Minor adjustments of caching for CveDB, based on code review

Update Windows usage.

.gitattributes

@@ -0,0 +1,2 @@
+*.html linguist-documentation
+(^|/)site/) linguist-documentation

.github/contributing.md

@@ -0,0 +1,34 @@
+# Contributing to OWASP dependency-check
+
+## Reporting Bugs
+
+- Ensure you're running the latest version of dependency-check.
+- Ensure the bug has not [already been reported](https://github.com/jeremylong/DependencyCheck/issues).
+- If you're unable to find an open issue addressing the problem, please [submit a new issue](https://github.com/jeremylong/DependencyCheck/issues/new).
+  - Please fill out the appropriate section of the bug report template provided. Please delete any sections not needed in the template.
+  
+## Reporting Vulnerabilities
+
+- If you believe you have found a vulnerability in dependency-check itself (not that dependency-check found a vulnerability); please email jeremy.long@owasp.org.
+
+## Asking Questions
+
+- Your question may be answered by taking a look at the [documentataion](https://jeremylong.github.io/DependencyCheck/).
+- If you still have a question consider:
+  - posting to the [Google Group](https://groups.google.com/forum/#!forum/dependency-check)
+  - opening a [new issue](https://github.com/jeremylong/DependencyCheck/issues/new)
+
+## Enhancement Requests
+
+- Suggest changes by [submitting a new issue](https://github.com/jeremylong/DependencyCheck/issues/new) and begin coding.
+
+## Contributing Code
+
+- If you have written a new feature or have fixed a bug please open a new pull request with the patch.
+- Ensure the PR description clearly describes the problem and solution. Include any related issue number(s) if applicable.
+- Please ensure the PR passes the automated checks performed (travis-ci, codacy, etc.)
+- Please consider adding test cases for any new functionality
+
+## Thank you for your contributions
+
+OWASP dependency-check team

.github/issue_template.md

@@ -0,0 +1,20 @@
+Please delete any un-needed section from the following issue template:
+
+### Reporting Bugs/Errors
+When reporting errors, 99% of the time log file output is required. Please post the log file as a [gist](https://gist.github.com/) and provide a link in the new issue.
+
+### Reporting False Positives
+When reporting a false positive please include:
+- The location of the dependency (Maven GAV, URL to download the dependency, etc.)
+- The CPE that is believed to be false positive
+  - Please report the CPE not the CVE
+
+#### Example
+False positive on library foo.jar - reported as cpe:/a:apache:tomcat:7.0
+```xml
+<dependency>
+   <groupId>org.sample</groupId>
+   <artifactId>foo</artifactId>
+   <version>1.0</version>
+</dependency>
+```

.github/pull_request_template.md

@@ -0,0 +1,9 @@
+## Fixes Issue #
+
+## Description of Change
+
+*Please add a description of the proposed change*
+
+## Have test cases been added to cover the new functionality?
+
+*yes/no*

.gitignore

@@ -26,3 +26,5 @@ _site/**
 .LCKpom.xml~
 #coverity
 /cov-int/
+/dependency-check-core/nbproject/
+cov-scan.bat

.travis.yml

@@ -0,0 +1,13 @@
+language: java
+jdk: oraclejdk7
+script: mvn install -DreleaseTesting
+env:
+  global:
+    secure: ZUzhWfpXJw/oAeDlUkDFkEJMT0T7kCN3d7ah8urkL2B0KFfKOqQagkbXkgvDa1SYud8VdcnoGa69LfkEr5IrdqW7R4bEYZAiN5swm4Z0iO8t53szVspm2f+O9jQ44O/sfOfpfLxWUUuhdc7Vbrszp+tSszxdPmssWL+f5a/mfWs=
+
+before_install:
+  - sudo apt-get install jq
+  - wget -O ~/codacy-coverage-reporter-assembly-latest.jar $(curl https://api.github.com/repos/codacy/codacy-coverage-reporter/releases/latest | jq -r .assets[0].browser_download_url)
+
+after_success:
+  - java -cp ~/codacy-coverage-reporter-assembly-latest.jar com.codacy.CodacyCoverageReporter -l Java -r build-reporting/target/site/jacoco-aggregate/jacoco.xml

Dockerfile

@@ -0,0 +1,29 @@
+FROM java:8
+
+MAINTAINER Timo Pagel <dependencycheckmaintainer@timo-pagel.de>
+
+ENV user=dependencycheck
+ENV version_url=https://jeremylong.github.io/DependencyCheck/current.txt
+ENV download_url=https://dl.bintray.com/jeremy-long/owasp
+
+RUN wget -O /tmp/current.txt ${version_url} && \
+ version=$(cat /tmp/current.txt) && \
+ file="dependency-check-${version}-release.zip" && \
+ wget "$download_url/$file" && \
+ unzip ${file} && \
+ rm ${file} && \
+ mv dependency-check /usr/share/
+
+RUN useradd -ms /bin/bash ${user} && \
+ chown -R ${user}:${user} /usr/share/dependency-check && \
+ mkdir /report && \
+ chown -R ${user}:${user} /report
+
+USER ${user}
+
+VOLUME ["/src" "/usr/share/dependency-check/data" "/report"]
+
+WORKDIR /report
+
+CMD ["--help"]
+ENTRYPOINT ["/usr/share/dependency-check/bin/dependency-check.sh"]

README.md

@@ -1,4 +1,7 @@
-[![Build Status](https://dependency-check.ci.cloudbees.com/buildStatus/icon?job=dependency-check)](https://dependency-check.ci.cloudbees.com/job/dependency-check/)
+[![Build Status](https://travis-ci.org/jeremylong/DependencyCheck.svg?branch=master)](https://travis-ci.org/jeremylong/DependencyCheck) [![Coverity Scan Build Status](https://scan.coverity.com/projects/1654/badge.svg)](https://scan.coverity.com/projects/dependencycheck) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/6b6021d481dc41a888c5da0d9ecf9494)](https://www.codacy.com/app/jeremylong/DependencyCheck?utm_source=github.com&utm_medium=referral&utm_content=jeremylong/DependencyCheck&utm_campaign=Badge_Grade) [![Apache 2.0 License](https://img.shields.io/badge/license-Apache%202-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0.txt)
+
+[![Black Hat Arsenal](https://www.toolswatch.org/badges/arsenal/2015.svg)](https://www.toolswatch.org/2015/06/black-hat-arsenal-usa-2015-speakers-lineup/) [![Black Hat Arsenal](https://www.toolswatch.org/badges/arsenal/2014.svg)](https://www.toolswatch.org/2014/06/black-hat-usa-2014-arsenal-tools-speaker-list/) [![Black Hat Arsenal](https://www.toolswatch.org/badges/arsenal/2013.svg)](https://www.toolswatch.org/2013/06/announcement-blackhat-arsenal-usa-2013-selected-tools/)
+
 Dependency-Check
 ================
 
@@ -22,18 +25,18 @@ The latest CLI can be downloaded from bintray's
 On *nix
 ```
 $ ./bin/dependency-check.sh -h
-$ ./bin/dependency-check.sh --app Testing --out . --scan [path to jar files to be scanned]
+$ ./bin/dependency-check.sh --project Testing --out . --scan [path to jar files to be scanned]
 ```
 On Windows
 ```
-> bin/dependency-check.bat -h
-> bin/dependency-check.bat --app Testing --out . --scan [path to jar files to be scanned]
+> .\bin\dependency-check.bat -h
+> .\bin\dependency-check.bat --project 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]
+$ dependency-check --project Testing --out . --scan [path to jar files to be scanned]
 ```
 
 ### Maven Plugin
@@ -85,17 +88,54 @@ On *nix
 ```
 $ mvn install
 $ ./dependency-check-cli/target/release/bin/dependency-check.sh -h
-$ ./dependency-check-cli/target/release/bin/dependency-check.sh --app Testing --out . --scan ./src/test/resources
+$ ./dependency-check-cli/target/release/bin/dependency-check.sh --project Testing --out . --scan ./src/test/resources
 ```
 On Windows
 ```
 > mvn install
-> dependency-check-cli/target/release/bin/dependency-check.bat -h
-> dependency-check-cli/target/release/bin/dependency-check.bat --app Testing --out . --scan ./src/test/resources
+> .\dependency-check-cli\target\release\bin\dependency-check.bat -h
+> .\dependency-check-cli\target\release\bin\dependency-check.bat --project Testing --out . --scan ./src/test/resources
 ```
 
 Then load the resulting 'DependencyCheck-Report.html' into your favorite browser.
 
+### Docker
+
+In the following example it is assumed that the source to be checked is in the current working directory. Persistent data and report directories are used, allowing you to destroy the container after running.
+
+```
+#!/bin/sh
+
+OWASPDC_DIRECTORY=$HOME/OWASP-Dependency-Check
+DATA_DIRECTORY="$OWASPDC_DIRECTORY/data"
+REPORT_DIRECTORY="$OWASPDC_DIRECTORY/reports"
+
+if [ ! -d "$DATA_DIRECTORY" ]; then
+    echo "Initially creating persistent directories"
+    mkdir -p "$DATA_DIRECTORY"
+    chmod -R 777 "$DATA_DIRECTORY"
+
+    mkdir -p "$REPORT_DIRECTORY"
+    chmod -R 777 "$REPORT_DIRECTORY"
+fi
+
+# Make sure we are using the latest version
+docker pull owasp/dependency-check
+
+docker run --rm \
+    --volume $(pwd):/src \
+    --volume "$DATA_DIRECTORY":/usr/share/dependency-check/data \
+    --volume "$REPORT_DIRECTORY":/report \
+    owasp/dependency-check \
+    --scan /src \
+    --format "ALL" \
+    --project "My OWASP Dependency Check Project"
+    # Use suppression like this: (/src == $pwd)
+    # --suppression "/src/security/dependency-check-suppression.xml"
+
+```
+
+
 Mailing List
 ------------
 
@@ -108,14 +148,14 @@ Archive: [google group](https://groups.google.com/forum/#!forum/dependency-check
 Copyright & License
 -
 
-Dependency-Check is Copyright (c) 2012-2015 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 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.
+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://github.com/jeremylong/DependencyCheck/blob/master/NOTICES.txt
+  [notices]: https://github.com/jeremylong/DependencyCheck/blob/master/NOTICE.txt

build-reporting/pom.xml

@@ -0,0 +1,80 @@
+<!--
+This file is part of dependency-check build-reporting.
+
+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) 2017 - 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>1.4.6-SNAPSHOT</version>
+    </parent>
+
+    <artifactId>build-reporting</artifactId>
+    <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
+    <distributionManagement>
+        <site>
+            <id>github-pages-site</id>
+            <name>Deployment through GitHub's site deployment plugin</name>
+            <url>${basedir}/../target/site/${project.version}/build-reporting</url>
+        </site>
+    </distributionManagement>
+    <!-- end copy -->
+    <dependencies>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-ant</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-cli</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-maven</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>report-aggregate</id>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>report-aggregate</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>

build-reporting/src/site/markdown/index.md

@@ -0,0 +1,5 @@
+About
+=====
+OWASP dependency-check build reporting is used to aggregate jacoco test coverage results
+so that they can be posted to [Codacy](https://www.codacy.com/app/OWASP_Reviews/DependencyCheck/dashboard)
+to track code coverage.

build-reporting/src/site/site.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
 <!--
-This file is part of dependency-check-gradle.
+This file is part of dependency-check build reporting.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -14,18 +14,19 @@ 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.
+Copyright (c) 2017 Jeremy Long. All Rights Reserved.
 -->
-<project name="dependency-check-gradle">
-    <bannerLeft>
-        <name>OWASP dependency-check-gradle</name>
-        <alt>OWASP dependency-check-gradle</alt>
-        <src>./images/dc-gradle.svg</src>
+<project name="dependency-check-build-reporting">
+	<bannerLeft>
+        <name>OWASP dependency-check build reporting</name>
+        <alt>OWASP dependency-check build reporting</alt>
+        <src>../images/dc.svg</src>
     </bannerLeft>
     <body>
         <breadcrumbs>
             <item name="dependency-check" href="../index.html"/>
         </breadcrumbs>
+        <menu ref="Project Documentation" />
         <menu ref="reports" />
     </body>
 </project>

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
 ------------

dependency-check-ant/pom.xml

@@ -20,7 +20,7 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.3.1</version>
+        <version>1.4.6-SNAPSHOT</version>
     </parent>
 
     <artifactId>dependency-check-ant</artifactId>
@@ -223,47 +223,6 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>cobertura-maven-plugin</artifactId>
-                <configuration>
-                    <check>
-                        <branchRate>85</branchRate>
-                        <lineRate>85</lineRate>
-                        <haltOnFailure>false</haltOnFailure>
-                        <totalBranchRate>85</totalBranchRate>
-                        <totalLineRate>85</totalLineRate>
-                        <packageLineRate>85</packageLineRate>
-                        <packageBranchRate>85</packageBranchRate>
-                        <regexes>
-                            <regex>
-                                <pattern>.*\$.*</pattern>
-                                <branchRate>0</branchRate>
-                                <lineRate>0</lineRate>
-                            </regex>
-                        </regexes>
-                    </check>
-                </configuration>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>clean</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <configuration>
-                    <systemProperties>
-                        <property>
-                            <name>data.directory</name>
-                            <value>${project.build.directory}/dependency-check-data</value>
-                        </property>
-                    </systemProperties>
-                </configuration>
-            </plugin>
         </plugins>
     </build>
     <reporting>
@@ -287,7 +246,7 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
                 <version>${reporting.pmd-plugin.version}</version>
                 <configuration>
                     <targetJdk>1.6</targetJdk>
-                    <linkXref>true</linkXref>
+                    <linkXRef>true</linkXRef>
                     <sourceEncoding>utf-8</sourceEncoding>
                     <excludes>
                         <exclude>**/generated/*.java</exclude>

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

@@ -24,16 +24,21 @@ 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.
+ * 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 {
 
+    /**
+     * serialization UID.
+     */
+    private static final long serialVersionUID = -1337;
     /**
      * A reference to the Ant task used for logging.
      */
-    private Task task;
+    private transient Task task;
 
     /**
      * Constructs an Ant Logger Adapter.
@@ -63,7 +68,9 @@ public class AntLoggerAdapter extends MarkerIgnoringBase {
 
     @Override
     public void trace(String msg) {
-        task.log(msg, Project.MSG_VERBOSE);
+        if (task != null) {
+            task.log(msg, Project.MSG_VERBOSE);
+        }
     }
 
     @Override

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

@@ -71,6 +71,36 @@ public class Purge extends Task {
         this.dataDirectory = dataDirectory;
     }
 
+    /**
+     * Indicates if dependency-check should fail the build if an exception
+     * occurs.
+     */
+    private boolean failOnError = true;
+
+    /**
+     * Get the value of failOnError.
+     *
+     * @return the value of failOnError
+     */
+    public boolean isFailOnError() {
+        return failOnError;
+    }
+
+    /**
+     * Set the value of failOnError.
+     *
+     * @param failOnError new value of failOnError
+     */
+    public void setFailOnError(boolean failOnError) {
+        this.failOnError = failOnError;
+    }
+
+    /**
+     * Executes the dependency-check purge to delete the existing local copy of
+     * the NVD CVE data.
+     *
+     * @throws BuildException thrown if there is a problem deleting the file(s)
+     */
     @Override
     public void execute() throws BuildException {
         populateSettings();
@@ -81,38 +111,47 @@ public class Purge extends Task {
                 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);
+                    final String msg = String.format("Unable to delete '%s'; please delete the file manually", db.getAbsolutePath());
+                    if (this.failOnError) {
+                        throw new BuildException(msg);
+                    }
+                    log(msg, Project.MSG_ERR);
                 }
             } else {
-                log(String.format("Unable to purge database; the database file does not exists: %s", db.getAbsolutePath()), Project.MSG_ERR);
+                final String msg = String.format("Unable to purge database; the database file does not exists: %s", db.getAbsolutePath());
+                if (this.failOnError) {
+                    throw new BuildException(msg);
+                }
+                log(msg, Project.MSG_ERR);
             }
         } catch (IOException ex) {
-            log("Unable to delete the database", Project.MSG_ERR);
+            final String msg = "Unable to delete the database";
+            if (this.failOnError) {
+                throw new BuildException(msg);
+            }
+            log(msg, 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.
+     * 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 if the properties file cannot be read.
      */
-    protected void populateSettings() {
+    protected void populateSettings() throws BuildException {
         Settings.initialize();
-        InputStream taskProperties = null;
-        try {
-            taskProperties = this.getClass().getClassLoader().getResourceAsStream(PROPERTIES_FILE);
+        try (InputStream 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);
-                }
+            final String msg = "Unable to load the dependency-check ant task.properties file.";
+            if (this.failOnError) {
+                throw new BuildException(msg, ex);
             }
+            log(msg, ex, Project.MSG_WARN);
         }
         if (dataDirectory != null) {
             Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);

