis exception
+     */
+    protected abstract void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException;
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    protected abstract String getAnalyzerEnabledSettingKey();
+
+//</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="Final implementations for the Analyzer interface">
+    /**
+     * Initializes the analyzer.
+     *
+     * @throws Exception thrown if there is an exception during initialization
+     */
+    @Override
+    public final void initialize() throws Exception {
+        if (filesMatched) {
+            initializeFileTypeAnalyzer();
+        } else {
+            enabled = false;
+        }
+    }
+
+    /**
+     * Resets the enabled flag on the analyzer.
+     */
+    @Override
+    public final void reset() {
+        final String key = getAnalyzerEnabledSettingKey();
+        try {
+            enabled = Settings.getBoolean(key, true);
+        } catch (InvalidSettingException ex) {
+            LOGGER.warn("Invalid setting for property '{}'", key);
+            LOGGER.debug("", ex);
+            LOGGER.warn("{} has been disabled", getName());
+        }
+    }
+
+    /**
+     * Analyzes a given dependency. If the dependency is an archive, such as a WAR or EAR, the contents are extracted, scanned,
+     * and added to the list of dependencies within the engine.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine scanning
+     * @throws AnalysisException thrown if there is an analysis exception
+     */
+    @Override
+    public final void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+        if (enabled) {
+            analyzeFileType(dependency, engine);
+        }
+    }
+
+    @Override
+    public boolean accept(File pathname) {
+        final FileFilter filter = getFileFilter();
+        boolean accepted = false;
+        if (null == filter) {
+            LOGGER.error("The '{}' analyzer is misconfigured and does not have a file filter; it will be disabled", getName());
+        } else if (enabled) {
+            accepted = filter.accept(pathname);
+            if (accepted) {
+                filesMatched = true;
+            }
+        }
+        return accepted;
+    }
+
+    //</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="Static utility methods">
+    /**
+     * <p>
+     * Utility method to help in the creation of the extensions set. This constructs a new Set that can be used in a final static
+     * declaration.</p>
+     * <p>
+     * This implementation was copied from
+     * http://stackoverflow.com/questions/2041778/initialize-java-hashset-values-by-construction</p>
+     *
+     * @param strings a list of strings to add to the set.
+     * @return a Set of strings.
+     */
+    protected static Set<String> newHashSet(String... strings) {
+        final Set<String> set = new HashSet<String>(strings.length);
+        Collections.addAll(set, strings);
+        return set;
+    }
+
+//</editor-fold>
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/AbstractSuppressionAnalyzer.java

@@ -0,0 +1,177 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.List;
+import java.util.Set;
+import java.util.regex.Pattern;
+import org.owasp.dependencycheck.suppression.SuppressionParseException;
+import org.owasp.dependencycheck.suppression.SuppressionParser;
+import org.owasp.dependencycheck.suppression.SuppressionRule;
+import org.owasp.dependencycheck.utils.DownloadFailedException;
+import org.owasp.dependencycheck.utils.Downloader;
+import org.owasp.dependencycheck.utils.FileUtils;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Abstract base suppression analyzer that contains methods for parsing the suppression xml file.
+ *
+ * @author Jeremy Long
+ */
+public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
+
+    /**
+     * The Logger for use throughout the class
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AbstractSuppressionAnalyzer.class);
+
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
+    /**
+     * Returns a list of file EXTENSIONS supported by this analyzer.
+     *
+     * @return a list of file EXTENSIONS supported by this analyzer.
+     */
+    public Set<String> getSupportedExtensions() {
+        return null;
+    }
+
+    //</editor-fold>
+    /**
+     * The initialize method loads the suppression XML file.
+     *
+     * @throws Exception thrown if there is an exception
+     */
+    @Override
+    public void initialize() throws Exception {
+        super.initialize();
+        loadSuppressionData();
+    }
+
+    /**
+     * The list of suppression rules
+     */
+    private List<SuppressionRule> rules;
+
+    /**
+     * Get the value of rules.
+     *
+     * @return the value of rules
+     */
+    public List<SuppressionRule> getRules() {
+        return rules;
+    }
+
+    /**
+     * Set the value of rules.
+     *
+     * @param rules new value of rules
+     */
+    public void setRules(List<SuppressionRule> rules) {
+        this.rules = rules;
+    }
+
+    /**
+     * Loads the suppression rules file.
+     *
+     * @throws SuppressionParseException thrown if the XML cannot be parsed.
+     */
+    private void loadSuppressionData() throws SuppressionParseException {
+        final SuppressionParser parser = new SuppressionParser();
+        File file = null;
+        try {
+            rules = parser.parseSuppressionRules(this.getClass().getClassLoader().getResourceAsStream("dependencycheck-base-suppression.xml"));
+        } catch (SuppressionParseException ex) {
+            LOGGER.debug("Unable to parse the base suppression data file", ex);
+        }
+        final String suppressionFilePath = Settings.getString(Settings.KEYS.SUPPRESSION_FILE);
+        if (suppressionFilePath == null) {
+            return;
+        }
+        boolean deleteTempFile = false;
+        try {
+            final Pattern uriRx = Pattern.compile("^(https?|file)\\:.*", Pattern.CASE_INSENSITIVE);
+            if (uriRx.matcher(suppressionFilePath).matches()) {
+                deleteTempFile = true;
+                file = FileUtils.getTempFile("suppression", "xml");
+                final URL url = new URL(suppressionFilePath);
+                try {
+                    Downloader.fetchFile(url, file, false);
+                } catch (DownloadFailedException ex) {
+                    Downloader.fetchFile(url, file, true);
+                }
+            } else {
+                file = new File(suppressionFilePath);
+                if (!file.exists()) {
+                    final InputStream suppressionsFromClasspath = this.getClass().getClassLoader().getResourceAsStream(suppressionFilePath);
+                    if (suppressionsFromClasspath != null) {
+                        deleteTempFile = true;
+                        file = FileUtils.getTempFile("suppression", "xml");
+                        try {
+                            org.apache.commons.io.FileUtils.copyInputStreamToFile(suppressionsFromClasspath, file);
+                        } catch (IOException ex) {
+                            throwSuppressionParseException("Unable to locate suppressions file in classpath", ex);
+                        }
+                    }
+                }
+            }
+
+            if (file != null) {
+                try {
+                    //rules = parser.parseSuppressionRules(file);
+                    rules.addAll(parser.parseSuppressionRules(file));
+                    LOGGER.debug("{} suppression rules were loaded.", rules.size());
+                } catch (SuppressionParseException ex) {
+                    LOGGER.warn("Unable to parse suppression xml file '{}'", file.getPath());
+                    LOGGER.warn(ex.getMessage());
+                    LOGGER.debug("", ex);
+                    throw ex;
+                }
+            }
+        } catch (DownloadFailedException ex) {
+            throwSuppressionParseException("Unable to fetch the configured suppression file", ex);
+        } catch (MalformedURLException ex) {
+            throwSuppressionParseException("Configured suppression file has an invalid URL", ex);
+        } catch (IOException ex) {
+            throwSuppressionParseException("Unable to create temp file for suppressions", ex);
+        } finally {
+            if (deleteTempFile && file != null) {
+                FileUtils.delete(file);
+            }
+        }
+    }
+
+    /**
+     * Utility method to throw parse exceptions.
+     *
+     * @param message the exception message
+     * @param exception the cause of the exception
+     * @throws SuppressionParseException throws the generated SuppressionParseException
+     */
+    private void throwSuppressionParseException(String message, Exception exception) throws SuppressionParseException {
+        LOGGER.warn(message);
+        LOGGER.debug("", exception);
+        throw new SuppressionParseException(message, exception);
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/AnalysisPhase.java

@@ -1,18 +1,17 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
@@ -21,7 +20,7 @@ package org.owasp.dependencycheck.analyzer;
 /**
  * An enumeration defining the phases of analysis.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public enum AnalysisPhase {
 
@@ -29,6 +28,10 @@ public enum AnalysisPhase {
      * Initialization phase.
      */
     INITIAL,
+    /**
+     * Pre information collection phase.
+     */
+    PRE_INFORMATION_COLLECTION,
     /**
      * Information collection phase.
      */

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/Analyzer.java

@@ -1,65 +1,46 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.util.Set;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
 
 /**
- * An interface that defines an Analyzer that is used to identify Dependencies.
- * An analyzer will collect information about the dependency in the form of
- * Evidence.
+ * An interface that defines an Analyzer that is used to identify Dependencies. An analyzer will collect information
+ * about the dependency in the form of Evidence.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public interface Analyzer {
 
     /**
-     * Analyzes the given dependency. The analysis could be anything from
-     * identifying an Identifier for the dependency, to finding vulnerabilities,
-     * etc. Additionally, if the analyzer collects enough information to add a
-     * description or license information for the dependency it should be added.
+     * Analyzes the given dependency. The analysis could be anything from identifying an Identifier for the dependency,
+     * to finding vulnerabilities, etc. Additionally, if the analyzer collects enough information to add a description
+     * or license information for the dependency it should be added.
      *
      * @param dependency a dependency to analyze.
-     * @param engine the engine that is scanning the dependencies - this is
-     * useful if we need to check other dependencies
-     * @throws AnalysisException is thrown if there is an error analyzing the
-     * dependency file
+     * @param engine the engine that is scanning the dependencies - this is useful if we need to check other
+     * dependencies
+     * @throws AnalysisException is thrown if there is an error analyzing the dependency file
      */
     void analyze(Dependency dependency, Engine engine) throws AnalysisException;
 
-    /**
-     * <p>Returns a list of supported file extensions. An example would be an
-     * analyzer that inspected java jar files. The getSupportedExtensions
-     * function would return a set with a single element "jar".</p>
-     *
-     * <p><b>Note:</b> when implementing this the extensions returned MUST be
-     * lowercase.</p>
-     *
-     * @return The file extensions supported by this analyzer.
-     *
-     * <p>If the analyzer returns null it will not cause additional files to be
-     * analyzed but will be executed against every file loaded</p>
-     */
-    Set<String> getSupportedExtensions();
-
     /**
      * Returns the name of the analyzer.
      *
@@ -67,15 +48,6 @@ public interface Analyzer {
      */
     String getName();
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this
-     * analyzer.
-     */
-    boolean supportsExtension(String extension);
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
@@ -84,17 +56,14 @@ public interface Analyzer {
     AnalysisPhase getAnalysisPhase();
 
     /**
-     * The initialize method is called (once) prior to the analyze method being
-     * called on all of the dependencies.
+     * The initialize method is called (once) prior to the analyze method being called on all of the dependencies.
      *
-     * @throws Exception is thrown if an exception occurs initializing the
-     * analyzer.
+     * @throws Exception is thrown if an exception occurs initializing the analyzer.
      */
     void initialize() throws Exception;
 
     /**
-     * The close method is called after all of the dependencies have been
-     * analyzed.
+     * The close method is called after all of the dependencies have been analyzed.
      *
      * @throws Exception is thrown if an exception occurs closing the analyzer.
      */

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/AnalyzerService.java

@@ -1,18 +1,17 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
@@ -22,15 +21,13 @@ import java.util.Iterator;
 import java.util.ServiceLoader;
 
 /**
+ * The Analyzer Service Loader. This class loads all services that implement
+ * org.owasp.dependencycheck.analyzer.Analyzer.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
-public final class AnalyzerService {
+public class AnalyzerService {
 
-    /**
-     * The analyzer service singleton.
-     */
-    private static AnalyzerService service;
     /**
      * The service loader for analyzers.
      */
@@ -38,21 +35,11 @@ public final class AnalyzerService {
 
     /**
      * Creates a new instance of AnalyzerService.
-     */
-    private AnalyzerService() {
-        loader = ServiceLoader.load(Analyzer.class);
-    }
-
-    /**
-     * Retrieve the singleton instance of AnalyzerService.
      *
-     * @return a singleton AnalyzerService.
+     * @param classLoader the ClassLoader to use when dynamically loading Analyzer and Update services
      */
-    public static synchronized AnalyzerService getInstance() {
-        if (service == null) {
-            service = new AnalyzerService();
-        }
-        return service;
+    public AnalyzerService(ClassLoader classLoader) {
+        loader = ServiceLoader.load(Analyzer.class, classLoader);
     }
 
     /**

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/ArchiveAnalyzer.java

@@ -1,64 +1,76 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
 import java.io.BufferedInputStream;
-import java.io.BufferedOutputStream;
+import java.io.Closeable;
 import java.io.File;
+import java.io.FileFilter;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
-import java.util.logging.Level;
-import java.util.logging.Logger;
+
 import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveInputStream;
 import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
 import org.apache.commons.compress.archivers.zip.ZipArchiveInputStream;
+import org.apache.commons.compress.archivers.zip.ZipFile;
 import org.apache.commons.compress.compressors.CompressorInputStream;
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
+import org.apache.commons.compress.compressors.bzip2.BZip2Utils;
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.apache.commons.compress.compressors.gzip.GzipUtils;
-import org.h2.store.fs.FileUtils;
+import org.apache.commons.compress.utils.IOUtils;
+
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.analyzer.exception.ArchiveExtractionException;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.FileUtils;
 import org.owasp.dependencycheck.utils.Settings;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 /**
- * <p>An analyzer that extracts files from archives and ensures any supported
- * files contained within the archive are added to the dependency list.</p>
+ * <p>
+ * An analyzer that extracts files from archives and ensures any supported files contained within the archive are added to the
+ * dependency list.</p>
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
-public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
+public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
-     * The buffer size to use when extracting files from the archive.
+     * The logger.
      */
-    private static final int BUFFER_SIZE = 4096;
+    private static final Logger LOGGER = LoggerFactory.getLogger(ArchiveAnalyzer.class);
     /**
-     * The count of directories created during analysis. This is used for
-     * creating temporary directories.
+     * The count of directories created during analysis. This is used for creating temporary directories.
      */
     private static int dirCount = 0;
     /**
@@ -66,15 +78,15 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      */
     private File tempFileLocation = null;
     /**
-     * The max scan depth that the analyzer will recursively extract nested
-     * archives.
+     * The max scan depth that the analyzer will recursively extract nested archives.
      */
     private static final int MAX_SCAN_DEPTH = Settings.getInt("archive.scan.depth", 3);
     /**
      * Tracks the current scan/extraction depth for nested archives.
      */
     private int scanDepth = 0;
-    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
+
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
      * The name of the analyzer.
      */
@@ -84,64 +96,84 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INITIAL;
     /**
-     * The set of file extensions supported by this analyzer.
+     * The set of things we can handle with Zip methods
      */
-    private static final Set<String> EXTENSIONS = newHashSet("zip", "ear", "war", "tar", "gz", "tgz");
+    private static final Set<String> ZIPPABLES = newHashSet("zip", "ear", "war", "jar", "sar", "apk", "nupkg");
+    /**
+     * The set of file extensions supported by this analyzer. Note for developers, any additions to this list will need to be
+     * explicitly handled in {@link #extractFiles(File, File, Engine)}.
+     */
+    private static final Set<String> EXTENSIONS = newHashSet("tar", "gz", "tgz", "bz2", "tbz2");
 
     /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
+     * Detects files with extensions to remove from the engine's collection of dependencies.
      */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
+    private static final FileFilter REMOVE_FROM_ANALYSIS = FileFilterBuilder.newInstance().addExtensions("zip", "tar", "gz", "tgz", "bz2", "tbz2")
+            .build();
+
+    static {
+        final String additionalZipExt = Settings.getString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS);
+        if (additionalZipExt != null) {
+            final String[] ext = additionalZipExt.split("\\s*,\\s*");
+            Collections.addAll(ZIPPABLES, ext);
+        }
+        EXTENSIONS.addAll(ZIPPABLES);
     }
 
+    /**
+     * The file filter used to filter supported files.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(EXTENSIONS).build();
+
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Detects files with .zip extension.
+     */
+    private static final FileFilter ZIP_FILTER = FileFilterBuilder.newInstance().addExtensions("zip").build();
+
     /**
      * Returns the name of the analyzer.
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this
-     * analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return EXTENSIONS.contains(extension);
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
      * @return the phase that the analyzer is intended to run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
     //</editor-fold>
 
     /**
-     * The initialize method does nothing for this Analyzer.
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
      *
-     * @throws Exception is thrown if there is an exception deleting or creating
-     * temporary files
+     * @return the analyzer's enabled property setting key
      */
     @Override
-    public void initialize() throws Exception {
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_ARCHIVE_ENABLED;
+    }
+
+    /**
+     * The initialize method does nothing for this Analyzer.
+     *
+     * @throws Exception is thrown if there is an exception deleting or creating temporary files
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
         final File baseDir = Settings.getTempDirectory();
-        if (!baseDir.exists()) {
-            if (!baseDir.mkdirs()) {
-                final String msg = String.format("Unable to make a temporary folder '%s'", baseDir.getPath());
-                throw new AnalysisException(msg);
-            }
-        }
         tempFileLocation = File.createTempFile("check", "tmp", baseDir);
         if (!tempFileLocation.delete()) {
             final String msg = String.format("Unable to delete temporary file '%s'.", tempFileLocation.getAbsolutePath());
@@ -154,68 +186,129 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
     }
 
     /**
-     * The close method does nothing for this Analyzer.
+     * The close method deletes any temporary files and directories created during analysis.
      *
-     * @throws Exception thrown if there is an exception deleting temporary
-     * files
+     * @throws Exception thrown if there is an exception deleting temporary files
      */
     @Override
     public void close() throws Exception {
         if (tempFileLocation != null && tempFileLocation.exists()) {
-            FileUtils.deleteRecursive(tempFileLocation.getAbsolutePath(), true);
+            LOGGER.debug("Attempting to delete temporary files");
+            final boolean success = FileUtils.delete(tempFileLocation);
+            if (!success && tempFileLocation.exists()) {
+                final String[] l = tempFileLocation.list();
+                if (l != null && l.length > 0) {
+                    LOGGER.warn("Failed to delete some temporary files, see the log for more details");
+                }
+            }
         }
     }
 
     /**
-     * Analyzes a given dependency. If the dependency is an archive, such as a
-     * WAR or EAR, the contents are extracted, scanned, and added to the list of
-     * dependencies within the engine.
+     * Analyzes a given dependency. If the dependency is an archive, such as a WAR or EAR, the contents are extracted, scanned,
+     * and added to the list of dependencies within the engine.
      *
      * @param dependency the dependency to analyze
      * @param engine the engine scanning
      * @throws AnalysisException thrown if there is an analysis exception
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
         final File f = new File(dependency.getActualFilePath());
         final File tmpDir = getNextTempDirectory();
         extractFiles(f, tmpDir, engine);
 
         //make a copy
-        final List<Dependency> dependencies = new ArrayList<Dependency>(engine.getDependencies());
-        engine.scan(tmpDir);
-        final List<Dependency> newDependencies = engine.getDependencies();
-        if (dependencies.size() != newDependencies.size()) {
-            //get the new dependencies
-            final Set<Dependency> dependencySet = new HashSet<Dependency>();
-            dependencySet.addAll(newDependencies);
-            dependencySet.removeAll(dependencies);
-
+        final Set<Dependency> dependencySet = findMoreDependencies(engine, tmpDir);
+        if (!dependencySet.isEmpty()) {
             for (Dependency d : dependencySet) {
                 //fix the dependency's display name and path
                 final String displayPath = String.format("%s%s",
                         dependency.getFilePath(),
                         d.getActualFilePath().substring(tmpDir.getAbsolutePath().length()));
-                final String displayName = String.format("%s%s%s",
+                final String displayName = String.format("%s: %s",
                         dependency.getFileName(),
-                        File.separator,
                         d.getFileName());
                 d.setFilePath(displayPath);
                 d.setFileName(displayName);
 
                 //TODO - can we get more evidence from the parent? EAR contains module name, etc.
-
                 //analyze the dependency (i.e. extract files) if it is a supported type.
-                if (this.supportsExtension(d.getFileExtension()) && scanDepth < MAX_SCAN_DEPTH) {
+                if (this.accept(d.getActualFile()) && scanDepth < MAX_SCAN_DEPTH) {
                     scanDepth += 1;
                     analyze(d, engine);
                     scanDepth -= 1;
                 }
             }
         }
+        if (REMOVE_FROM_ANALYSIS.accept(dependency.getActualFile())) {
+            addDisguisedJarsToDependencies(dependency, engine);
+            engine.getDependencies().remove(dependency);
+        }
         Collections.sort(engine.getDependencies());
     }
 
+    /**
+     * If a zip file was identified as a possible JAR, this method will add the zip to the list of dependencies.
+     *
+     * @param dependency the zip file
+     * @param engine the engine
+     * @throws AnalysisException thrown if there is an issue
+     */
+    private void addDisguisedJarsToDependencies(Dependency dependency, Engine engine) throws AnalysisException {
+        if (ZIP_FILTER.accept(dependency.getActualFile()) && isZipFileActuallyJarFile(dependency)) {
+            final File tdir = getNextTempDirectory();
+            final String fileName = dependency.getFileName();
+
+            LOGGER.info("The zip file '{}' appears to be a JAR file, making a copy and analyzing it as a JAR.", fileName);
+
+            final File tmpLoc = new File(tdir, fileName.substring(0, fileName.length() - 3) + "jar");
+            try {
+                org.apache.commons.io.FileUtils.copyFile(tdir, tmpLoc);
+                final Set<Dependency> dependencySet = findMoreDependencies(engine, tmpLoc);
+                if (!dependencySet.isEmpty()) {
+                    if (dependencySet.size() != 1) {
+                        LOGGER.info("Deep copy of ZIP to JAR file resulted in more than one dependency?");
+                    }
+                    for (Dependency d : dependencySet) {
+                        //fix the dependency's display name and path
+                        d.setFilePath(dependency.getFilePath());
+                        d.setDisplayFileName(dependency.getFileName());
+                    }
+                }
+            } catch (IOException ex) {
+                LOGGER.debug("Unable to perform deep copy on '{}'", dependency.getActualFile().getPath(), ex);
+            }
+        }
+    }
+    /**
+     * An empty dependency set.
+     */
+    private static final Set<Dependency> EMPTY_DEPENDENCY_SET = Collections.emptySet();
+
+    /**
+     * Scan the given file/folder, and return any new dependencies found.
+     *
+     * @param engine used to scan
+     * @param file target of scanning
+     * @return any dependencies that weren't known to the engine before
+     */
+    private static Set<Dependency> findMoreDependencies(Engine engine, File file) {
+        final List<Dependency> before = new ArrayList<Dependency>(engine.getDependencies());
+        engine.scan(file);
+        final List<Dependency> after = engine.getDependencies();
+        final boolean sizeChanged = before.size() != after.size();
+        final Set<Dependency> newDependencies;
+        if (sizeChanged) {
+            //get the new dependencies
+            newDependencies = new HashSet<Dependency>(after);
+            newDependencies.removeAll(before);
+        } else {
+            newDependencies = EMPTY_DEPENDENCY_SET;
+        }
+        return newDependencies;
+    }
+
     /**
      * Retrieves the next temporary directory to extract an archive too.
      *
@@ -245,43 +338,41 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      * @throws AnalysisException thrown if the archive is not found
      */
     private void extractFiles(File archive, File destination, Engine engine) throws AnalysisException {
-        if (archive == null || destination == null) {
-            return;
-        }
-
-        FileInputStream fis = null;
-        try {
-            fis = new FileInputStream(archive);
-        } catch (FileNotFoundException ex) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.INFO, null, ex);
-            throw new AnalysisException("Archive file was not found.", ex);
-        }
-        final String archiveExt = org.owasp.dependencycheck.utils.FileUtils.getFileExtension(archive.getName()).toLowerCase();
-        try {
-            if ("zip".equals(archiveExt) || "war".equals(archiveExt) || "ear".equals(archiveExt)) {
-                extractArchive(new ZipArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
-            } else if ("tar".equals(archiveExt)) {
-                extractArchive(new TarArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
-            } else if ("gz".equals(archiveExt) || "tgz".equals(archiveExt)) {
-                final String uncompressedName = GzipUtils.getUncompressedFilename(archive.getName());
-                final String uncompressedExt = org.owasp.dependencycheck.utils.FileUtils.getFileExtension(uncompressedName).toLowerCase();
-                if (engine.supportsExtension(uncompressedExt)) {
-                    decompressFile(new GzipCompressorInputStream(new BufferedInputStream(fis)), new File(destination, uncompressedName));
-                }
-            }
-        } catch (ArchiveExtractionException ex) {
-            final String msg = String.format("Exception extracting archive '%s'.", archive.getName());
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING, msg);
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
-        } catch (IOException ex) {
-            final String msg = String.format("Exception reading archive '%s'.", archive.getName());
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING, msg);
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
-        } finally {
+        if (archive != null && destination != null) {
+            FileInputStream fis;
             try {
-                fis.close();
+                fis = new FileInputStream(archive);
+            } catch (FileNotFoundException ex) {
+                LOGGER.debug("", ex);
+                throw new AnalysisException("Archive file was not found.", ex);
+            }
+            final String archiveExt = FileUtils.getFileExtension(archive.getName()).toLowerCase();
+            try {
+                if (ZIPPABLES.contains(archiveExt)) {
+                    extractArchive(new ZipArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
+                } else if ("tar".equals(archiveExt)) {
+                    extractArchive(new TarArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
+                } else if ("gz".equals(archiveExt) || "tgz".equals(archiveExt)) {
+                    final String uncompressedName = GzipUtils.getUncompressedFilename(archive.getName());
+                    final File f = new File(destination, uncompressedName);
+                    if (engine.accept(f)) {
+                        decompressFile(new GzipCompressorInputStream(new BufferedInputStream(fis)), f);
+                    }
+                } else if ("bz2".equals(archiveExt) || "tbz2".equals(archiveExt)) {
+                    final String uncompressedName = BZip2Utils.getUncompressedFilename(archive.getName());
+                    final File f = new File(destination, uncompressedName);
+                    if (engine.accept(f)) {
+                        decompressFile(new BZip2CompressorInputStream(new BufferedInputStream(fis)), f);
+                    }
+                }
+            } catch (ArchiveExtractionException ex) {
+                LOGGER.warn("Exception extracting archive '{}'.", archive.getName());
+                LOGGER.debug("", ex);
             } catch (IOException ex) {
-                Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                LOGGER.warn("Exception reading archive '{}'.", archive.getName());
+                LOGGER.debug("", ex);
+            } finally {
+                close(fis);
             }
         }
     }
@@ -292,71 +383,57 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      * @param input the archive to extract files from
      * @param destination the location to write the files too
      * @param engine the dependency-check engine
-     * @throws ArchiveExtractionException thrown if there is an exception
-     * extracting files from the archive
+     * @throws ArchiveExtractionException thrown if there is an exception extracting files from the archive
      */
     private void extractArchive(ArchiveInputStream input, File destination, Engine engine) throws ArchiveExtractionException {
         ArchiveEntry entry;
         try {
             while ((entry = input.getNextEntry()) != null) {
+                final File file = new File(destination, entry.getName());
                 if (entry.isDirectory()) {
-                    final File d = new File(destination, entry.getName());
-                    if (!d.exists()) {
-                        if (!d.mkdirs()) {
-                            final String msg = String.format("Unable to create '%s'.", d.getAbsolutePath());
-                            throw new AnalysisException(msg);
-                        }
-                    }
-                } else {
-                    final File file = new File(destination, entry.getName());
-                    final String ext = org.owasp.dependencycheck.utils.FileUtils.getFileExtension(file.getName());
-                    if (engine.supportsExtension(ext)) {
-                        BufferedOutputStream bos = null;
-                        FileOutputStream fos;
-                        try {
-                            fos = new FileOutputStream(file);
-                            bos = new BufferedOutputStream(fos, BUFFER_SIZE);
-                            int count;
-                            final byte data[] = new byte[BUFFER_SIZE];
-                            while ((count = input.read(data, 0, BUFFER_SIZE)) != -1) {
-                                bos.write(data, 0, count);
-                            }
-                            bos.flush();
-                        } catch (FileNotFoundException ex) {
-                            Logger.getLogger(ArchiveAnalyzer.class
-                                    .getName()).log(Level.FINE, null, ex);
-                            final String msg = String.format("Unable to find file '%s'.", file.getName());
-                            throw new AnalysisException(msg, ex);
-                        } catch (IOException ex) {
-                            Logger.getLogger(ArchiveAnalyzer.class
-                                    .getName()).log(Level.FINE, null, ex);
-                            final String msg = String.format("IO Exception while parsing file '%s'.", file.getName());
-                            throw new AnalysisException(msg, ex);
-                        } finally {
-                            if (bos != null) {
-                                try {
-                                    bos.close();
-                                } catch (IOException ex) {
-                                    Logger.getLogger(ArchiveAnalyzer.class
-                                            .getName()).log(Level.FINEST, null, ex);
-                                }
-                            }
-                        }
+                    if (!file.exists() && !file.mkdirs()) {
+                        final String msg = String.format("Unable to create directory '%s'.", file.getAbsolutePath());
+                        throw new AnalysisException(msg);
                     }
+                } else if (engine.accept(file)) {
+                    extractAcceptedFile(input, file);
                 }
             }
-        } catch (IOException ex) {
-            throw new ArchiveExtractionException(ex);
         } catch (Throwable ex) {
             throw new ArchiveExtractionException(ex);
         } finally {
-            if (input != null) {
-                try {
-                    input.close();
-                } catch (IOException ex) {
-                    Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINEST, null, ex);
-                }
+            close(input);
+        }
+    }
+
+    /**
+     * Extracts a file from an archive.
+     *
+     * @param input the archives input stream
+     * @param file the file to extract
+     * @throws AnalysisException thrown if there is an error
+     */
+    private static void extractAcceptedFile(ArchiveInputStream input, File file) throws AnalysisException {
+        LOGGER.debug("Extracting '{}'", file.getPath());
+        FileOutputStream fos = null;
+        try {
+            final File parent = file.getParentFile();
+            if (!parent.isDirectory() && !parent.mkdirs()) {
+                final String msg = String.format("Unable to build directory '%s'.", parent.getAbsolutePath());
+                throw new AnalysisException(msg);
             }
+            fos = new FileOutputStream(file);
+            IOUtils.copy(input, fos);
+        } catch (FileNotFoundException ex) {
+            LOGGER.debug("", ex);
+            final String msg = String.format("Unable to find file '%s'.", file.getName());
+            throw new AnalysisException(msg, ex);
+        } catch (IOException ex) {
+            LOGGER.debug("", ex);
+            final String msg = String.format("IO Exception while parsing file '%s'.", file.getName());
+            throw new AnalysisException(msg, ex);
+        } finally {
+            close(fos);
         }
     }
 