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

@@ -18,19 +18,83 @@
 package org.owasp.dependencycheck.taskdefs;
 
 import org.apache.tools.ant.BuildException;
+import org.apache.tools.ant.Project;
 import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.update.exception.UpdateException;
 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.
+ * 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 {
 
+    /**
+     * The Proxy Server.
+     */
+    private String proxyServer;
+    /**
+     * The Proxy Port.
+     */
+    private String proxyPort;
+    /**
+     * The Proxy username.
+     */
+    private String proxyUsername;
+    /**
+     * The Proxy password.
+     */
+    private String proxyPassword;
+    /**
+     * The Connection Timeout.
+     */
+    private String connectionTimeout;
+    /**
+     * The database driver name; such as org.h2.Driver.
+     */
+    private String databaseDriverName;
+    /**
+     * The path to the database driver JAR file if it is not on the class path.
+     */
+    private String databaseDriverPath;
+    /**
+     * The database connection string.
+     */
+    private String connectionString;
+    /**
+     * The user name for connecting to the database.
+     */
+    private String databaseUser;
+    /**
+     * The password to use when connecting to the database.
+     */
+    private String databasePassword;
+    /**
+     * The url for the modified NVD CVE (1.2 schema).
+     */
+    private String cveUrl12Modified;
+    /**
+     * Base Data Mirror URL for CVE 1.2.
+     */
+    private String cveUrl12Base;
+    /**
+     * Data Mirror URL for CVE 2.0.
+     */
+    private String cveUrl20Base;
+    /**
+     * The number of hours to wait before re-checking for updates.
+     */
+    private Integer cveValidForHours;
+    /**
+     * The url for the modified NVD CVE (2.0 schema).
+     */
+    private String cveUrl20Modified;
+
     /**
      * Construct a new UpdateTask.
      */
@@ -41,11 +105,6 @@ public class Update extends Purge {
         StaticLoggerBinder.getSingleton().setTask(this);
     }
 
-    /**
-     * The Proxy Server.
-     */
-    private String proxyServer;
-
     /**
      * Get the value of proxyServer.
      *
@@ -64,11 +123,6 @@ public class Update extends Purge {
         this.proxyServer = server;
     }
 
-    /**
-     * The Proxy Port.
-     */
-    private String proxyPort;
-
     /**
      * Get the value of proxyPort.
      *
@@ -86,10 +140,6 @@ public class Update extends Purge {
     public void setProxyPort(String proxyPort) {
         this.proxyPort = proxyPort;
     }
-    /**
-     * The Proxy username.
-     */
-    private String proxyUsername;
 
     /**
      * Get the value of proxyUsername.
@@ -108,10 +158,6 @@ public class Update extends Purge {
     public void setProxyUsername(String proxyUsername) {
         this.proxyUsername = proxyUsername;
     }
-    /**
-     * The Proxy password.
-     */
-    private String proxyPassword;
 
     /**
      * Get the value of proxyPassword.
@@ -130,10 +176,6 @@ public class Update extends Purge {
     public void setProxyPassword(String proxyPassword) {
         this.proxyPassword = proxyPassword;
     }
-    /**
-     * The Connection Timeout.
-     */
-    private String connectionTimeout;
 
     /**
      * Get the value of connectionTimeout.
@@ -152,10 +194,6 @@ public class Update extends Purge {
     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.
@@ -175,11 +213,6 @@ public class Update extends Purge {
         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.
      *
@@ -197,10 +230,6 @@ public class Update extends Purge {
     public void setDatabaseDriverPath(String databaseDriverPath) {
         this.databaseDriverPath = databaseDriverPath;
     }
-    /**
-     * The database connection string.
-     */
-    private String connectionString;
 
     /**
      * Get the value of connectionString.
@@ -219,10 +248,6 @@ public class Update extends Purge {
     public void setConnectionString(String connectionString) {
         this.connectionString = connectionString;
     }
-    /**
-     * The user name for connecting to the database.
-     */
-    private String databaseUser;
 
     /**
      * Get the value of databaseUser.
@@ -242,11 +267,6 @@ public class Update extends Purge {
         this.databaseUser = databaseUser;
     }
 
-    /**
-     * The password to use when connecting to the database.
-     */
-    private String databasePassword;
-
     /**
      * Get the value of databasePassword.
      *
@@ -265,11 +285,6 @@ public class Update extends Purge {
         this.databasePassword = databasePassword;
     }
 
-    /**
-     * The url for the modified NVD CVE (1.2 schema).
-     */
-    private String cveUrl12Modified;
-
     /**
      * Get the value of cveUrl12Modified.
      *
@@ -288,11 +303,6 @@ public class Update extends Purge {
         this.cveUrl12Modified = cveUrl12Modified;
     }
 
-    /**
-     * The url for the modified NVD CVE (2.0 schema).
-     */
-    private String cveUrl20Modified;
-
     /**
      * Get the value of cveUrl20Modified.
      *
@@ -311,11 +321,6 @@ public class Update extends Purge {
         this.cveUrl20Modified = cveUrl20Modified;
     }
 
-    /**
-     * Base Data Mirror URL for CVE 1.2.
-     */
-    private String cveUrl12Base;
-
     /**
      * Get the value of cveUrl12Base.
      *
@@ -334,11 +339,6 @@ public class Update extends Purge {
         this.cveUrl12Base = cveUrl12Base;
     }
 
-    /**
-     * Data Mirror URL for CVE 2.0.
-     */
-    private String cveUrl20Base;
-
     /**
      * Get the value of cveUrl20Base.
      *
@@ -358,10 +358,29 @@ public class Update extends Purge {
     }
 
     /**
-     * Executes the update by initializing the settings, downloads the NVD XML data, and then processes the data storing it in the
-     * local database.
+     * Get the value of cveValidForHours.
      *
-     * @throws BuildException thrown if a connection to the local database cannot be made.
+     * @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 {
@@ -369,9 +388,20 @@ public class Update extends Purge {
         Engine engine = null;
         try {
             engine = new Engine(Update.class.getClassLoader());
-            engine.doUpdates();
+            try {
+                engine.doUpdates();
+            } catch (UpdateException ex) {
+                if (this.isFailOnError()) {
+                    throw new BuildException(ex);
+                }
+                log(ex.getMessage(), Project.MSG_ERR);
+            }
         } catch (DatabaseException ex) {
-            throw new BuildException("Unable to connect to the dependency-check database; unable to update the NVD data", ex);
+            final String msg = "Unable to connect to the dependency-check database; unable to update the NVD data";
+            if (this.isFailOnError()) {
+                throw new BuildException(msg, ex);
+            }
+            log(msg, Project.MSG_ERR);
         } finally {
             Settings.cleanup(true);
             if (engine != null) {
@@ -381,53 +411,35 @@ public class Update extends Purge {
     }
 
     /**
-     * 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.
+     * 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() {
+    protected void populateSettings() throws BuildException {
         super.populateSettings();
-        if (proxyServer != null && !proxyServer.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_SERVER, proxyServer);
-        }
-        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);
-        }
-        if (databaseDriverName != null && !databaseDriverName.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
-        }
-        if (databaseDriverPath != null && !databaseDriverPath.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
-        }
-        if (connectionString != null && !connectionString.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
-        }
-        if (databaseUser != null && !databaseUser.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_USER, databaseUser);
-        }
-        if (databasePassword != null && !databasePassword.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
-        }
-        if (cveUrl12Modified != null && !cveUrl12Modified.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
-        }
-        if (cveUrl20Modified != null && !cveUrl20Modified.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
-        }
-        if (cveUrl12Base != null && !cveUrl12Base.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
-        }
-        if (cveUrl20Base != null && !cveUrl20Base.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
+        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/slf4j/impl/StaticLoggerBinder.java

@@ -23,18 +23,25 @@ import org.slf4j.ILoggerFactory;
 import org.slf4j.spi.LoggerFactoryBinder;
 
 /**
- * The binding of {@link LoggerFactory} class with an actual instance of {@link ILoggerFactory} is performed using information
- * returned by this class.
+ * 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
  */
+//CSOFF: FinalClass
 public class StaticLoggerBinder implements LoggerFactoryBinder {
+//CSON: FinalClass
 
     /**
      * The unique instance of this class
-     *
      */
     private static final StaticLoggerBinder SINGLETON = new StaticLoggerBinder();
+    /**
+     * Ant tasks have the log method we actually want to call. So we hang onto
+     * the task as a delegate
+     */
+    private Task task = null;
 
     /**
      * Return the singleton of this class.
@@ -45,11 +52,6 @@ public class StaticLoggerBinder implements LoggerFactoryBinder {
         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.
      *
@@ -61,16 +63,24 @@ public class StaticLoggerBinder implements LoggerFactoryBinder {
     }
 
     /**
-     * Declare the version of the SLF4J API this implementation is compiled against. The value of this filed is usually modified
-     * with each release.
+     * 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
+    //CSOFF: StaticVariableName
+    //CSOFF: VisibilityModifier
     public static String REQUESTED_API_VERSION = "1.7.12"; // final
+    //CSON: VisibilityModifier
+    //CSON: StaticVariableName
 
+    /**
+     * The logger factory class string.
+     */
     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
+     * The ILoggerFactory instance returned by the {@link #getLoggerFactory}
+     * method should always be the smae object
      */
     private ILoggerFactory loggerFactory;
 