@@ -365,32 +442,71 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      *
      * @param inputStream the compressed file
      * @param outputFile the location to write the decompressed file
-     * @throws ArchiveExtractionException thrown if there is an exception
-     * decompressing the file
+     * @throws ArchiveExtractionException thrown if there is an exception decompressing the file
      */
     private void decompressFile(CompressorInputStream inputStream, File outputFile) throws ArchiveExtractionException {
+        LOGGER.debug("Decompressing '{}'", outputFile.getPath());
         FileOutputStream out = null;
         try {
             out = new FileOutputStream(outputFile);
-            final byte[] buffer = new byte[BUFFER_SIZE];
-            int n = 0;
-            while (-1 != (n = inputStream.read(buffer))) {
-                out.write(buffer, 0, n);
-            }
+            IOUtils.copy(inputStream, out);
         } catch (FileNotFoundException ex) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.debug("", ex);
             throw new ArchiveExtractionException(ex);
         } catch (IOException ex) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.debug("", ex);
             throw new ArchiveExtractionException(ex);
         } finally {
-            if (out != null) {
-                try {
-                    out.close();
-                } catch (IOException ex) {
-                    Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINEST, null, ex);
-                }
+            close(out);
+        }
+    }
+
+    /**
+     * Close the given {@link Closeable} instance, ignoring nulls, and logging any thrown {@link IOException}.
+     *
+     * @param closeable to be closed
+     */
+    private static void close(Closeable closeable) {
+        if (null != closeable) {
+            try {
+                closeable.close();
+            } catch (IOException ex) {
+                LOGGER.trace("", ex);
             }
         }
     }
+
+    /**
+     * Attempts to determine if a zip file is actually a JAR file.
+     *
+     * @param dependency the dependency to check
+     * @return true if the dependency appears to be a JAR file; otherwise false
+     */
+    private boolean isZipFileActuallyJarFile(Dependency dependency) {
+        boolean isJar = false;
+        ZipFile zip = null;
+        try {
+            zip = new ZipFile(dependency.getActualFilePath());
+            if (zip.getEntry("META-INF/MANIFEST.MF") != null
+                    || zip.getEntry("META-INF/maven") != null) {
+                final Enumeration<ZipArchiveEntry> entries = zip.getEntries();
+                while (entries.hasMoreElements()) {
+                    final ZipArchiveEntry entry = entries.nextElement();
+                    if (!entry.isDirectory()) {
+                        final String name = entry.getName().toLowerCase();
+                        if (name.endsWith(".class")) {
+                            isJar = true;
+                            break;
+                        }
+                    }
+                }
+            }
+        } catch (IOException ex) {
+            LOGGER.debug("Unable to unzip zip file '{}'", dependency.getFilePath(), ex);
+        } finally {
+            ZipFile.closeQuietly(zip);
+        }
+
+        return isJar;
+    }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/ArchiveExtractionException.java

@@ -1,67 +0,0 @@
-/*
- * This file is part of dependency-check-core.
- *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
- *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
- *
- * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
- */
-package org.owasp.dependencycheck.analyzer;
-
-/**
- * An exception thrown when the analysis of a dependency fails.
- *
- * @author Jeremy Long (jeremy.long@owasp.org)
- */
-public class ArchiveExtractionException extends Exception {
-
-    /**
-     * The serial version UID for serialization.
-     */
-    private static final long serialVersionUID = 1L;
-
-    /**
-     * Creates a new AnalysisException.
-     */
-    public ArchiveExtractionException() {
-        super();
-    }
-
-    /**
-     * Creates a new AnalysisException.
-     *
-     * @param msg a message for the exception.
-     */
-    public ArchiveExtractionException(String msg) {
-        super(msg);
-    }
-
-    /**
-     * Creates a new AnalysisException.
-     *
-     * @param ex the cause of the failure.
-     */
-    public ArchiveExtractionException(Throwable ex) {
-        super(ex);
-    }
-
-    /**
-     * Creates a new DownloadFailedException.
-     *
-     * @param msg a message for the exception.
-     * @param ex the cause of the failure.
-     */
-    public ArchiveExtractionException(String msg, Throwable ex) {
-        super(msg, ex);
-    }
-}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/AssemblyAnalyzer.java

@@ -0,0 +1,307 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.output.NullOutputStream;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.w3c.dom.Document;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathExpressionException;
+import javax.xml.xpath.XPathFactory;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Analyzer for getting company, product, and version information from a .NET assembly.
+ *
+ * @author colezlaw
+ *
+ */
+public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The analyzer name
+     */
+    private static final String ANALYZER_NAME = "Assembly Analyzer";
+    /**
+     * The analysis phase
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+    /**
+     * The list of supported extensions
+     */
+    private static final String[] SUPPORTED_EXTENSIONS = {"dll", "exe"};
+    /**
+     * The temp value for GrokAssembly.exe
+     */
+    private File grokAssemblyExe = null;
+    /**
+     * The DocumentBuilder for parsing the XML
+     */
+    private DocumentBuilder builder;
+    /**
+     * Logger
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AssemblyAnalyzer.class);
+
+    /**
+     * Builds the beginnings of a List for ProcessBuilder
+     *
+     * @return the list of arguments to begin populating the ProcessBuilder
+     */
+    private List<String> buildArgumentList() {
+        // Use file.separator as a wild guess as to whether this is Windows
+        final List<String> args = new ArrayList<String>();
+        if (!"\\".equals(System.getProperty("file.separator"))) {
+            if (Settings.getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH) != null) {
+                args.add(Settings.getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH));
+            } else {
+                args.add("mono");
+            }
+        }
+        args.add(grokAssemblyExe.getPath());
+
+        return args;
+    }
+
+    /**
+     * Performs the analysis on a single Dependency.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine to perform the analysis under
+     * @throws AnalysisException if anything goes sideways
+     */
+    @Override
+    public void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        if (grokAssemblyExe == null) {
+            LOGGER.warn("GrokAssembly didn't get deployed");
+            return;
+        }
+
+        final List<String> args = buildArgumentList();
+        args.add(dependency.getActualFilePath());
+        final ProcessBuilder pb = new ProcessBuilder(args);
+        Document doc = null;
+        try {
+            final Process proc = pb.start();
+
+            doc = builder.parse(proc.getInputStream());
+
+            // Try evacuating the error stream
+            final String errorStream = IOUtils.toString(proc.getErrorStream(), "UTF-8");
+            if (null != errorStream && !errorStream.isEmpty()) {
+                LOGGER.warn("Error from GrokAssembly: {}", errorStream);
+            }
+
+            int rc = 0;
+            try {
+                rc = proc.waitFor();
+            } catch (InterruptedException ie) {
+                return;
+            }
+            if (rc == 3) {
+                LOGGER.debug("{} is not a .NET assembly or executable and as such cannot be analyzed by dependency-check",
+                        dependency.getActualFilePath());
+                return;
+            } else if (rc != 0) {
+                LOGGER.warn("Return code {} from GrokAssembly", rc);
+            }
+
+            final XPath xpath = XPathFactory.newInstance().newXPath();
+
+            // First, see if there was an error
+            final String error = xpath.evaluate("/assembly/error", doc);
+            if (error != null && !error.isEmpty()) {
+                throw new AnalysisException(error);
+            }
+
+            final String version = xpath.evaluate("/assembly/version", doc);
+            if (version != null) {
+                dependency.getVersionEvidence().addEvidence(new Evidence("grokassembly", "version",
+                        version, Confidence.HIGHEST));
+            }
+
+            final String vendor = xpath.evaluate("/assembly/company", doc);
+            if (vendor != null) {
+                dependency.getVendorEvidence().addEvidence(new Evidence("grokassembly", "vendor",
+                        vendor, Confidence.HIGH));
+            }
+
+            final String product = xpath.evaluate("/assembly/product", doc);
+            if (product != null) {
+                dependency.getProductEvidence().addEvidence(new Evidence("grokassembly", "product",
+                        product, Confidence.HIGH));
+            }
+
+        } catch (IOException ioe) {
+            throw new AnalysisException(ioe);
+        } catch (SAXException saxe) {
+            throw new AnalysisException("Couldn't parse GrokAssembly result", saxe);
+        } catch (XPathExpressionException xpe) {
+            // This shouldn't happen
+            throw new AnalysisException(xpe);
+        }
+    }
+
+    /**
+     * Initialize the analyzer. In this case, extract GrokAssembly.exe to a temporary location.
+     *
+     * @throws Exception if anything goes wrong
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+        final File tempFile = File.createTempFile("GKA", ".exe", Settings.getTempDirectory());
+        FileOutputStream fos = null;
+        InputStream is = null;
+        try {
+            fos = new FileOutputStream(tempFile);
+            is = AssemblyAnalyzer.class.getClassLoader().getResourceAsStream("GrokAssembly.exe");
+            IOUtils.copy(is, fos);
+
+            grokAssemblyExe = tempFile;
+            // Set the temp file to get deleted when we're done
+            grokAssemblyExe.deleteOnExit();
+            LOGGER.debug("Extracted GrokAssembly.exe to {}", grokAssemblyExe.getPath());
+        } catch (IOException ioe) {
+            this.setEnabled(false);
+            LOGGER.warn("Could not extract GrokAssembly.exe: {}", ioe.getMessage());
+            throw new AnalysisException("Could not extract GrokAssembly.exe", ioe);
+        } finally {
+            if (fos != null) {
+                try {
+                    fos.close();
+                } catch (Throwable e) {
+                    LOGGER.debug("Error closing output stream");
+                }
+            }
+            if (is != null) {
+                try {
+                    is.close();
+                } catch (Throwable e) {
+                    LOGGER.debug("Error closing input stream");
+                }
+            }
+        }
+
+        // Now, need to see if GrokAssembly actually runs from this location.
+        final List<String> args = buildArgumentList();
+        try {
+            final ProcessBuilder pb = new ProcessBuilder(args);
+            final Process p = pb.start();
+            // Try evacuating the error stream
+            IOUtils.copy(p.getErrorStream(), NullOutputStream.NULL_OUTPUT_STREAM);
+
+            final Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(p.getInputStream());
+            final XPath xpath = XPathFactory.newInstance().newXPath();
+            final String error = xpath.evaluate("/assembly/error", doc);
+            if (p.waitFor() != 1 || error == null || error.isEmpty()) {
+                LOGGER.warn("An error occurred with the .NET AssemblyAnalyzer, please see the log for more details.");
+                LOGGER.debug("GrokAssembly.exe is not working properly");
+                grokAssemblyExe = null;
+                this.setEnabled(false);
+                throw new AnalysisException("Could not execute .NET AssemblyAnalyzer");
+            }
+        } catch (AnalysisException e) {
+            throw e;
+        } catch (Throwable e) {
+            LOGGER.warn("An error occurred with the .NET AssemblyAnalyzer;\n"
+                    + "this can be ignored unless you are scanning .NET DLLs. Please see the log for more details.");
+            LOGGER.debug("Could not execute GrokAssembly {}", e.getMessage());
+            this.setEnabled(false);
+            throw new AnalysisException("An error occurred with the .NET AssemblyAnalyzer", e);
+        }
+        builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+    }
+
+    /**
+     * Removes resources used from the local file system.
+     *
+     * @throws Exception thrown if there is a problem closing the analyzer
+     */
+    @Override
+    public void close() throws Exception {
+        super.close();
+        try {
+            if (grokAssemblyExe != null && !grokAssemblyExe.delete()) {
+                grokAssemblyExe.deleteOnExit();
+            }
+        } catch (SecurityException se) {
+            LOGGER.debug("Can't delete temporary GrokAssembly.exe");
+        }
+    }
+
+    /**
+     * The File Filter used to filter supported extensions.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(
+            SUPPORTED_EXTENSIONS).build();
+
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Gets this analyzer's name.
+     *
+     * @return the analyzer name
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase this analyzer runs under.
+     *
+     * @return the phase this runs under
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/AutoconfAnalyzer.java

@@ -0,0 +1,279 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.EvidenceCollection;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.utils.UrlStringUtils;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Used to analyze Autoconf input files named configure.ac or configure.in. Files simply named "configure" are also analyzed,
+ * assuming they are generated by Autoconf, and contain certain special package descriptor variables.
+ *
+ * @author Dale Visser
+ * @see <a href="https://www.gnu.org/software/autoconf/">Autoconf - GNU Project - Free Software Foundation (FSF)</a>
+ */
+public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * Autoconf output filename.
+     */
+    private static final String CONFIGURE = "configure";
+
+    /**
+     * Autoconf input filename.
+     */
+    private static final String CONFIGURE_IN = "configure.in";
+
+    /**
+     * Autoconf input filename.
+     */
+    private static final String CONFIGURE_AC = "configure.ac";
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Autoconf Analyzer";
+
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The set of file extensions supported by this analyzer.
+     */
+    private static final String[] EXTENSIONS = {"ac", "in"};
+
+    /**
+     * Matches AC_INIT variables in the output configure script.
+     */
+    private static final Pattern PACKAGE_VAR = Pattern.compile(
+            "PACKAGE_(.+?)='(.*?)'", Pattern.DOTALL | Pattern.CASE_INSENSITIVE);
+
+    /**
+     * Matches AC_INIT statement in configure.ac file.
+     */
+    private static final Pattern AC_INIT_PATTERN;
+
+    static {
+        // each instance of param or sep_param has a capture group
+        final String param = "\\[{0,2}(.+?)\\]{0,2}";
+        final String sepParam = "\\s*,\\s*" + param;
+        // Group 1: Package
+        // Group 2: Version
+        // Group 3: optional
+        // Group 4: Bug report address (if it exists)
+        // Group 5: optional
+        // Group 6: Tarname (if it exists)
+        // Group 7: optional
+        // Group 8: URL (if it exists)
+        AC_INIT_PATTERN = Pattern.compile(String.format(
+                "AC_INIT\\(%s%s(%s)?(%s)?(%s)?\\s*\\)", param, sepParam,
+                sepParam, sepParam, sepParam), Pattern.DOTALL
+                | Pattern.CASE_INSENSITIVE);
+    }
+
+    /**
+     * The file filter used to determine which files this analyzer supports.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addFilenames(CONFIGURE).addExtensions(
+            EXTENSIONS).build();
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase that the analyzer is intended to run in.
+     *
+     * @return the phase that the analyzer is intended to run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED;
+    }
+
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        final File actualFile = dependency.getActualFile();
+        final String name = actualFile.getName();
+        if (name.startsWith(CONFIGURE)) {
+            final File parent = actualFile.getParentFile();
+            final String parentName = parent.getName();
+            dependency.setDisplayFileName(parentName + "/" + name);
+            final boolean isOutputScript = CONFIGURE.equals(name);
+            if (isOutputScript || CONFIGURE_AC.equals(name)
+                    || CONFIGURE_IN.equals(name)) {
+                final String contents = getFileContents(actualFile);
+                if (!contents.isEmpty()) {
+                    if (isOutputScript) {
+                        extractConfigureScriptEvidence(dependency, name,
+                                contents);
+                    } else {
+                        gatherEvidence(dependency, name, contents);
+                    }
+                }
+            }
+        } else {
+            // copy, alter and set in case some other thread is iterating over
+            final List<Dependency> dependencies = new ArrayList<Dependency>(
+                    engine.getDependencies());
+            dependencies.remove(dependency);
+            engine.setDependencies(dependencies);
+        }
+    }
+
+    /**
+     * Extracts evidence from the configuration.
+     *
+     * @param dependency the dependency being analyzed
+     * @param name the name of the source of evidence
+     * @param contents the contents to analyze for evidence
+     */
+    private void extractConfigureScriptEvidence(Dependency dependency,
+            final String name, final String contents) {
+        final Matcher matcher = PACKAGE_VAR.matcher(contents);
+        while (matcher.find()) {
+            final String variable = matcher.group(1);
+            final String value = matcher.group(2);
+            if (!value.isEmpty()) {
+                if (variable.endsWith("NAME")) {
+                    dependency.getProductEvidence().addEvidence(name, variable,
+                            value, Confidence.HIGHEST);
+                } else if ("VERSION".equals(variable)) {
+                    dependency.getVersionEvidence().addEvidence(name, variable,
+                            value, Confidence.HIGHEST);
+                } else if ("BUGREPORT".equals(variable)) {
+                    dependency.getVendorEvidence().addEvidence(name, variable,
+                            value, Confidence.HIGH);
+                } else if ("URL".equals(variable)) {
+                    dependency.getVendorEvidence().addEvidence(name, variable,
+                            value, Confidence.HIGH);
+                }
+            }
+        }
+    }
+
+    /**
+     * Retrieves the contents of a given file.
+     *
+     * @param actualFile the file to read
+     * @return the contents of the file
+     * @throws AnalysisException thrown if there is an IO Exception
+     */
+    private String getFileContents(final File actualFile)
+            throws AnalysisException {
+        String contents = "";
+        try {
+            contents = FileUtils.readFileToString(actualFile).trim();
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+        return contents;
+    }
+
+    /**
+     * Gathers evidence from a given file
+     *
+     * @param dependency the dependency to add evidence to
+     * @param name the source of the evidence
+     * @param contents the evidence to analyze
+     */
+    private void gatherEvidence(Dependency dependency, final String name,
+            String contents) {
+        final Matcher matcher = AC_INIT_PATTERN.matcher(contents);
+        if (matcher.find()) {
+            final EvidenceCollection productEvidence = dependency
+                    .getProductEvidence();
+            productEvidence.addEvidence(name, "Package", matcher.group(1),
+                    Confidence.HIGHEST);
+            dependency.getVersionEvidence().addEvidence(name,
+                    "Package Version", matcher.group(2), Confidence.HIGHEST);
+            final EvidenceCollection vendorEvidence = dependency
+                    .getVendorEvidence();
+            if (null != matcher.group(3)) {
+                vendorEvidence.addEvidence(name, "Bug report address",
+                        matcher.group(4), Confidence.HIGH);
+            }
+            if (null != matcher.group(5)) {
+                productEvidence.addEvidence(name, "Tarname", matcher.group(6),
+                        Confidence.HIGH);
+            }
+            if (null != matcher.group(7)) {
+                final String url = matcher.group(8);
+                if (UrlStringUtils.isUrl(url)) {
+                    vendorEvidence.addEvidence(name, "URL", url,
+                            Confidence.HIGH);
+                }
+            }
+        }
+    }
+
+    /**
+     * Initializes the file type analyzer.
+     *
+     * @throws Exception thrown if there is an exception during initialization
+     */
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        // No initialization needed.
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/CMakeAnalyzer.java