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

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

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

@@ -2,7 +2,7 @@ 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.
+the rare circumstance that the local H2 database becomes corrupt.
 
 ```xml
 <target name="dependency-check-purge" description="Dependency-Check purge">
@@ -14,6 +14,7 @@ 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
+Property              | Description                                                            | Default Value
+----------------------|------------------------------------------------------------------------|------------------
+dataDirectory         | Data directory that is used to store the local copy of the NVD         | data
+failOnError           | Whether the build should fail if there is an error executing the purge | true

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

@@ -3,7 +3,7 @@ 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
+than 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.
 
@@ -24,6 +24,7 @@ proxyPort             | The Proxy Port.                    |  
 proxyUsername         | Defines the proxy user name.       |  
 proxyPassword         | Defines the proxy password.        |  
 connectionTimeout     | The URL Connection Timeout.        |  
+failOnError           | Whether the build should fail if there is an error executing the update | true
 
 Advanced Configuration
 ====================
@@ -32,10 +33,10 @@ may be the cvedUrl properties, which can be used to host a mirror of the NVD wit
 
 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
+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.                                              |  
 databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path.           |  

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

@@ -27,21 +27,25 @@ the project's dependencies.
 
 Configuration: dependency-check Task
 --------------------
-The following properties can be set on the dependency-check-update task.
+The following properties can be set on the dependency-check 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
-projectName           | The name of the project being scanned. | Dependency-Check
-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'
-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
-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
-suppressionFile       | The file path to the XML suppression file \- used to suppress [false positives](../general/suppression.html) |  
-proxyServer           | The Proxy Server.                  |  
-proxyPort             | The Proxy Port.                    |  
-proxyUsername         | Defines the proxy user name.       |  
-proxyPassword         | Defines the proxy password.        |  
-connectionTimeout     | The URL Connection Timeout.        |  
+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
+failOnError           | Whether the build should fail if there is an error executing the dependency-check analysis                                                                                                         | true
+projectName           | The name of the project being scanned.                                                                                                                                                             | Dependency-Check
+reportFormat          | The report format to be generated (HTML, XML, CSV, JSON, 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)                                                                                       |  
+hintsFile             | The file path to the XML hints file \- used to resolve [false negatives](../general/hints.html)                                                                                                    |  
+proxyServer           | The Proxy Server; see the [proxy configuration](../data/proxy.html) page for more information.                                                                                                     |  
+proxyPort             | The Proxy Port.                                                                                                                                                                                    |  
+proxyUsername         | Defines the proxy user name.                                                                                                                                                                       |  
+proxyPassword         | Defines the proxy password.                                                                                                                                                                        |  
+connectionTimeout     | The URL Connection Timeout.                                                                                                                                                                        |  
+enableExperimental    | Enable the [experimental analyzers](../analyzers/index.html). If not enabled the experimental analyzers (see below) will not be loaded or used.                                                                             | false
 
 Analyzer Configuration
 ====================
@@ -51,26 +55,30 @@ 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
+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. |  
-jarAnalyzer                   | Sets whether the Jar Analyzer will be used.                               | true
+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. |  
-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.       |  
+nexusUsesProxy                | Whether or not the defined proxy should be used when connecting to Nexus.         | true
+pyDistributionAnalyzerEnabled | Sets whether the [experimental](../analyzers/index.html) Python Distribution Analyzer will be used.        | true
+pyPackageAnalyzerEnabled      | Sets whether the [experimental](../analyzers/index.html) Python Package Analyzer will be used.             | true
+rubygemsAnalyzerEnabled       | Sets whether the [experimental](../analyzers/index.html) Ruby Gemspec Analyzer will be used.               | true
+opensslAnalyzerEnabled        | Sets whether the openssl Analyzer should be used.                                 | true
+cmakeAnalyzerEnabled          | Sets whether the [experimental](../analyzers/index.html) CMake Analyzer should be used.                    | true
+autoconfAnalyzerEnabled       | Sets whether the [experimental](../analyzers/index.html) autoconf Analyzer should be used.                 | true
+composerAnalyzerEnabled       | Sets whether the [experimental](../analyzers/index.html) PHP Composer Lock File Analyzer should be used.   | true
+nodeAnalyzerEnabled           | Sets whether the [experimental](../analyzers/index.html) Node.js Analyzer should be used.                  | true
+nuspecAnalyzerEnabled         | Sets whether the .NET Nuget Nuspec Analyzer will be used.                                                  | true
+cocoapodsAnalyzerEnabled      | Sets whether the [experimental](../analyzers/index.html) Cocoapods Analyzer should be used.                | true
+bundleAuditAnalyzerEnabled    | Sets whether the [experimental](../analyzers/index.html) Bundle Audit Analyzer should be used.             | true
+bundleAuditPath               | Sets the path to the bundle audit executable; only used if bundle audit analyzer is enabled and experimental analyzers are enabled.  |  
+swiftPackageManagerAnalyzerEnabled | Sets whether the [experimental](../analyzers/index.html) Switft Package Analyzer should be used.      | true
+assemblyAnalyzerEnabled       | Sets whether the .NET Assembly Analyzer should be used.                                                    | true
+pathToMono                    | The path to Mono for .NET assembly analysis on non-windows systems.                                        |  
 
 Advanced Configuration
 ====================

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

@@ -16,8 +16,11 @@ Installation
     <property name="dependency-check.home" value="C:/tools/dependency-check-ant"/>
     <path id="dependency-check.path">
        <pathelement location="${dependency-check.home}/dependency-check-ant.jar"/>
+        <fileset dir="${dependency-check.home}/lib">
+            <include name="*.jar"/>
+        </fileset>
     </path>
-       <taskdef resource="dependency-check-taskdefs.properties">
+    <taskdef resource="dependency-check-taskdefs.properties">
        <classpath refid="dependency-check.path" />
     </taskdef>
     ```

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

@@ -27,7 +27,7 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
             <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="configuration.html"/>
         </menu>
         <menu ref="reports" />

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

@@ -26,12 +26,11 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
-import org.owasp.dependencycheck.data.nvdcve.BaseDBTestCase;
+import org.owasp.dependencycheck.BaseDBTestCase;
 import org.owasp.dependencycheck.utils.Settings;
 
 import static org.junit.Assert.assertTrue;
 
-
 /**
  *
  * @author Jeremy Long
@@ -65,15 +64,11 @@ public class DependencyCheckTaskTest {
     @Test
     public void testAddFileSet() throws Exception {
         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.");
-            }
+        if (report.exists() && !report.delete()) {
+            throw new Exception("Unable to delete 'target/DependencyCheck-Report.html' prior to test.");
         }
         buildFileRule.executeTarget("test.fileset");
-
         assertTrue("DependencyCheck report was not generated", report.exists());
-
     }
 
     /**

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

@@ -61,11 +61,14 @@
 
     <target name="failCVSS">
         <dependency-check
-            applicationName="test formatBAD"
+            applicationName="test failCVSS"
             reportOutputDirectory="${project.build.directory}"
             reportFormat="XML"
             autoupdate="false"
-            failBuildOnCVSS="8">
+            failBuildOnCVSS="3">
+            <fileset dir="${project.build.directory}/test-classes/jars">
+                <include name="axis-1.4.jar"/>
+            </fileset>
         </dependency-check>
     </target>
 </project>

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
 ------------

dependency-check-cli/pom.xml

@@ -20,7 +20,7 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.3.1</version>
+        <version>1.4.6-SNAPSHOT</version>
     </parent>
 
     <artifactId>dependency-check-cli</artifactId>
@@ -69,61 +69,6 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                     </archive>
                 </configuration>
             </plugin>
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>cobertura-maven-plugin</artifactId>
-                <configuration>
-                    <!--instrumentation>
-                        <ignoreTrivial>true</ignoreTrivial>
-                    </instrumentation-->
-                    <check>
-                        <branchRate>85</branchRate>
-                        <lineRate>85</lineRate>
-                        <haltOnFailure>false</haltOnFailure>
-                        <totalBranchRate>85</totalBranchRate>
-                        <totalLineRate>85</totalLineRate>
-                        <packageLineRate>85</packageLineRate>
-                        <packageBranchRate>85</packageBranchRate>
-                        <regexes>
-                            <regex>
-                                <pattern>.*\$.*</pattern>
-                                <branchRate>0</branchRate>
-                                <lineRate>0</lineRate>
-                            </regex>
-                            <regex>
-                                <pattern>org.owasp.dependencycheck.App</pattern>
-                                <branchRate>0</branchRate>
-                                <lineRate>0</lineRate>
-                            </regex>
-                        </regexes>
-                    </check>
-                </configuration>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>clean</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <configuration>
-                    <systemProperties>
-                        <property>
-                            <name>cpe</name>
-                            <value>data/cpe</value>
-                            <workingDirectory>target</workingDirectory>
-                        </property>
-                        <property>
-                            <name>cve</name>
-                            <value>data/cpe</value>
-                            <workingDirectory>target</workingDirectory>
-                        </property>
-                    </systemProperties>
-                </configuration>
-            </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>appassembler-maven-plugin</artifactId>
@@ -139,6 +84,8 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                     <binFileExtensions>
                         <unix>.sh</unix>
                     </binFileExtensions>
+                    <configurationDirectory>plugins/*</configurationDirectory>
+                    <includeConfigurationDirectoryInClasspath>true</includeConfigurationDirectoryInClasspath>
                 </configuration>
                 <executions>
                     <execution>
@@ -193,7 +140,7 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                 <version>${reporting.pmd-plugin.version}</version>
                 <configuration>
                     <targetJdk>1.6</targetJdk>
-                    <linkXref>true</linkXref>
+                    <linkXRef>true</linkXRef>
                     <sourceEncoding>utf-8</sourceEncoding>
                     <excludes>
                         <exclude>**/generated/*.java</exclude>

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

@@ -29,6 +29,13 @@
             <outputDirectory>dependency-check/repo</outputDirectory>
             <directory>${project.build.directory}/release/repo</directory>
         </fileSet>
+        <fileSet>
+            <directory>.</directory>
+            <outputDirectory>dependency-check/plugins</outputDirectory>
+            <excludes>
+                <exclude>*/**</exclude>
+            </excludes>
+        </fileSet>
         <fileSet>
             <outputDirectory>dependency-check</outputDirectory>
             <includes>
@@ -53,21 +60,4 @@
             </includes>
         </fileSet>
     </fileSets>
-    <!--
-            <fileSets>
-            <fileSet>
-                <outputDirectory>/</outputDirectory>
-                <directory>${project.build.directory}</directory>
-                <includes>
-                    <include>dependency-check*.jar</include>
-                </includes>
-            </fileSet>
-        </fileSets>
-        <dependencySets>
-            <dependencySet>
-                <outputDirectory>/lib</outputDirectory>
-                <scope>runtime</scope>
-            </dependencySet>
-        </dependencySets>
-    -->
 </assembly>

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

@@ -19,6 +19,7 @@ package org.owasp.dependencycheck;
 
 import ch.qos.logback.classic.LoggerContext;
 import ch.qos.logback.classic.encoder.PatternLayoutEncoder;
+import ch.qos.logback.classic.spi.ILoggingEvent;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
@@ -32,11 +33,16 @@ import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.apache.tools.ant.DirectoryScanner;
+import org.owasp.dependencycheck.dependency.Vulnerability;
 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.owasp.dependencycheck.data.update.exception.UpdateException;
+import org.owasp.dependencycheck.exception.ExceptionCollection;
+import org.owasp.dependencycheck.exception.ReportException;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.slf4j.impl.StaticLoggerBinder;
 
 /**
@@ -57,21 +63,26 @@ public class App {
      * @param args the command line arguments
      */
     public static void main(String[] args) {
+        int exitCode = 0;
         try {
             Settings.initialize();
             final App app = new App();
-            app.run(args);
+            exitCode = app.run(args);
+            LOGGER.debug("Exit code: " + exitCode);
         } finally {
             Settings.cleanup(true);
         }
+        System.exit(exitCode);
     }
 
     /**
      * Main CLI entry-point into the application.
      *
      * @param args the command line arguments
+     * @return the exit code to return
      */
-    public void run(String[] args) {
+    public int run(String[] args) {
+        int exitCode = 0;
         final CliParser cli = new CliParser();
 
         try {
@@ -79,11 +90,11 @@ public class App {
         } catch (FileNotFoundException ex) {
             System.err.println(ex.getMessage());
             cli.printHelp();
-            return;
+            return -1;
         } catch (ParseException ex) {
             System.err.println(ex.getMessage());
             cli.printHelp();
-            return;
+            return -2;
         }
 
         if (cli.getVerboseLog() != null) {
@@ -93,8 +104,15 @@ public class App {
         if (cli.isPurge()) {
             if (cli.getConnectionString() != null) {
                 LOGGER.error("Unable to purge the database when using a non-default connection string");
+                exitCode = -3;
             } else {
-                populateSettings(cli);
+                try {
+                    populateSettings(cli);
+                } catch (InvalidSettingException ex) {
+                    LOGGER.error(ex.getMessage());
+                    LOGGER.debug("Error loading properties file", ex);
+                    exitCode = -4;
+                }
                 File db;
                 try {
                     db = new File(Settings.getDataDirectory(), "dc.h2.db");
@@ -103,56 +121,115 @@ public class App {
                             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());
+                            exitCode = -5;
                         }
                     } else {
                         LOGGER.error("Unable to purge database; the database file does not exists: {}", db.getAbsolutePath());
+                        exitCode = -6;
                     }
                 } catch (IOException ex) {
                     LOGGER.error("Unable to delete the database");
+                    exitCode = -7;
                 }
             }
         } else if (cli.isGetVersion()) {
             cli.printVersionInfo();
         } else if (cli.isUpdateOnly()) {
-            populateSettings(cli);
-            runUpdateOnly();
-        } else if (cli.isRunScan()) {
-            populateSettings(cli);
             try {
-                runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getProjectName(), cli.getScanFiles(),
-                        cli.getExcludeList(), cli.getSymLinkDepth());
+                populateSettings(cli);
+            } catch (InvalidSettingException ex) {
+                LOGGER.error(ex.getMessage());
+                LOGGER.debug("Error loading properties file", ex);
+                exitCode = -4;
+            }
+            try {
+                runUpdateOnly();
+            } catch (UpdateException ex) {
+                LOGGER.error(ex.getMessage());
+                exitCode = -8;
+            } catch (DatabaseException ex) {
+                LOGGER.error(ex.getMessage());
+                exitCode = -9;
+            }
+        } else if (cli.isRunScan()) {
+            try {
+                populateSettings(cli);
+            } catch (InvalidSettingException ex) {
+                LOGGER.error(ex.getMessage());
+                LOGGER.debug("Error loading properties file", ex);
+                exitCode = -4;
+            }
+            try {
+                final String[] scanFiles = cli.getScanFiles();
+                if (scanFiles != null) {
+                    exitCode = runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getProjectName(), scanFiles,
+                            cli.getExcludeList(), cli.getSymLinkDepth(), cli.getFailOnCVSS());
+                } else {
+                    LOGGER.error("No scan files configured");
+                }
             } catch (InvalidScanPathException ex) {
                 LOGGER.error("An invalid scan path was detected; unable to scan '//*' paths");
+                exitCode = -10;
+            } catch (DatabaseException ex) {
+                LOGGER.error(ex.getMessage());
+                exitCode = -11;
+            } catch (ReportException ex) {
+                LOGGER.error(ex.getMessage());
+                exitCode = -12;
+            } catch (ExceptionCollection ex) {
+                if (ex.isFatal()) {
+                    exitCode = -13;
+                    LOGGER.error("One or more fatal errors occurred");
+                } else {
+                    exitCode = -14;
+                }
+                for (Throwable e : ex.getExceptions()) {
+                    LOGGER.error(e.getMessage());
+                }
             }
         } else {
             cli.printHelp();
         }
+        return exitCode;
     }
 
     /**
-     * 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
+     * @param cvssFailScore the score to fail on if a vulnerability is found
+     * @return the exit code if there was an error
      *
-     * @throws InvalidScanPathException thrown if the path to scan starts with "//"
+     * @throws InvalidScanPathException thrown if the path to scan starts with
+     * "//"
+     * @throws ReportException thrown when the report cannot be generated
+     * @throws DatabaseException thrown when there is an error connecting to the
+     * database