@@ -0,0 +1,237 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Checksum;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * <p>
+ * Used to analyze CMake build files, and collect information that can be used to determine the associated CPE.</p>
+ * <p>
+ * Note: This analyzer catches straightforward invocations of the project command, plus some other observed patterns of version
+ * inclusion in real CMake projects. Many projects make use of older versions of CMake and/or use custom "homebrew" ways to insert
+ * version information. Hopefully as the newer CMake call pattern grows in usage, this analyzer allow more CPEs to be
+ * identified.</p>
+ *
+ * @author Dale Visser
+ */
+public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(CMakeAnalyzer.class);
+
+    /**
+     * Used when compiling file scanning regex patterns.
+     */
+    private static final int REGEX_OPTIONS = Pattern.DOTALL
+            | Pattern.CASE_INSENSITIVE | Pattern.MULTILINE;
+
+    /**
+     * Regex to extract the product information.
+     */
+    private static final Pattern PROJECT = Pattern.compile(
+            "^ *project *\\([ \\n]*(\\w+)[ \\n]*.*?\\)", REGEX_OPTIONS);
+
+    /**
+     * Regex to extract product and version information.
+     *
+     * Group 1: Product
+     *
+     * Group 2: Version
+     */
+    private static final Pattern SET_VERSION = Pattern
+            .compile(
+                    "^ *set\\s*\\(\\s*(\\w+)_version\\s+\"?(\\d+(?:\\.\\d+)+)[\\s\"]?\\)",
+                    REGEX_OPTIONS);
+
+    /**
+     * Detects files that can be analyzed.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(".cmake")
+            .addFilenames("CMakeLists.txt").build();
+
+    /**
+     * A reference to SHA1 message digest.
+     */
+    private static MessageDigest sha1 = null;
+
+    static {
+        try {
+            sha1 = MessageDigest.getInstance("SHA1");
+        } catch (NoSuchAlgorithmException e) {
+            LOGGER.error(e.getMessage());
+        }
+    }
+
+    /**
+     * Returns the name of the CMake analyzer.
+     *
+     * @return the name of the analyzer
+     *
+     */
+    @Override
+    public String getName() {
+        return "CMake Analyzer";
+    }
+
+    /**
+     * Tell that we are used for information collection.
+     *
+     * @return INFORMATION_COLLECTION
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return AnalysisPhase.INFORMATION_COLLECTION;
+    }
+
+    /**
+     * Returns the set of supported file extensions.
+     *
+     * @return the set of supported file extensions
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * No-op initializer implementation.
+     *
+     * @throws Exception never thrown
+     */
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        // Nothing to do here.
+    }
+
+    /**
+     * Analyzes python packages and adds evidence to the dependency.
+     *
+     * @param dependency the dependency being analyzed
+     * @param engine the engine being used to perform the scan
+     * @throws AnalysisException thrown if there is an unrecoverable error analyzing the dependency
+     */
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        final File file = dependency.getActualFile();
+        final String parentName = file.getParentFile().getName();
+        final String name = file.getName();
+        dependency.setDisplayFileName(String.format("%s%c%s", parentName, File.separatorChar, name));
+        String contents;
+        try {
+            contents = FileUtils.readFileToString(file).trim();
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+
+        if (StringUtils.isNotBlank(contents)) {
+            final Matcher m = PROJECT.matcher(contents);
+            int count = 0;
+            while (m.find()) {
+                count++;
+                LOGGER.debug(String.format(
+                        "Found project command match with %d groups: %s",
+                        m.groupCount(), m.group(0)));
+                final String group = m.group(1);
+                LOGGER.debug("Group 1: " + group);
+                dependency.getProductEvidence().addEvidence(name, "Project",
+                        group, Confidence.HIGH);
+            }
+            LOGGER.debug("Found {} matches.", count);
+            analyzeSetVersionCommand(dependency, engine, contents);
+        }
+    }
+
+    /**
+     * Extracts the version information from the contents. If more then one version is found additional dependencies are added to
+     * the dependency list.
+     *
+     * @param dependency the dependency being analyzed
+     * @param engine the dependency-check engine
+     * @param contents the version information
+     */
+    private void analyzeSetVersionCommand(Dependency dependency, Engine engine, String contents) {
+        Dependency currentDep = dependency;
+
+        final Matcher m = SET_VERSION.matcher(contents);
+        int count = 0;
+        while (m.find()) {
+            count++;
+            LOGGER.debug("Found project command match with {} groups: {}",
+                    m.groupCount(), m.group(0));
+            String product = m.group(1);
+            final String version = m.group(2);
+            LOGGER.debug("Group 1: " + product);
+            LOGGER.debug("Group 2: " + version);
+            final String aliasPrefix = "ALIASOF_";
+            if (product.startsWith(aliasPrefix)) {
+                product = product.replaceFirst(aliasPrefix, "");
+            }
+            if (count > 1) {
+                //TODO - refactor so we do not assign to the parameter (checkstyle)
+                currentDep = new Dependency(dependency.getActualFile());
+                currentDep.setDisplayFileName(String.format("%s:%s", dependency.getDisplayFileName(), product));
+                final String filePath = String.format("%s:%s", dependency.getFilePath(), product);
+                currentDep.setFilePath(filePath);
+
+                byte[] path;
+                try {
+                    path = filePath.getBytes("UTF-8");
+                } catch (UnsupportedEncodingException ex) {
+                    path = filePath.getBytes();
+                }
+                currentDep.setSha1sum(Checksum.getHex(sha1.digest(path)));
+                engine.getDependencies().add(currentDep);
+            }
+            final String source = currentDep.getDisplayFileName();
+            currentDep.getProductEvidence().addEvidence(source, "Product",
+                    product, Confidence.MEDIUM);
+            currentDep.getVersionEvidence().addEvidence(source, "Version",
+                    version, Confidence.MEDIUM);
+        }
+        LOGGER.debug(String.format("Found %d matches.", count));
+    }
+
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_CMAKE_ENABLED;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/CPEAnalyzer.java

@@ -1,18 +1,17 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
@@ -21,44 +20,48 @@ package org.owasp.dependencycheck.analyzer;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
-import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 import java.util.StringTokenizer;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.index.CorruptIndexException;
 import org.apache.lucene.queryparser.classic.ParseException;
 import org.apache.lucene.search.ScoreDoc;
 import org.apache.lucene.search.TopDocs;
 import org.owasp.dependencycheck.Engine;
-import org.owasp.dependencycheck.data.lucene.LuceneUtils;
-import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.dependency.Evidence;
-import org.owasp.dependencycheck.dependency.Evidence.Confidence;
-import org.owasp.dependencycheck.dependency.EvidenceCollection;
-import org.owasp.dependencycheck.data.cpe.CpeIndexReader;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.data.cpe.CpeMemoryIndex;
 import org.owasp.dependencycheck.data.cpe.Fields;
 import org.owasp.dependencycheck.data.cpe.IndexEntry;
+import org.owasp.dependencycheck.data.cpe.IndexException;
+import org.owasp.dependencycheck.data.lucene.LuceneUtils;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.dependency.EvidenceCollection;
 import org.owasp.dependencycheck.dependency.Identifier;
 import org.owasp.dependencycheck.dependency.VulnerableSoftware;
 import org.owasp.dependencycheck.utils.DependencyVersion;
 import org.owasp.dependencycheck.utils.DependencyVersionUtil;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
- * CPEAnalyzer is a utility class that takes a project dependency and attempts
- * to discern if there is an associated CPE. It uses the evidence contained
- * within the dependency to search the Lucene index.
+ * CPEAnalyzer is a utility class that takes a project dependency and attempts to discern if there is an associated CPE. It uses
+ * the evidence contained within the dependency to search the Lucene index.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class CPEAnalyzer implements Analyzer {
 
+    /**
+     * The Logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(CPEAnalyzer.class);
     /**
      * The maximum number of query results to return.
      */
@@ -68,91 +71,107 @@ public class CPEAnalyzer implements Analyzer {
      */
     static final String WEIGHTING_BOOST = "^5";
     /**
-     * A string representation of a regular expression defining characters
-     * utilized within the CPE Names.
+     * A string representation of a regular expression defining characters utilized within the CPE Names.
      */
     static final String CLEANSE_CHARACTER_RX = "[^A-Za-z0-9 ._-]";
     /**
-     * A string representation of a regular expression used to remove all but
-     * alpha characters.
+     * A string representation of a regular expression used to remove all but alpha characters.
      */
     static final String CLEANSE_NONALPHA_RX = "[^A-Za-z]*";
     /**
-     * The additional size to add to a new StringBuilder to account for extra
-     * data that will be written into the string.
+     * The additional size to add to a new StringBuilder to account for extra data that will be written into the string.
      */
     static final int STRING_BUILDER_BUFFER = 20;
     /**
-     * The CPE Index Reader.
+     * The CPE in memory index.
      */
-    private CpeIndexReader cpe;
+    private CpeMemoryIndex cpe;
     /**
      * The CVE Database.
      */
     private CveDB cve;
 
+    /**
+     * The URL to perform a search of the NVD CVE data at NIST.
+     */
+    public static final String NVD_SEARCH_URL = "https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=%s";
+
+    /**
+     * Returns the name of this analyzer.
+     *
+     * @return the name of this analyzer.
+     */
+    @Override
+    public String getName() {
+        return "CPE Analyzer";
+    }
+
+    /**
+     * Returns the analysis phase that this analyzer should run in.
+     *
+     * @return the analysis phase that this analyzer should run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return AnalysisPhase.IDENTIFIER_ANALYSIS;
+    }
+
+    /**
+     * Creates the CPE Lucene Index.
+     *
+     * @throws Exception is thrown if there is an issue opening the index.
+     */
+    @Override
+    public void initialize() throws Exception {
+        this.open();
+    }
+
     /**
      * Opens the data source.
      *
-     * @throws IOException when the Lucene directory to be queried does not
-     * exist or is corrupt.
-     * @throws DatabaseException when the database throws an exception. This
-     * usually occurs when the database is in use by another process.
+     * @throws IOException when the Lucene directory to be queried does not exist or is corrupt.
+     * @throws DatabaseException when the database throws an exception. This usually occurs when the database is in use by another
+     * process.
      */
     public void open() throws IOException, DatabaseException {
-        cpe = new CpeIndexReader();
-        cpe.open();
-        cve = new CveDB();
-        try {
+        if (!isOpen()) {
+            cve = new CveDB();
             cve.open();
-        } catch (SQLException ex) {
-            Logger.getLogger(CPEAnalyzer.class.getName()).log(Level.FINE, null, ex);
-            throw new DatabaseException("Unable to open the cve db", ex);
-        } catch (ClassNotFoundException ex) {
-            Logger.getLogger(CPEAnalyzer.class.getName()).log(Level.FINE, null, ex);
-            throw new DatabaseException("Unable to open the cve db", ex);
+            cpe = CpeMemoryIndex.getInstance();
+            try {
+                LOGGER.info("Creating the CPE Index");
+                final long creationStart = System.currentTimeMillis();
+                cpe.open(cve);
+                LOGGER.info("CPE Index Created ({} ms)", System.currentTimeMillis() - creationStart);
+            } catch (IndexException ex) {
+                LOGGER.debug("IndexException", ex);
+                throw new DatabaseException(ex);
+            }
         }
     }
 
     /**
-     * Closes the data source.
+     * Closes the data sources.
      */
     @Override
     public void close() {
         if (cpe != null) {
             cpe.close();
+            cpe = null;
         }
         if (cve != null) {
             cve.close();
+            cve = null;
         }
     }
 
-    /**
-     * Returns the status of the data source - is the index open.
-     *
-     * @return true or false.
-     */
     public boolean isOpen() {
-        return (cpe != null) && cpe.isOpen();
+        return cpe != null && cpe.isOpen();
     }
 
     /**
-     * Ensures that the Lucene index is closed.
-     *
-     * @throws Throwable when a throwable is thrown.
-     */
-    @Override
-    protected void finalize() throws Throwable {
-        super.finalize();
-        if (isOpen()) {
-            close();
-        }
-    }
-
-    /**
-     * Searches the data store of CPE entries, trying to identify the CPE for
-     * the given dependency based on the evidence contained within. The
-     * dependency passed in is updated with any identified CPE values.
+     * Searches the data store of CPE entries, trying to identify the CPE for the given dependency based on the evidence contained
+     * within. The dependency passed in is updated with any identified CPE values.
      *
      * @param dependency the dependency to search for CPE entries on.
      * @throws CorruptIndexException is thrown when the Lucene index is corrupt.
@@ -160,42 +179,45 @@ public class CPEAnalyzer implements Analyzer {
      * @throws ParseException is thrown when the Lucene query cannot be parsed.
      */
     protected void determineCPE(Dependency dependency) throws CorruptIndexException, IOException, ParseException {
-        Confidence vendorConf = Confidence.HIGHEST;
-        Confidence productConf = Confidence.HIGHEST;
-
-        String vendors = addEvidenceWithoutDuplicateTerms("", dependency.getVendorEvidence(), vendorConf);
-        String products = addEvidenceWithoutDuplicateTerms("", dependency.getProductEvidence(), productConf);
-
-        int ctr = 0;
-        do {
+        //TODO test dojo-war against this. we shold get dojo-toolkit:dojo-toolkit AND dojo-toolkit:toolkit
+        String vendors = "";
+        String products = "";
+        for (Confidence confidence : Confidence.values()) {
+            if (dependency.getVendorEvidence().contains(confidence)) {
+                vendors = addEvidenceWithoutDuplicateTerms(vendors, dependency.getVendorEvidence(), confidence);
+                LOGGER.debug("vendor search: {}", vendors);
+            }
+            if (dependency.getProductEvidence().contains(confidence)) {
+                products = addEvidenceWithoutDuplicateTerms(products, dependency.getProductEvidence(), confidence);
+                LOGGER.debug("product search: {}", products);
+            }
             if (!vendors.isEmpty() && !products.isEmpty()) {
                 final List<IndexEntry> entries = searchCPE(vendors, products, dependency.getProductEvidence().getWeighting(),
                         dependency.getVendorEvidence().getWeighting());
-
+                if (entries == null) {
+                    continue;
+                }
+                boolean identifierAdded = false;
                 for (IndexEntry e : entries) {
+                    LOGGER.debug("Verifying entry: {}", e);
                     if (verifyEntry(e, dependency)) {
                         final String vendor = e.getVendor();
                         final String product = e.getProduct();
-                        determineIdentifiers(dependency, vendor, product);
+                        LOGGER.debug("identified vendor/product: {}/{}", vendor, product);
+                        identifierAdded |= determineIdentifiers(dependency, vendor, product, confidence);
                     }
                 }
+                if (identifierAdded) {
+                    break;
+                }
             }
-            vendorConf = reduceConfidence(vendorConf);
-            if (dependency.getVendorEvidence().contains(vendorConf)) {
-                vendors = addEvidenceWithoutDuplicateTerms(vendors, dependency.getVendorEvidence(), vendorConf);
-            }
-            productConf = reduceConfidence(productConf);
-            if (dependency.getProductEvidence().contains(productConf)) {
-                products = addEvidenceWithoutDuplicateTerms(products, dependency.getProductEvidence(), productConf);
-            }
-        } while ((++ctr) < 4);
+        }
     }
 
     /**
-     * Returns the text created by concatenating the text and the values from
-     * the EvidenceCollection (filtered for a specific confidence). This
-     * attempts to prevent duplicate terms from being added.<br/<br/> Note, if
-     * the evidence is longer then 200 characters it will be truncated.
+     * Returns the text created by concatenating the text and the values from the EvidenceCollection (filtered for a specific
+     * confidence). This attempts to prevent duplicate terms from being added.<br/<br/> Note, if the evidence is longer then 200
+     * characters it will be truncated.
      *
      * @param text the base text.
      * @param ec an EvidenceCollection
@@ -225,87 +247,66 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * Reduces the given confidence by one level. This returns LOW if the
-     * confidence passed in is not HIGH.
+     * <p>
+     * Searches the Lucene CPE index to identify possible CPE entries associated with the supplied vendor, product, and
+     * version.</p>
      *
-     * @param c the confidence to reduce.
-     * @return One less then the confidence passed in.
-     */
-    private Confidence reduceConfidence(final Confidence c) {
-        if (c == Confidence.HIGHEST) {
-            return Confidence.HIGH;
-        } else if (c == Confidence.HIGH) {
-            return Confidence.MEDIUM;
-        } else {
-            return Confidence.LOW;
-        }
-    }
-
-    /**
-     * <p>Searches the Lucene CPE index to identify possible CPE entries
-     * associated with the supplied vendor, product, and version.</p>
-     *
-     * <p>If either the vendorWeightings or productWeightings lists have been
-     * populated this data is used to add weighting factors to the search.</p>
+     * <p>
+     * If either the vendorWeightings or productWeightings lists have been populated this data is used to add weighting factors to
+     * the search.</p>
      *
      * @param vendor the text used to search the vendor field
      * @param product the text used to search the product field
-     * @param vendorWeightings a list of strings to use to add weighting factors
-     * to the vendor field
-     * @param productWeightings Adds a list of strings that will be used to add
-     * weighting factors to the product search
+     * @param vendorWeightings a list of strings to use to add weighting factors to the vendor field
+     * @param productWeightings Adds a list of strings that will be used to add weighting factors to the product search
      * @return a list of possible CPE values
-     * @throws CorruptIndexException when the Lucene index is corrupt
-     * @throws IOException when the Lucene index is not found
-     * @throws ParseException when the generated query is not valid
      */
     protected List<IndexEntry> searchCPE(String vendor, String product,
-            Set<String> vendorWeightings, Set<String> productWeightings)
-            throws CorruptIndexException, IOException, ParseException {
-        final ArrayList<IndexEntry> ret = new ArrayList<IndexEntry>(MAX_QUERY_RESULTS);
+            Set<String> vendorWeightings, Set<String> productWeightings) {
+
+        final List<IndexEntry> ret = new ArrayList<IndexEntry>(MAX_QUERY_RESULTS);
 
         final String searchString = buildSearch(vendor, product, vendorWeightings, productWeightings);
         if (searchString == null) {
             return ret;
         }
-
-        final TopDocs docs = cpe.search(searchString, MAX_QUERY_RESULTS);
-        for (ScoreDoc d : docs.scoreDocs) {
-            if (d.score >= 0.08) {
-                final Document doc = cpe.getDocument(d.doc);
-                final IndexEntry entry = new IndexEntry();
-                entry.setVendor(doc.get(Fields.VENDOR));
-                entry.setProduct(doc.get(Fields.PRODUCT));
-//                if (d.score < 0.08) {
-//                    System.out.print(entry.getVendor());
-//                    System.out.print(":");
-//                    System.out.print(entry.getProduct());
-//                    System.out.print(":");
-//                    System.out.println(d.score);
-//                }
-                entry.setSearchScore(d.score);
-                if (!ret.contains(entry)) {
-                    ret.add(entry);
+        try {
+            final TopDocs docs = cpe.search(searchString, MAX_QUERY_RESULTS);
+            for (ScoreDoc d : docs.scoreDocs) {
+                if (d.score >= 0.08) {
+                    final Document doc = cpe.getDocument(d.doc);
+                    final IndexEntry entry = new IndexEntry();
+                    entry.setVendor(doc.get(Fields.VENDOR));
+                    entry.setProduct(doc.get(Fields.PRODUCT));
+                    entry.setSearchScore(d.score);
+                    if (!ret.contains(entry)) {
+                        ret.add(entry);
+                    }
                 }
             }
+            return ret;
+        } catch (ParseException ex) {
+            LOGGER.warn("An error occurred querying the CPE data. See the log for more details.");
+            LOGGER.info("Unable to parse: {}", searchString, ex);
+        } catch (IOException ex) {
+            LOGGER.warn("An error occurred reading CPE data. See the log for more details.");
+            LOGGER.info("IO Error with search string: {}", searchString, ex);
         }
-        return ret;
+        return null;
     }
 
     /**
-     * <p>Builds a Lucene search string by properly escaping data and
-     * constructing a valid search query.</p>
+     * <p>
+     * Builds a Lucene search string by properly escaping data and constructing a valid search query.</p>
      *
-     * <p>If either the possibleVendor or possibleProducts lists have been
-     * populated this data is used to add weighting factors to the search string
-     * generated.</p>
+     * <p>
+     * If either the possibleVendor or possibleProducts lists have been populated this data is used to add weighting factors to
+     * the search string generated.</p>
      *
      * @param vendor text to search the vendor field
      * @param product text to search the product field
-     * @param vendorWeighting a list of strings to apply to the vendor to boost
-     * the terms weight
-     * @param productWeightings a list of strings to apply to the product to
-     * boost the terms weight
+     * @param vendorWeighting a list of strings to apply to the vendor to boost the terms weight
+     * @param productWeightings a list of strings to apply to the product to boost the terms weight
      * @return the Lucene query
      */
     protected String buildSearch(String vendor, String product,
@@ -326,25 +327,21 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * This method constructs a Lucene query for a given field. The searchText
-     * is split into separate words and if the word is within the list of
-     * weighted words then an additional weighting is applied to the term as it
-     * is appended into the query.
+     * This method constructs a Lucene query for a given field. The searchText is split into separate words and if the word is
+     * within the list of weighted words then an additional weighting is applied to the term as it is appended into the query.
      *
      * @param sb a StringBuilder that the query text will be appended to.
-     * @param field the field within the Lucene index that the query is
-     * searching.
+     * @param field the field within the Lucene index that the query is searching.
      * @param searchText text used to construct the query.
-     * @param weightedText a list of terms that will be considered higher
-     * importance when searching.
+     * @param weightedText a list of terms that will be considered higher importance when searching.
      * @return if the append was successful.
      */
     private boolean appendWeightedSearch(StringBuilder sb, String field, String searchText, Set<String> weightedText) {
-        sb.append(" ").append(field).append(":( ");
+        sb.append(' ').append(field).append(":( ");
 
         final String cleanText = cleanseText(searchText);
 
-        if ("".equals(cleanText)) {
+        if (cleanText.isEmpty()) {
             return false;
         }
 
@@ -354,20 +351,27 @@ public class CPEAnalyzer implements Analyzer {
             final StringTokenizer tokens = new StringTokenizer(cleanText);
             while (tokens.hasMoreElements()) {
                 final String word = tokens.nextToken();
-                String temp = null;
+                StringBuilder temp = null;
                 for (String weighted : weightedText) {
                     final String weightedStr = cleanseText(weighted);
                     if (equalsIgnoreCaseAndNonAlpha(word, weightedStr)) {
-                        temp = LuceneUtils.escapeLuceneQuery(word) + WEIGHTING_BOOST;
+                        temp = new StringBuilder(word.length() + 2);
+                        LuceneUtils.appendEscapedLuceneQuery(temp, word);
+                        temp.append(WEIGHTING_BOOST);
                         if (!word.equalsIgnoreCase(weightedStr)) {
-                            temp += " " + LuceneUtils.escapeLuceneQuery(weightedStr) + WEIGHTING_BOOST;
+                            temp.append(' ');
+                            LuceneUtils.appendEscapedLuceneQuery(temp, weightedStr);
+                            temp.append(WEIGHTING_BOOST);
                         }
+                        break;
                     }
                 }
+                sb.append(' ');
                 if (temp == null) {
-                    temp = LuceneUtils.escapeLuceneQuery(word);
+                    LuceneUtils.appendEscapedLuceneQuery(sb, word);
+                } else {
+                    sb.append(temp);
                 }
-                sb.append(" ").append(temp);
             }
         }
         sb.append(" ) ");
@@ -375,8 +379,7 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * Removes characters from the input text that are not used within the CPE
-     * index.
+     * Removes characters from the input text that are not used within the CPE index.
      *
      * @param text is the text to remove the characters from.
      * @return the text having removed some characters.
@@ -386,8 +389,7 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * Compares two strings after lower casing them and removing the non-alpha
-     * characters.
+     * Compares two strings after lower casing them and removing the non-alpha characters.
      *
      * @param l string one to compare.
      * @param r string two to compare.
@@ -404,9 +406,8 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * Ensures that the CPE Identified matches the dependency. This validates
-     * that the product, vendor, and version information for the CPE are
-     * contained within the dependencies evidence.
+     * Ensures that the CPE Identified matches the dependency. This validates that the product, vendor, and version information
+     * for the CPE are contained within the dependencies evidence.
      *
      * @param entry a CPE entry.
      * @param dependency the dependency that the CPE entries could be for.
@@ -415,6 +416,8 @@ public class CPEAnalyzer implements Analyzer {
     private boolean verifyEntry(final IndexEntry entry, final Dependency dependency) {
         boolean isValid = false;
 