+     * @throws ExceptionCollection thrown when an exception occurs during
+     * analysis; there may be multiple exceptions contained within the
+     * collection.
      */
-    private void runScan(String reportDirectory, String outputFormat, String applicationName, String[] files,
-            String[] excludes, int symLinkDepth) throws InvalidScanPathException {
+    private int runScan(String reportDirectory, String outputFormat, String applicationName, String[] files,
+            String[] excludes, int symLinkDepth, int cvssFailScore) throws InvalidScanPathException, DatabaseException,
+            ExceptionCollection, ReportException {
         Engine engine = null;
+        int retCode = 0;
         try {
             engine = new Engine();
-            final List<String> antStylePaths = new ArrayList<String>();
+            final List<String> antStylePaths = new ArrayList<>();
             for (String file : files) {
                 final String antPath = ensureCanonicalPath(file);
                 antStylePaths.add(antPath);
             }
 
-            final Set<File> paths = new HashSet<File>();
+            final Set<File> paths = new HashSet<>();
             for (String file : antStylePaths) {
                 LOGGER.debug("Scanning {}", file);
                 final DirectoryScanner scanner = new DirectoryScanner();
@@ -174,8 +251,6 @@ public class App {
                         include = "**/*";
                     }
                 }
-                //LOGGER.debug("baseDir: {}", baseDir);
-                //LOGGER.debug("include: {}", include);
                 scanner.setBasedir(baseDir);
                 final String[] includes = {include};
                 scanner.setIncludes(includes);
@@ -197,34 +272,52 @@ public class App {
             }
             engine.scan(paths);
 
-            engine.analyzeDependencies();
+            ExceptionCollection exCol = null;
+            try {
+                engine.analyzeDependencies();
+            } catch (ExceptionCollection ex) {
+                if (ex.isFatal()) {
+                    throw ex;
+                }
+                exCol = ex;
+            }
             final List<Dependency> dependencies = engine.getDependencies();
             DatabaseProperties prop = null;
-            CveDB cve = null;
-            try {
-                cve = new CveDB();
-                cve.open();
+            try (CveDB cve = CveDB.getInstance()) {
                 prop = cve.getDatabaseProperties();
             } catch (DatabaseException ex) {
+                //TODO shouldn't this be a fatal exception
                 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 (ReportException ex) {
+                if (exCol != null) {
+                    exCol.addException(ex);
+                    throw exCol;
+                } else {
+                    throw ex;
+                }
             }
-        } catch (DatabaseException ex) {
-            LOGGER.error("Unable to connect to the dependency-check database; analysis has stopped");
-            LOGGER.debug("", ex);
+            if (exCol != null && exCol.getExceptions().size() > 0) {
+                throw exCol;
+            }
+
+            //Set the exit code based on whether we found a high enough vulnerability
+            for (Dependency dep : dependencies) {
+                if (!dep.getVulnerabilities().isEmpty()) {
+                    for (Vulnerability vuln : dep.getVulnerabilities()) {
+                        LOGGER.debug("VULNERABILITY FOUND " + dep.getDisplayFileName());
+                        if (vuln.getCvssScore() > cvssFailScore) {
+                            retCode = 1;
+                        }
+                    }
+                }
+            }
+
+            return retCode;
         } finally {
             if (engine != null) {
                 engine.cleanup();
@@ -234,15 +327,16 @@ public class App {
 
     /**
      * Only executes the update phase of dependency-check.
+     *
+     * @throws UpdateException thrown if there is an error updating
+     * @throws DatabaseException thrown if a fatal error occurred and a
+     * connection to the database could not be established
      */
-    private void runUpdateOnly() {
+    private void runUpdateOnly() throws UpdateException, DatabaseException {
         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();
@@ -253,12 +347,13 @@ public class App {
     /**
      * Updates the global Settings.
      *
-     * @param cli a reference to the CLI Parser that contains the command line arguments used to set the corresponding settings in
-     * the core engine.
+     * @param cli a reference to the CLI Parser that contains the command line
+     * arguments used to set the corresponding settings in the core engine.
+     *
+     * @throws InvalidSettingException thrown when a user defined properties
+     * file is unable to be loaded.
      */
-    private void populateSettings(CliParser cli) {
-
-        final boolean autoUpdate = cli.isAutoUpdate();
+    protected void populateSettings(CliParser cli) throws InvalidSettingException {
         final String connectionTimeout = cli.getConnectionTimeout();
         final String proxyServer = cli.getProxyServer();
         final String proxyPort = cli.getProxyPort();
@@ -267,6 +362,7 @@ public class App {
         final String dataDirectory = cli.getDataDirectory();
         final File propertiesFile = cli.getPropertiesFile();
         final String suppressionFile = cli.getSuppressionFile();
+        final String hintsFile = cli.getHintsFile();
         final String nexusUrl = cli.getNexusUrl();
         final String databaseDriverName = cli.getDatabaseDriverName();
         final String databaseDriverPath = cli.getDatabaseDriverPath();
@@ -279,21 +375,22 @@ public class App {
         final String cveMod20 = cli.getModifiedCve20Url();
         final String cveBase12 = cli.getBaseCve12Url();
         final String cveBase20 = cli.getBaseCve20Url();
+        final Integer cveValidForHours = cli.getCveValidForHours();
+        final Boolean autoUpdate = cli.isAutoUpdate();
+        final Boolean experimentalEnabled = cli.isExperimentalEnabled();
 
         if (propertiesFile != null) {
             try {
                 Settings.mergeProperties(propertiesFile);
             } catch (FileNotFoundException ex) {
-                LOGGER.error("Unable to load properties file '{}'", propertiesFile.getPath());
-                LOGGER.debug("", ex);
+                throw new InvalidSettingException("Unable to find properties file '" + propertiesFile.getPath() + "'", ex);
             } catch (IOException ex) {
-                LOGGER.error("Unable to find properties file '{}'", propertiesFile.getPath());
-                LOGGER.debug("", ex);
+                throw new InvalidSettingException("Error reading properties file '" + propertiesFile.getPath() + "'", 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
+        // on the command line.  This is true of other boolean values set below not using the setBooleanIfNotNull.
         final boolean nexusUsesProxy = cli.isNexusUsesProxy();
         if (dataDirectory != null) {
             Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
@@ -307,27 +404,19 @@ public class App {
             final File dataDir = new File(base, sub);
             Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
         }
-        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
-        if (proxyServer != null && !proxyServer.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_SERVER, proxyServer);
-        }
-        if (proxyPort != null && !proxyPort.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);
-        }
-        if (proxyUser != null && !proxyUser.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_USERNAME, proxyUser);
-        }
-        if (proxyPass != null && !proxyPass.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PASSWORD, proxyPass);
-        }
-        if (connectionTimeout != null && !connectionTimeout.isEmpty()) {
-            Settings.setString(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
-        }
-        if (suppressionFile != null && !suppressionFile.isEmpty()) {
-            Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
-        }
+        Settings.setBooleanIfNotNull(Settings.KEYS.AUTO_UPDATE, autoUpdate);
+        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.setStringIfNotEmpty(Settings.KEYS.HINTS_FILE, hintsFile);
+        Settings.setIntIfNotNull(Settings.KEYS.CVE_CHECK_VALID_FOR_HOURS, cveValidForHours);
 
         //File Type Analyzer Settings
+        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, experimentalEnabled);
+
         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());
@@ -336,38 +425,26 @@ public class App {
         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_SWIFT_PACKAGE_MANAGER_ENABLED, !cli.isSwiftPackageAnalyzerDisabled());
+        Settings.setBoolean(Settings.KEYS.ANALYZER_COCOAPODS_ENABLED, !cli.isCocoapodsAnalyzerDisabled());
         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());
-        if (nexusUrl != null && !nexusUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
-        }
-        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY, nexusUsesProxy);
-        if (databaseDriverName != null && !databaseDriverName.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
-        }
-        if (databaseDriverPath != null && !databaseDriverPath.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
-        }
-        if (connectionString != null && !connectionString.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
-        }
-        if (databaseUser != null && !databaseUser.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_USER, databaseUser);
-        }
-        if (databasePassword != null && !databasePassword.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
-        }
-        if (additionalZipExtensions != null && !additionalZipExtensions.isEmpty()) {
-            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, additionalZipExtensions);
-        }
-        if (pathToMono != null && !pathToMono.isEmpty()) {
-            Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
-        }
+
+        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);
@@ -389,7 +466,7 @@ public class App {
         encoder.setPattern("%d %C:%L%n%-5level - %msg%n");
         encoder.setContext(context);
         encoder.start();
-        final FileAppender fa = new FileAppender();
+        final FileAppender<ILoggingEvent> fa = new FileAppender<>();
         fa.setAppend(true);
         fa.setEncoder(encoder);
         fa.setContext(context);
@@ -407,15 +484,16 @@ public class App {
     }
 
     /**
-     * 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 ?).
+     * 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 basePath;
         String wildCards = null;
         final String file = path.replace('\\', '/');
         if (file.contains("*") || file.contains("?")) {

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

@@ -58,7 +58,8 @@ public final class CliParser {
      * 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 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 {
@@ -85,11 +86,25 @@ public final class CliParser {
     /**
      * 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.
+     * @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 (isUpdateOnly() || isRunScan()) {
+            final String value = line.getOptionValue(ARGUMENT.CVE_VALID_FOR_HOURS);
+            if (value != null) {
+                try {
+                    final int i = Integer.parseInt(value);
+                    if (i < 0) {
+                        throw new ParseException("Invalid Setting: cveValidForHours must be a number greater than or equal to 0.");
+                    }
+                } catch (NumberFormatException ex) {
+                    throw new ParseException("Invalid Setting: cveValidForHours must be a number greater than or equal to 0.");
+                }
+            }
+        }
         if (isRunScan()) {
             validatePathExists(getScanFiles(), ARGUMENT.SCAN);
             validatePathExists(getReportDirectory(), ARGUMENT.OUT);
@@ -105,7 +120,7 @@ public final class CliParser {
                     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);
+                            + "Supported output formats are HTML, XML, CSV, JSON, VULN, or ALL", format);
                     throw new ParseException(msg);
                 }
             }
@@ -128,12 +143,14 @@ public final class CliParser {
     }
 
     /**
-     * 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.
+     * 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.
+     * @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) {
@@ -142,12 +159,14 @@ public final class CliParser {
     }
 
     /**
-     * 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.
+     * 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 argumentName the argument being validated (e.g. scan, out, etc.)
-     * @throws FileNotFoundException is thrown if the path being validated does not exist.
+     * @throws FileNotFoundException is thrown if the path being validated does
+     * not exist.
      */
     private void validatePathExists(String path, String argumentName) throws FileNotFoundException {
         if (path == null) {
@@ -168,22 +187,25 @@ public final class CliParser {
                         throw new FileNotFoundException(msg);
                     }
                 }
-            } else {
-                if (!f.exists()) {
-                    isValid = false;
-                    final String msg = String.format("Invalid '%s' argument: '%s'", argumentName, path);
-                    throw new FileNotFoundException(msg);
-                }
+            } else if (!f.exists()) {
+                isValid = false;
+                final String msg = String.format("Invalid '%s' argument: '%s'", argumentName, path);
+                throw new FileNotFoundException(msg);
             }
         } else if (path.startsWith("//") || path.startsWith("\\\\")) {
             isValid = false;
             final String msg = String.format("Invalid '%s' argument: '%s'%nUnable to scan paths that start with '//'.", argumentName, path);
             throw new FileNotFoundException(msg);
+        } else if ((path.endsWith("/*") && !path.endsWith("**/*")) || (path.endsWith("\\*") && path.endsWith("**\\*"))) {
+            final String msg = String.format("Possibly incorrect path '%s' from argument '%s' because it ends with a slash star; "
+                    + "dependency-check uses ant-style paths", path, argumentName);
+            LOGGER.warn(msg);
         }
     }
 
     /**
-     * Generates an Options collection that is used to parse the command line and to display the help message.
+     * 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
      */
@@ -227,7 +249,7 @@ public final class CliParser {
 
         final Option excludes = Option.builder().argName("pattern").hasArg().longOpt(ARGUMENT.EXCLUDE)
                 .desc("Specify and exclusion pattern. This option can be specified multiple times"
-                        + " and it accepts Ant style excludsions.")
+                        + " and it accepts Ant style exclusions.")
                 .build();
 
         final Option props = Option.builder(ARGUMENT.PROP_SHORT).argName("file").hasArg().longOpt(ARGUMENT.PROP)
@@ -240,7 +262,7 @@ public final class CliParser {
                 .build();
 
         final Option outputFormat = Option.builder(ARGUMENT.OUTPUT_FORMAT_SHORT).argName("format").hasArg().longOpt(ARGUMENT.OUTPUT_FORMAT)
-                .desc("The output format to write to (XML, HTML, VULN, ALL). The default is HTML.")
+                .desc("The output format to write to (XML, JSON, HTML, VULN, ALL). The default is HTML.")
                 .build();
 
         final Option verboseLog = Option.builder(ARGUMENT.VERBOSE_LOG_SHORT).argName("file").hasArg().longOpt(ARGUMENT.VERBOSE_LOG)
@@ -255,6 +277,23 @@ public final class CliParser {
                 .desc("The file path to the suppression XML file.")
                 .build();
 
+        final Option hintsFile = Option.builder().argName("file").hasArg().longOpt(ARGUMENT.HINTS_FILE)
+                .desc("The file path to the hints XML file.")
+                .build();
+
+        final Option cveValidForHours = Option.builder().argName("hours").hasArg().longOpt(ARGUMENT.CVE_VALID_FOR_HOURS)
+                .desc("The number of hours to wait before checking for new updates from the NVD.")
+                .build();
+
+        final Option experimentalEnabled = Option.builder().longOpt(ARGUMENT.EXPERIMENTAL)
+                .desc("Enables the experimental analyzers.")
+                .build();
+
+        final Option failOnCVSS = Option.builder().argName("score").hasArg().longOpt(ARGUMENT.FAIL_ON_CVSS)
+                .desc("Specifies if the build should be failed if a CVSS score above a specified level is identified. "
+                        + "The default is 11; since the CVSS scores are 0-10, by default the build will never fail.")
+                .build();
+
         //This is an option group because it can be specified more then once.
         final OptionGroup og = new OptionGroup();
         og.addOption(path);
@@ -274,12 +313,17 @@ public final class CliParser {
                 .addOption(symLinkDepth)
                 .addOption(props)
                 .addOption(verboseLog)
-                .addOption(suppressionFile);
+                .addOption(suppressionFile)
+                .addOption(hintsFile)
+                .addOption(cveValidForHours)
+                .addOption(experimentalEnabled)
+                .addOption(failOnCVSS);
     }
 
     /**
-     * Adds the advanced command line options to the given options collection. These are split out for purposes of being able to
-     * display two different help messages.
+     * Adds the advanced command line options to the given options collection.
+     * These are split out for purposes of being able to display two different
+     * help messages.
      *
      * @param options a collection of command line arguments
      * @throws IllegalArgumentException thrown if there is an exception
@@ -327,6 +371,10 @@ public final class CliParser {
                 .desc("The path to Mono for .NET Assembly analysis on non-windows systems.")
                 .build();
 
+        final Option pathToBundleAudit = Option.builder().argName("path").hasArg()
+                .longOpt(ARGUMENT.PATH_TO_BUNDLE_AUDIT)
+                .desc("The path to bundle-audit for Gem bundle analysis.").build();
+
         final Option connectionTimeout = Option.builder(ARGUMENT.CONNECTION_TIMEOUT_SHORT).argName("timeout").hasArg()
                 .longOpt(ARGUMENT.CONNECTION_TIMEOUT).desc("The connection timeout (in milliseconds) to use when downloading resources.")
                 .build();
@@ -389,6 +437,11 @@ public final class CliParser {
         final Option disableCmakeAnalyzer = Option.builder().longOpt(ARGUMENT.DISABLE_CMAKE)
                 .desc("Disable the Cmake Analyzer.").build();
 
+        final Option cocoapodsAnalyzerEnabled = Option.builder().longOpt(ARGUMENT.DISABLE_COCOAPODS)
+                .desc("Disable the CocoaPods Analyzer.").build();
+        final Option swiftPackageManagerAnalyzerEnabled = Option.builder().longOpt(ARGUMENT.DISABLE_SWIFT)
+                .desc("Disable the swift package Analyzer.").build();
+
         final Option disableCentralAnalyzer = Option.builder().longOpt(ARGUMENT.DISABLE_CENTRAL)
                 .desc("Disable the Central Analyzer. If this analyzer is disabled it is likely you also want to disable "
                         + "the Nexus Analyzer.").build();
@@ -419,29 +472,37 @@ public final class CliParser {
                 .addOption(disableJarAnalyzer)
                 .addOption(disableArchiveAnalyzer)
                 .addOption(disableAssemblyAnalyzer)
+                .addOption(pathToBundleAudit)
                 .addOption(disablePythonDistributionAnalyzer)
                 .addOption(disableCmakeAnalyzer)
                 .addOption(disablePythonPackageAnalyzer)
                 .addOption(Option.builder().longOpt(ARGUMENT.DISABLE_RUBYGEMS)
                         .desc("Disable the Ruby Gemspec Analyzer.").build())
+                .addOption(Option.builder().longOpt(ARGUMENT.DISABLE_BUNDLE_AUDIT)
+                        .desc("Disable the Ruby Bundler-Audit Analyzer.").build())
                 .addOption(disableAutoconfAnalyzer)
                 .addOption(disableComposerAnalyzer)
                 .addOption(disableOpenSSLAnalyzer)
                 .addOption(disableNuspecAnalyzer)
                 .addOption(disableCentralAnalyzer)
                 .addOption(disableNexusAnalyzer)
+                .addOption(cocoapodsAnalyzerEnabled)
+                .addOption(swiftPackageManagerAnalyzerEnabled)
                 .addOption(Option.builder().longOpt(ARGUMENT.DISABLE_NODE_JS)
                         .desc("Disable the Node.js Package Analyzer.").build())
                 .addOption(nexusUrl)
                 .addOption(nexusUsesProxy)
                 .addOption(additionalZipExtensions)
                 .addOption(pathToMono)
+                .addOption(pathToBundleAudit)
                 .addOption(purge);
     }
 
     /**
-     * Adds the deprecated command line options to the given options collection. These are split out for purposes of not including
-     * them in the help message. We need to add the deprecated options so as not to break existing scripts.
+     * Adds the deprecated command line options to the given options collection.
+     * These are split out for purposes of not including them in the help
+     * message. We need to add the deprecated options so as not to break
+     * existing scripts.
      *
      * @param options a collection of command line arguments
      * @throws IllegalArgumentException thrown if there is an exception
@@ -488,7 +549,8 @@ public final class CliParser {
     }
 
     /**
-     * Returns the symbolic link depth (how deeply symbolic links will be followed).
+     * Returns the symbolic link depth (how deeply symbolic links will be
+     * followed).
      *
      * @return the symbolic link depth
      */
@@ -505,136 +567,210 @@ public final class CliParser {
         return value;
     }
 
+    /**
+     * Utility method to determine if one of the disable options has been set.
+     * If not set, this method will check the currently configured settings for
+     * the current value to return.
+     *
+     * Example given `--disableArchive` on the command line would cause this
+     * method to return true for the disable archive setting.
+     *
+     * @param argument the command line argument
+     * @param setting the corresponding settings key
+     * @return true if the disable option was set, if not set the currently
+     * configured value will be returned
+     */
+    private boolean hasDisableOption(String argument, String setting) {
+        if (line == null || !line.hasOption(argument)) {
+            try {
+                return !Settings.getBoolean(setting);
+            } catch (InvalidSettingException ise) {
+                LOGGER.warn("Invalid property setting '{}' defaulting to false", setting);
+                return false;
+            }
+        } else {
+            return true;
+        }
+    }
+
     /**
      * Returns true if the disableJar command line argument was specified.
      *
-     * @return true if the disableJar command line argument was specified; otherwise false
+     * @return true if the disableJar command line argument was specified;
+     * otherwise false
      */
     public boolean isJarDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_JAR);
+        return hasDisableOption(ARGUMENT.DISABLE_JAR, Settings.KEYS.ANALYZER_JAR_ENABLED);
     }
 
     /**
      * Returns true if the disableArchive command line argument was specified.
      *
-     * @return true if the disableArchive command line argument was specified; otherwise false
+     * @return true if the disableArchive command line argument was specified;
+     * otherwise false
      */
     public boolean isArchiveDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_ARCHIVE);
+        return hasDisableOption(ARGUMENT.DISABLE_ARCHIVE, Settings.KEYS.ANALYZER_ARCHIVE_ENABLED);
     }
 
     /**
      * Returns true if the disableNuspec command line argument was specified.
      *
-     * @return true if the disableNuspec command line argument was specified; otherwise false
+     * @return true if the disableNuspec command line argument was specified;
+     * otherwise false
      */
     public boolean isNuspecDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_NUSPEC);
+        return hasDisableOption(ARGUMENT.DISABLE_NUSPEC, Settings.KEYS.ANALYZER_NUSPEC_ENABLED);
     }
 
     /**
      * Returns true if the disableAssembly command line argument was specified.
      *
-     * @return true if the disableAssembly command line argument was specified; otherwise false
+     * @return true if the disableAssembly command line argument was specified;
+     * otherwise false
      */
     public boolean isAssemblyDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_ASSEMBLY);
+        return hasDisableOption(ARGUMENT.DISABLE_ASSEMBLY, Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED);
+    }
+
+    /**
+     * Returns true if the disableBundleAudit command line argument was
+     * specified.
+     *
+     * @return true if the disableBundleAudit command line argument was
+     * specified; otherwise false
+     */
+    public boolean isBundleAuditDisabled() {
+        return hasDisableOption(ARGUMENT.DISABLE_BUNDLE_AUDIT, Settings.KEYS.ANALYZER_BUNDLE_AUDIT_ENABLED);
     }
 
     /**
      * Returns true if the disablePyDist command line argument was specified.
      *
-     * @return true if the disablePyDist command line argument was specified; otherwise false
+     * @return true if the disablePyDist command line argument was specified;
+     * otherwise false
      */
     public boolean isPythonDistributionDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_PY_DIST);
+        return hasDisableOption(ARGUMENT.DISABLE_PY_DIST, Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED);
     }
 
     /**
      * Returns true if the disablePyPkg command line argument was specified.
      *
-     * @return true if the disablePyPkg command line argument was specified; otherwise false
+     * @return true if the disablePyPkg command line argument was specified;
+     * otherwise false
      */
     public boolean isPythonPackageDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_PY_PKG);
+        return hasDisableOption(ARGUMENT.DISABLE_PY_PKG, Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED);
     }
 
     /**
      * Returns whether the Ruby gemspec analyzer is disabled.
      *
-     * @return true if the {@link ARGUMENT#DISABLE_RUBYGEMS} command line argument was specified; otherwise false
+     * @return true if the {@link ARGUMENT#DISABLE_RUBYGEMS} command line
+     * argument was specified; otherwise false
      */
     public boolean isRubyGemspecDisabled() {
-        return (null != line) && line.hasOption(ARGUMENT.DISABLE_RUBYGEMS);
+        return hasDisableOption(ARGUMENT.DISABLE_RUBYGEMS, Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED);
     }
 
     /**
      * Returns true if the disableCmake command line argument was specified.
      *
-     * @return true if the disableCmake command line argument was specified; otherwise false
+     * @return true if the disableCmake command line argument was specified;
+     * otherwise false
      */
     public boolean isCmakeDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_CMAKE);
+        return hasDisableOption(ARGUMENT.DISABLE_CMAKE, Settings.KEYS.ANALYZER_CMAKE_ENABLED);
     }
 
     /**
      * Returns true if the disableAutoconf command line argument was specified.
      *
-     * @return true if the disableAutoconf command line argument was specified; otherwise false
+     * @return true if the disableAutoconf command line argument was specified;
+     * otherwise false
      */
     public boolean isAutoconfDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_AUTOCONF);
+        return hasDisableOption(ARGUMENT.DISABLE_AUTOCONF, Settings.KEYS.ANALYZER_AUTOCONF_ENABLED);
     }
 
     /**
      * Returns true if the disableComposer command line argument was specified.
      *
-     * @return true if the disableComposer command line argument was specified; otherwise false
+     * @return true if the disableComposer command line argument was specified;
+     * otherwise false
      */
     public boolean isComposerDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_COMPOSER);
+        return hasDisableOption(ARGUMENT.DISABLE_COMPOSER, Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED);
     }
 
     /**
      * Returns true if the disableNexus command line argument was specified.
      *
-     * @return true if the disableNexus command line argument was specified; otherwise false
+     * @return true if the disableNexus command line argument was specified;
+     * otherwise false
      */
     public boolean isNexusDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_NEXUS);
+        return hasDisableOption(ARGUMENT.DISABLE_NEXUS, Settings.KEYS.ANALYZER_NEXUS_ENABLED);
     }
 
     /**
      * Returns true if the disableOpenSSL command line argument was specified.
      *
-     * @return true if the disableOpenSSL command line argument was specified; otherwise false
+     * @return true if the disableOpenSSL command line argument was specified;
+     * otherwise false
      */
     public boolean isOpenSSLDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_OPENSSL);
+        return hasDisableOption(ARGUMENT.DISABLE_OPENSSL, Settings.KEYS.ANALYZER_OPENSSL_ENABLED);
     }
 
     /**
      * Returns true if the disableNodeJS command line argument was specified.
      *
-     * @return true if the disableNodeJS command line argument was specified; otherwise false
+     * @return true if the disableNodeJS command line argument was specified;
+     * otherwise false
      */
     public boolean isNodeJsDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_NODE_JS);
+        return hasDisableOption(ARGUMENT.DISABLE_NODE_JS, Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED);
+    }
+
+    /**
+     * Returns true if the disableCocoapodsAnalyzer command line argument was
+     * specified.
+     *
+     * @return true if the disableCocoapodsAnalyzer command line argument was
+     * specified; otherwise false
+     */
+    public boolean isCocoapodsAnalyzerDisabled() {
+        return hasDisableOption(ARGUMENT.DISABLE_COCOAPODS, Settings.KEYS.ANALYZER_COCOAPODS_ENABLED);
+    }
+
+    /**
+     * Returns true if the disableSwiftPackageManagerAnalyzer command line
+     * argument was specified.
+     *
+     * @return true if the disableSwiftPackageManagerAnalyzer command line
+     * argument was specified; otherwise false
+     */
+    public boolean isSwiftPackageAnalyzerDisabled() {
+        return hasDisableOption(ARGUMENT.DISABLE_SWIFT, Settings.KEYS.ANALYZER_SWIFT_PACKAGE_MANAGER_ENABLED);
     }
 
     /**
      * Returns true if the disableCentral command line argument was specified.
      *
-     * @return true if the disableCentral command line argument was specified; otherwise false
+     * @return true if the disableCentral command line argument was specified;
+     * otherwise false
      */
     public boolean isCentralDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_CENTRAL);
+        return hasDisableOption(ARGUMENT.DISABLE_CENTRAL, Settings.KEYS.ANALYZER_CENTRAL_ENABLED);
     }
 
     /**
      * Returns the url to the nexus server if one was specified.
      *
-     * @return the url to the nexus server; if none was specified this will return null;
+     * @return the url to the nexus server; if none was specified this will
+     * return null;
      */
     public String getNexusUrl() {
         if (line == null || !line.hasOption(ARGUMENT.NEXUS_URL)) {
@@ -645,16 +781,18 @@ public final class CliParser {
     }
 
     /**
-     * Returns true if the Nexus Analyzer should use the configured proxy to connect to Nexus; otherwise false is returned.
+     * Returns true if the Nexus Analyzer should use the configured proxy to
+     * connect to Nexus; otherwise false is returned.
      *
-     * @return true if the Nexus Analyzer should use the configured proxy to connect to Nexus; otherwise false
+     * @return true if the Nexus Analyzer should use the configured proxy to
+     * connect to Nexus; otherwise false
      */
     public boolean isNexusUsesProxy() {
         // If they didn't specify whether Nexus needs to use the proxy, we should
         // still honor the property if it's set.
         if (line == null || !line.hasOption(ARGUMENT.NEXUS_USES_PROXY)) {
             try {
-                return Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY);
+                return Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY);
             } catch (InvalidSettingException ise) {
                 return true;
             }
@@ -687,7 +825,8 @@ public final class CliParser {
     }
 
     /**
-     * Retrieves the file command line parameter(s) specified for the 'scan' argument.
+     * Retrieves the file command line parameter(s) specified for the 'scan'
+     * argument.
      *
      * @return the file paths specified on the command line for scan
      */
@@ -696,7 +835,8 @@ public final class CliParser {
     }
 
     /**
-     * Retrieves the list of excluded file patterns specified by the 'exclude' argument.
+     * Retrieves the list of excluded file patterns specified by the 'exclude'
+     * argument.
      *
      * @return the excluded file patterns
      */
@@ -705,7 +845,8 @@ public final class CliParser {
     }
 
     /**
-     * Returns the directory to write the reports to specified on the command line.
+     * Returns the directory to write the reports to specified on the command
+     * line.
      *
      * @return the path to the reports directory.
      */
@@ -714,7 +855,8 @@ public final class CliParser {
     }
 
     /**
-     * Returns the path to Mono for .NET Assembly analysis on non-windows systems.
+     * Returns the path to Mono for .NET Assembly analysis on non-windows
+     * systems.
      *
      * @return the path to Mono
      */
@@ -723,7 +865,17 @@ public final class CliParser {
     }
 
     /**
-     * Returns the output format specified on the command line. Defaults to HTML if no format was specified.
+     * Returns the path to bundle-audit for Ruby bundle analysis.
+     *
+     * @return the path to Mono
+     */
+    public String getPathToBundleAudit() {
+        return line.getOptionValue(ARGUMENT.PATH_TO_BUNDLE_AUDIT);
+    }
+
+    /**
+     * Returns the output format specified on the command line. Defaults to HTML
+     * if no format was specified.
      *
      * @return the output format name.
      */
@@ -876,6 +1028,15 @@ public final class CliParser {
         return line.getOptionValue(ARGUMENT.SUPPRESSION_FILE);
     }
 
+    /**
+     * Returns the path to the hints file.
+     *
+     * @return the path to the hints file
+     */
+    public String getHintsFile() {
+        return line.getOptionValue(ARGUMENT.HINTS_FILE);
+    }
+
     /**
      * <p>
      * Prints the manifest information to standard output.</p>
@@ -884,24 +1045,27 @@ public final class CliParser {
      */
     public void printVersionInfo() {
         final String version = String.format("%s version %s",
-                Settings.getString(Settings.KEYS.APPLICATION_VAME, "dependency-check"),
+                Settings.getString(Settings.KEYS.APPLICATION_NAME, "dependency-check"),
                 Settings.getString(Settings.KEYS.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.
+     * Checks if the auto update feature has been disabled. If it has been
+     * disabled via the command line this will return false.
      *
-     * @return <code>true</code> if auto-update is allowed; otherwise <code>false</code>
+     * @return <code>true</code> if auto-update is allowed; otherwise
+     * <code>null</code>
      */
-    public boolean isAutoUpdate() {
-        return line != null && !line.hasOption(ARGUMENT.DISABLE_AUTO_UPDATE);
+    public Boolean isAutoUpdate() {
+        return (line != null && line.hasOption(ARGUMENT.DISABLE_AUTO_UPDATE)) ? false : null;
     }
 
     /**
      * Checks if the update only flag has been set.
      *
-     * @return <code>true</code> if the update only flag has been set; otherwise <code>false</code>.
+     * @return <code>true</code> if the update only flag has been set; otherwise
+     * <code>false</code>.
      */
     public boolean isUpdateOnly() {
         return line != null && line.hasOption(ARGUMENT.UPDATE_ONLY);
@@ -910,14 +1074,16 @@ public final class CliParser {
     /**
      * Checks if the purge NVD flag has been set.
      *
-     * @return <code>true</code> if the purge nvd flag has been set; otherwise <code>false</code>.
+     * @return <code>true</code> if the purge nvd flag has been set; otherwise
+     * <code>false</code>.
      */
     public boolean isPurge() {
         return line != null && line.hasOption(ARGUMENT.PURGE_NVD);
     }
 
     /**
-     * Returns the database driver name if specified; otherwise null is returned.
+     * Returns the database driver name if specified; otherwise null is
+     * returned.
      *
      * @return the database driver name if specified; otherwise null is returned
      */
@@ -926,7 +1092,8 @@ public final class CliParser {
     }
 
     /**
-     * Returns the database driver path if specified; otherwise null is returned.
+     * Returns the database driver path if specified; otherwise null is
+     * returned.
      *
      * @return the database driver name if specified; otherwise null is returned
      */
@@ -935,34 +1102,41 @@ public final class CliParser {
     }
 
     /**
-     * Returns the database connection string if specified; otherwise null is returned.
+     * Returns the database connection string if specified; otherwise null is
+     * returned.
      *
-     * @return the database connection string if specified; otherwise null is returned
+     * @return the database connection string if specified; otherwise null is
+     * returned
      */
     public String getConnectionString() {
         return line.getOptionValue(ARGUMENT.CONNECTION_STRING);
     }
 
     /**
-     * Returns the database database user name if specified; otherwise null is returned.
+     * Returns the database database user name if specified; otherwise null is
+     * returned.
      *
-     * @return the database database user name if specified; otherwise null is returned
+     * @return the database database user name if specified; otherwise null is
+     * returned
      */
     public String getDatabaseUser() {
         return line.getOptionValue(ARGUMENT.DB_NAME);
     }
 
     /**
-     * Returns the database database password if specified; otherwise null is returned.
+     * Returns the database database password if specified; otherwise null is
+     * returned.
      *
-     * @return the database database password if specified; otherwise null is returned
+     * @return the database database password if specified; otherwise null is
+     * returned
      */
     public String getDatabasePassword() {
         return line.getOptionValue(ARGUMENT.DB_PASSWORD);
     }
 
     /**
-     * Returns the additional Extensions if specified; otherwise null is returned.
+     * Returns the additional Extensions if specified; otherwise null is
+     * returned.
      *
      * @return the additional Extensions; otherwise null is returned
      */
@@ -971,7 +1145,49 @@ public final class CliParser {
     }
 
     /**
-     * A collection of static final strings that represent the possible command line arguments.
+     * Get the value of cveValidForHours.
+     *
+     * @return the value of cveValidForHours
+     */
+    public Integer getCveValidForHours() {
+        final String v = line.getOptionValue(ARGUMENT.CVE_VALID_FOR_HOURS);
+        if (v != null) {
+            return Integer.parseInt(v);
+        }
+        return null;
+    }
+
+    /**
+     * Returns true if the experimental analyzers are enabled.
+     *
+     * @return true if the experimental analyzers are enabled; otherwise null
+     */
+    public Boolean isExperimentalEnabled() {
+        return (line != null && line.hasOption(ARGUMENT.EXPERIMENTAL)) ? true : null;
+    }
+
+    /**
+     * Returns the CVSS value to fail on.
+     *
+     * @return 11 if nothing is set. Otherwise it returns the int passed from
+     * the command line arg
+     */
+    public int getFailOnCVSS() {
+        if (line.hasOption(ARGUMENT.FAIL_ON_CVSS)) {
+            final String value = line.getOptionValue(ARGUMENT.FAIL_ON_CVSS);
+            try {
+                return Integer.parseInt(value);
+            } catch (NumberFormatException nfe) {
+                return 11;
+            }
+        } else {
+            return 11;
+        }
+    }
+
+    /**
+     * A collection of static final strings that represent the possible command
+     * line arguments.
      */
     public static class ARGUMENT {
 
@@ -984,50 +1200,61 @@ public final class CliParser {
          */
         public static final String SCAN_SHORT = "s";
         /**
-         * The long CLI argument name specifying that the CPE/CVE/etc. data should not be automatically updated.
+         * 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.
+         * 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 that only the update phase should be executed; no scan should be run.
+         * The long CLI argument name specifying that only the update phase
+         * should be executed; no scan should be run.
          */
         public static final String UPDATE_ONLY = "updateonly";
         /**
-         * The long CLI argument name specifying that only the update phase should be executed; no scan should be run.
+         * The long CLI argument name specifying that only the update phase
+         * should be executed; no scan should be run.
          */
         public static final String PURGE_NVD = "purge";
         /**
-         * The long CLI argument name specifying the directory to write the reports to.
+         * 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.
+         * 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.
+         * 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.
+         * 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 project to be scanned.
+         * The long CLI argument name specifying the name of the project to be
+         * scanned.
          */
         public static final String PROJECT = "project";
         /**
-         * The long CLI argument name specifying the name of the application to be scanned.
+         * The long CLI argument name specifying the name of the application to
+         * be scanned.
          *
          * @deprecated project should be used instead
          */
         @Deprecated
         public static final String APP_NAME = "app";
         /**
-         * The short CLI argument name specifying the name of the application to be scanned.
+         * The short CLI argument name specifying the name of the application to
+         * be scanned.
          *
          * @deprecated project should be used instead
          */
@@ -1085,11 +1312,13 @@ public final class CliParser {
          */
         public static final String CONNECTION_TIMEOUT = "connectiontimeout";