+        //TODO - does this nullify some of the fuzzy matching that happens in the lucene search?
+        // for instance CPE some-component and in the evidence we have SomeComponent.
         if (collectionContainsString(dependency.getProductEvidence(), entry.getProduct())
                 && collectionContainsString(dependency.getVendorEvidence(), entry.getVendor())) {
             //&& collectionContainsVersion(dependency.getVersionEvidence(), entry.getVersion())
@@ -431,18 +434,6 @@ public class CPEAnalyzer implements Analyzer {
      * @return whether or not the EvidenceCollection contains the string
      */
     private boolean collectionContainsString(EvidenceCollection ec, String text) {
-
-        //<editor-fold defaultstate="collapsed" desc="This code fold contains an old version of the code, delete once more testing is done">
-        //        String[] splitText = text.split("[\\s_-]");
-        //
-        //        for (String search : splitText) {
-        //            //final String search = text.replaceAll("[\\s_-]", "").toLowerCase();
-        //            if (ec.containsUsedString(search)) {
-        //                return true;
-        //            }
-        //        }
-        //</editor-fold>
-
         //TODO - likely need to change the split... not sure if this will work for CPE with special chars
         if (text == null) {
             return false;
@@ -451,8 +442,10 @@ public class CPEAnalyzer implements Analyzer {
         final List<String> list = new ArrayList<String>();
         String tempWord = null;
         for (String word : words) {
-            //single letter words should be concatonated with the next word.
-            // so { "m", "core", "sample" } -> { "mcore", "sample" }
+            /*
+             single letter words should be concatenated with the next word.
+             so { "m", "core", "sample" } -> { "mcore", "sample" }
+             */
             if (tempWord != null) {
                 list.add(tempWord + word);
                 tempWord = null;
@@ -462,9 +455,16 @@ public class CPEAnalyzer implements Analyzer {
                 list.add(word);
             }
         }
-        if (tempWord != null && !list.isEmpty()) {
-            final String tmp = list.get(list.size() - 1) + tempWord;
-            list.add(tmp);
+        if (tempWord != null) {
+            if (!list.isEmpty()) {
+                final String tmp = list.get(list.size() - 1) + tempWord;
+                list.add(tmp);
+            } else {
+                list.add(tempWord);
+            }
+        }
+        if (list.isEmpty()) {
+            return false;
         }
         boolean contains = true;
         for (String word : list) {
@@ -474,16 +474,14 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * Analyzes a dependency and attempts to determine if there are any CPE
-     * identifiers for this dependency.
+     * Analyzes a dependency and attempts to determine if there are any CPE identifiers for this dependency.
      *
      * @param dependency The Dependency to analyze.
      * @param engine The analysis engine
-     * @throws AnalysisException is thrown if there is an issue analyzing the
-     * dependency.
+     * @throws AnalysisException is thrown if there is an issue analyzing the dependency.
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    public synchronized void analyze(Dependency dependency, Engine engine) throws AnalysisException {
         try {
             determineCPE(dependency);
         } catch (CorruptIndexException ex) {
@@ -496,74 +494,28 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @return true.
-     */
-    @Override
-    public Set<String> getSupportedExtensions() {
-        return null;
-    }
-
-    /**
-     * Returns the name of this analyzer.
-     *
-     * @return the name of this analyzer.
-     */
-    @Override
-    public String getName() {
-        return "CPE Analyzer";
-    }
-
-    /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @param extension the file extension of the dependency being analyzed.
-     * @return true.
-     */
-    @Override
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
-    /**
-     * Returns the analysis phase that this analyzer should run in.
-     *
-     * @return the analysis phase that this analyzer should run in.
-     */
-    @Override
-    public AnalysisPhase getAnalysisPhase() {
-        return AnalysisPhase.IDENTIFIER_ANALYSIS;
-    }
-
-    /**
-     * Opens the CPE Lucene Index.
-     *
-     * @throws Exception is thrown if there is an issue opening the index.
-     */
-    @Override
-    public void initialize() throws Exception {
-        this.open();
-    }
-
-    /**
-     * Retrieves a list of CPE values from the CveDB based on the vendor and
-     * product passed in. The list is then validated to find only CPEs that are
-     * valid for the given dependency. It is possible that the CPE identified is
-     * a best effort "guess" based on the vendor, product, and version
-     * information.
+     * Retrieves a list of CPE values from the CveDB based on the vendor and product passed in. The list is then validated to find
+     * only CPEs that are valid for the given dependency. It is possible that the CPE identified is a best effort "guess" based on
+     * the vendor, product, and version information.
      *
      * @param dependency the Dependency being analyzed
      * @param vendor the vendor for the CPE being analyzed
      * @param product the product for the CPE being analyzed
+     * @param currentConfidence the current confidence being used during analysis
+     * @return <code>true</code> if an identifier was added to the dependency; otherwise <code>false</code>
      * @throws UnsupportedEncodingException is thrown if UTF-8 is not supported
      */
-    private void determineIdentifiers(Dependency dependency, String vendor, String product) throws UnsupportedEncodingException {
+    protected boolean determineIdentifiers(Dependency dependency, String vendor, String product,
+            Confidence currentConfidence) throws UnsupportedEncodingException {
         final Set<VulnerableSoftware> cpes = cve.getCPEs(vendor, product);
         DependencyVersion bestGuess = new DependencyVersion("-");
         Confidence bestGuessConf = null;
+        boolean hasBroadMatch = false;
         final List<IdentifierMatch> collected = new ArrayList<IdentifierMatch>();
         for (Confidence conf : Confidence.values()) {
+//            if (conf.compareTo(currentConfidence) > 0) {
+//                break;
+//            }
             for (Evidence evidence : dependency.getVersionEvidence().iterator(conf)) {
                 final DependencyVersion evVer = DependencyVersionUtil.parseVersion(evidence.getValue());
                 if (evVer == null) {
@@ -571,14 +523,18 @@ public class CPEAnalyzer implements Analyzer {
                 }
                 for (VulnerableSoftware vs : cpes) {
                     DependencyVersion dbVer;
-                    if (vs.getRevision() != null && !vs.getRevision().isEmpty()) {
-                        dbVer = DependencyVersionUtil.parseVersion(vs.getVersion() + "." + vs.getRevision());
+                    if (vs.getUpdate() != null && !vs.getUpdate().isEmpty()) {
+                        dbVer = DependencyVersionUtil.parseVersion(vs.getVersion() + '.' + vs.getUpdate());
                     } else {
                         dbVer = DependencyVersionUtil.parseVersion(vs.getVersion());
                     }
-                    if (dbVer == null //special case, no version specified - everything is vulnerable
-                            || evVer.equals(dbVer)) { //woot exect match
-                        final String url = String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(vs.getName(), "UTF-8"));
+                    if (dbVer == null) { //special case, no version specified - everything is vulnerable
+                        hasBroadMatch = true;
+                        final String url = String.format(NVD_SEARCH_URL, URLEncoder.encode(vs.getName(), "UTF-8"));
+                        final IdentifierMatch match = new IdentifierMatch("cpe", vs.getName(), url, IdentifierConfidence.BROAD_MATCH, conf);
+                        collected.add(match);
+                    } else if (evVer.equals(dbVer)) { //yeah! exact match
+                        final String url = String.format(NVD_SEARCH_URL, URLEncoder.encode(vs.getName(), "UTF-8"));
                         final IdentifierMatch match = new IdentifierMatch("cpe", vs.getName(), url, IdentifierConfidence.EXACT_MATCH, conf);
                         collected.add(match);
                     } else {
@@ -603,7 +559,11 @@ public class CPEAnalyzer implements Analyzer {
             }
         }
         final String cpeName = String.format("cpe:/a:%s:%s:%s", vendor, product, bestGuess.toString());
-        final String url = null; //String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(cpeName, "UTF-8"));
+        String url = null;
+        if (hasBroadMatch) { //if we have a broad match we can add the URL to the best guess.
+            final String cpeUrlName = String.format("cpe:/a:%s:%s", vendor, product);
+            url = String.format(NVD_SEARCH_URL, URLEncoder.encode(cpeUrlName, "UTF-8"));
+        }
         if (bestGuessConf == null) {
             bestGuessConf = Confidence.LOW;
         }
@@ -613,12 +573,21 @@ public class CPEAnalyzer implements Analyzer {
         Collections.sort(collected);
         final IdentifierConfidence bestIdentifierQuality = collected.get(0).getConfidence();
         final Confidence bestEvidenceQuality = collected.get(0).getEvidenceConfidence();
+        boolean identifierAdded = false;
         for (IdentifierMatch m : collected) {
             if (bestIdentifierQuality.equals(m.getConfidence())
                     && bestEvidenceQuality.equals(m.getEvidenceConfidence())) {
-                dependency.addIdentifier(m.getIdentifier());
+                final Identifier i = m.getIdentifier();
+                if (bestIdentifierQuality == IdentifierConfidence.BEST_GUESS) {
+                    i.setConfidence(Confidence.LOW);
+                } else {
+                    i.setConfidence(bestEvidenceQuality);
+                }
+                dependency.addIdentifier(i);
+                identifierAdded = true;
             }
         }
+        return identifierAdded;
     }
 
     /**
@@ -633,25 +602,27 @@ public class CPEAnalyzer implements Analyzer {
         /**
          * A best guess for the CPE.
          */
-        BEST_GUESS
+        BEST_GUESS,
+        /**
+         * The entire vendor/product group must be added (without a guess at version) because there is a CVE with a VS that only
+         * specifies vendor/product.
+         */
+        BROAD_MATCH
     }
 
     /**
-     * A simple object to hold an identifier and carry information about the
-     * confidence in the identifier.
+     * A simple object to hold an identifier and carry information about the confidence in the identifier.
      */
     private static class IdentifierMatch implements Comparable<IdentifierMatch> {
 
         /**
-         * Constructs an IdentiferMatch.
+         * Constructs an IdentifierMatch.
          *
          * @param type the type of identifier (such as CPE)
          * @param value the value of the identifier
          * @param url the URL of the identifier
-         * @param identifierConfidence the confidence in the identifier: best
-         * guess or exact match
-         * @param evidenceConfidence the confidence of the evidence used to find
-         * the identifier
+         * @param identifierConfidence the confidence in the identifier: best guess or exact match
+         * @param evidenceConfidence the confidence of the evidence used to find the identifier
          */
         IdentifierMatch(String type, String value, String url, IdentifierConfidence identifierConfidence, Confidence evidenceConfidence) {
             this.identifier = new Identifier(type, value, url);
@@ -782,8 +753,7 @@ public class CPEAnalyzer implements Analyzer {
         //</editor-fold>
 
         /**
-         * Standard implementation of compareTo that compares identifier
-         * confidence, evidence confidence, and then the identifier.
+         * Standard implementation of compareTo that compares identifier confidence, evidence confidence, and then the identifier.
          *
          * @param o the IdentifierMatch to compare to
          * @return the natural ordering of IdentifierMatch

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/CentralAnalyzer.java

@@ -0,0 +1,238 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.data.central.CentralSearch;
+import org.owasp.dependencycheck.data.nexus.MavenArtifact;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.xml.pom.PomUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URL;
+import java.util.List;
+import org.owasp.dependencycheck.utils.DownloadFailedException;
+import org.owasp.dependencycheck.utils.Downloader;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * Analyzer which will attempt to locate a dependency, and the GAV information, by querying Central for the dependency's SHA-1
+ * digest.
+ *
+ * @author colezlaw
+ */
+public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(CentralAnalyzer.class);
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Central Analyzer";
+
+    /**
+     * The phase in which this analyzer runs.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The types of files on which this will work.
+     */
+    private static final String SUPPORTED_EXTENSIONS = "jar";
+
+    /**
+     * The analyzer should be disabled if there are errors, so this is a flag to determine if such an error has occurred.
+     */
+    private boolean errorFlag = false;
+
+    /**
+     * The searcher itself.
+     */
+    private CentralSearch searcher;
+    /**
+     * Field indicating if the analyzer is enabled.
+     */
+    private final boolean enabled = checkEnabled();
+
+    /**
+     * Determine whether to enable this analyzer or not.
+     *
+     * @return whether the analyzer should be enabled
+     */
+    @Override
+    public boolean isEnabled() {
+        return enabled;
+    }
+
+    /**
+     * Determines if this analyzer is enabled.
+     *
+     * @return <code>true</code> if the analyzer is enabled; otherwise <code>false</code>
+     */
+    private boolean checkEnabled() {
+        boolean retval = false;
+
+        try {
+            if (Settings.getBoolean(Settings.KEYS.ANALYZER_CENTRAL_ENABLED)) {
+                if (!Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED)
+                        || NexusAnalyzer.DEFAULT_URL.equals(Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL))) {
+                    LOGGER.debug("Enabling the Central analyzer");
+                    retval = true;
+                } else {
+                    LOGGER.info("Nexus analyzer is enabled, disabling the Central Analyzer");
+                }
+            } else {
+                LOGGER.info("Central analyzer disabled");
+            }
+        } catch (InvalidSettingException ise) {
+            LOGGER.warn("Invalid setting. Disabling the Central analyzer");
+        }
+        return retval;
+    }
+
+    /**
+     * Initializes the analyzer once before any analysis is performed.
+     *
+     * @throws Exception if there's an error during initialization
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+        LOGGER.debug("Initializing Central analyzer");
+        LOGGER.debug("Central analyzer enabled: {}", isEnabled());
+        if (isEnabled()) {
+            final String searchUrl = Settings.getString(Settings.KEYS.ANALYZER_CENTRAL_URL);
+            LOGGER.debug("Central Analyzer URL: {}", searchUrl);
+            searcher = new CentralSearch(new URL(searchUrl));
+        }
+    }
+
+    /**
+     * Returns the analyzer's name.
+     *
+     * @return the name of the analyzer
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the key used in the properties file to to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key.
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_CENTRAL_ENABLED;
+    }
+
+    /**
+     * Returns the analysis phase under which the analyzer runs.
+     *
+     * @return the phase under which the analyzer runs
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * The file filter used to determine which files this analyzer supports.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(SUPPORTED_EXTENSIONS).build();
+
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Performs the analysis.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine
+     * @throws AnalysisException when there's an exception during analysis
+     */
+    @Override
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        if (errorFlag || !isEnabled()) {
+            return;
+        }
+
+        try {
+            final List<MavenArtifact> mas = searcher.searchSha1(dependency.getSha1sum());
+            final Confidence confidence = mas.size() > 1 ? Confidence.HIGH : Confidence.HIGHEST;
+            for (MavenArtifact ma : mas) {
+                LOGGER.debug("Central analyzer found artifact ({}) for dependency ({})", ma, dependency.getFileName());
+                dependency.addAsEvidence("central", ma, confidence);
+                boolean pomAnalyzed = false;
+                for (Evidence e : dependency.getVendorEvidence()) {
+                    if ("pom".equals(e.getSource())) {
+                        pomAnalyzed = true;
+                        break;
+                    }
+                }
+                if (!pomAnalyzed && ma.getPomUrl() != null) {
+                    File pomFile = null;
+                    try {
+                        final File baseDir = Settings.getTempDirectory();
+                        pomFile = File.createTempFile("pom", ".xml", baseDir);
+                        if (!pomFile.delete()) {
+                            LOGGER.warn("Unable to fetch pom.xml for {} from Central; "
+                                    + "this could result in undetected CPE/CVEs.", dependency.getFileName());
+                            LOGGER.debug("Unable to delete temp file");
+                        }
+                        LOGGER.debug("Downloading {}", ma.getPomUrl());
+                        Downloader.fetchFile(new URL(ma.getPomUrl()), pomFile);
+                        PomUtils.analyzePOM(dependency, pomFile);
+
+                    } catch (DownloadFailedException ex) {
+                        LOGGER.warn("Unable to download pom.xml for {} from Central; "
+                                + "this could result in undetected CPE/CVEs.", dependency.getFileName());
+                    } finally {
+                        if (pomFile != null && !FileUtils.deleteQuietly(pomFile)) {
+                            pomFile.deleteOnExit();
+                        }
+                    }
+                }
+
+            }
+        } catch (IllegalArgumentException iae) {
+            LOGGER.info("invalid sha1-hash on {}", dependency.getFileName());
+        } catch (FileNotFoundException fnfe) {
+            LOGGER.debug("Artifact not found in repository: '{}", dependency.getFileName());
+        } catch (IOException ioe) {
+            LOGGER.debug("Could not connect to Central search", ioe);
+            errorFlag = true;
+        }
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/ComposerLockAnalyzer.java

@@ -0,0 +1,162 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 The OWASP Foundation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.data.composer.ComposerDependency;
+import org.owasp.dependencycheck.data.composer.ComposerException;
+import org.owasp.dependencycheck.data.composer.ComposerLockParser;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Checksum;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.FileFilter;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.nio.charset.Charset;
+import java.security.MessageDigest;
+
+/**
+ * Used to analyze a composer.lock file for a composer PHP app.
+ *
+ * @author colezlaw
+ */
+public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(ComposerLockAnalyzer.class);
+
+    /**
+     * The analyzer name.
+     */
+    private static final String ANALYZER_NAME = "Composer.lock analyzer";
+
+    /**
+     * composer.json.
+     */
+    private static final String COMPOSER_LOCK = "composer.lock";
+
+    /**
+     * The FileFilter.
+     */
+    private static final FileFilter FILE_FILTER = FileFilterBuilder.newInstance().addFilenames(COMPOSER_LOCK).build();
+
+    /**
+     * Returns the FileFilter.
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILE_FILTER;
+    }
+
+    /**
+     * Initializes the analyzer.
+     *
+     * @throws Exception thrown if an exception occurs getting an instance of SHA1
+     */
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        sha1 = MessageDigest.getInstance("SHA1");
+    }
+
+    /**
+     * The MessageDigest for calculating a new digest for the new dependencies added.
+     */
+    private MessageDigest sha1 = null;
+
+    /**
+     * Entry point for the analyzer.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine scanning
+     * @throws AnalysisException if there's a failure during analysis
+     */
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        FileInputStream fis = null;
+        try {
+            fis = new FileInputStream(dependency.getActualFile());
+            final ComposerLockParser clp = new ComposerLockParser(fis);
+            LOGGER.info("Checking composer.lock file {}", dependency.getActualFilePath());
+            clp.process();
+            for (ComposerDependency dep : clp.getDependencies()) {
+                final Dependency d = new Dependency(dependency.getActualFile());
+                d.setDisplayFileName(String.format("%s:%s/%s", dependency.getDisplayFileName(), dep.getGroup(), dep.getProject()));
+                final String filePath = String.format("%s:%s/%s", dependency.getFilePath(), dep.getGroup(), dep.getProject());
+                d.setFilePath(filePath);
+                d.setSha1sum(Checksum.getHex(sha1.digest(filePath.getBytes(Charset.defaultCharset()))));
+                d.getVendorEvidence().addEvidence(COMPOSER_LOCK, "vendor", dep.getGroup(), Confidence.HIGHEST);
+                d.getProductEvidence().addEvidence(COMPOSER_LOCK, "product", dep.getProject(), Confidence.HIGHEST);
+                d.getVersionEvidence().addEvidence(COMPOSER_LOCK, "version", dep.getVersion(), Confidence.HIGHEST);
+                LOGGER.info("Adding dependency {}", d);
+                engine.getDependencies().add(d);
+            }
+        } catch (FileNotFoundException fnfe) {
+            LOGGER.warn("Error opening dependency {}", dependency.getActualFilePath());
+        } catch (ComposerException ce) {
+            LOGGER.warn("Error parsing composer.json {}", dependency.getActualFilePath(), ce);
+        } finally {
+            if (fis != null) {
+                try {
+                    fis.close();
+                } catch (Exception e) {
+                    LOGGER.debug("Unable to close file", e);
+                }
+            }
+        }
+    }
+
+    /**
+     * Gets the key to determine whether the analyzer is enabled.
+     *
+     * @return the key specifying whether the analyzer is enabled
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED;
+    }
+
+    /**
+     * Returns the analyzer's name.
+     *
+     * @return the analyzer's name
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase this analyzer should run under.
+     *
+     * @return the analysis phase
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return AnalysisPhase.INFORMATION_COLLECTION;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/CpeSuppressionAnalyzer.java

@@ -0,0 +1,75 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.suppression.SuppressionRule;
+
+/**
+ * The suppression analyzer processes an externally defined XML document that complies with the suppressions.xsd schema.
+ * Any identified CPE entries within the dependencies that match will be removed.
+ *
+ * @author Jeremy Long
+ */
+public class CpeSuppressionAnalyzer extends AbstractSuppressionAnalyzer {
+
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Cpe Suppression Analyzer";
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.POST_IDENTIFIER_ANALYSIS;
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase that the analyzer is intended to run in.
+     *
+     * @return the phase that the analyzer is intended to run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+    //</editor-fold>
+
+    @Override
+    public void analyze(final Dependency dependency, final Engine engine) throws AnalysisException {
+
+        if (getRules() == null || getRules().size() <= 0) {
+            return;
+        }
+
+        for (final SuppressionRule rule : getRules()) {
+            rule.process(dependency);
+        }
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/DependencyBundlingAnalyzer.java

@@ -1,18 +1,17 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
@@ -23,44 +22,45 @@ import java.util.HashSet;
 import java.util.Iterator;
 import java.util.ListIterator;
 import java.util.Set;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Identifier;
 import org.owasp.dependencycheck.utils.DependencyVersion;
 import org.owasp.dependencycheck.utils.DependencyVersionUtil;
-import org.owasp.dependencycheck.utils.LogUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
- * <p>This analyzer ensures dependencies that should be grouped together, to
- * remove excess noise from the report, are grouped. An example would be Spring,
- * Spring Beans, Spring MVC, etc. If they are all for the same version and have
- * the same relative path then these should be grouped into a single dependency
- * under the core/main library.</p>
- * <p>Note, this grouping only works on dependencies with identified CVE
- * entries</p>
+ * <p>
+ * This analyzer ensures dependencies that should be grouped together, to remove excess noise from the report, are grouped. An
+ * example would be Spring, Spring Beans, Spring MVC, etc. If they are all for the same version and have the same relative path
+ * then these should be grouped into a single dependency under the core/main library.</p>
+ * <p>
+ * Note, this grouping only works on dependencies with identified CVE entries</p>
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Analyzer {
 
+    /**
+     * The Logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(DependencyBundlingAnalyzer.class);
+
     //<editor-fold defaultstate="collapsed" desc="Constants and Member Variables">
     /**
      * A pattern for obtaining the first part of a filename.
      */
-    private static final Pattern STARTING_TEXT_PATTERN = Pattern.compile("^[a-zA-Z]*");
+    private static final Pattern STARTING_TEXT_PATTERN = Pattern.compile("^[a-zA-Z0-9]*");
     /**
      * a flag indicating if this analyzer has run. This analyzer only runs once.
      */
     private boolean analyzed = false;
     //</editor-fold>
-    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = null;
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
      * The name of the analyzer.
      */
@@ -70,54 +70,34 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.PRE_FINDING_ANALYSIS;
 
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
-
     /**
      * Returns the name of the analyzer.
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support
-     * @return whether or not the specified file extension is supported by this
-     * analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
      * @return the phase that the analyzer is intended to run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
     //</editor-fold>
 
     /**
-     * Analyzes a set of dependencies. If they have been found to have the same
-     * base path and the same set of identifiers they are likely related. The
-     * related dependencies are bundled into a single reportable item.
+     * Analyzes a set of dependencies. If they have been found to have the same base path and the same set of identifiers they are
+     * likely related. The related dependencies are bundled into a single reportable item.
      *
      * @param ignore this analyzer ignores the dependency being analyzed
      * @param engine the engine that is scanning the dependencies
-     * @throws AnalysisException is thrown if there is an error reading the JAR
-     * file.
+     * @throws AnalysisException is thrown if there is an error reading the JAR file.
      */
     @Override
     public void analyze(Dependency ignore, Engine engine) throws AnalysisException {
@@ -128,33 +108,35 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
             //for (Dependency nextDependency : engine.getDependencies()) {
             while (mainIterator.hasNext()) {
                 final Dependency dependency = mainIterator.next();
-                if (mainIterator.hasNext()) {
+                if (mainIterator.hasNext() && !dependenciesToRemove.contains(dependency)) {
                     final ListIterator<Dependency> subIterator = engine.getDependencies().listIterator(mainIterator.nextIndex());
                     while (subIterator.hasNext()) {
                         final Dependency nextDependency = subIterator.next();
-
-                        if (identifiersMatch(dependency, nextDependency)
+                        if (hashesMatch(dependency, nextDependency) && !containedInWar(dependency.getFilePath())
+                                && !containedInWar(nextDependency.getFilePath())) {
+                            if (firstPathIsShortest(dependency.getFilePath(), nextDependency.getFilePath())) {
+                                mergeDependencies(dependency, nextDependency, dependenciesToRemove);
+                            } else {
+                                mergeDependencies(nextDependency, dependency, dependenciesToRemove);
+                                break; //since we merged into the next dependency - skip forward to the next in mainIterator
+                            }
+                        } else if (isShadedJar(dependency, nextDependency)) {
+                            if (dependency.getFileName().toLowerCase().endsWith("pom.xml")) {
+                                mergeDependencies(nextDependency, dependency, dependenciesToRemove);
+                                nextDependency.getRelatedDependencies().remove(dependency);
+                                break;
+                            } else {
+                                mergeDependencies(dependency, nextDependency, dependenciesToRemove);
+                                dependency.getRelatedDependencies().remove(nextDependency);
+                            }
+                        } else if (cpeIdentifiersMatch(dependency, nextDependency)
                                 && hasSameBasePath(dependency, nextDependency)
                                 && fileNameMatch(dependency, nextDependency)) {
-
                             if (isCore(dependency, nextDependency)) {
-                                dependency.addRelatedDependency(nextDependency);
-                                //move any "related dependencies" to the new "parent" dependency
-                                final Iterator<Dependency> i = nextDependency.getRelatedDependencies().iterator();
-                                while (i.hasNext()) {
-                                    dependency.addRelatedDependency(i.next());
-                                    i.remove();
-                                }
-                                dependenciesToRemove.add(nextDependency);
+                                mergeDependencies(dependency, nextDependency, dependenciesToRemove);
                             } else {
-                                nextDependency.addRelatedDependency(dependency);
-                                //move any "related dependencies" to the new "parent" dependency
-                                final Iterator<Dependency> i = dependency.getRelatedDependencies().iterator();
-                                while (i.hasNext()) {
-                                    nextDependency.addRelatedDependency(i.next());
-                                    i.remove();
-                                }
-                                dependenciesToRemove.add(dependency);
+                                mergeDependencies(nextDependency, dependency, dependenciesToRemove);
+                                break; //since we merged into the next dependency - skip forward to the next in mainIterator
                             }
                         }
                     }
@@ -162,15 +144,34 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
             }
             //removing dependencies here as ensuring correctness and avoiding ConcurrentUpdateExceptions
             // was difficult because of the inner iterator.
-            for (Dependency d : dependenciesToRemove) {
-                engine.getDependencies().remove(d);
-            }
+            engine.getDependencies().removeAll(dependenciesToRemove);
         }
     }
 
     /**
-     * Attempts to trim a maven repo to a common base path. This is typically
-     * [drive]\[repo_location]\repository\[path1]\[path2].
+     * Adds the relatedDependency to the dependency's related dependencies.
+     *
+     * @param dependency the main dependency
+     * @param relatedDependency a collection of dependencies to be removed from the main analysis loop, this is the source of
+     * dependencies to remove
+     * @param dependenciesToRemove a collection of dependencies that will be removed from the main analysis loop, this function
+     * adds to this collection
+     */
+    private void mergeDependencies(final Dependency dependency, final Dependency relatedDependency, final Set<Dependency> dependenciesToRemove) {
+        dependency.addRelatedDependency(relatedDependency);
+        final Iterator<Dependency> i = relatedDependency.getRelatedDependencies().iterator();
+        while (i.hasNext()) {
+            dependency.addRelatedDependency(i.next());
+            i.remove();
+        }
+        if (dependency.getSha1sum().equals(relatedDependency.getSha1sum())) {
+            dependency.addAllProjectReferences(relatedDependency.getProjectReferences());
+        }
+        dependenciesToRemove.add(relatedDependency);
+    }
+
+    /**
+     * Attempts to trim a maven repo to a common base path. This is typically [drive]\[repo_location]\repository\[path1]\[path2].
      *
      * @param path the path to trim
      * @return a string representing the base path.
@@ -195,46 +196,25 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * Returns true if the file names (and version if it exists) of the two
-     * dependencies are sufficiently similiar.
+     * Returns true if the file names (and version if it exists) of the two dependencies are sufficiently similar.
      *
      * @param dependency1 a dependency2 to compare
      * @param dependency2 a dependency2 to compare
-     * @return true if the identifiers in the two supplied dependencies are
-     * equal
+     * @return true if the identifiers in the two supplied dependencies are equal
      */
     private boolean fileNameMatch(Dependency dependency1, Dependency dependency2) {
         if (dependency1 == null || dependency1.getFileName() == null
                 || dependency2 == null || dependency2.getFileName() == null) {
             return false;
         }
-        String fileName1 = dependency1.getFileName();
-        String fileName2 = dependency2.getFileName();
-
-        //update to deal with archive analyzer, the starting name maybe the same
-        // as this is incorrectly looking at the starting path
-        final File one = new File(fileName1);
-        final File two = new File(fileName2);
-        final String oneParent = one.getParent();
-        final String twoParent = two.getParent();
-        if (oneParent != null) {
-            if (twoParent != null && oneParent.equals(twoParent)) {
-                fileName1 = one.getName();
-                fileName2 = two.getName();
-            } else {
-                return false;
-            }
-        } else if (twoParent != null) {
-            return false;
-        }
+        final String fileName1 = dependency1.getActualFile().getName();
+        final String fileName2 = dependency2.getActualFile().getName();
 