         /**
-         * The short CLI argument name for setting the location of an additional properties file.
+         * 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.
+         * The CLI argument name for setting the location of an additional
+         * properties file.
          */
         public static final String PROP = "propertyfile";
         /**
@@ -1113,7 +1342,8 @@ public final class CliParser {
          */
         public static final String CVE_BASE_20 = "cveUrl20Base";
         /**
-         * The short CLI argument name for setting the location of the data directory.
+         * The short CLI argument name for setting the location of the data
+         * directory.
          */
         public static final String DATA_DIRECTORY_SHORT = "d";
         /**
@@ -1121,18 +1351,30 @@ public final class CliParser {
          */
         public static final String VERBOSE_LOG = "log";
         /**
-         * The short CLI argument name for setting the location of the data directory.
+         * The short CLI argument name for setting the location of the data
+         * directory.
          */
         public static final String VERBOSE_LOG_SHORT = "l";
 
         /**
-         * The CLI argument name for setting the depth of symbolic links that will be followed.
+         * The CLI argument name for setting the depth of symbolic links that
+         * will be followed.
          */
         public static final String SYM_LINK_DEPTH = "symLink";
         /**
-         * The CLI argument name for setting the location of the suppression file.
+         * The CLI argument name for setting the location of the suppression
+         * file.
          */
         public static final String SUPPRESSION_FILE = "suppression";
+        /**
+         * The CLI argument name for setting the location of the hint file.
+         */
+        public static final String HINTS_FILE = "hints";
+        /**
+         * The CLI argument name for setting the number of hours to wait before
+         * checking for new updates from the NVD.
+         */
+        public static final String CVE_VALID_FOR_HOURS = "cveValidForHours";
         /**
          * Disables the Jar Analyzer.
          */
@@ -1165,10 +1407,22 @@ public final class CliParser {
          * Disables the Cmake Analyzer.
          */
         public static final String DISABLE_CMAKE = "disableCmake";
+        /**
+         * Disables the cocoapods analyzer.
+         */
+        public static final String DISABLE_COCOAPODS = "disableCocoapodsAnalyzer";
+        /**
+         * Disables the swift package manager analyzer.
+         */
+        public static final String DISABLE_SWIFT = "disableSwiftPackageManagerAnalyzer";
         /**
          * Disables the Assembly Analyzer.
          */
         public static final String DISABLE_ASSEMBLY = "disableAssembly";
+        /**
+         * Disables the Ruby Bundler Audit Analyzer.
+         */
+        public static final String DISABLE_BUNDLE_AUDIT = "disableBundleAudit";
         /**
          * Disables the Nuspec Analyzer.
          */
@@ -1194,7 +1448,8 @@ public final class CliParser {
          */
         public static final String NEXUS_URL = "nexus";
         /**
-         * Whether or not the defined proxy should be used when connecting to Nexus.
+         * Whether or not the defined proxy should be used when connecting to
+         * Nexus.
          */
         public static final String NEXUS_USES_PROXY = "nexusUsesProxy";
         /**
@@ -1214,11 +1469,13 @@ public final class CliParser {
          */
         public static final String DB_DRIVER = "dbDriverName";
         /**
-         * The CLI argument name for setting the path to the database driver; in case it is not on the class path.
+         * The CLI argument name for setting the path to the database driver; in
+         * case it is not on the class path.
          */
         public static final String DB_DRIVER_PATH = "dbDriverPath";
         /**
-         * The CLI argument name for setting the path to mono for .NET Assembly analysis on non-windows systems.
+         * The CLI argument name for setting the path to mono for .NET Assembly
+         * analysis on non-windows systems.
          */
         public static final String PATH_TO_MONO = "mono";
         /**
@@ -1229,5 +1486,18 @@ public final class CliParser {
          * Exclude path argument.
          */
         public static final String EXCLUDE = "exclude";
+        /**
+         * The CLI argument name for setting the path to bundle-audit for Ruby
+         * bundle analysis.
+         */
+        public static final String PATH_TO_BUNDLE_AUDIT = "bundleAudit";
+        /**
+         * The CLI argument to enable the experimental analyzers.
+         */
+        private static final String EXPERIMENTAL = "enableExperimental";
+        /**
+         * The CLI argument to enable the experimental analyzers.
+         */
+        private static final String FAIL_ON_CVSS = "failOnCVSS";
     }
 }

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

@@ -22,7 +22,7 @@ package org.owasp.dependencycheck;
  *
  * @author Jeremy Long
  */
-class InvalidScanPathException extends Exception {
+public class InvalidScanPathException extends Exception {
 
     /**
      * The serial version UID for serialization.

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

@@ -4,41 +4,47 @@ 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
+-------|------------------------|-----------------|-------------|------------
+       | \-\-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, CSV, JSON, VULN, ALL). The default is HTML. | Required
+       | \-\-failOnCvss         | \<score\>       | If the score set between 0 and 10 the exit code from dependency-check will indicate if a vulnerability with a CVSS score equal to or higher was identified. | Optional
+ \-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
+       | \-\-enableExperimental |                 | Enable the [experimental analyzers](../analyzers/index.html). If not set the analyzers marked as experimental below will not be loaded or used. | 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                                                     | http://nvd.nist.gov/download/nvdcve-modified.xml
-       | \-\-cveUrl20Modified  | \<url\>         | URL for the modified CVE 2.0                                                     | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
-       | \-\-cveUrl12Base      | \<url\>         | 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      | \<url\>         | 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
+       | \-\-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
-       | \-\-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
+       | \-\-disablePyDist     |                 | Sets whether the [experimental](../analyzers/index.html) Python Distribution Analyzer will be used.                      | false
+       | \-\-disablePyPkg      |                 | Sets whether the [experimental](../analyzers/index.html) Python Package Analyzer will be used.                           | false
+       | \-\-disableNodeJS     |                 | Sets whether the [experimental](../analyzers/index.html) Node.js Package Analyzer will be used.                          | false
+       | \-\-disableRubygems   |                 | Sets whether the [experimental](../analyzers/index.html) Ruby Gemspec Analyzer will be used.                             | false
+       | \-\-disableBundleAudit |                | Sets whether the [experimental](../analyzers/index.html) Ruby Bundler Audit Analyzer will be used.                       | false
+       | \-\-disableCocoapodsAnalyzer |          | Sets whether the [experimental](../analyzers/index.html) Cocoapods Analyzer will be used.                                | false
+       | \-\-disableSwiftPackageManagerAnalyzer | | Sets whether the [experimental](../analyzers/index.html) Swift Package Manager Analyzer will be used.                   | false
+       | \-\-disableAutoconf   |                 | Sets whether the [experimental](../analyzers/index.html) Autoconf Analyzer will be used.                                 | false
+       | \-\-disableOpenSSL    |                 | Sets whether the OpenSSL Analyzer will be used.                                                                          | false
+       | \-\-disableCmake      |                 | Sets whether the [experimental](../analyzers/index.html) 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
+       | \-\-disableJar        |                 | Sets whether the Jar Analyzer will be disabled.                                                                          | false
+       | \-\-disableComposer   |                 | Sets whether the [experimental](../analyzers/index.html) 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;
@@ -46,7 +52,8 @@ Short  | Argument&nbsp;Name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; | Paramete
        | \-\-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;
-       | \-\-proxyserver       | \<server\>      | The proxy server to use when downloading resources.                              | &nbsp;
+       | \-\-bundleAudit       |                 | The path to the bundle-audit executable. | &nbsp;
+       | \-\-proxyserver       | \<server\>      | The proxy server to use when downloading resources; see the [proxy configuration](../data/proxy.html) page for more information. | &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;

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

@@ -9,10 +9,7 @@ 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
+path environment variable.
 
 #set( $H = '#' )
 
@@ -25,10 +22,10 @@ your homebrew installation.
 To scan a folder on the system you can run:
 
 $H$H$H Windows
-    dependency-check.bat --app "My App Name" --scan "c:\java\application\lib"
+    dependency-check.bat --project "My App Name" --scan "c:\java\application\lib"
 
 $H$H$H *nix
-    dependency-check.sh --app "My App Name" --scan "/java/application/lib"
+    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:
 

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

@@ -13,16 +13,21 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *
- * Copyright (c) 2015 The OWASP Foundatio. All Rights Reserved.
+ * Copyright (c) 2017 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 java.io.File;
+import java.io.FileNotFoundException;
+import java.net.URISyntaxException;
+import java.util.HashMap;
+import java.util.Map;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.UnrecognizedOptionException;
 import org.junit.Test;
 import static org.junit.Assert.*;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  *
@@ -30,25 +35,6 @@ import static org.junit.Assert.*;
  */
 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.
      */
@@ -59,17 +45,83 @@ public class AppTest {
         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();
+        file = "../some/skip/../path/file.txt";
         String expResult = "/some/path/file.txt";
-        String result = instance.ensureCanonicalPath(file);
+        result = instance.ensureCanonicalPath(file);
         assertTrue("result=" + result, result.endsWith(expResult));
     }
+
+    @Test(expected = UnrecognizedOptionException.class)
+    public void testPopulateSettingsException() throws FileNotFoundException, ParseException, InvalidSettingException, URISyntaxException {
+        String[] args = {"-invalidPROPERTY"};
+        assertTrue(testBooleanProperties(args, null));
+    }
+
+    @Test
+    public void testPopulateSettings() throws FileNotFoundException, ParseException, InvalidSettingException, URISyntaxException {
+        File prop = new File(this.getClass().getClassLoader().getResource("sample.properties").toURI().getPath());
+        String[] args = {"-P", prop.getAbsolutePath()};
+        Map<String, Boolean> expected = new HashMap<>();
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.FALSE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.TRUE);
+        
+        assertTrue(testBooleanProperties(args, expected));
+
+        String[] args2 = {"-n"};
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.FALSE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.TRUE);
+        assertTrue(testBooleanProperties(args2, expected));
+
+        String[] args3 = {"-h"};
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.TRUE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.TRUE);
+        assertTrue(testBooleanProperties(args3, expected));
+
+        String[] args4 = {"--disableArchive"};
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.TRUE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.FALSE);
+        assertTrue(testBooleanProperties(args4, expected));
+
+        String[] args5 = {"-P", prop.getAbsolutePath(), "--disableArchive"};
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.FALSE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.FALSE);
+        assertTrue(testBooleanProperties(args5, expected));
+
+        prop = new File(this.getClass().getClassLoader().getResource("sample2.properties").toURI().getPath());
+        String[] args6 = {"-P", prop.getAbsolutePath(), "--disableArchive"};
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.TRUE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.FALSE);
+        assertTrue(testBooleanProperties(args6, expected));
+
+        String[] args7 = {"-P", prop.getAbsolutePath(), "--noupdate"};
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.FALSE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.FALSE);
+        assertTrue(testBooleanProperties(args7, expected));
+
+        String[] args8 = {"-P", prop.getAbsolutePath(), "--noupdate", "--disableArchive"};
+        expected.put(Settings.KEYS.AUTO_UPDATE, Boolean.FALSE);
+        expected.put(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, Boolean.FALSE);
+        assertTrue(testBooleanProperties(args8, expected));
+
+        
+    }
+
+    private boolean testBooleanProperties(String[] args, Map<String, Boolean> expected) throws URISyntaxException, FileNotFoundException, ParseException, InvalidSettingException {
+        Settings.initialize();
+        try {
+            final CliParser cli = new CliParser();
+            cli.parse(args);
+            App instance = new App();
+            instance.populateSettings(cli);
+            boolean results = true;
+            for (Map.Entry<String, Boolean> entry : expected.entrySet()) {
+                results &= Settings.getBoolean(entry.getKey()) == entry.getValue();
+            }
+
+            return results;
+        } finally {
+            Settings.cleanup();
+        }
+    }
 }

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

@@ -17,17 +17,14 @@
  */
 package org.owasp.dependencycheck;
 
-import org.owasp.dependencycheck.CliParser;
 import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.PrintStream;
 import org.apache.commons.cli.ParseException;
-import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Assert;
-import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.owasp.dependencycheck.utils.Settings;
@@ -48,14 +45,6 @@ public class CliParserTest {
         Settings.cleanup(true);
     }
 
-    @Before
-    public void setUp() throws Exception {
-    }
-
-    @After
-    public void tearDown() throws Exception {
-    }
-
     /**
      * Test of parse method, of class CliParser.
      *
@@ -115,6 +104,63 @@ public class CliParserTest {
 
     }
 
+    /**
+     * Test of parse method with failOnCVSS without an argument
+     *
+     * @throws Exception thrown when an exception occurs.
+     */
+    @Test
+    public void testParse_failOnCVSSNoArg() throws Exception {
+
+        String[] args = {"--failOnCVSS"};
+
+        CliParser instance = new CliParser();
+        try {
+            instance.parse(args);
+        } catch (ParseException ex) {
+            Assert.assertTrue(ex.getMessage().contains("Missing argument"));
+        }
+        Assert.assertFalse(instance.isGetVersion());
+        Assert.assertFalse(instance.isGetHelp());
+        Assert.assertFalse(instance.isRunScan());
+    }
+
+    /**
+     * Test of parse method with failOnCVSS invalid argument. It should default to 11
+     *
+     * @throws Exception thrown when an exception occurs.
+     */
+    @Test
+    public void testParse_failOnCVSSInvalidArgument() throws Exception {
+
+        String[] args = {"--failOnCVSS","bad"};
+
+        CliParser instance = new CliParser();
+        instance.parse(args);
+        Assert.assertEquals("Default should be 11", 11, instance.getFailOnCVSS());
+        Assert.assertFalse(instance.isGetVersion());
+        Assert.assertFalse(instance.isGetHelp());
+        Assert.assertFalse(instance.isRunScan());
+    }
+
+    /**
+     * Test of parse method with failOnCVSS invalid argument. It should default to 11
+     *
+     * @throws Exception thrown when an exception occurs.
+     */
+    @Test
+    public void testParse_failOnCVSSValidArgument() throws Exception {
+
+        String[] args = {"--failOnCVSS","6"};
+
+        CliParser instance = new CliParser();
+        instance.parse(args);
+        Assert.assertEquals(6, instance.getFailOnCVSS());
+        Assert.assertFalse(instance.isGetVersion());
+        Assert.assertFalse(instance.isGetHelp());
+        Assert.assertFalse(instance.isRunScan());
+    }
+
     /**
      * Test of parse method with jar and cpe args, of class CliParser.
      *
@@ -196,7 +242,7 @@ public class CliParserTest {
      */
     @Test
     public void testParse_scan_withFileExists() throws Exception {
-        File path = new File(this.getClass().getClassLoader().getResource("checkSumTest.file").getPath());
+        File path = new File(this.getClass().getClassLoader().getResource("checkSumTest.file").toURI().getPath());
         String[] args = {"-scan", path.getCanonicalPath(), "-out", "./", "-app", "test"};
 
         CliParser instance = new CliParser();

dependency-check-cli/src/test/resources/sample.properties

@@ -0,0 +1,33 @@
+autoupdate=false
+
+analyzer.experimental.enabled=false
+analyzer.jar.enabled=true
+analyzer.archive.enabled=true
+analyzer.node.package.enabled=true
+analyzer.composer.lock.enabled=true
+analyzer.python.distribution.enabled=true
+analyzer.python.package.enabled=true
+analyzer.ruby.gemspec.enabled=true
+analyzer.autoconf.enabled=true
+analyzer.cmake.enabled=true
+analyzer.assembly.enabled=true
+analyzer.nuspec.enabled=true
+analyzer.openssl.enabled=true
+analyzer.central.enabled=true
+analyzer.nexus.enabled=false
+analyzer.cocoapods.enabled=true
+analyzer.swift.package.manager.enabled=true
+#whether the nexus analyzer uses the proxy
+analyzer.nexus.proxy=true
+analyzer.cpe.enabled=true
+analyzer.cpesuppression.enabled=true
+analyzer.dependencybundling.enabled=true
+analyzer.dependencymerging.enabled=true
+analyzer.falsepositive.enabled=true
+analyzer.filename.enabled=true
+analyzer.hint.enabled=true
+analyzer.nvdcve.enabled=true
+analyzer.vulnerabilitysuppression.enabled=true
+updater.nvdcve.enabled=true
+updater.versioncheck.enabled=true
+analyzer.versionfilter.enabled=true

dependency-check-cli/src/test/resources/sample2.properties

@@ -0,0 +1,33 @@
+autoupdate=true
+
+analyzer.experimental.enabled=true
+analyzer.jar.enabled=false
+analyzer.archive.enabled=false
+analyzer.node.package.enabled=false
+analyzer.composer.lock.enabled=false
+analyzer.python.distribution.enabled=false
+analyzer.python.package.enabled=false
+analyzer.ruby.gemspec.enabled=false
+analyzer.autoconf.enabled=false
+analyzer.cmake.enabled=false
+analyzer.assembly.enabled=false
+analyzer.nuspec.enabled=false
+analyzer.openssl.enabled=false
+analyzer.central.enabled=false
+analyzer.nexus.enabled=true
+analyzer.cocoapods.enabled=false
+analyzer.swift.package.manager.enabled=false
+#whether the nexus analyzer uses the proxy
+analyzer.nexus.proxy=false
+analyzer.cpe.enabled=false
+analyzer.cpesuppression.enabled=false
+analyzer.dependencybundling.enabled=false
+analyzer.dependencymerging.enabled=false
+analyzer.falsepositive.enabled=false
+analyzer.filename.enabled=false
+analyzer.hint.enabled=false
+analyzer.nvdcve.enabled=false
+analyzer.vulnerabilitysuppression.enabled=false
+updater.nvdcve.enabled=false
+updater.versioncheck.enabled=false
+analyzer.versionfilter.enabled=false

dependency-check-core/pom.xml

@@ -20,7 +20,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.3.1</version>
+        <version>1.4.6-SNAPSHOT</version>
     </parent>
 
     <artifactId>dependency-check-core</artifactId>
@@ -83,9 +83,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             </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>
@@ -124,92 +121,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>cobertura-maven-plugin</artifactId>
-                <configuration>
-                    <instrumentation>
-                        <!--ignoreTrivial>true</ignoreTrivial-->
-                        <ignores>
-                            <ignore>.*\$KEYS\.class</ignore>
-                            <ignore>.*\$Element\.class</ignore>
-                        </ignores>
-                        <excludes>
-                            <exclude>.*\$KEYS\.class</exclude>
-                            <exclude>.*\$Element\.class</exclude>
-                        </excludes>
-                    </instrumentation>
-                    <check>
-                        <branchRate>85</branchRate>
-                        <lineRate>85</lineRate>
-                        <haltOnFailure>false</haltOnFailure>
-                        <totalBranchRate>85</totalBranchRate>
-                        <totalLineRate>85</totalLineRate>
-                        <packageLineRate>85</packageLineRate>
-                        <packageBranchRate>85</packageBranchRate>
-                        <regexes>
-                            <regex>
-                                <pattern>.*\$.*</pattern>
-                                <branchRate>0</branchRate>
-                                <lineRate>0</lineRate>
-                            </regex>
-                            <regex>
-                                <pattern>org.owasp.dependencycheck.data.cpe.Fields</pattern>
-                                <branchRate>0</branchRate>
-                                <lineRate>0</lineRate>
-                            </regex>
-                            <regex>
-                                <pattern>org.owasp.dependencycheck.App</pattern>
-                                <branchRate>0</branchRate>
-                                <lineRate>0</lineRate>
-                            </regex>
-                        </regexes>
-                    </check>
-                </configuration>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>clean</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <configuration>
-                    <systemProperties>
-                        <property>
-                            <name>data.directory</name>
-                            <value>${project.build.directory}/data</value>
-                        </property>
-                        <property>
-                            <name>temp.directory</name>
-                            <value>${project.build.directory}/temp</value>
-                        </property>
-                    </systemProperties>
-                    <excludes>
-                        <exclude>**/*IntegrationTest.java</exclude>
-                        <exclude>**/*MySQLTest.java</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-failsafe-plugin</artifactId>
-                <configuration>
-                    <systemProperties>
-                        <property>
-                            <name>data.directory</name>
-                            <value>${project.build.directory}/data</value>
-                        </property>
-                        <property>
-                            <name>temp.directory</name>
-                            <value>${project.build.directory}/temp</value>
-                        </property>
-                    </systemProperties>
-                </configuration>
-            </plugin>
         </plugins>
     </build>
     <reporting>
@@ -246,7 +157,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 <version>${reporting.pmd-plugin.version}</version>
                 <configuration>
                     <targetJdk>1.6</targetJdk>
-                    <linkXref>true</linkXref>
+                    <linkXRef>true</linkXRef>
                     <sourceEncoding>utf-8</sourceEncoding>
                     <excludes>
                         <exclude>**/generated/*.java</exclude>
@@ -263,6 +174,10 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
     </reporting>
     <dependencies>
         <!-- Note, to stay compatible with Jenkins installations only JARs compiled to 1.6 can be used -->
+        <dependency>
+            <groupId>joda-time</groupId>
+            <artifactId>joda-time</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.google.code.findbugs</groupId>
             <artifactId>annotations</artifactId>
@@ -338,6 +253,10 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <groupId>com.sun.mail</groupId>
             <artifactId>mailapi</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+        </dependency>
         <!-- The following dependencies are only used during testing -->
         <dependency>
             <groupId>org.apache.maven.scm</groupId>
@@ -454,6 +373,21 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <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>
+        <dependency>
+            <groupId>com.thoughtworks.xstream</groupId>
+            <artifactId>xstream</artifactId>
+            <version>1.4.8</version>
+            <scope>test</scope>
+            <optional>true</optional>
+        </dependency>
+
     </dependencies>
     <profiles>
         <profile>
@@ -465,23 +399,14 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             </activation>
             <build>
                 <plugins>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-surefire-plugin</artifactId>
-                        <version>2.18.1</version>
-                        <configuration>
-                            <skip>true</skip>
-                        </configuration>
-                    </plugin>
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-failsafe-plugin</artifactId>
-                        <version>2.18.1</version>
                         <configuration>
                             <systemProperties>
                                 <property>
                                     <name>data.driver_path</name>
-                                    <value>${basedir}/${driver_path}</value>
+                                    <value>${driver_path}</value>
                                 </property>
                                 <property>
                                     <name>data.driver_name</name>
@@ -493,7 +418,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                                 </property>
                             </systemProperties>
                             <includes>
-                                <include>**/*MySQLTest.java</include>
+                                <include>**/*MySqlIT.java</include>
                             </includes>
                         </configuration>
                         <executions>
@@ -509,14 +434,68 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             </build>
         </profile>
         <profile>
-            <!-- The following profile adds additional
-            dependencies that are only used during testing.
-            Additionally, these are only added when using "allTests" to
-            make the build slightly faster in most cases. -->
+            <id>Postgresql-IntegrationTest</id>
+            <activation>
+                <property>
+                    <name>postgresql</name>
+                </property>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>org.postgresql</groupId>
+                    <artifactId>postgresql</artifactId>
+                    <version>9.4-1204-jdbc42</version>
+                </dependency>
+            </dependencies>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-failsafe-plugin</artifactId>
+                        <configuration>
+                            <systemProperties>
+                                <property>
+                                    <name>data.driver_path</name>
+                                    <value>${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>**/*MySqlIT.java</include>
+                            </includes>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <goals>
+                                    <goal>integration-test</goal>
+                                    <goal>verify</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+        <!-- 
+            The following profile adds additional dependencies that are only 
+            used during testing.
+        
+            TODO move the following FP tests to a seperate invoker test in the
+            maven plugin project. Add checks against the XML to validate that
+            these do not report FP.
+        -->
+        <!--profile>
             <id>False Positive Tests</id>
             <activation>
                 <property>
-                    <name>allTests</name>
+                    <name>releaseTesting</name>
                 </property>
             </activation>
             <dependencies>
@@ -527,13 +506,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                     <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>
@@ -604,20 +576,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                     <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>
@@ -668,6 +626,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                     <optional>true</optional>
                 </dependency>
             </dependencies>
-        </profile>
+        </profile-->
     </profiles>
 </project>

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

@@ -0,0 +1,129 @@
+/*
+ * 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) 2016 Stefan Neuhaus. All Rights Reserved.
+ */
+package org.owasp.dependencycheck;
+
+import org.owasp.dependencycheck.analyzer.Analyzer;
+import org.owasp.dependencycheck.analyzer.FileTypeAnalyzer;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
+import java.util.concurrent.Callable;
+
+/**
+ * Task to support parallelism of dependency-check analysis. Analyses a single
+ * {@link Dependency} by a specific {@link Analyzer}.
+ *
+ * @author Stefan Neuhaus
+ */
+public class AnalysisTask implements Callable<Void> {
+
+    /**
+     * Instance of the logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AnalysisTask.class);
+
+    /**
+     * A reference to the analyzer.
+     */
+    private final Analyzer analyzer;
+    /**
+     * The dependency to analyze.
+     */
+    private final Dependency dependency;
+    /**
+     * A reference to the dependency-check engine.
+     */
+    private final Engine engine;
+    /**
+     * The list of exceptions that may occur during analysis.
+     */
+    private final List<Throwable> exceptions;
+    /**
+     * A reference to the global settings object.
+     */
+    private final Settings settings;
+
+    /**
+     * Creates a new analysis task.
+     *
+     * @param analyzer a reference of the analyzer to execute
+     * @param dependency the dependency to analyze
+     * @param engine the dependency-check engine
+     * @param exceptions exceptions that occur during analysis will be added to
+     * this collection of exceptions
+     * @param settings a reference to the global settings object; this is
+     * necessary so that when the thread is started the dependencies have a
+     * correct reference to the global settings.
+     */
+    AnalysisTask(Analyzer analyzer, Dependency dependency, Engine engine, List<Throwable> exceptions, Settings settings) {
+        this.analyzer = analyzer;
+        this.dependency = dependency;
+        this.engine = engine;
+        this.exceptions = exceptions;
+        this.settings = settings;
+    }
+
+    /**
+     * Executes the analysis task.
+     *
+     * @return null
+     */
+    @Override
+    public Void call() {
+        try {
+            Settings.setInstance(settings);
+
+            if (shouldAnalyze()) {
+                LOGGER.debug("Begin Analysis of '{}' ({})", dependency.getActualFilePath(), analyzer.getName());
+                try {
+                    analyzer.analyze(dependency, engine);
+                } catch (AnalysisException ex) {
+                    LOGGER.warn("An error occurred while analyzing '{}' ({}).", dependency.getActualFilePath(), analyzer.getName());
+                    LOGGER.debug("", ex);
+                    exceptions.add(ex);
+                } catch (Throwable ex) {
+                    LOGGER.warn("An unexpected error occurred during analysis of '{}' ({}): {}",
+                            dependency.getActualFilePath(), analyzer.getName(), ex.getMessage());
+                    LOGGER.debug("", ex);
+                    exceptions.add(ex);
+                }
+            }
+        } finally {
+            Settings.cleanup(false);
+        }
+        return null;
+    }
+
+    /**
+     * Determines if the analyzer can analyze the given dependency.
+     *
+     * @return whether or not the analyzer can analyze the dependency
+     */
+    protected boolean shouldAnalyze() {
+        if (analyzer instanceof FileTypeAnalyzer) {
+            final FileTypeAnalyzer fileTypeAnalyzer = (FileTypeAnalyzer) analyzer;
+            return fileTypeAnalyzer.accept(dependency.getActualFile());
+        }
+
+        return true;
+    }
+}

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

@@ -21,7 +21,6 @@ import org.owasp.dependencycheck.analyzer.AnalysisPhase;
 import org.owasp.dependencycheck.analyzer.Analyzer;
 import org.owasp.dependencycheck.analyzer.AnalyzerService;
 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;
@@ -29,6 +28,8 @@ 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.exception.ExceptionCollection;
+import org.owasp.dependencycheck.exception.InitializationException;
 import org.owasp.dependencycheck.exception.NoDataException;
 import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.owasp.dependencycheck.utils.Settings;
@@ -37,17 +38,28 @@ import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.io.FileFilter;
+import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
 import java.util.EnumMap;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.concurrent.CancellationException;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.concurrent.TimeUnit;
 
 /**
- * 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
  */
@@ -56,21 +68,26 @@ public class Engine implements FileFilter {
     /**
      * The list of dependencies.
      */
-    private List<Dependency> dependencies = new ArrayList<Dependency>();
+    private final List<Dependency> dependencies = Collections.synchronizedList(new ArrayList<Dependency>());
     /**
      * A Map of analyzers grouped by Analysis phase.
      */
-    private Map<AnalysisPhase, List<Analyzer>> analyzers = new EnumMap<AnalysisPhase, List<Analyzer>>(AnalysisPhase.class);
+    private final Map<AnalysisPhase, List<Analyzer>> analyzers = new EnumMap<>(AnalysisPhase.class);
 
     /**
      * A Map of analyzers grouped by Analysis phase.
      */
-    private Set<FileTypeAnalyzer> fileTypeAnalyzers = new HashSet<FileTypeAnalyzer>();
+    private final Set<FileTypeAnalyzer> fileTypeAnalyzers = new HashSet<>();
 
     /**
-     * The ClassLoader to use when dynamically loading Analyzer and Update services.
+     * The ClassLoader to use when dynamically loading Analyzer and Update
+     * services.
      */
     private ClassLoader serviceClassLoader = Thread.currentThread().getContextClassLoader();
+    /**
+     * A reference to the database.
+     */
+    private CveDB database = null;
     /**
      * The Logger for use throughout the class.
      */
@@ -79,7 +96,8 @@ public class Engine implements FileFilter {
     /**
      * Creates a new Engine.
      *
-     * @throws DatabaseException thrown if there is an error connecting to the database
+     * @throws DatabaseException thrown if there is an error connecting to the
+     * database
      */
     public Engine() throws DatabaseException {
         initializeEngine();
@@ -89,7 +107,8 @@ public class Engine implements FileFilter {
      * Creates a new Engine.
      *
      * @param serviceClassLoader a reference the class loader being used
-     * @throws DatabaseException thrown if there is an error connecting to the database
+     * @throws DatabaseException thrown if there is an error connecting to the
+     * database
      */
     public Engine(ClassLoader serviceClassLoader) throws DatabaseException {
         this.serviceClassLoader = serviceClassLoader;
@@ -97,9 +116,11 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Creates a new Engine using the specified classloader to dynamically load Analyzer and Update services.
+     * 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
+     * @throws DatabaseException thrown if there is an error connecting to the
+     * database
      */
     protected final void initializeEngine() throws DatabaseException {
         ConnectionFactory.initialize();
@@ -110,11 +131,16 @@ public class Engine implements FileFilter {
      * Properly cleans up resources allocated during analysis.
      */
     public void cleanup() {
+        if (database != null) {
+            database.close();
+            database = null;
+        }
         ConnectionFactory.cleanup();
     }
 
     /**
-     * Loads the analyzers specified in the configuration file (or system properties).
+     * Loads the analyzers specified in the configuration file (or system
+     * properties).
      */
     private void loadAnalyzers() {
         if (!analyzers.isEmpty()) {
@@ -125,9 +151,8 @@ public class Engine implements FileFilter {
         }
 
         final AnalyzerService service = new AnalyzerService(serviceClassLoader);
-        final Iterator<Analyzer> iterator = service.getAnalyzers();
-        while (iterator.hasNext()) {
-            final Analyzer a = iterator.next();
+        final List<Analyzer> iterator = service.getAnalyzers();
+        for (Analyzer a : iterator) {
             analyzers.get(a.getAnalysisPhase()).add(a);
             if (a instanceof FileTypeAnalyzer) {
                 this.fileTypeAnalyzers.add((FileTypeAnalyzer) a);
@@ -146,11 +171,17 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Get the dependencies identified.
+     * Get the dependencies identified. The returned list is a reference to the
+     * engine's synchronized list. <b>You must synchronize on the returned
+     * list</b> when you modify and iterate over it from multiple threads. E.g.
+     * this holds for analyzers supporting parallel processing during their
+     * analysis phase.
      *
      * @return the dependencies identified
+     * @see Collections#synchronizedList(List)
+     * @see Analyzer#supportsParallelProcessing()
      */
-    public List<Dependency> getDependencies() {
+    public synchronized List<Dependency> getDependencies() {
         return dependencies;
     }
 
@@ -160,22 +191,40 @@ public class Engine implements FileFilter {
      * @param dependencies the dependencies
      */
     public void setDependencies(List<Dependency> dependencies) {
-        this.dependencies = dependencies;
+        synchronized (this.dependencies) {
+            this.dependencies.clear();
+            this.dependencies.addAll(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.
+     * 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>();
+        return scan(paths, null);
+    }
+
+    /**
+     * 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
+     * @param projectReference the name of the project or scope in which the
+     * dependency was identified
+     * @return the list of dependencies scanned
+     * @since v1.4.4
+     */
+    public List<Dependency> scan(String[] paths, String projectReference) {
+        final List<Dependency> deps = new ArrayList<>();
         for (String path : paths) {
-            final File file = new File(path);
-            final List<Dependency> d = scan(file);
+            final List<Dependency> d = scan(path, projectReference);
             if (d != null) {
                 deps.addAll(d);
             }
@@ -184,29 +233,61 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * 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.
+     * 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
      * @return the list of dependencies scanned
      */
     public List<Dependency> scan(String path) {
-        final File file = new File(path);
-        return scan(file);
+        return scan(path, null);
     }
 
     /**
-     * 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.
+     * 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
+     * @param projectReference the name of the project or scope in which the
+     * dependency was identified
+     * @return the list of dependencies scanned
+     * @since v1.4.4
+     */
+    public List<Dependency> scan(String path, String projectReference) {
+        final File file = new File(path);
+        return scan(file, projectReference);
+    }
+
+    /**
+     * 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>();
+        return scan(files, null);
+    }
+
+    /**
+     * 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.
+     * @param projectReference the name of the project or scope in which the
+     * dependency was identified
+     * @return the list of dependencies
+     * @since v1.4.4
+     */
+    public List<Dependency> scan(File[] files, String projectReference) {
+        final List<Dependency> deps = new ArrayList<>();
         for (File file : files) {
-            final List<Dependency> d = scan(file);
+            final List<Dependency> d = scan(file, projectReference);
             if (d != null) {
                 deps.addAll(d);
             }
@@ -215,36 +296,33 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * 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.
+     * 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(Set<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;
+    public List<Dependency> scan(Collection<File> files) {
+        return scan(files, null);
     }
 
     /**
-     * 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.
+     * 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
+     * @param projectReference the name of the project or scope in which the
+     * dependency was identified
      * @return the list of dependencies scanned
-     * @since v0.3.2.5
+     * @since v1.4.4
      */
-    public List<Dependency> scan(List<File> files) {
-        final List<Dependency> deps = new ArrayList<Dependency>();
+    public List<Dependency> scan(Collection<File> files, String projectReference) {
+        final List<Dependency> deps = new ArrayList<>();
         for (File file : files) {
-            final List<Dependency> d = scan(file);
+            final List<Dependency> d = scan(file, projectReference);
             if (d != null) {
                 deps.addAll(d);
             }
@@ -253,21 +331,37 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * 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.
+     * 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) {
+        return scan(file, null);
+    }
+
+    /**
+     * 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
+     * @param projectReference the name of the project or scope in which the