         //version check
         final DependencyVersion version1 = DependencyVersionUtil.parseVersion(fileName1);
         final DependencyVersion version2 = DependencyVersionUtil.parseVersion(fileName2);
-        if (version1 != null && version2 != null) {
-            if (!version1.equals(version2)) {
-                return false;
-            }
+        if (version1 != null && version2 != null && !version1.equals(version2)) {
+            return false;
         }
 
         //filename check
@@ -248,25 +228,41 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * Returns true if the identifiers in the two supplied dependencies are
-     * equal.
+     * Returns true if the CPE identifiers in the two supplied dependencies are equal.
      *
      * @param dependency1 a dependency2 to compare
      * @param dependency2 a dependency2 to compare
-     * @return true if the identifiers in the two supplied dependencies are
-     * equal
+     * @return true if the identifiers in the two supplied dependencies are equal
      */
-    private boolean identifiersMatch(Dependency dependency1, Dependency dependency2) {
+    private boolean cpeIdentifiersMatch(Dependency dependency1, Dependency dependency2) {
         if (dependency1 == null || dependency1.getIdentifiers() == null
                 || dependency2 == null || dependency2.getIdentifiers() == null) {
             return false;
         }
-        final boolean matches = dependency1.getIdentifiers().size() > 0
-                && dependency2.getIdentifiers().equals(dependency1.getIdentifiers());
-        if (LogUtils.isVerboseLoggingEnabled()) {
-            final String msg = String.format("IdentifiersMatch=%s (%s, %s)", matches, dependency1.getFileName(), dependency2.getFileName());
-            Logger.getLogger(DependencyBundlingAnalyzer.class.getName()).log(Level.FINE, msg);
+        boolean matches = false;
+        int cpeCount1 = 0;
+        int cpeCount2 = 0;
+        for (Identifier i : dependency1.getIdentifiers()) {
+            if ("cpe".equals(i.getType())) {
+                cpeCount1 += 1;
+            }
         }
+        for (Identifier i : dependency2.getIdentifiers()) {
+            if ("cpe".equals(i.getType())) {
+                cpeCount2 += 1;
+            }
+        }
+        if (cpeCount1 > 0 && cpeCount1 == cpeCount2) {
+            for (Identifier i : dependency1.getIdentifiers()) {
+                if ("cpe".equals(i.getType())) {
+                    matches |= dependency2.getIdentifiers().contains(i);
+                    if (!matches) {
+                        break;
+                    }
+                }
+            }
+        }
+        LOGGER.debug("IdentifiersMatch={} ({}, {})", matches, dependency1.getFileName(), dependency2.getFileName());
         return matches;
     }
 
@@ -286,10 +282,7 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
         final File rFile = new File(dependency2.getFilePath());
         String right = rFile.getParent();
         if (left == null) {
-            if (right == null) {
-                return true;
-            }
-            return false;
+            return right == null;
         }
         if (left.equalsIgnoreCase(right)) {
             return true;
@@ -298,46 +291,138 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
             left = getBaseRepoPath(left);
             right = getBaseRepoPath(right);
         }
-        return left.equalsIgnoreCase(right);
+        if (left.equalsIgnoreCase(right)) {
+            return true;
+        }
+        //new code
+        for (Dependency child : dependency2.getRelatedDependencies()) {
+            if (hasSameBasePath(dependency1, child)) {
+                return true;
+            }
+        }
+        return false;
     }
 
     /**
-     * This is likely a very broken attempt at determining if the 'left'
-     * dependency is the 'core' library in comparison to the 'right' library.
+     * This is likely a very broken attempt at determining if the 'left' dependency is the 'core' library in comparison to the
+     * 'right' library.
      *
      * @param left the dependency to test
      * @param right the dependency to test against
-     * @return a boolean indicating whether or not the left dependency should be
-     * considered the "core" version.
+     * @return a boolean indicating whether or not the left dependency should be considered the "core" version.
      */
-    private boolean isCore(Dependency left, Dependency right) {
+    boolean isCore(Dependency left, Dependency right) {
         final String leftName = left.getFileName().toLowerCase();
         final String rightName = right.getFileName().toLowerCase();
+
         final boolean returnVal;
-        if (rightName.contains("core") && !leftName.contains("core")) {
+        if (!rightName.matches(".*\\.(tar|tgz|gz|zip|ear|war).+") && leftName.matches(".*\\.(tar|tgz|gz|zip|ear|war).+")
+                || rightName.contains("core") && !leftName.contains("core")
+                || rightName.contains("kernel") && !leftName.contains("kernel")) {
             returnVal = false;
-        } else if (!rightName.contains("core") && leftName.contains("core")) {
+        } else if (rightName.matches(".*\\.(tar|tgz|gz|zip|ear|war).+") && !leftName.matches(".*\\.(tar|tgz|gz|zip|ear|war).+")
+                || !rightName.contains("core") && leftName.contains("core")
+                || !rightName.contains("kernel") && leftName.contains("kernel")) {
             returnVal = true;
+//        } else if (leftName.matches(".*struts2\\-core.*") && rightName.matches(".*xwork\\-core.*")) {
+//            returnVal = true;
+//        } else if (rightName.matches(".*struts2\\-core.*") && leftName.matches(".*xwork\\-core.*")) {
+//            returnVal = false;
         } else {
             /*
              * considered splitting the names up and comparing the components,
              * but decided that the file name length should be sufficient as the
-             * "core" component, if this follows a normal namming protocol should
+             * "core" component, if this follows a normal naming protocol should
              * be shorter:
              * axis2-saaj-1.4.1.jar
              * axis2-1.4.1.jar       <-----
-             * axis2-kernal-1.4.1.jar
+             * axis2-kernel-1.4.1.jar
              */
-            if (leftName.length() > rightName.length()) {
-                returnVal = false;
-            } else {
-                returnVal = true;
-            }
-        }
-        if (LogUtils.isVerboseLoggingEnabled()) {
-            final String msg = String.format("IsCore=%s (%s, %s)", returnVal, left.getFileName(), right.getFileName());
-            Logger.getLogger(DependencyBundlingAnalyzer.class.getName()).log(Level.FINE, msg);
+            returnVal = leftName.length() <= rightName.length();
         }
+        LOGGER.debug("IsCore={} ({}, {})", returnVal, left.getFileName(), right.getFileName());
         return returnVal;
     }
+
+    /**
+     * Compares the SHA1 hashes of two dependencies to determine if they are equal.
+     *
+     * @param dependency1 a dependency object to compare
+     * @param dependency2 a dependency object to compare
+     * @return true if the sha1 hashes of the two dependencies match; otherwise false
+     */
+    private boolean hashesMatch(Dependency dependency1, Dependency dependency2) {
+        if (dependency1 == null || dependency2 == null || dependency1.getSha1sum() == null || dependency2.getSha1sum() == null) {
+            return false;
+        }
+        return dependency1.getSha1sum().equals(dependency2.getSha1sum());
+    }
+
+    /**
+     * Determines if the jar is shaded and the created pom.xml identified the same CPE as the jar - if so, the pom.xml dependency
+     * should be removed.
+     *
+     * @param dependency a dependency to check
+     * @param nextDependency another dependency to check
+     * @return true if on of the dependencies is a pom.xml and the identifiers between the two collections match; otherwise false
+     */
+    private boolean isShadedJar(Dependency dependency, Dependency nextDependency) {
+        final String mainName = dependency.getFileName().toLowerCase();
+        final String nextName = nextDependency.getFileName().toLowerCase();
+        if (mainName.endsWith(".jar") && nextName.endsWith("pom.xml")) {
+            return dependency.getIdentifiers().containsAll(nextDependency.getIdentifiers());
+        } else if (nextName.endsWith(".jar") && mainName.endsWith("pom.xml")) {
+            return nextDependency.getIdentifiers().containsAll(dependency.getIdentifiers());
+        }
+        return false;
+    }
+
+    /**
+     * Determines which path is shortest; if path lengths are equal then we use compareTo of the string method to determine if the
+     * first path is smaller.
+     *
+     * @param left the first path to compare
+     * @param right the second path to compare
+     * @return <code>true</code> if the leftPath is the shortest; otherwise <code>false</code>
+     */
+    protected boolean firstPathIsShortest(String left, String right) {
+        final String leftPath = left.replace('\\', '/');
+        final String rightPath = right.replace('\\', '/');
+
+        final int leftCount = countChar(leftPath, '/');
+        final int rightCount = countChar(rightPath, '/');
+        if (leftCount == rightCount) {
+            return leftPath.compareTo(rightPath) <= 0;
+        } else {
+            return leftCount < rightCount;
+        }
+    }
+
+    /**
+     * Counts the number of times the character is present in the string.
+     *
+     * @param string the string to count the characters in
+     * @param c the character to count
+     * @return the number of times the character is present in the string
+     */
+    private int countChar(String string, char c) {
+        int count = 0;
+        final int max = string.length();
+        for (int i = 0; i < max; i++) {
+            if (c == string.charAt(i)) {
+                count++;
+            }
+        }
+        return count;
+    }
+
+    /**
+     * Checks if the given file path is contained within a war or ear file.
+     *
+     * @param filePath the file path to check
+     * @return true if the path contains '.war\' or '.ear\'.
+     */
+    private boolean containedInWar(String filePath) {
+        return filePath == null ? false : filePath.matches(".*\\.(ear|war)[\\\\/].*");
+    }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/FalsePositiveAnalyzer.java

@@ -1,23 +1,23 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
+import java.io.FileFilter;
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.util.ArrayList;
@@ -26,28 +26,35 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.ListIterator;
 import java.util.Set;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Identifier;
 import org.owasp.dependencycheck.dependency.VulnerableSoftware;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
- * This analyzer attempts to remove some well known false positives -
- * specifically regarding the java runtime.
+ * This analyzer attempts to remove some well known false positives - specifically regarding the java runtime.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class FalsePositiveAnalyzer extends AbstractAnalyzer {
 
-    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
     /**
-     * The set of file extensions supported by this analyzer.
+     * The Logger.
      */
-    private static final Set<String> EXTENSIONS = null;
+    private static final Logger LOGGER = LoggerFactory.getLogger(FalsePositiveAnalyzer.class);
+
+    /**
+     * The file filter used to find DLL and EXE.
+     */
+    private static final FileFilter DLL_EXE_FILTER = FileFilterBuilder.newInstance().addExtensions("dll", "exe").build();
+
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
      * The name of the analyzer.
      */
@@ -57,73 +64,90 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.POST_IDENTIFIER_ANALYSIS;
 
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
-
     /**
      * Returns the name of the analyzer.
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support
-     * @return whether or not the specified file extension is supported by this
-     * analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
      * @return the phase that the analyzer is intended to run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
     //</editor-fold>
 
     /**
-     * Analyzes the dependencies and removes bad/incorrect CPE associations
-     * based on various heuristics.
+     * Analyzes the dependencies and removes bad/incorrect CPE associations based on various heuristics.
      *
      * @param dependency the dependency to analyze.
      * @param engine the engine that is scanning the dependencies
-     * @throws AnalysisException is thrown if there is an error reading the JAR
-     * file.
+     * @throws AnalysisException is thrown if there is an error reading the JAR file.
      */
     @Override
     public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
         removeJreEntries(dependency);
         removeBadMatches(dependency);
+        removeBadSpringMatches(dependency);
         removeWrongVersionMatches(dependency);
         removeSpuriousCPE(dependency);
+        removeDuplicativeEntriesFromJar(dependency, engine);
         addFalseNegativeCPEs(dependency);
     }
 
     /**
-     * <p>Intended to remove spurious CPE entries. By spurious we mean
-     * duplicate, less specific CPE entries.</p>
-     * <p>Example:</p>
+     * Removes inaccurate matches on springframework CPEs.
+     *
+     * @param dependency the dependency to test for and remove known inaccurate CPE matches
+     */
+    private void removeBadSpringMatches(Dependency dependency) {
+        String mustContain = null;
+        for (Identifier i : dependency.getIdentifiers()) {
+            if ("maven".contains(i.getType())) {
+                if (i.getValue() != null && i.getValue().startsWith("org.springframework.")) {
+                    final int endPoint = i.getValue().indexOf(':', 19);
+                    if (endPoint >= 0) {
+                        mustContain = i.getValue().substring(19, endPoint).toLowerCase();
+                        break;
+                    }
+                }
+            }
+        }
+        if (mustContain != null) {
+            final Iterator<Identifier> itr = dependency.getIdentifiers().iterator();
+            while (itr.hasNext()) {
+                final Identifier i = itr.next();
+                if ("cpe".contains(i.getType())
+                        && i.getValue() != null
+                        && i.getValue().startsWith("cpe:/a:springsource:")
+                        && !i.getValue().toLowerCase().contains(mustContain)) {
+                    itr.remove();
+                    //dependency.getIdentifiers().remove(i);
+                }
+            }
+        }
+    }
+
+    /**
+     * <p>
+     * Intended to remove spurious CPE entries. By spurious we mean duplicate, less specific CPE entries.</p>
+     * <p>
+     * Example:</p>
      * <code>
      * cpe:/a:some-vendor:some-product
      * cpe:/a:some-vendor:some-product:1.5
      * cpe:/a:some-vendor:some-product:1.5.2
      * </code>
-     * <p>Should be trimmed to:</p>
+     * <p>
+     * Should be trimmed to:</p>
      * <code>
      * cpe:/a:some-vendor:some-product:1.5.2
      * </code>
@@ -132,8 +156,7 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
      */
     @SuppressWarnings("null")
     private void removeSpuriousCPE(Dependency dependency) {
-        final List<Identifier> ids = new ArrayList<Identifier>();
-        ids.addAll(dependency.getIdentifiers());
+        final List<Identifier> ids = new ArrayList<Identifier>(dependency.getIdentifiers());
         Collections.sort(ids);
         final ListIterator<Identifier> mainItr = ids.listIterator();
         while (mainItr.hasNext()) {
@@ -157,8 +180,7 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
                         final String nextVersion = nextCpe.getVersion();
                         if (currentVersion == null && nextVersion == null) {
                             //how did we get here?
-                            Logger.getLogger(FalsePositiveAnalyzer.class
-                                    .getName()).log(Level.FINE, "currentVersion and nextVersion are both null?");
+                            LOGGER.debug("currentVersion and nextVersion are both null?");
                         } else if (currentVersion == null && nextVersion != null) {
                             dependency.getIdentifiers().remove(currentId);
                         } else if (nextVersion == null && currentVersion != null) {
@@ -178,20 +200,27 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
         }
     }
     /**
-     * Regex to identify core java libraries and a few other commonly
-     * misidentified ones.
+     * Regex to identify core java libraries and a few other commonly misidentified ones.
      */
     public static final Pattern CORE_JAVA = Pattern.compile("^cpe:/a:(sun|oracle|ibm):(j2[ems]e|"
-            + "java(_platfrom_micro_edition|_runtime_environment|_se|virtual_machine|se_development_kit|fx)?|"
-            + "jdk|jre|jsf|jsse)($|:.*)");
+            + "java(_platform_micro_edition|_runtime_environment|_se|virtual_machine|se_development_kit|fx)?|"
+            + "jdk|jre|jsse)($|:.*)");
+
+    /**
+     * Regex to identify core jsf libraries.
+     */
+    public static final Pattern CORE_JAVA_JSF = Pattern.compile("^cpe:/a:(sun|oracle|ibm):jsf($|:.*)");
     /**
      * Regex to identify core java library files. This is currently incomplete.
      */
-    public static final Pattern CORE_FILES = Pattern.compile("^((alt[-])?rt|jsf[-].*|jsse|jfxrt|jfr|jce|javaws|deploy|charsets)\\.jar$");
+    public static final Pattern CORE_FILES = Pattern.compile("(^|/)((alt[-])?rt|jsse|jfxrt|jfr|jce|javaws|deploy|charsets)\\.jar$");
+    /**
+     * Regex to identify core jsf java library files. This is currently incomplete.
+     */
+    public static final Pattern CORE_JSF_FILES = Pattern.compile("(^|/)jsf[-][^/]*\\.jar$");
 
     /**
-     * Removes any CPE entries for the JDK/JRE unless the filename ends with
-     * rt.jar
+     * Removes any CPE entries for the JDK/JRE unless the filename ends with rt.jar
      *
      * @param dependency the dependency to remove JRE CPEs from
      */
@@ -205,27 +234,11 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
             if (coreCPE.matches() && !coreFiles.matches()) {
                 itr.remove();
             }
-
-            //replacecd with the regex above.
-            //            if (("cpe:/a:sun:java".equals(i.getValue())
-            //                    || "cpe:/a:oracle:java".equals(i.getValue())
-            //                    || "cpe:/a:ibm:java".equals(i.getValue())
-            //                    || "cpe:/a:sun:j2se".equals(i.getValue())
-            //                    || "cpe:/a:oracle:j2se".equals(i.getValue())
-            //                    || i.getValue().startsWith("cpe:/a:sun:java:")
-            //                    || i.getValue().startsWith("cpe:/a:sun:j2se:")
-            //                    || i.getValue().startsWith("cpe:/a:sun:java:jre")
-            //                    || i.getValue().startsWith("cpe:/a:sun:java:jdk")
-            //                    || i.getValue().startsWith("cpe:/a:sun:java_se")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:java_se")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:java:")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:j2se:")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:jre")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:jdk")
-            //                    || i.getValue().startsWith("cpe:/a:ibm:java:"))
-            //                    && !dependency.getFileName().toLowerCase().endsWith("rt.jar")) {
-            //                itr.remove();
-            //            }
+            final Matcher coreJsfCPE = CORE_JAVA_JSF.matcher(i.getValue());
+            final Matcher coreJsfFiles = CORE_JSF_FILES.matcher(dependency.getFileName());
+            if (coreJsfCPE.matches() && !coreJsfFiles.matches()) {
+                itr.remove();
+            }
         }
     }
 
@@ -244,16 +257,15 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
         try {
             cpe.parseName(value);
         } catch (UnsupportedEncodingException ex) {
-            Logger.getLogger(FalsePositiveAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+            LOGGER.trace("", ex);
             return null;
         }
         return cpe;
     }
 
     /**
-     * Removes bad CPE matches for a dependency. Unfortunately, right now these
-     * are hard-coded patches for specific problems identified when testing this
-     * on a LARGE volume of jar files.
+     * Removes bad CPE matches for a dependency. Unfortunately, right now these are hard-coded patches for specific problems
+     * identified when testing this on a LARGE volume of jar files.
      *
      * @param dependency the dependency to analyze
      */
@@ -266,36 +278,69 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
          * found based on LOW confidence evidence should have a different CPE type? (this
          * might be a better solution then just removing the URL for "best-guess" matches).
          */
-
         //Set<Evidence> groupId = dependency.getVendorEvidence().getEvidence("pom", "groupid");
         //Set<Evidence> artifactId = dependency.getVendorEvidence().getEvidence("pom", "artifactid");
-
         while (itr.hasNext()) {
             final Identifier i = itr.next();
-            //TODO move this startswith expression to a configuration file?
+            //TODO move this startsWith expression to the base suppression file
             if ("cpe".equals(i.getType())) {
                 if ((i.getValue().matches(".*c\\+\\+.*")
-                        || i.getValue().startsWith("cpe:/a:jquery:jquery")
-                        || i.getValue().startsWith("cpe:/a:prototypejs:prototype")
-                        || i.getValue().startsWith("cpe:/a:yahoo:yui")
                         || i.getValue().startsWith("cpe:/a:file:file")
                         || i.getValue().startsWith("cpe:/a:mozilla:mozilla")
                         || i.getValue().startsWith("cpe:/a:cvs:cvs")
                         || i.getValue().startsWith("cpe:/a:ftp:ftp")
-                        || i.getValue().startsWith("cpe:/a:ssh:ssh"))
-                        && dependency.getFileName().toLowerCase().endsWith(".jar")) {
+                        || i.getValue().startsWith("cpe:/a:tcp:tcp")
+                        || i.getValue().startsWith("cpe:/a:ssh:ssh")
+                        || i.getValue().startsWith("cpe:/a:lookup:lookup"))
+                        && (dependency.getFileName().toLowerCase().endsWith(".jar")
+                        || dependency.getFileName().toLowerCase().endsWith("pom.xml")
+                        || dependency.getFileName().toLowerCase().endsWith(".dll")
+                        || dependency.getFileName().toLowerCase().endsWith(".exe")
+                        || dependency.getFileName().toLowerCase().endsWith(".nuspec")
+                        || dependency.getFileName().toLowerCase().endsWith(".zip")
+                        || dependency.getFileName().toLowerCase().endsWith(".sar")
+                        || dependency.getFileName().toLowerCase().endsWith(".apk")
+                        || dependency.getFileName().toLowerCase().endsWith(".tar")
+                        || dependency.getFileName().toLowerCase().endsWith(".gz")
+                        || dependency.getFileName().toLowerCase().endsWith(".tgz")
+                        || dependency.getFileName().toLowerCase().endsWith(".ear")
+                        || dependency.getFileName().toLowerCase().endsWith(".war"))) {
+                    itr.remove();
+                } else if ((i.getValue().startsWith("cpe:/a:jquery:jquery")
+                        || i.getValue().startsWith("cpe:/a:prototypejs:prototype")
+                        || i.getValue().startsWith("cpe:/a:yahoo:yui"))
+                        && (dependency.getFileName().toLowerCase().endsWith(".jar")
+                        || dependency.getFileName().toLowerCase().endsWith("pom.xml")
+                        || dependency.getFileName().toLowerCase().endsWith(".dll")
+                        || dependency.getFileName().toLowerCase().endsWith(".exe"))) {
+                    itr.remove();
+                } else if ((i.getValue().startsWith("cpe:/a:microsoft:excel")
+                        || i.getValue().startsWith("cpe:/a:microsoft:word")
+                        || i.getValue().startsWith("cpe:/a:microsoft:visio")
+                        || i.getValue().startsWith("cpe:/a:microsoft:powerpoint")
+                        || i.getValue().startsWith("cpe:/a:microsoft:office")
+                        || i.getValue().startsWith("cpe:/a:core_ftp:core_ftp"))
+                        && (dependency.getFileName().toLowerCase().endsWith(".jar")
+                        || dependency.getFileName().toLowerCase().endsWith(".ear")
+                        || dependency.getFileName().toLowerCase().endsWith(".war")
+                        || dependency.getFileName().toLowerCase().endsWith("pom.xml"))) {
                     itr.remove();
                 } else if (i.getValue().startsWith("cpe:/a:apache:maven")
                         && !dependency.getFileName().toLowerCase().matches("maven-core-[\\d\\.]+\\.jar")) {
                     itr.remove();
+                } else if (i.getValue().startsWith("cpe:/a:m-core:m-core")
+                        && !dependency.getEvidenceUsed().containsUsedString("m-core")) {
+                    itr.remove();
+                } else if (i.getValue().startsWith("cpe:/a:jboss:jboss")
+                        && !dependency.getFileName().toLowerCase().matches("jboss-?[\\d\\.-]+(GA)?\\.jar")) {
+                    itr.remove();
                 }
             }
         }
     }
 
     /**
-     * Removes CPE matches for the wrong version of a dependency. Currently,
-     * this only covers Axis 1 & 2.
+     * Removes CPE matches for the wrong version of a dependency. Currently, this only covers Axis 1 & 2.
      *
      * @param dependency the dependency to analyze
      */
@@ -328,44 +373,111 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     }
 
     /**
-     * There are some known CPE entries, specifically regarding sun and oracle
-     * products due to the acquisition and changes in product names, that based
-     * on given evidence we can add the related CPE entries to ensure a complete
-     * list of CVE entries.
+     * There are some known CPE entries, specifically regarding sun and oracle products due to the acquisition and changes in
+     * product names, that based on given evidence we can add the related CPE entries to ensure a complete list of CVE entries.
      *
      * @param dependency the dependency being analyzed
      */
     private void addFalseNegativeCPEs(Dependency dependency) {
-        final Iterator<Identifier> itr = dependency.getIdentifiers().iterator();
-        while (itr.hasNext()) {
-            final Identifier i = itr.next();
-            if ("cpe".equals(i.getType()) && i.getValue() != null
-                    && (i.getValue().startsWith("cpe:/a:oracle:opensso:")
-                    || i.getValue().startsWith("cpe:/a:oracle:opensso_enterprise:")
-                    || i.getValue().startsWith("cpe:/a:sun:opensso_enterprise:")
-                    || i.getValue().startsWith("cpe:/a:sun:opensso:"))) {
-                final String newCpe = String.format("cpe:/a:sun:opensso_enterprise:%s", i.getValue().substring(22));
-                final String newCpe2 = String.format("cpe:/a:oracle:opensso_enterprise:%s", i.getValue().substring(22));
-                final String newCpe3 = String.format("cpe:/a:sun:opensso:%s", i.getValue().substring(22));
-                final String newCpe4 = String.format("cpe:/a:oracle:opensso:%s", i.getValue().substring(22));
+        //TODO move this to the hint analyzer
+        for (final Identifier identifier : dependency.getIdentifiers()) {
+            if ("cpe".equals(identifier.getType()) && identifier.getValue() != null
+                    && (identifier.getValue().startsWith("cpe:/a:oracle:opensso:")
+                    || identifier.getValue().startsWith("cpe:/a:oracle:opensso_enterprise:")
+                    || identifier.getValue().startsWith("cpe:/a:sun:opensso_enterprise:")
+                    || identifier.getValue().startsWith("cpe:/a:sun:opensso:"))) {
+                final String newCpe = String.format("cpe:/a:sun:opensso_enterprise:%s", identifier.getValue().substring(22));
+                final String newCpe2 = String.format("cpe:/a:oracle:opensso_enterprise:%s", identifier.getValue().substring(22));
+                final String newCpe3 = String.format("cpe:/a:sun:opensso:%s", identifier.getValue().substring(22));
+                final String newCpe4 = String.format("cpe:/a:oracle:opensso:%s", identifier.getValue().substring(22));
                 try {
                     dependency.addIdentifier("cpe",
                             newCpe,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe, "UTF-8")));
                     dependency.addIdentifier("cpe",
                             newCpe2,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe2, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe2, "UTF-8")));
                     dependency.addIdentifier("cpe",
                             newCpe3,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe3, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe3, "UTF-8")));
                     dependency.addIdentifier("cpe",
                             newCpe4,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe4, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe4, "UTF-8")));
                 } catch (UnsupportedEncodingException ex) {
-                    Logger.getLogger(FalsePositiveAnalyzer.class
-                            .getName()).log(Level.FINE, null, ex);
+                    LOGGER.debug("", ex);
                 }
             }
         }
     }
+
+    /**
+     * Removes duplicate entries identified that are contained within JAR files. These occasionally crop up due to POM entries or
+     * other types of files (such as DLLs and EXEs) being contained within the JAR.
+     *
+     * @param dependency the dependency that might be a duplicate
+     * @param engine the engine used to scan all dependencies
+     */
+    private void removeDuplicativeEntriesFromJar(Dependency dependency, Engine engine) {
+        if (dependency.getFileName().toLowerCase().endsWith("pom.xml")
+                || DLL_EXE_FILTER.accept(dependency.getActualFile())) {
+            String parentPath = dependency.getFilePath().toLowerCase();
+            if (parentPath.contains(".jar")) {
+                parentPath = parentPath.substring(0, parentPath.indexOf(".jar") + 4);
+                final Dependency parent = findDependency(parentPath, engine.getDependencies());
+                if (parent != null) {
+                    boolean remove = false;
+                    for (Identifier i : dependency.getIdentifiers()) {
+                        if ("cpe".equals(i.getType())) {
+                            final String trimmedCPE = trimCpeToVendor(i.getValue());
+                            for (Identifier parentId : parent.getIdentifiers()) {
+                                if ("cpe".equals(parentId.getType()) && parentId.getValue().startsWith(trimmedCPE)) {
+                                    remove |= true;
+                                }
+                            }
+                        }
+                        if (!remove) { //we can escape early
+                            return;
+                        }
+                    }
+                    if (remove) {
+                        engine.getDependencies().remove(dependency);
+                    }
+                }
+            }
+
+        }
+    }
+
+    /**
+     * Retrieves a given dependency, based on a given path, from a list of dependencies.
+     *
+     * @param dependencyPath the path of the dependency to return
+     * @param dependencies the collection of dependencies to search
+     * @return the dependency object for the given path, otherwise null
+     */
+    private Dependency findDependency(String dependencyPath, List<Dependency> dependencies) {
+        for (Dependency d : dependencies) {
+            if (d.getFilePath().equalsIgnoreCase(dependencyPath)) {
+                return d;
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Takes a full CPE and returns the CPE trimmed to include only vendor and product.
+     *
+     * @param value the CPE value to trim
+     * @return a CPE value that only includes the vendor and product
+     */
+    private String trimCpeToVendor(String value) {
+        //cpe:/a:jruby:jruby:1.0.8
+        final int pos1 = value.indexOf(':', 7); //right of vendor
+        final int pos2 = value.indexOf(':', pos1 + 1); //right of product
+        if (pos2 < 0) {
+            return value;
+        } else {
+            return value.substring(0, pos2);
+        }
+    }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/FileNameAnalyzer.java

@@ -1,28 +1,30 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
 import java.io.File;
-import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.dependency.Evidence;
-import java.util.Set;
+
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.filefilter.NameFileFilter;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.utils.DependencyVersion;
 import org.owasp.dependencycheck.utils.DependencyVersionUtil;
 
@@ -30,11 +32,11 @@ import org.owasp.dependencycheck.utils.DependencyVersionUtil;
  *
  * Takes a dependency and analyzes the filename and determines the hashes.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
 
-    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
      * The name of the analyzer.
      */
@@ -43,91 +45,77 @@ public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
      * The phase that this analyzer is intended to run in.
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = null;
-
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
 
     /**
      * Returns the name of the analyzer.
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this
-     * analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
      * @return the phase that the analyzer is intended to run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
     //</editor-fold>
 
+    // Python init files
+    private static final NameFileFilter IGNORED_FILES = new NameFileFilter(new String[] {
+        "__init__.py",
+        "__init__.pyc",
+        "__init__.pyo"
+    });
+
     /**
      * Collects information about the file name.
      *
      * @param dependency the dependency to analyze.
      * @param engine the engine that is scanning the dependencies
-     * @throws AnalysisException is thrown if there is an error reading the JAR
-     * file.
+     * @throws AnalysisException is thrown if there is an error reading the JAR file.
      */
     @Override
     public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
 
         //strip any path information that may get added by ArchiveAnalyzer, etc.
-        final File f = new File(dependency.getFileName());
-        String fileName = f.getName();
-
-        //remove file extension
-        final int pos = fileName.lastIndexOf(".");
-        if (pos > 0) {
-            fileName = fileName.substring(0, pos);
-        }
+        final File f = dependency.getActualFile();
+        final String fileName = FilenameUtils.removeExtension(f.getName());
 
         //add version evidence
         final DependencyVersion version = DependencyVersionUtil.parseVersion(fileName);
         if (version != null) {
+            // If the version number is just a number like 2 or 23, reduce the confidence
+            // a shade. This should hopefully correct for cases like log4j.jar or
+            // struts2-core.jar
+            if (version.getVersionParts() == null || version.getVersionParts().size() < 2) {
+                dependency.getVersionEvidence().addEvidence("file", "name",
+                        version.toString(), Confidence.MEDIUM);
+            } else {
+                dependency.getVersionEvidence().addEvidence("file", "name",
+                        version.toString(), Confidence.HIGHEST);
+            }
             dependency.getVersionEvidence().addEvidence("file", "name",
-                    version.toString(), Evidence.Confidence.HIGHEST);
-            dependency.getVersionEvidence().addEvidence("file", "name",
-                    fileName, Evidence.Confidence.MEDIUM);
+                    fileName, Confidence.MEDIUM);
         }
 
         //add as vendor and product evidence
         if (fileName.contains("-")) {
             dependency.getProductEvidence().addEvidence("file", "name",
-                    fileName, Evidence.Confidence.HIGHEST);
+                    fileName, Confidence.HIGHEST);
             dependency.getVendorEvidence().addEvidence("file", "name",
-                    fileName, Evidence.Confidence.HIGHEST);
-        } else {
+                    fileName, Confidence.HIGHEST);
+        } else if (!IGNORED_FILES.accept(f)) {
             dependency.getProductEvidence().addEvidence("file", "name",
-                    fileName, Evidence.Confidence.HIGH);
+                    fileName, Confidence.HIGH);
             dependency.getVendorEvidence().addEvidence("file", "name",
-                    fileName, Evidence.Confidence.HIGH);
+                    fileName, Confidence.HIGH);
         }
     }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/FileTypeAnalyzer.java

@@ -0,0 +1,33 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.FileFilter;
+
+/**
+ * An Analyzer that scans specific file types.
+ *
+ * @author Jeremy Long
+ */
+public interface FileTypeAnalyzer extends Analyzer, FileFilter {
+
+    /**
+     * Resets the analyzers state.
+     */
+    void reset();
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/HintAnalyzer.java

@@ -1,18 +1,17 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
@@ -20,18 +19,21 @@ package org.owasp.dependencycheck.analyzer;
 
 import java.util.ArrayList;
 import java.util.Iterator;
+import java.util.List;
 import java.util.Set;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Evidence;
 
 /**
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class HintAnalyzer extends AbstractAnalyzer implements Analyzer {
 
-    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
      * The name of the analyzer.
      */
@@ -40,91 +42,122 @@ public class HintAnalyzer extends AbstractAnalyzer implements Analyzer {
      * The phase that this analyzer is intended to run in.
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.PRE_IDENTIFIER_ANALYSIS;
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = null;
-
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
 
     /**
      * Returns the name of the analyzer.
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this
-     * analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
      * @return the phase that the analyzer is intended to run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
     //</editor-fold>
 
     /**
-     * The HintAnalyzer uses knowledge about a dependency to add additional
-     * information to help in identification of identifiers or vulnerabilities.
+     * The HintAnalyzer uses knowledge about a dependency to add additional information to help in identification of identifiers
+     * or vulnerabilities.
      *
      * @param dependency The dependency being analyzed
      * @param engine The scanning engine
-     * @throws AnalysisException is thrown if there is an exception analyzing
-     * the dependency.
+     * @throws AnalysisException is thrown if there is an exception analyzing the dependency.
      */
     @Override
     public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
         final Evidence springTest1 = new Evidence("Manifest",
                 "Implementation-Title",
                 "Spring Framework",
-                Evidence.Confidence.HIGH);
+                Confidence.HIGH);
 
         final Evidence springTest2 = new Evidence("Manifest",
                 "Implementation-Title",
                 "org.springframework.core",
-                Evidence.Confidence.HIGH);
+                Confidence.HIGH);
 
         final Evidence springTest3 = new Evidence("Manifest",
-                "Bundle-Vendor",
-                "SpringSource",
-                Evidence.Confidence.HIGH);
+                "Implementation-Title",
+                "spring-core",
+                Confidence.HIGH);
 
+        final Evidence springTest4 = new Evidence("jar",
+                "package name",
+                "springframework",
+                Confidence.LOW);
 
-        Set<Evidence> evidence = dependency.getProductEvidence().getEvidence();
-        if (evidence.contains(springTest1) || evidence.contains(springTest2)) {
-            dependency.getProductEvidence().addEvidence("hint analyzer", "product", "springsource_spring_framework", Evidence.Confidence.HIGH);
-            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "SpringSource", Evidence.Confidence.HIGH);
-            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "vmware", Evidence.Confidence.HIGH);
+        final Evidence springSecurityTest1 = new Evidence("Manifest",
+                "Bundle-Name",
+                "Spring Security Core",
+                Confidence.MEDIUM);
+
+        final Evidence springSecurityTest2 = new Evidence("pom",
+                "artifactid",
+                "spring-security-core",
+                Confidence.HIGH);
+
+        final Evidence symfony = new Evidence("composer.lock",
+            "vendor",
+            "symfony",
+            Confidence.HIGHEST);
+
+        final Evidence zendframeworkVendor = new Evidence("composer.lock",
+            "vendor",
+            "zendframework",
+            Confidence.HIGHEST);
+
+        final Evidence zendframeworkProduct = new Evidence("composer.lock",
+            "product",
+            "zendframework",
+            Confidence.HIGHEST);
+
+        //springsource/vware problem
+        final Set<Evidence> product = dependency.getProductEvidence().getEvidence();
+        final Set<Evidence> vendor = dependency.getVendorEvidence().getEvidence();
+
+        if (product.contains(springTest1) || product.contains(springTest2) || product.contains(springTest3)
+                || (dependency.getFileName().contains("spring") && product.contains(springTest4))) {
+            dependency.getProductEvidence().addEvidence("hint analyzer", "product", "springsource spring framework", Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "SpringSource", Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "vmware", Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "pivotal", Confidence.HIGH);
         }
 
-        evidence = dependency.getVendorEvidence().getEvidence();
-        if (evidence.contains(springTest3)) {
-            dependency.getProductEvidence().addEvidence("hint analyzer", "product", "springsource_spring_framework", Evidence.Confidence.HIGH);
-            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "vmware", Evidence.Confidence.HIGH);
+        if (vendor.contains(springTest4)) {
+            dependency.getProductEvidence().addEvidence("hint analyzer", "product", "springsource_spring_framework", Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "vmware", Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "pivotal", Confidence.HIGH);
         }
+
+        if (product.contains(springSecurityTest1) || product.contains(springSecurityTest2)) {
+            dependency.getProductEvidence().addEvidence("hint analyzer", "product", "springsource_spring_security", Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "SpringSource", Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "vmware", Confidence.HIGH);
+        }
+
+        if (vendor.contains(symfony)) {
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "sensiolabs", Confidence.HIGHEST);
+        }
+
+        if (vendor.contains(zendframeworkVendor)) {
+            dependency.getVendorEvidence().addEvidence("hint analyzer", "vendor", "zend", Confidence.HIGHEST);
+        }
+
+        if (product.contains(zendframeworkProduct)) {
+            dependency.getProductEvidence().addEvidence("hint analyzer", "vendor", "zend_framework", Confidence.HIGHEST);
+        }
+
+        //sun/oracle problem
         final Iterator<Evidence> itr = dependency.getVendorEvidence().iterator();
-        final ArrayList<Evidence> newEntries = new ArrayList<Evidence>();
+        final List<Evidence> newEntries = new ArrayList<Evidence>();
         while (itr.hasNext()) {
             final Evidence e = itr.next();
             if ("sun".equalsIgnoreCase(e.getValue(false))) {
@@ -139,6 +172,5 @@ public class HintAnalyzer extends AbstractAnalyzer implements Analyzer {
             dependency.getVendorEvidence().addEvidence(e);
         }
 
-
     }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/JavaScriptAnalyzer.java

@@ -1,122 +0,0 @@
-/*
- * This file is part of dependency-check-core.
- *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
- *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
- *
- * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
- */
-package org.owasp.dependencycheck.analyzer;
-
-import org.owasp.dependencycheck.Engine;
-import org.owasp.dependencycheck.dependency.Dependency;
-import java.util.Set;
-import java.util.regex.Pattern;
-
-/**
- *
- * Used to load a JAR file and collect information that can be used to determine
- * the associated CPE.
- *
- * @author Jeremy Long (jeremy.long@owasp.org)
- */
-public class JavaScriptAnalyzer extends AbstractAnalyzer implements Analyzer {
-
-    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
-    /**
-     * The name of the analyzer.
-     */
-    private static final String ANALYZER_NAME = "JavaScript Analyzer";
-    /**
-     * The phase that this analyzer is intended to run in.
-     */
-    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = newHashSet("js");
-
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
-
-    /**
-     * Returns the name of the analyzer.
-     *
-     * @return the name of the analyzer.
-     */
-    public String getName() {
-        return ANALYZER_NAME;
-    }
-
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this
-     * analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return EXTENSIONS.contains(extension);
-    }
-
-    /**
-     * Returns the phase that the analyzer is intended to run in.
-     *
-     * @return the phase that the analyzer is intended to run in.
-     */
-    public AnalysisPhase getAnalysisPhase() {
-        return ANALYSIS_PHASE;
-    }
-    //</editor-fold>
-
-    /**
-     * Loads a specified JAR file and collects information from the manifest and
-     * checksums to identify the correct CPE information.
-     *
-     * @param dependency the dependency to analyze.
-     * @param engine the engine that is scanning the dependencies
-     * @throws AnalysisException is thrown if there is an error reading the JAR
-     * file.
-     */
-    @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
-        final Pattern extractComments = Pattern.compile("(/\\*([^*]|[\\r\\n]|(\\*+([^*/]|[\\r\\n])))*\\*+/)|(//.*)");
-
-    }
-
-    /**
-     * The initialize method does nothing for this Analyzer.
-     *
-     * @throws Exception thrown if there is an exception
-     */
-    @Override
-    public void initialize() throws Exception {
-        //do nothing
-    }
-
-    /**
-     * The close method does nothing for this Analyzer.
-     *
-     * @throws Exception thrown if there is an exception
-     */
-    @Override
-    public void close() throws Exception {
-        //do nothing
-    }
-}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/NexusAnalyzer.java

@@ -0,0 +1,260 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.data.nexus.MavenArtifact;
+import org.owasp.dependencycheck.data.nexus.NexusSearch;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.xml.pom.PomUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import org.owasp.dependencycheck.utils.DownloadFailedException;
+import org.owasp.dependencycheck.utils.Downloader;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * Analyzer which will attempt to locate a dependency on a Nexus service by SHA-1 digest of the dependency.
+ *
+ * There are two settings which govern this behavior:
+ *
+ * <ul>
+ * <li>{@link org.owasp.dependencycheck.utils.Settings.KEYS#ANALYZER_NEXUS_ENABLED} determines whether this analyzer is even
+ * enabled. This can be overridden by setting the system property.</li>
+ * <li>{@link org.owasp.dependencycheck.utils.Settings.KEYS#ANALYZER_NEXUS_URL} the URL to a Nexus service to search by SHA-1.
+ * There is an expected <code>%s</code> in this where the SHA-1 will get entered.</li>
+ * </ul>
+ *
+ * @author colezlaw
+ */
+public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The default URL - this will be used by the CentralAnalyzer to determine whether to enable this.
+     */
+    public static final String DEFAULT_URL = "https://repository.sonatype.org/service/local/";
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(NexusAnalyzer.class);
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Nexus Analyzer";
+
+    /**
+     * The phase in which the analyzer runs.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The types of files on which this will work.
+     */
+    private static final String SUPPORTED_EXTENSIONS = "jar";
+
+    /**
+     * The Nexus Search to be set up for this analyzer.
+     */
+    private NexusSearch searcher;
+
+    /**
+     * Field indicating if the analyzer is enabled.
+     */
+    private final boolean enabled = checkEnabled();
+
+    /**
+     * Determines if this analyzer is enabled
+     *
+     * @return <code>true</code> if the analyzer is enabled; otherwise <code>false</code>
+     */
+    private boolean checkEnabled() {
+        /* Enable this analyzer ONLY if the Nexus URL has been set to something
+         other than the default one (if it's the default one, we'll use the
+         central one) and it's enabled by the user.
+         */
+        boolean retval = false;
+        try {
+            if (!DEFAULT_URL.equals(Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL))
+                    && Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED)) {
+                LOGGER.info("Enabling Nexus analyzer");
+                retval = true;
+            } else {
+                LOGGER.debug("Nexus analyzer disabled, using Central instead");
+            }
+        } catch (InvalidSettingException ise) {
+            LOGGER.warn("Invalid setting. Disabling Nexus analyzer");
+        }
+
+        return retval;
+    }
+
+    /**
+     * Determine whether to enable this analyzer or not.
+     *
+     * @return whether the analyzer should be enabled
+     */
+    @Override
+    public boolean isEnabled() {
+        return enabled;
+    }
+
+    /**
+     * Initializes the analyzer once before any analysis is performed.
+     *
+     * @throws Exception if there's an error during initialization
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+        LOGGER.debug("Initializing Nexus Analyzer");
+        LOGGER.debug("Nexus Analyzer enabled: {}", isEnabled());
+        if (isEnabled()) {
+            final String searchUrl = Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL);
+            LOGGER.debug("Nexus Analyzer URL: {}", searchUrl);
+            try {
+                searcher = new NexusSearch(new URL(searchUrl));
+                if (!searcher.preflightRequest()) {
+                    LOGGER.warn("There was an issue getting Nexus status. Disabling analyzer.");
+                    setEnabled(false);
+                }
+            } catch (MalformedURLException mue) {
+                // I know that initialize can throw an exception, but we'll
+                // just disable the analyzer if the URL isn't valid
+                LOGGER.warn("Property {} not a valid URL. Nexus Analyzer disabled", searchUrl);
+                setEnabled(false);
+            }
+        }
+    }
+
+    /**
+     * Returns the analyzer's name.
+     *
+     * @return the name of the analyzer
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_NEXUS_ENABLED;
+    }
+
+    /**
+     * Returns the analysis phase under which the analyzer runs.
+     *
+     * @return the phase under which this analyzer runs
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * The file filter used to determine which files this analyzer supports.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(SUPPORTED_EXTENSIONS).build();
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Performs the analysis.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine
+     * @throws AnalysisException when there's an exception during analysis
+     */
+    @Override
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        if (!isEnabled()) {
+            return;
+        }
+        try {
+            final MavenArtifact ma = searcher.searchSha1(dependency.getSha1sum());
+            dependency.addAsEvidence("nexus", ma, Confidence.HIGH);
+            boolean pomAnalyzed = false;
+            LOGGER.debug("POM URL {}", ma.getPomUrl());
+            for (Evidence e : dependency.getVendorEvidence()) {
+                if ("pom".equals(e.getSource())) {
+                    pomAnalyzed = true;
+                    break;
+                }
+            }
+            if (!pomAnalyzed && ma.getPomUrl() != null) {
+                File pomFile = null;
+                try {
+                    final File baseDir = Settings.getTempDirectory();
+                    pomFile = File.createTempFile("pom", ".xml", baseDir);
+                    if (!pomFile.delete()) {
+                        LOGGER.warn("Unable to fetch pom.xml for {} from Nexus repository; "
+                                + "this could result in undetected CPE/CVEs.", dependency.getFileName());
+                        LOGGER.debug("Unable to delete temp file");
+                    }
+                    LOGGER.debug("Downloading {}", ma.getPomUrl());
+                    Downloader.fetchFile(new URL(ma.getPomUrl()), pomFile);
+                    PomUtils.analyzePOM(dependency, pomFile);
+                } catch (DownloadFailedException ex) {
+                    LOGGER.warn("Unable to download pom.xml for {} from Nexus repository; "
+                            + "this could result in undetected CPE/CVEs.", dependency.getFileName());
+                } finally {
+                    if (pomFile != null && !FileUtils.deleteQuietly(pomFile)) {
+                        pomFile.deleteOnExit();
+                    }
+                }
+            }
+        } catch (IllegalArgumentException iae) {
+            //dependency.addAnalysisException(new AnalysisException("Invalid SHA-1"));
+            LOGGER.info("invalid sha-1 hash on {}", dependency.getFileName());
+        } catch (FileNotFoundException fnfe) {
+            //dependency.addAnalysisException(new AnalysisException("Artifact not found on repository"));
+            LOGGER.debug("Artifact not found in repository '{}'", dependency.getFileName());
+            LOGGER.debug(fnfe.getMessage(), fnfe);
+        } catch (IOException ioe) {
+            //dependency.addAnalysisException(new AnalysisException("Could not connect to repository", ioe));
+            LOGGER.debug("Could not connect to nexus repository", ioe);
+        }
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/NodePackageAnalyzer.java

@@ -0,0 +1,187 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.EvidenceCollection;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.util.Map;
+import javax.json.Json;
+import javax.json.JsonException;
+import javax.json.JsonObject;
+import javax.json.JsonReader;
+import javax.json.JsonString;
+import javax.json.JsonValue;
+
+/**
+ * Used to analyze Node Package Manager (npm) package.json files, and collect information that can be used to determine the
+ * associated CPE.
+ *
+ * @author Dale Visser
+ */
+public class NodePackageAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(NodePackageAnalyzer.class);
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Node.js Package Analyzer";
+
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The file name to scan.
+     */
+    public static final String PACKAGE_JSON = "package.json";
+    /**
+     * Filter that detects files named "package.json".
+     */
+    private static final FileFilter PACKAGE_JSON_FILTER = FileFilterBuilder.newInstance()
+            .addFilenames(PACKAGE_JSON).build();
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return PACKAGE_JSON_FILTER;
+    }
+
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        // NO-OP
+    }
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase that the analyzer is intended to run in.
+     *
+     * @return the phase that the analyzer is intended to run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED;
+    }
+
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        final File file = dependency.getActualFile();
+        JsonReader jsonReader;
+        try {
+            jsonReader = Json.createReader(FileUtils.openInputStream(file));
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+        try {
+            final JsonObject json = jsonReader.readObject();
+            final EvidenceCollection productEvidence = dependency.getProductEvidence();
+            final EvidenceCollection vendorEvidence = dependency.getVendorEvidence();
+            if (json.containsKey("name")) {
+                final Object value = json.get("name");
+                if (value instanceof JsonString) {
+                    final String valueString = ((JsonString) value).getString();
+                    productEvidence.addEvidence(PACKAGE_JSON, "name", valueString, Confidence.HIGHEST);
+                    vendorEvidence.addEvidence(PACKAGE_JSON, "name_project", String.format("%s_project", valueString), Confidence.LOW);
+                } else {
+                    LOGGER.warn("JSON value not string as expected: {}", value);
+                }
+            }
+            addToEvidence(json, productEvidence, "description");
+            addToEvidence(json, vendorEvidence, "author");
+            addToEvidence(json, dependency.getVersionEvidence(), "version");
+            dependency.setDisplayFileName(String.format("%s/%s", file.getParentFile().getName(), file.getName()));
+        } catch (JsonException e) {
+            LOGGER.warn("Failed to parse package.json file.", e);
+        } finally {
+            jsonReader.close();
+        }
+    }
+
+    /**
+     * Adds information to an evidence collection from the node json configuration.
+     *
+     * @param json information from node.js
+     * @param collection a set of evidence about a dependency
+     * @param key the key to obtain the data from the json information
+     */
+    private void addToEvidence(JsonObject json, EvidenceCollection collection, String key) {
+        if (json.containsKey(key)) {
+            final JsonValue value = json.get(key);
+            if (value instanceof JsonString) {
+                collection.addEvidence(PACKAGE_JSON, key, ((JsonString) value).getString(), Confidence.HIGHEST);
+            } else if (value instanceof JsonObject) {
+                final JsonObject jsonObject = (JsonObject) value;
+                for (final Map.Entry<String, JsonValue> entry : jsonObject.entrySet()) {
+                    final String property = entry.getKey();
+                    final JsonValue subValue = entry.getValue();
+                    if (subValue instanceof JsonString) {
+                        collection.addEvidence(PACKAGE_JSON,
+                                String.format("%s.%s", key, property),
+                                ((JsonString) subValue).getString(),
+                                Confidence.HIGHEST);
+                    } else {
+                        LOGGER.warn("JSON sub-value not string as expected: {}", subValue);
+                    }
+                }
+            } else {
+                LOGGER.warn("JSON value not string or JSON object as expected: {}", value);
+            }
+        }
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/NuspecAnalyzer.java

@@ -0,0 +1,164 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.data.nuget.NugetPackage;
+import org.owasp.dependencycheck.data.nuget.NuspecParseException;
+import org.owasp.dependencycheck.data.nuget.NuspecParser;
+import org.owasp.dependencycheck.data.nuget.XPathNuspecParser;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.FileFilter;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+/**
+ * Analyzer which will parse a Nuspec file to gather module information.
+ *
+ * @author colezlaw
+ */
+public class NuspecAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(NuspecAnalyzer.class);
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Nuspec Analyzer";
+
+    /**
+     * The phase in which the analyzer runs.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The types of files on which this will work.
+     */
+    private static final String SUPPORTED_EXTENSIONS = "nuspec";
+
+    /**
+     * Initializes the analyzer once before any analysis is performed.
+     *
+     * @throws Exception if there's an error during initialization
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+    }
+
+    /**
+     * Returns the analyzer's name.
+     *
+     * @return the name of the analyzer
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_NUSPEC_ENABLED;
+    }
+
+    /**
+     * Returns the analysis phase under which the analyzer runs.
+     *
+     * @return the phase under which this analyzer runs
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * The file filter used to determine which files this analyzer supports.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(
+            SUPPORTED_EXTENSIONS).build();
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Performs the analysis.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine
+     * @throws AnalysisException when there's an exception during analysis
+     */
+    @Override
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        LOGGER.debug("Checking Nuspec file {}", dependency);
+        try {
+            final NuspecParser parser = new XPathNuspecParser();
+            NugetPackage np = null;
+            FileInputStream fis = null;
+            try {
+                fis = new FileInputStream(dependency.getActualFilePath());
+                np = parser.parse(fis);
+            } catch (NuspecParseException ex) {
+                throw new AnalysisException(ex);
+            } catch (FileNotFoundException ex) {
+                throw new AnalysisException(ex);
+            } finally {
+                if (fis != null) {
+                    try {
+                        fis.close();
+                    } catch (IOException e) {
+                        LOGGER.debug("Error closing input stream");
+                    }
+                }
+            }
+
+            if (np.getOwners() != null) {
+                dependency.getVendorEvidence().addEvidence("nuspec", "owners", np.getOwners(), Confidence.HIGHEST);
+            }
+            dependency.getVendorEvidence().addEvidence("nuspec", "authors", np.getAuthors(), Confidence.HIGH);
+            dependency.getVersionEvidence().addEvidence("nuspec", "version", np.getVersion(), Confidence.HIGHEST);
+            dependency.getProductEvidence().addEvidence("nuspec", "id", np.getId(), Confidence.HIGHEST);
+            if (np.getTitle() != null) {
+                dependency.getProductEvidence().addEvidence("nuspec", "title", np.getTitle(), Confidence.MEDIUM);
+            }
+        } catch (Throwable e) {
+            throw new AnalysisException(e);
+        }
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/NvdCveAnalyzer.java

@@ -1,18 +1,17 @@
 /*
  * This file is part of dependency-check-core.
  *
- * Dependency-check-core is free software: you can redistribute it and/or modify it
- * under the terms of the GNU General Public License as published by the Free
- * Software Foundation, either version 3 of the License, or (at your option) any
- * later version.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
  *
- * Dependency-check-core is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
- * details.
+ *     http://www.apache.org/licenses/LICENSE-2.0
  *
- * You should have received a copy of the GNU General Public License along with
- * dependency-check-core. If not, see http://www.gnu.org/licenses/.
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
@@ -21,20 +20,19 @@ package org.owasp.dependencycheck.analyzer;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.List;
-import java.util.Set;
 import org.owasp.dependencycheck.Engine;
-import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.dependency.Vulnerability;
-import org.owasp.dependencycheck.dependency.Identifier;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Identifier;
+import org.owasp.dependencycheck.dependency.Vulnerability;
 
 /**
- * NvdCveAnalyzer is a utility class that takes a project dependency and
- * attempts to discern if there is an associated CVEs. It uses the the
- * identifiers found by other analyzers to lookup the CVE data.
+ * NvdCveAnalyzer is a utility class that takes a project dependency and attempts to discern if there is an associated
+ * CVEs. It uses the the identifiers found by other analyzers to lookup the CVE data.
  *
- * @author Jeremy Long (jeremy.long@owasp.org)
+ * @author Jeremy Long
  */
 public class NvdCveAnalyzer implements Analyzer {
 
@@ -53,8 +51,7 @@ public class NvdCveAnalyzer implements Analyzer {
      * @throws SQLException thrown when there is a SQL Exception
      * @throws IOException thrown when there is an IO Exception
      * @throws DatabaseException thrown when there is a database exceptions
-     * @throws ClassNotFoundException thrown if the h2 database driver cannot be
-     * loaded
+     * @throws ClassNotFoundException thrown if the h2 database driver cannot be loaded
      */
     public void open() throws SQLException, IOException, DatabaseException, ClassNotFoundException {
         cveDB = new CveDB();
@@ -64,6 +61,7 @@ public class NvdCveAnalyzer implements Analyzer {
     /**
      * Closes the data source.
      */
+    @Override
     public void close() {
         cveDB.close();
         cveDB = null;
@@ -75,7 +73,7 @@ public class NvdCveAnalyzer implements Analyzer {
      * @return true or false.
      */
     public boolean isOpen() {
-        return (cveDB != null);
+        return cveDB != null;
     }
 
     /**
@@ -92,14 +90,13 @@ public class NvdCveAnalyzer implements Analyzer {
     }
 
     /**
-     * Analyzes a dependency and attempts to determine if there are any CPE
-     * identifiers for this dependency.
+     * Analyzes a dependency and attempts to determine if there are any CPE identifiers for this dependency.
      *
      * @param dependency The Dependency to analyze
      * @param engine The analysis engine
-     * @throws AnalysisException is thrown if there is an issue analyzing the
-     * dependency
+     * @throws AnalysisException is thrown if there is an issue analyzing the dependency
      */
+    @Override
     public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
         for (Identifier id : dependency.getIdentifiers()) {
             if ("cpe".equals(id.getType())) {
@@ -107,13 +104,17 @@ public class NvdCveAnalyzer implements Analyzer {
                     final String value = id.getValue();
                     final List<Vulnerability> vulns = cveDB.getVulnerabilities(value);
                     dependency.getVulnerabilities().addAll(vulns);
-//TODO - remove this comment block after additional testing is completed
-//note - valid match functionality has been moved into the CveDB class.
-////                    for (Vulnerability v : vulns) {
-////                        if (isValidMatch(dependency, v)) {
-////                            dependency.addVulnerability(v);
-////                        }
-////                    }
+                } catch (DatabaseException ex) {
+                    throw new AnalysisException(ex);
+                }
+            }
+        }
+        for (Identifier id : dependency.getSuppressedIdentifiers()) {
+            if ("cpe".equals(id.getType())) {
+                try {
+                    final String value = id.getValue();
+                    final List<Vulnerability> vulns = cveDB.getVulnerabilities(value);
+                    dependency.getSuppressedVulnerabilities().addAll(vulns);
                 } catch (DatabaseException ex) {
                     throw new AnalysisException(ex);
                 }
@@ -121,102 +122,33 @@ public class NvdCveAnalyzer implements Analyzer {
         }
     }
 
-    /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @return true.
-     */
-    public Set<String> getSupportedExtensions() {
-        return null;
-    }
-
     /**
      * Returns the name of this analyzer.
      *
      * @return the name of this analyzer.
      */
+    @Override
     public String getName() {
         return "NVD CVE Analyzer";
     }
 
-    /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @param extension the file extension of the dependency being analyzed.
-     * @return true.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the analysis phase that this analyzer should run in.
      *
      * @return the analysis phase that this analyzer should run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return AnalysisPhase.FINDING_ANALYSIS;
     }
 
     /**
-     * Opens the NVD CVE Lucene Index.
+     * Opens the database used to gather NVD CVE data.
      *
      * @throws Exception is thrown if there is an issue opening the index.
      */
+    @Override
     public void initialize() throws Exception {
         this.open();
     }
-//TODO - remove this comment block after additional testing is completed
-// The following check has been moved into the CveDB class.
-////    /**
-////     * <p>Determines if this is a valid vulnerability match for the given
-////     * dependency. Specifically, this is concerned with ensuring the version
-////     * numbers are correct.</p>
-////     * <p>Currently, this is focused on the issues with the versions for Struts
-////     * 1 and Struts 2. In the future this will due better matching on more
-////     * version numbers.</p>
-////     *
-////     * @param dependency the dependency
-////     * @param v the vulnerability
-////     * @return returns true if the vulnerability is for the given dependency
-////     */
-////    private boolean isValidMatch(final Dependency dependency, final Vulnerability v) {
-////        //right now I only know of the issue with Struts1/2
-////        // start with fixing this problem.
-////
-////        //TODO extend this solution to do better version matching for the vulnerable software.
-////        boolean struts1 = false;
-////        boolean struts2 = false;
-////        for (Identifier i : dependency.getIdentifiers()) {
-////            if (i.getValue().startsWith("cpe:/a:apache:struts:")) {
-////                final char version = i.getValue().charAt(21);
-////                if (version == '1') {
-////                    struts1 = true;
-////                }
-////                if (version == '2') {
-////                    struts2 = true;
-////                }
-////            }
-////        }
-////        if (!struts1 && !struts2) {
-////            return true; //we are not looking at struts, so return true.
-////        }
-////        if (struts1 && struts2) {
-////            return true; //there is a mismatch here, but we can't solve it here so we return valid.
-////        }
-////        if (struts1) {
-////            boolean hasStruts1Vuln = false;
-////            boolean hasStruts2PreviousVersion = false;
-////            for (VulnerableSoftware vs : v.getVulnerableSoftware()) {
-////                //TODO FIX THIS
-////                //hasStruts2PreviousVersion |= vs.hasPreviousVersion() && vs.getName().charAt(21) == '2';
-////                //hasStruts1Vuln |= vs.getName().charAt(21) == '1';
-////            }
-////            if (!hasStruts1Vuln && hasStruts2PreviousVersion) {
-////                return false;
-////            }
-////        }
-////
-////        return true;
-////    }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/OpenSSLAnalyzer.java

@@ -0,0 +1,175 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Used to analyze OpenSSL source code present in the file system.
+ *
+ * @author Dale Visser
+ */
+public class OpenSSLAnalyzer extends AbstractFileTypeAnalyzer {
+
+    private static final int HEXADECIMAL = 16;
+    /**
+     * Filename to analyze. All other .h files get removed from consideration.
+     */
+    private static final String OPENSSLV_H = "opensslv.h";
+
+    /**
+     * Filter that detects files named "__init__.py".
+     */
+    private static final FileFilter OPENSSLV_FILTER = FileFilterBuilder.newInstance().addFilenames(OPENSSLV_H).build();
+    private static final Pattern VERSION_PATTERN = Pattern.compile(
+            "define\\s+OPENSSL_VERSION_NUMBER\\s+0x([0-9a-zA-Z]{8})L", Pattern.DOTALL
+            | Pattern.CASE_INSENSITIVE);
+    private static final int MAJOR_OFFSET = 28;
+    private static final long MINOR_MASK = 0x0ff00000L;
+    private static final int MINOR_OFFSET = 20;
+    private static final long FIX_MASK = 0x000ff000L;
+    private static final int FIX_OFFSET = 12;
+    private static final long PATCH_MASK = 0x00000ff0L;
+    private static final int PATCH_OFFSET = 4;
+    private static final int NUM_LETTERS = 26;
+    private static final int STATUS_MASK = 0x0000000f;
+
+    /**
+     * Returns the open SSL version as a string.
+     *
+     * @param openSSLVersionConstant The open SSL version
+     * @return the version of openssl
+     */
+    static String getOpenSSLVersion(long openSSLVersionConstant) {
+        final long major = openSSLVersionConstant >>> MAJOR_OFFSET;
+        final long minor = (openSSLVersionConstant & MINOR_MASK) >>> MINOR_OFFSET;
+        final long fix = (openSSLVersionConstant & FIX_MASK) >>> FIX_OFFSET;
+        final long patchLevel = (openSSLVersionConstant & PATCH_MASK) >>> PATCH_OFFSET;
+        final String patch = 0 == patchLevel || patchLevel > NUM_LETTERS ? "" : String.valueOf((char) (patchLevel + 'a' - 1));
+        final int statusCode = (int) (openSSLVersionConstant & STATUS_MASK);
+        final String status = 0xf == statusCode ? "" : (0 == statusCode ? "-dev" : "-beta" + statusCode);
+        return String.format("%d.%d.%d%s%s", major, minor, fix, patch, status);
+    }
+
+    /**
+     * Returns the name of the Python Package Analyzer.
+     *
+     * @return the name of the analyzer
+     */
+    @Override
+    public String getName() {
+        return "OpenSSL Source Analyzer";
+    }
+
+    /**
+     * Tell that we are used for information collection.
+     *
+     * @return INFORMATION_COLLECTION
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return AnalysisPhase.INFORMATION_COLLECTION;
+    }
+
+    /**
+     * Returns the set of supported file extensions.
+     *
+     * @return the set of supported file extensions
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return OPENSSLV_FILTER;
+    }
+
+    /**
+     * No-op initializer implementation.
+     *
+     * @throws Exception never thrown
+     */
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        // Nothing to do here.
+    }
+
+    /**
+     * Analyzes python packages and adds evidence to the dependency.
+     *
+     * @param dependency the dependency being analyzed
+     * @param engine the engine being used to perform the scan
+     * @throws AnalysisException thrown if there is an unrecoverable error analyzing the dependency
+     */
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        final File file = dependency.getActualFile();
+        final String parentName = file.getParentFile().getName();
+        boolean found = false;
+        final String contents = getFileContents(file);
+        if (!contents.isEmpty()) {
+            final Matcher matcher = VERSION_PATTERN.matcher(contents);
+            if (matcher.find()) {
+                dependency.getVersionEvidence().addEvidence(OPENSSLV_H, "Version Constant",
+                        getOpenSSLVersion(Long.parseLong(matcher.group(1), HEXADECIMAL)), Confidence.HIGH);
+                found = true;
+            }
+        }
+        if (found) {
+            dependency.setDisplayFileName(parentName + File.separatorChar + OPENSSLV_H);
+            dependency.getVendorEvidence().addEvidence(OPENSSLV_H, "Vendor", "OpenSSL", Confidence.HIGHEST);
+            dependency.getProductEvidence().addEvidence(OPENSSLV_H, "Product", "OpenSSL", Confidence.HIGHEST);
+        } else {
+            engine.getDependencies().remove(dependency);
+        }
+    }
+
+    /**
+     * Retrieves the contents of a given file.
+     *
+     * @param actualFile the file to read
+     * @return the contents of the file
+     * @throws AnalysisException thrown if there is an IO Exception
+     */
+    private String getFileContents(final File actualFile)
+            throws AnalysisException {
+        String contents;
+        try {
+            contents = FileUtils.readFileToString(actualFile).trim();
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+        return contents;
+    }
+
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_OPENSSL_ENABLED;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/PythonDistributionAnalyzer.java

@@ -0,0 +1,374 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FilenameFilter;
+import org.apache.commons.io.filefilter.NameFileFilter;
+import org.apache.commons.io.filefilter.SuffixFileFilter;
+import org.apache.commons.io.input.AutoCloseInputStream;
+import org.apache.commons.lang3.StringUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.EvidenceCollection;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.mail.MessagingException;
+import javax.mail.internet.InternetHeaders;
+import org.owasp.dependencycheck.utils.ExtractionException;
+import org.owasp.dependencycheck.utils.ExtractionUtil;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.FileUtils;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.utils.UrlStringUtils;
+
+/**
+ * Used to analyze a Wheel or egg distribution files, or their contents in unzipped form, and collect information that can be used
+ * to determine the associated CPE.
+ *
+ * @author Dale Visser
+ */
+public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * Name of egg metadata files to analyze.
+     */
+    private static final String PKG_INFO = "PKG-INFO";
+
+    /**
+     * Name of wheel metadata files to analyze.
+     */
+    private static final String METADATA = "METADATA";
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory
+            .getLogger(PythonDistributionAnalyzer.class);
+
+    /**
+     * The count of directories created during analysis. This is used for creating temporary directories.
+     */
+    private static int dirCount = 0;
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Python Distribution Analyzer";
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The set of file extensions supported by this analyzer.
+     */
+    private static final String[] EXTENSIONS = {"whl", "egg", "zip"};
+
+    /**
+     * Used to match on egg archive candidate extensions.
+     */
+    private static final FileFilter EGG_OR_ZIP = FileFilterBuilder.newInstance().addExtensions("egg", "zip").build();
+
+    /**
+     * Used to detect files with a .whl extension.
+     */
+    private static final FileFilter WHL_FILTER = FileFilterBuilder.newInstance().addExtensions("whl").build();
+
+    /**
+     * The parent directory for the individual directories per archive.
+     */
+    private File tempFileLocation;
+
+    /**
+     * Filter that detects *.dist-info files (but doesn't verify they are directories.
+     */
+    private static final FilenameFilter DIST_INFO_FILTER = new SuffixFileFilter(
+            ".dist-info");
+
+    /**
+     * Filter that detects files named "METADATA".
+     */
+    private static final FilenameFilter EGG_INFO_FILTER = new NameFileFilter(
+            "EGG-INFO");
+
+    /**
+     * Filter that detects files named "METADATA".
+     */
+    private static final NameFileFilter METADATA_FILTER = new NameFileFilter(
+            METADATA);
+
+    /**
+     * Filter that detects files named "PKG-INFO".
+     */
+    private static final NameFileFilter PKG_INFO_FILTER = new NameFileFilter(
+            PKG_INFO);
+
+    /**
+     * The file filter used to determine which files this analyzer supports.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addFileFilters(
+            METADATA_FILTER, PKG_INFO_FILTER).addExtensions(EXTENSIONS).build();
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase that the analyzer is intended to run in.
+     *
+     * @return the phase that the analyzer is intended to run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED;
+    }
+
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        final File actualFile = dependency.getActualFile();
+        if (WHL_FILTER.accept(actualFile)) {
+            collectMetadataFromArchiveFormat(dependency, DIST_INFO_FILTER,
+                    METADATA_FILTER);
+        } else if (EGG_OR_ZIP.accept(actualFile)) {
+            collectMetadataFromArchiveFormat(dependency, EGG_INFO_FILTER,
+                    PKG_INFO_FILTER);
+        } else {
+            final String name = actualFile.getName();
+            final boolean metadata = METADATA.equals(name);
+            if (metadata || PKG_INFO.equals(name)) {
+                final File parent = actualFile.getParentFile();
+                final String parentName = parent.getName();
+                dependency.setDisplayFileName(parentName + "/" + name);
+                if (parent.isDirectory()
+                        && (metadata && parentName.endsWith(".dist-info")
+                        || parentName.endsWith(".egg-info") || "EGG-INFO"
+                        .equals(parentName))) {
+                    collectWheelMetadata(dependency, actualFile);
+                }
+            }
+        }
+    }
+
+    /**
+     * Collects the meta data from an archive.
+     *
+     * @param dependency the archive being scanned
+     * @param folderFilter the filter to apply to the folder
+     * @param metadataFilter the filter to apply to the meta data
+     * @throws AnalysisException thrown when there is a problem analyzing the dependency
+     */
+    private void collectMetadataFromArchiveFormat(Dependency dependency,
+            FilenameFilter folderFilter, FilenameFilter metadataFilter)
+            throws AnalysisException {
+        final File temp = getNextTempDirectory();
+        LOGGER.debug("{} exists? {}", temp, temp.exists());
+        try {
+            ExtractionUtil.extractFilesUsingFilter(
+                    new File(dependency.getActualFilePath()), temp,
+                    metadataFilter);
+        } catch (ExtractionException ex) {
+            throw new AnalysisException(ex);
+        }
+
+        collectWheelMetadata(
+                dependency,
+                getMatchingFile(getMatchingFile(temp, folderFilter),
+                        metadataFilter));
+    }
+
+    /**
+     * Makes sure a usable temporary directory is available.
+     *
+     * @throws Exception an AnalyzeException is thrown when the temp directory cannot be created
+     */
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        final File baseDir = Settings.getTempDirectory();
+        tempFileLocation = File.createTempFile("check", "tmp", baseDir);
+        if (!tempFileLocation.delete()) {
+            final String msg = String.format(
+                    "Unable to delete temporary file '%s'.",
+                    tempFileLocation.getAbsolutePath());
+            throw new AnalysisException(msg);
+        }
+        if (!tempFileLocation.mkdirs()) {
+            final String msg = String.format(
+                    "Unable to create directory '%s'.",
+                    tempFileLocation.getAbsolutePath());
+            throw new AnalysisException(msg);
+        }
+    }
+
+    /**
+     * Deletes any files extracted from the Wheel during analysis.
+     */
+    @Override
+    public void close() {
+        if (tempFileLocation != null && tempFileLocation.exists()) {
+            LOGGER.debug("Attempting to delete temporary files");
+            final boolean success = FileUtils.delete(tempFileLocation);
+            if (!success) {
+                LOGGER.warn(
+                        "Failed to delete some temporary files, see the log for more details");
+            }
+        }
+    }
+
+    /**
+     * Gathers evidence from the METADATA file.
+     *
+     * @param dependency the dependency being analyzed
+     * @param file a reference to the manifest/properties file
+     */
+    private static void collectWheelMetadata(Dependency dependency, File file) {
+        final InternetHeaders headers = getManifestProperties(file);
+        addPropertyToEvidence(headers, dependency.getVersionEvidence(),
+                "Version", Confidence.HIGHEST);
+        addPropertyToEvidence(headers, dependency.getProductEvidence(), "Name",
+                Confidence.HIGHEST);
+        final String url = headers.getHeader("Home-page", null);
+        final EvidenceCollection vendorEvidence = dependency
+                .getVendorEvidence();
+        if (StringUtils.isNotBlank(url)) {
+            if (UrlStringUtils.isUrl(url)) {
+                vendorEvidence.addEvidence(METADATA, "vendor", url,
+                        Confidence.MEDIUM);
+            }
+        }
+        addPropertyToEvidence(headers, vendorEvidence, "Author", Confidence.LOW);
+        final String summary = headers.getHeader("Summary", null);
+        if (StringUtils.isNotBlank(summary)) {
+            JarAnalyzer
+                    .addDescription(dependency, summary, METADATA, "summary");
+        }
+    }
+
+    /**
+     * Adds a value to the evidence collection.
+     *
+     * @param headers the properties collection
+     * @param evidence the evidence collection to add the value
+     * @param property the property name
+     * @param confidence the confidence of the evidence
+     */
+    private static void addPropertyToEvidence(InternetHeaders headers,
+            EvidenceCollection evidence, String property, Confidence confidence) {
+        final String value = headers.getHeader(property, null);
+        LOGGER.debug("Property: {}, Value: {}", property, value);
+        if (StringUtils.isNotBlank(value)) {
+            evidence.addEvidence(METADATA, property, value, confidence);
+        }
+    }
+
+    /**
+     * Returns a list of files that match the given filter, this does not recursively scan the directory.
+     *
+     * @param folder the folder to filter
+     * @param filter the filter to apply to the files in the directory
+     * @return the list of Files in the directory that match the provided filter
+     */
+    private static File getMatchingFile(File folder, FilenameFilter filter) {
+        File result = null;
+        final File[] matches = folder.listFiles(filter);
+        if (null != matches && 1 == matches.length) {
+            result = matches[0];
+        }
+        return result;
+    }
+
+    /**
+     * Reads the manifest entries from the provided file.
+     *
+     * @param manifest the manifest
+     * @return the manifest entries
+     */
+    private static InternetHeaders getManifestProperties(File manifest) {
+        final InternetHeaders result = new InternetHeaders();
+        if (null == manifest) {
+            LOGGER.debug("Manifest file not found.");
+        } else {
+            try {
+                result.load(new AutoCloseInputStream(new BufferedInputStream(
+                        new FileInputStream(manifest))));
+            } catch (MessagingException e) {
+                LOGGER.warn(e.getMessage(), e);
+            } catch (FileNotFoundException e) {
+                LOGGER.warn(e.getMessage(), e);
+            }
+        }
+        return result;
+    }
+
+    /**
+     * Retrieves the next temporary destination directory for extracting an archive.
+     *
+     * @return a directory
+     * @throws AnalysisException thrown if unable to create temporary directory
+     */
+    private File getNextTempDirectory() throws AnalysisException {
+        File directory;
+
+        // getting an exception for some directories not being able to be
+        // created; might be because the directory already exists?
+        do {
+            dirCount += 1;
+            directory = new File(tempFileLocation, String.valueOf(dirCount));
+        } while (directory.exists());
+        if (!directory.mkdirs()) {
+            throw new AnalysisException(String.format(
+                    "Unable to create temp directory '%s'.",
+                    directory.getAbsolutePath()));
+        }
+        return directory;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/PythonPackageAnalyzer.java

@@ -0,0 +1,316 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.filefilter.NameFileFilter;
+import org.apache.commons.io.filefilter.SuffixFileFilter;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.EvidenceCollection;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.utils.UrlStringUtils;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Used to analyze a Python package, and collect information that can be used to determine the associated CPE.
+ *
+ * @author Dale Visser
+ */
+public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * Used when compiling file scanning regex patterns.
+     */
+    private static final int REGEX_OPTIONS = Pattern.DOTALL
+            | Pattern.CASE_INSENSITIVE;
+
+    /**
+     * Filename extensions for files to be analyzed.
+     */
+    private static final String EXTENSIONS = "py";
+
+    /**
+     * Pattern for matching the module docstring in a source file.
+     */
+    private static final Pattern MODULE_DOCSTRING = Pattern.compile(
+            "^(['\\\"]{3})(.*?)\\1", REGEX_OPTIONS);
+
+    /**
+     * Matches assignments to version variables in Python source code.
+     */
+    private static final Pattern VERSION_PATTERN = Pattern.compile(
+            "\\b(__)?version(__)? *= *(['\"]+)(\\d+\\.\\d+.*?)\\3",
+            REGEX_OPTIONS);
+
+    /**
+     * Matches assignments to title variables in Python source code.
+     */
+    private static final Pattern TITLE_PATTERN = compileAssignPattern("title");
+
+    /**
+     * Matches assignments to summary variables in Python source code.
+     */
+    private static final Pattern SUMMARY_PATTERN = compileAssignPattern("summary");
+
+    /**
+     * Matches assignments to URL/URL variables in Python source code.
+     */
+    private static final Pattern URI_PATTERN = compileAssignPattern("ur[il]");
+
+    /**
+     * Matches assignments to home page variables in Python source code.
+     */
+    private static final Pattern HOMEPAGE_PATTERN = compileAssignPattern("home_?page");
+
+    /**
+     * Matches assignments to author variables in Python source code.
+     */
+    private static final Pattern AUTHOR_PATTERN = compileAssignPattern("author");
+
+    /**
+     * Filter that detects files named "__init__.py".
+     */
+    private static final FileFilter INIT_PY_FILTER = new NameFileFilter("__init__.py");
+
+    /**
+     * The file filter for python files.
+     */
+    private static final FileFilter PY_FILTER = new SuffixFileFilter(".py");
+
+    /**
+     * Returns the name of the Python Package Analyzer.
+     *
+     * @return the name of the analyzer
+     */
+    @Override
+    public String getName() {
+        return "Python Package Analyzer";
+    }
+
+    /**
+     * Tell that we are used for information collection.
+     *
+     * @return INFORMATION_COLLECTION
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return AnalysisPhase.INFORMATION_COLLECTION;
+    }
+
+    /**
+     * The file filter used to determine which files this analyzer supports.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(EXTENSIONS).build();
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * No-op initializer implementation.
+     *
+     * @throws Exception never thrown
+     */
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        // Nothing to do here.
+    }
+
+    /**
+     * Utility function to create a regex pattern matcher.
+     *
+     * @param name the value to use when constructing the assignment pattern
+     * @return the compiled Pattern
+     */
+    private static Pattern compileAssignPattern(String name) {
+        return Pattern.compile(
+                String.format("\\b(__)?%s(__)?\\b *= *(['\"]+)(.*?)\\3", name),
+                REGEX_OPTIONS);
+    }
+
+    /**
+     * Analyzes python packages and adds evidence to the dependency.
+     *
+     * @param dependency the dependency being analyzed
+     * @param engine the engine being used to perform the scan
+     * @throws AnalysisException thrown if there is an unrecoverable error analyzing the dependency
+     */
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        final File file = dependency.getActualFile();
+        final File parent = file.getParentFile();
+        final String parentName = parent.getName();
+        boolean found = false;
+        if (INIT_PY_FILTER.accept(file)) {
+            final File[] fileList = parent.listFiles(PY_FILTER);
+            if (fileList != null) {
+                for (final File sourceFile : fileList) {
+                    found |= analyzeFileContents(dependency, sourceFile);
+                }
+            }
+        }
+        if (found) {
+            dependency.setDisplayFileName(parentName + "/__init__.py");
+            dependency.getProductEvidence().addEvidence(file.getName(),
+                    "PackageName", parentName, Confidence.HIGH);
+        } else {
+            // copy, alter and set in case some other thread is iterating over
+            final List<Dependency> dependencies = new ArrayList<Dependency>(
+                    engine.getDependencies());
+            dependencies.remove(dependency);
+            engine.setDependencies(dependencies);
+        }
+    }
+
+    /**
+     * This should gather information from leading docstrings, file comments, and assignments to __version__, __title__,
+     * __summary__, __uri__, __url__, __home*page__, __author__, and their all caps equivalents.
+     *
+     * @param dependency the dependency being analyzed
+     * @param file the file name to analyze
+     * @return whether evidence was found
+     * @throws AnalysisException thrown if there is an unrecoverable error
+     */
+    private boolean analyzeFileContents(Dependency dependency, File file)
+            throws AnalysisException {
+        String contents;
+        try {
+            contents = FileUtils.readFileToString(file).trim();
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+        boolean found = false;
+        if (!contents.isEmpty()) {
+            final String source = file.getName();
+            found = gatherEvidence(VERSION_PATTERN, contents, source,
+                    dependency.getVersionEvidence(), "SourceVersion",
+                    Confidence.MEDIUM);
+            found |= addSummaryInfo(dependency, SUMMARY_PATTERN, 4, contents,
+                    source, "summary");
+            if (INIT_PY_FILTER.accept(file)) {
+                found |= addSummaryInfo(dependency, MODULE_DOCSTRING, 2,
+                        contents, source, "docstring");
+            }
+            found |= gatherEvidence(TITLE_PATTERN, contents, source,
+                    dependency.getProductEvidence(), "SourceTitle",
+                    Confidence.LOW);
+            final EvidenceCollection vendorEvidence = dependency
+                    .getVendorEvidence();
+            found |= gatherEvidence(AUTHOR_PATTERN, contents, source,
+                    vendorEvidence, "SourceAuthor", Confidence.MEDIUM);
+            found |= gatherHomePageEvidence(URI_PATTERN, vendorEvidence,
+                    source, "URL", contents);
+            found |= gatherHomePageEvidence(HOMEPAGE_PATTERN,
+                    vendorEvidence, source, "HomePage", contents);
+        }
+        return found;
+    }
+
+    /**
+     * Adds summary information to the dependency
+     *
+     * @param dependency the dependency being analyzed
+     * @param pattern the pattern used to perform analysis
+     * @param group the group from the pattern that indicates the data to use
+     * @param contents the data being analyzed
+     * @param source the source name to use when recording the evidence
+     * @param key the key name to use when recording the evidence
+     * @return true if evidence was collected; otherwise false
+     */
+    private boolean addSummaryInfo(Dependency dependency, Pattern pattern,
+            int group, String contents, String source, String key) {
+        final Matcher matcher = pattern.matcher(contents);
+        final boolean found = matcher.find();
+        if (found) {
+            JarAnalyzer.addDescription(dependency, matcher.group(group),
+                    source, key);
+        }
+        return found;
+    }
+
+    /**
+     * Collects evidence from the home page URL.
+     *
+     * @param pattern the pattern to match
+     * @param evidence the evidence collection to add the evidence to
+     * @param source the source of the evidence
+     * @param name the name of the evidence
+     * @param contents the home page URL
+     * @return true if evidence was collected; otherwise false
+     */
+    private boolean gatherHomePageEvidence(Pattern pattern,
+            EvidenceCollection evidence, String source, String name,
+            String contents) {
+        final Matcher matcher = pattern.matcher(contents);
+        boolean found = false;
+        if (matcher.find()) {
+            final String url = matcher.group(4);
+            if (UrlStringUtils.isUrl(url)) {
+                found = true;
+                evidence.addEvidence(source, name, url, Confidence.MEDIUM);
+            }
+        }
+        return found;
+    }
+
+    /**
+     * Gather evidence from a Python source file using the given string assignment regex pattern.
+     *
+     * @param pattern to scan contents with
+     * @param contents of Python source file
+     * @param source for storing evidence
+     * @param evidence to store evidence in
+     * @param name of evidence
+     * @param confidence in evidence
+     * @return whether evidence was found
+     */
+    private boolean gatherEvidence(Pattern pattern, String contents,
+            String source, EvidenceCollection evidence, String name,
+            Confidence confidence) {
+        final Matcher matcher = pattern.matcher(contents);
+        final boolean found = matcher.find();
+        if (found) {
+            evidence.addEvidence(source, name, matcher.group(4), confidence);
+        }
+        return found;
+    }
+
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/RubyBundleAuditAnalyzer.java

@@ -0,0 +1,342 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Reference;
+import org.owasp.dependencycheck.dependency.Vulnerability;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ * Used to analyze Ruby Bundler Gemspec.lock files utilizing the 3rd party bundle-audit tool.
+ *
+ * @author Dale Visser
+ */
+public class RubyBundleAuditAnalyzer extends AbstractFileTypeAnalyzer {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(RubyBundleAuditAnalyzer.class);
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Ruby Bundle Audit Analyzer";
+
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.PRE_INFORMATION_COLLECTION;
+
+    private static final FileFilter FILTER
+            = FileFilterBuilder.newInstance().addFilenames("Gemfile.lock").build();
+    public static final String NAME = "Name: ";
+    public static final String VERSION = "Version: ";
+    public static final String ADVISORY = "Advisory: ";
+    public static final String CRITICALITY = "Criticality: ";
+
+    /**
+     * @return a filter that accepts files named Gemfile.lock
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Launch bundle-audit.
+     *
+     * @return a handle to the process
+     */
+    private Process launchBundleAudit(File folder) throws AnalysisException {
+        if (!folder.isDirectory()) {
+            throw new AnalysisException(String.format("%s should have been a directory.", folder.getAbsolutePath()));
+        }
+        final List<String> args = new ArrayList<String>();
+        final String bundleAuditPath = Settings.getString(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_PATH);
+        args.add(null == bundleAuditPath ? "bundle-audit" : bundleAuditPath);
+        args.add("check");
+        args.add("--verbose");
+        final ProcessBuilder builder = new ProcessBuilder(args);
+        builder.directory(folder);
+        try {
+        	LOGGER.info("Launching: " + args + " from " + folder);
+            return builder.start();
+        } catch (IOException ioe) {
+            throw new AnalysisException("bundle-audit failure", ioe);
+        }
+    }
+
+    /**
+     * Initialize the analyzer. In this case, extract GrokAssembly.exe to a temporary location.
+     *
+     * @throws Exception if anything goes wrong
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+        // Now, need to see if bundle-audit actually runs from this location.
+    	Process process = null;
+    	try {
+	        process = launchBundleAudit(Settings.getTempDirectory());
+    	}
+    	catch(AnalysisException ae) {
+    		LOGGER.warn("Exception from bundle-audit process: {}. Disabling {}", ae.getCause(), ANALYZER_NAME);
+            setEnabled(false);
+            throw ae;
+    	}
+    	
+        int exitValue = process.waitFor();
+        if (0 == exitValue) {
+            LOGGER.warn("Unexpected exit code from bundle-audit process. Disabling {}: {}", ANALYZER_NAME, exitValue);
+            setEnabled(false);
+            throw new AnalysisException("Unexpected exit code from bundle-audit process.");
+        } else {
+            BufferedReader reader = null;
+            try {
+                reader = new BufferedReader(new InputStreamReader(process.getErrorStream(), "UTF-8"));
+                if (!reader.ready()) {
+                    LOGGER.warn("Bundle-audit error stream unexpectedly not ready. Disabling " + ANALYZER_NAME);
+                    setEnabled(false);
+                    throw new AnalysisException("Bundle-audit error stream unexpectedly not ready.");
+                } else {
+                    final String line = reader.readLine();
+                    if (line == null || !line.contains("Errno::ENOENT")) {
+                        LOGGER.warn("Unexpected bundle-audit output. Disabling {}: {}", ANALYZER_NAME, line);
+                        setEnabled(false);
+                        throw new AnalysisException("Unexpected bundle-audit output.");
+                    }
+                }
+            } finally {
+                if (null != reader) {
+                    reader.close();
+                }
+            }
+        }
+    	
+        if (isEnabled()) {
+            LOGGER.info(ANALYZER_NAME + " is enabled. It is necessary to manually run \"bundle-audit update\" "
+                    + "occasionally to keep its database up to date.");
+        }
+    }
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase that the analyzer is intended to run in.
+     *
+     * @return the phase that the analyzer is intended to run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_BUNDLE_AUDIT_ENABLED;
+    }
+
+    /**
+     * If {@link #analyzeFileType(Dependency, Engine)} is called, then we have successfully initialized, and it will be necessary
+     * to disable {@link RubyGemspecAnalyzer}.
+     */
+    private boolean needToDisableGemspecAnalyzer = true;
+
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        if (needToDisableGemspecAnalyzer) {
+            boolean failed = true;
+            final String className = RubyGemspecAnalyzer.class.getName();
+            for (FileTypeAnalyzer analyzer : engine.getFileTypeAnalyzers()) {
+                if (analyzer instanceof RubyGemspecAnalyzer) {
+                    ((RubyGemspecAnalyzer) analyzer).setEnabled(false);
+                    LOGGER.info("Disabled " + className + " to avoid noisy duplicate results.");
+                    failed = false;
+                }
+            }
+            if (failed) {
+                LOGGER.warn("Did not find" + className + '.');
+            }
+            needToDisableGemspecAnalyzer = false;
+        }
+        final File parentFile = dependency.getActualFile().getParentFile();
+        final Process process = launchBundleAudit(parentFile);
+        try {
+            process.waitFor();
+        } catch (InterruptedException ie) {
+            throw new AnalysisException("bundle-audit process interrupted", ie);
+        }
+        BufferedReader rdr = null;
+        try {
+        	BufferedReader errReader = new BufferedReader(new InputStreamReader(process.getErrorStream(), "UTF-8"));
+        	while(errReader.ready()) {
+        		String error = errReader.readLine();
+        		LOGGER.warn(error);
+        	}
+            rdr = new BufferedReader(new InputStreamReader(process.getInputStream(), "UTF-8"));
+            processBundlerAuditOutput(dependency, engine, rdr);
+        } catch (IOException ioe) {
+            LOGGER.warn("bundle-audit failure", ioe);
+        } finally {
+            if (null != rdr) {
+                try {
+                    rdr.close();
+                } catch (IOException ioe) {
+                    LOGGER.warn("bundle-audit close failure", ioe);
+                }
+            }
+        }
+
+    }
+
+    private void processBundlerAuditOutput(Dependency original, Engine engine, BufferedReader rdr) throws IOException {
+        final String parentName = original.getActualFile().getParentFile().getName();
+        final String fileName = original.getFileName();
+        Dependency dependency = null;
+        Vulnerability vulnerability = null;
+        String gem = null;
+        final Map<String, Dependency> map = new HashMap<String, Dependency>();
+        boolean appendToDescription = false;
+        while (rdr.ready()) {
+            final String nextLine = rdr.readLine();
+            if (null == nextLine) {
+                break;
+            } else if (nextLine.startsWith(NAME)) {
+                appendToDescription = false;
+                gem = nextLine.substring(NAME.length());
+                if (!map.containsKey(gem)) {
+                    map.put(gem, createDependencyForGem(engine, parentName, fileName, gem));
+                }
+                dependency = map.get(gem);
+                LOGGER.debug(String.format("bundle-audit (%s): %s", parentName, nextLine));
+            } else if (nextLine.startsWith(VERSION)) {
+                vulnerability = createVulnerability(parentName, dependency, vulnerability, gem, nextLine);
+            } else if (nextLine.startsWith(ADVISORY)) {
+                setVulnerabilityName(parentName, dependency, vulnerability, nextLine);
+            } else if (nextLine.startsWith(CRITICALITY)) {
+                addCriticalityToVulnerability(parentName, vulnerability, nextLine);
+            } else if (nextLine.startsWith("URL: ")) {
+                addReferenceToVulnerability(parentName, vulnerability, nextLine);
+            } else if (nextLine.startsWith("Description:")) {
+                appendToDescription = true;
+                if (null != vulnerability) {
+                    vulnerability.setDescription("*** Vulnerability obtained from bundle-audit verbose report. Title link may not work. CPE below is guessed. CVSS score is estimated (-1.0 indicates unknown). See link below for full details. *** ");
+                }
+            } else if (appendToDescription) {
+                if (null != vulnerability) {
+                    vulnerability.setDescription(vulnerability.getDescription() + nextLine + "\n");
+                }
+            }
+        }
+    }
+
+    private void setVulnerabilityName(String parentName, Dependency dependency, Vulnerability vulnerability, String nextLine) {
+        final String advisory = nextLine.substring((ADVISORY.length()));
+        if (null != vulnerability) {
+            vulnerability.setName(advisory);
+        }
+        if (null != dependency) {
+            dependency.getVulnerabilities().add(vulnerability); // needed to wait for vulnerability name to avoid NPE
+        }
+        LOGGER.debug(String.format("bundle-audit (%s): %s", parentName, nextLine));
+    }
+
+    private void addReferenceToVulnerability(String parentName, Vulnerability vulnerability, String nextLine) {
+        final String url = nextLine.substring(("URL: ").length());
+        if (null != vulnerability) {
+            Reference ref = new Reference();
+            ref.setName(vulnerability.getName());
+            ref.setSource("bundle-audit");
+            ref.setUrl(url);
+            vulnerability.getReferences().add(ref);
+        }
+        LOGGER.debug(String.format("bundle-audit (%s): %s", parentName, nextLine));
+    }
+
+    private void addCriticalityToVulnerability(String parentName, Vulnerability vulnerability, String nextLine) {
+        if (null != vulnerability) {
+            final String criticality = nextLine.substring(CRITICALITY.length()).trim();
+            if ("High".equals(criticality)) {
+                vulnerability.setCvssScore(8.5f);
+            } else if ("Medium".equals(criticality)) {
+                vulnerability.setCvssScore(5.5f);
+            } else if ("Low".equals(criticality)) {
+                vulnerability.setCvssScore(2.0f);
+            } else {
+                vulnerability.setCvssScore(-1.0f);
+            }
+        }
+        LOGGER.debug(String.format("bundle-audit (%s): %s", parentName, nextLine));
+    }
+
+    private Vulnerability createVulnerability(String parentName, Dependency dependency, Vulnerability vulnerability, String gem, String nextLine) {
+        if (null != dependency) {
+            final String version = nextLine.substring(VERSION.length());
+            dependency.getVersionEvidence().addEvidence(
+                    "bundler-audit",
+                    "Version",
+                    version,
+                    Confidence.HIGHEST);
+            vulnerability = new Vulnerability(); // don't add to dependency until we have name set later
+            vulnerability.setMatchedCPE(
+                    String.format("cpe:/a:%1$s_project:%1$s:%2$s::~~~ruby~~", gem, version),
+                    null);
+            vulnerability.setCvssAccessVector("-");
+            vulnerability.setCvssAccessComplexity("-");
+            vulnerability.setCvssAuthentication("-");
+            vulnerability.setCvssAvailabilityImpact("-");
+            vulnerability.setCvssConfidentialityImpact("-");
+            vulnerability.setCvssIntegrityImpact("-");
+        }
+        LOGGER.debug(String.format("bundle-audit (%s): %s", parentName, nextLine));
+        return vulnerability;
+    }
+
+    private Dependency createDependencyForGem(Engine engine, String parentName, String fileName, String gem) throws IOException {
+        final File tempFile = File.createTempFile("Gemfile-" + gem, ".lock", Settings.getTempDirectory());
+        final String displayFileName = String.format("%s%c%s:%s", parentName, File.separatorChar, fileName, gem);
+        FileUtils.write(tempFile, displayFileName); // unique contents to avoid dependency bundling
+        final Dependency dependency = new Dependency(tempFile);
+        dependency.getProductEvidence().addEvidence("bundler-audit", "Name", gem, Confidence.HIGHEST);
+        dependency.setDisplayFileName(displayFileName);
+        engine.getDependencies().add(dependency);
+        return dependency;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/RubyGemspecAnalyzer.java

@@ -0,0 +1,161 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2015 Institute for Defense Analyses. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.EvidenceCollection;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+
+import java.io.FileFilter;
+import java.io.IOException;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Used to analyze Ruby Gem specifications and collect information that can be used to determine the associated CPE. Regular
+ * expressions are used to parse the well-defined Ruby syntax that forms the specification.
+ *
+ * @author Dale Visser
+ */
+public class RubyGemspecAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Ruby Gemspec Analyzer";
+
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    private static final String GEMSPEC = "gemspec";
+
+    private static final FileFilter FILTER
+            = FileFilterBuilder.newInstance().addExtensions(GEMSPEC).addFilenames("Rakefile").build();
+
+    private static final String EMAIL = "email";
+
+    /**
+     * @return a filter that accepts files named Rakefile or matching the glob pattern, *.gemspec
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+        // NO-OP
+    }
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase that the analyzer is intended to run in.
+     *
+     * @return the phase that the analyzer is intended to run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED;
+    }
+
+    /**
+     * The capture group #1 is the block variable.
+     */
+    private static final Pattern GEMSPEC_BLOCK_INIT
+            = Pattern.compile("Gem::Specification\\.new\\s+?do\\s+?\\|(.+?)\\|");
+
+    @Override
+    protected void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        String contents;
+        try {
+            contents = FileUtils.readFileToString(dependency.getActualFile());
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+        final Matcher matcher = GEMSPEC_BLOCK_INIT.matcher(contents);
+        if (matcher.find()) {
+            contents = contents.substring(matcher.end());
+            final String blockVariable = matcher.group(1);
+            final EvidenceCollection vendor = dependency.getVendorEvidence();
+            addStringEvidence(vendor, contents, blockVariable, "author", Confidence.HIGHEST);
+            addListEvidence(vendor, contents, blockVariable, "authors", Confidence.HIGHEST);
+            final String email = addStringEvidence(vendor, contents, blockVariable, EMAIL, Confidence.MEDIUM);
+            if (email.isEmpty()) {
+                addListEvidence(vendor, contents, blockVariable, EMAIL, Confidence.MEDIUM);
+            }
+            addStringEvidence(vendor, contents, blockVariable, "homepage", Confidence.MEDIUM);
+            final EvidenceCollection product = dependency.getProductEvidence();
+            final String name = addStringEvidence(product, contents, blockVariable, "name", Confidence.HIGHEST);
+            if (!name.isEmpty()) {
+                vendor.addEvidence(GEMSPEC, "name_project", name + "_project", Confidence.LOW);
+            }
+            addStringEvidence(product, contents, blockVariable, "summary", Confidence.LOW);
+            addStringEvidence(dependency.getVersionEvidence(), contents, blockVariable, "version", Confidence.HIGHEST);
+        }
+    }
+
+    private void addListEvidence(EvidenceCollection evidences, String contents,
+            String blockVariable, String field, Confidence confidence) {
+        final Matcher matcher = Pattern.compile(
+                String.format("\\s+?%s\\.%s\\s*?=\\s*?\\[(.*?)\\]", blockVariable, field)).matcher(contents);
+        if (matcher.find()) {
+            final String value = matcher.group(1).replaceAll("['\"]", " ").trim();
+            evidences.addEvidence(GEMSPEC, field, value, confidence);
+        }
+    }
+
+    private String addStringEvidence(EvidenceCollection evidences, String contents,
+            String blockVariable, String field, Confidence confidence) {
+        final Matcher matcher = Pattern.compile(
+                String.format("\\s+?%s\\.%s\\s*?=\\s*?(['\"])(.*?)\\1", blockVariable, field)).matcher(contents);
+        String value = "";
+        if (matcher.find()) {
+            value = matcher.group(2);
+            evidences.addEvidence(GEMSPEC, field, value, confidence);
+        }
+        return value;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/analyzer/VulnerabilitySuppressionAnalyzer.java

@@ -0,0 +1,75 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.suppression.SuppressionRule;
+
+/**
+ * The suppression analyzer processes an externally defined XML document that complies with the suppressions.xsd schema.
+ * Any identified Vulnerability entries within the dependencies that match will be removed.
+ *
+ * @author Jeremy Long
+ */
+public class VulnerabilitySuppressionAnalyzer extends AbstractSuppressionAnalyzer {
+
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Vulnerability Suppression Analyzer";
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.POST_FINDING_ANALYSIS;
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase that the analyzer is intended to run in.
+     *
+     * @return the phase that the analyzer is intended to run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+    //</editor-fold>
+
+    @Override
+    public void analyze(final Dependency dependency, final Engine engine) throws AnalysisException {
+
+        if (getRules() == null || getRules().size() <= 0) {
+            return;
+        }
+
+        for (final SuppressionRule rule : getRules()) {
+            rule.process(dependency);
+        }
+    }
+}