+     * dependency was identified
+     * @return the list of dependencies scanned
+     * @since v1.4.4
+     */
+    public List<Dependency> scan(File file, String projectReference) {
         if (file.exists()) {
             if (file.isDirectory()) {
-                return scanDirectory(file);
+                return scanDirectory(file, projectReference);
             } else {
-                final Dependency d = scanFile(file);
+                final Dependency d = scanFile(file, projectReference);
                 if (d != null) {
-                    final List<Dependency> deps = new ArrayList<Dependency>();
+                    final List<Dependency> deps = new ArrayList<>();
                     deps.add(d);
                     return deps;
                 }
@@ -277,23 +371,38 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Recursively scans files and directories. Any dependencies identified are added to the dependency collection.
+     * Recursively scans files and directories. Any dependencies identified are
+     * added to the dependency collection.
      *
      * @param dir the directory to scan
      * @return the list of Dependency objects scanned
      */
     protected List<Dependency> scanDirectory(File dir) {
+        return scanDirectory(dir, null);
+    }
+
+    /**
+     * Recursively scans files and directories. Any dependencies identified are
+     * added to the dependency collection.
+     *
+     * @param dir the directory to scan
+     * @param projectReference the name of the project or scope in which the
+     * dependency was identified
+     * @return the list of Dependency objects scanned
+     * @since v1.4.4
+     */
+    protected List<Dependency> scanDirectory(File dir, String projectReference) {
         final File[] files = dir.listFiles();
-        final List<Dependency> deps = new ArrayList<Dependency>();
+        final List<Dependency> deps = new ArrayList<>();
         if (files != null) {
             for (File f : files) {
                 if (f.isDirectory()) {
-                    final List<Dependency> d = scanDirectory(f);
+                    final List<Dependency> d = scanDirectory(f, projectReference);
                     if (d != null) {
                         deps.addAll(d);
                     }
                 } else {
-                    final Dependency d = scanFile(f);
+                    final Dependency d = scanFile(f, projectReference);
                     deps.add(d);
                 }
             }
@@ -302,91 +411,117 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Scans a specified file. If a dependency is identified it is added to the dependency collection.
+     * 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) {
+        return scanFile(file, null);
+    }
+
+    /**
+     * Scans a specified file. If a dependency is identified it is added to the
+     * dependency collection.
+     *
+     * @param file The file to scan
+     * @param projectReference the name of the project or scope in which the
+     * dependency was identified
+     * @return the scanned dependency
+     * @since v1.4.4
+     */
+    protected Dependency scanFile(File file, String projectReference) {
         Dependency dependency = null;
         if (file.isFile()) {
             if (accept(file)) {
                 dependency = new Dependency(file);
-                dependencies.add(dependency);
+                if (projectReference != null) {
+                    dependency.addProjectReference(projectReference);
+                }
+                final String sha1 = dependency.getSha1sum();
+                boolean found = false;
+                synchronized (dependencies) {
+                    if (sha1 != null) {
+                        for (Dependency existing : dependencies) {
+                            if (sha1.equals(existing.getSha1sum())) {
+                                found = true;
+                                if (projectReference != null) {
+                                    existing.addProjectReference(projectReference);
+                                }
+                                if (existing.getActualFilePath() != null && dependency.getActualFilePath() != null
+                                        && !existing.getActualFilePath().equals(dependency.getActualFilePath())) {
+                                    existing.addRelatedDependency(dependency);
+                                } else {
+                                    dependency = existing;
+                                }
+                                break;
+                            }
+                        }
+                    }
+                    if (!found) {
+                        dependencies.add(dependency);
+                    }
+                }
+            } else {
+                LOGGER.debug("Path passed to scanFile(File) is not a file: {}. Skipping the file.", file);
             }
-        } else {
-            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. 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.
+     * 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.
+     * <p>
+     * Every effort is made to complete analysis on the dependencies. In some
+     * cases an exception will occur with part of the analysis being performed
+     * which may not affect the entire analysis. If an exception occurs it will
+     * be included in the thrown exception collection.
+     *
+     * @throws ExceptionCollection a collections of any exceptions that occurred
+     * during analysis
      */
-    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();
-        }
+    public void analyzeDependencies() throws ExceptionCollection {
+        final List<Throwable> exceptions = Collections.synchronizedList(new ArrayList<Throwable>());
+
+        initializeAndUpdateDatabase(exceptions);
 
         //need to ensure that data exists
         try {
             ensureDataExists();
         } catch (NoDataException 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;
-
+            throwFatalExceptionCollection("Unable to continue dependency-check analysis.", ex, exceptions);
         }
 
         LOGGER.debug("\n----------------------------------------------------\nBEGIN ANALYSIS\n----------------------------------------------------");
-        LOGGER.info("Analysis Starting");
+        LOGGER.info("Analysis Started");
         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);
+            for (final Analyzer analyzer : analyzerList) {
+                final long analyzerStart = System.currentTimeMillis();
+                try {
+                    initializeAnalyzer(analyzer);
+                } catch (InitializationException ex) {
+                    exceptions.add(ex);
+                    continue;
+                }
 
-                /* 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.
-                 */
-                LOGGER.debug("Begin Analyzer '{}'", a.getName());
-                final Set<Dependency> dependencySet = new HashSet<Dependency>(dependencies);
-                for (Dependency d : dependencySet) {
-                    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) {
-                            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);
-                        }
-                    }
+                if (analyzer.isEnabled()) {
+                    executeAnalysisTasks(analyzer, exceptions);
+
+                    final long analyzerDurationMillis = System.currentTimeMillis() - analyzerStart;
+                    final long analyzerDurationSeconds = TimeUnit.MILLISECONDS.toSeconds(analyzerDurationMillis);
+                    LOGGER.info("Finished {} ({} seconds)", analyzer.getName(), analyzerDurationSeconds);
+                } else {
+                    LOGGER.debug("Skipping {} (not enabled)", analyzer.getName());
                 }
             }
         }
@@ -399,20 +534,134 @@ public class Engine implements FileFilter {
         }
 
         LOGGER.debug("\n----------------------------------------------------\nEND ANALYSIS\n----------------------------------------------------");
-        LOGGER.info("Analysis Complete ({} ms)", System.currentTimeMillis() - analysisStart);
+        final long analysisDurationSeconds = TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - analysisStart);
+        LOGGER.info("Analysis Complete ({} seconds)", analysisDurationSeconds);
+        if (exceptions.size() > 0) {
+            throw new ExceptionCollection("One or more exceptions occurred during dependency-check analysis", exceptions);
+        }
+    }
+
+    /**
+     * Performs any necessary updates and initializes the database.
+     *
+     * @param exceptions a collection to store non-fatal exceptions
+     * @throws ExceptionCollection thrown if fatal exceptions occur
+     */
+    private void initializeAndUpdateDatabase(final List<Throwable> exceptions) throws ExceptionCollection {
+        boolean autoUpdate = true;
+        try {
+            autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
+        } catch (InvalidSettingException ex) {
+            LOGGER.debug("Invalid setting for auto-update; using true.");
+            exceptions.add(ex);
+        }
+        if (autoUpdate) {
+            try {
+                database = CveDB.getInstance();
+                doUpdates();
+            } catch (UpdateException ex) {
+                exceptions.add(ex);
+                LOGGER.warn("Unable to update Cached Web DataSource, using local "
+                        + "data instead. Results may not include recent vulnerabilities.");
+                LOGGER.debug("Update Error", ex);
+            } catch (DatabaseException ex) {
+                throw new ExceptionCollection("Unable to connect to the database", ex);
+            }
+        } else {
+            try {
+                if (ConnectionFactory.isH2Connection() && !ConnectionFactory.h2DataFileExists()) {
+                    throw new ExceptionCollection(new NoDataException("Autoupdate is disabled and the database does not exist"), true);
+                } else {
+                    database = CveDB.getInstance();
+                }
+            } catch (IOException ex) {
+                throw new ExceptionCollection(new DatabaseException("Autoupdate is disabled and unable to connect to the database"), true);
+            } catch (DatabaseException ex) {
+                throwFatalExceptionCollection("Unable to connect to the dependency-check database.", ex, exceptions);
+            }
+        }
+    }
+
+    /**
+     * Executes executes the analyzer using multiple threads.
+     *
+     * @param exceptions a collection of exceptions that occurred during
+     * analysis
+     * @param analyzer the analyzer to execute
+     * @throws ExceptionCollection thrown if exceptions occurred during analysis
+     */
+    protected void executeAnalysisTasks(Analyzer analyzer, List<Throwable> exceptions) throws ExceptionCollection {
+        LOGGER.debug("Starting {}", analyzer.getName());
+        final List<AnalysisTask> analysisTasks = getAnalysisTasks(analyzer, exceptions);
+        final ExecutorService executorService = getExecutorService(analyzer);
+
+        try {
+            final List<Future<Void>> results = executorService.invokeAll(analysisTasks, 10, TimeUnit.MINUTES);
+
+            // ensure there was no exception during execution
+            for (Future<Void> result : results) {
+                try {
+                    result.get();
+                } catch (ExecutionException e) {
+                    throwFatalExceptionCollection("Analysis task failed with a fatal exception.", e, exceptions);
+                } catch (CancellationException e) {
+                    throwFatalExceptionCollection("Analysis task timed out.", e, exceptions);
+                }
+            }
+        } catch (InterruptedException e) {
+            throwFatalExceptionCollection("Analysis has been interrupted.", e, exceptions);
+        } finally {
+            executorService.shutdown();
+        }
+    }
+
+    /**
+     * Returns the analysis tasks for the dependencies.
+     *
+     * @param analyzer the analyzer to create tasks for
+     * @param exceptions the collection of exceptions to collect
+     * @return a collection of analysis tasks
+     */
+    protected List<AnalysisTask> getAnalysisTasks(Analyzer analyzer, List<Throwable> exceptions) {
+        final List<AnalysisTask> result = new ArrayList<>();
+        synchronized (dependencies) {
+            for (final Dependency dependency : dependencies) {
+                final AnalysisTask task = new AnalysisTask(analyzer, dependency, this, exceptions, Settings.getInstance());
+                result.add(task);
+            }
+        }
+        return result;
+    }
+
+    /**
+     * Returns the executor service for a given analyzer.
+     *
+     * @param analyzer the analyzer to obtain an executor
+     * @return the executor service
+     */
+    protected ExecutorService getExecutorService(Analyzer analyzer) {
+        if (analyzer.supportsParallelProcessing()) {
+            final int maximumNumberOfThreads = Runtime.getRuntime().availableProcessors();
+            LOGGER.debug("Parallel processing with up to {} threads: {}.", maximumNumberOfThreads, analyzer.getName());
+            return Executors.newFixedThreadPool(maximumNumberOfThreads);
+        } else {
+            LOGGER.debug("Parallel processing is not supported: {}.", analyzer.getName());
+            return Executors.newSingleThreadExecutor();
+        }
     }
 
     /**
      * Initializes the given analyzer.
      *
      * @param analyzer the analyzer to initialize
-     * @return the initialized analyzer
+     * @throws InitializationException thrown when there is a problem
+     * initializing the analyzer
      */
-    protected Analyzer initializeAnalyzer(Analyzer analyzer) {
+    protected void initializeAnalyzer(Analyzer analyzer) throws InitializationException {
         try {
             LOGGER.debug("Initializing {}", analyzer.getName());
             analyzer.initialize();
-        } catch (Throwable ex) {
+        } catch (InitializationException ex) {
             LOGGER.error("Exception occurred initializing {}.", analyzer.getName());
             LOGGER.debug("", ex);
             try {
@@ -420,8 +669,17 @@ public class Engine implements FileFilter {
             } catch (Throwable ex1) {
                 LOGGER.trace("", ex1);
             }
+            throw ex;
+        } catch (Throwable ex) {
+            LOGGER.error("Unexpected exception occurred initializing {}.", analyzer.getName());
+            LOGGER.debug("", ex);
+            try {
+                analyzer.close();
+            } catch (Throwable ex1) {
+                LOGGER.trace("", ex1);
+            }
+            throw new InitializationException("Unexpected Exception", ex);
         }
-        return analyzer;
     }
 
     /**
@@ -439,33 +697,31 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * 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.
+     *
+     * @throws UpdateException thrown if the operation fails
      */
-    public void doUpdates() {
+    public void doUpdates() throws UpdateException {
         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.warn(
-                        "Unable to update Cached Web DataSource, using local data instead. Results may not include recent vulnerabilities.");
-                LOGGER.debug("Unable to update details for {}", source.getClass().getName(), ex);
-            }
+            source.update();
         }
         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
      */
     public List<Analyzer> getAnalyzers() {
-        final List<Analyzer> ret = new ArrayList<Analyzer>();
+        final List<Analyzer> ret = new ArrayList<>();
         for (AnalysisPhase phase : AnalysisPhase.values()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
             ret.addAll(analyzerList);
@@ -477,7 +733,8 @@ public class Engine implements FileFilter {
      * Checks all analyzers to see if an extension is supported.
      *
      * @param file a file extension
-     * @return true or false depending on whether or not the file extension is supported
+     * @return true or false depending on whether or not the file extension is
+     * supported
      */
     @Override
     public boolean accept(File file) {
@@ -503,22 +760,40 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Checks the CPE Index to ensure documents exists. If none exist a NoDataException is thrown.
+     * Adds a file type analyzer. This has been added solely to assist in unit
+     * testing the Engine.
+     *
+     * @param fta the file type analyzer to add
+     */
+    protected void addFileTypeAnalyzer(FileTypeAnalyzer fta) {
+        this.fileTypeAnalyzers.add(fta);
+    }
+
+    /**
+     * 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, DatabaseException {
-        final CveDB cve = new CveDB();
-        try {
-            cve.open();
-            if (!cve.dataExists()) {
-                throw new NoDataException("No documents exist");
-            }
-        } catch (DatabaseException ex) {
-            throw new NoDataException(ex.getMessage(), ex);
-        } finally {
-            cve.close();
+    private void ensureDataExists() throws NoDataException {
+        if (database == null || !database.dataExists()) {
+            throw new NoDataException("No documents exist");
         }
     }
+
+    /**
+     * Constructs and throws a fatal exception collection.
+     *
+     * @param message the exception message
+     * @param throwable the cause
+     * @param exceptions a collection of exception to include
+     * @throws ExceptionCollection a collection of exceptions that occurred
+     * during analysis
+     */
+    private void throwFatalExceptionCollection(String message, Throwable throwable, List<Throwable> exceptions) throws ExceptionCollection {
+        LOGGER.error("{}\n\n{}", throwable.getMessage(), message);
+        LOGGER.debug("", throwable);
+        exceptions.add(throwable);
+        throw new ExceptionCollection(message, exceptions, true);
+    }
 }

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

@@ -27,6 +27,8 @@ 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.exception.ExceptionCollection;
+import org.owasp.dependencycheck.exception.ReportException;
 import org.owasp.dependencycheck.exception.ScanAgentException;
 import org.owasp.dependencycheck.reporting.ReportGenerator;
 import org.owasp.dependencycheck.utils.Settings;
@@ -34,14 +36,16 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * This class provides a way to easily conduct a scan solely based on existing evidence metadata rather than collecting evidence
- * from the files themselves. This class is based on the Ant task and Maven plugin with the exception that it takes a list of
- * dependencies that can be programmatically added from data in a spreadsheet, database or some other datasource and conduct a
- * scan based on this pre-defined evidence.
+ * This class provides a way to easily conduct a scan solely based on existing
+ * evidence metadata rather than collecting evidence from the files themselves.
+ * This class is based on the Ant task and Maven plugin with the exception that
+ * it takes a list of dependencies that can be programmatically added from data
+ * in a spreadsheet, database or some other datasource and conduct a scan based
+ * on this pre-defined evidence.
  *
  * <h2>Example:</h2>
  * <pre>
- * List<Dependency> dependencies = new ArrayList<Dependency>();
+ * List&lt;Dependency&gt; dependencies = new ArrayList&lt;Dependency&gt;();
  * Dependency dependency = new Dependency(new File(FileUtils.getBitBucket()));
  * dependency.getProductEvidence().addEvidence("my-datasource", "name", "Jetty", Confidence.HIGH);
  * dependency.getVersionEvidence().addEvidence("my-datasource", "version", "5.1.10", Confidence.HIGH);
@@ -55,11 +59,12 @@ import org.slf4j.LoggerFactory;
  * scan.execute();
  * </pre>
  *
- * @author Steve Springett <steve.springett@owasp.org>
+ * @author Steve Springett
  */
 @SuppressWarnings("unused")
 public class DependencyCheckScanAgent {
 
+    //<editor-fold defaultstate="collapsed" desc="private fields">
     /**
      * System specific new line character.
      */
@@ -72,6 +77,141 @@ public class DependencyCheckScanAgent {
      * The application name for the report.
      */
     private String applicationName = "Dependency-Check";
+    /**
+     * The pre-determined dependencies to scan
+     */
+    private List<Dependency> dependencies;
+    /**
+     * The location of the data directory that contains
+     */
+    private String dataDirectory = null;
+    /**
+     * Specifies the destination directory for the generated Dependency-Check
+     * report.
+     */
+    private String 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;
+    /**
+     * 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;
+    /**
+     * flag indicating whether or not to generate a report of findings.
+     */
+    private boolean generateReport = true;
+    /**
+     * 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 ReportGenerator.Format reportFormat = ReportGenerator.Format.HTML;
+    /**
+     * The Proxy Server.
+     */
+    private String proxyServer;
+    /**
+     * The Proxy Port.
+     */
+    private String proxyPort;
+    /**
+     * The Proxy username.
+     */
+    private String proxyUsername;
+    /**
+     * The Proxy password.
+     */
+    private String proxyPassword;
+    /**
+     * The Connection Timeout.
+     */
+    private String connectionTimeout;
+    /**
+     * The file path used for verbose logging.
+     */
+    private String logFile = null;
+    /**
+     * flag indicating whether or not to show a summary of findings.
+     */
+    private boolean showSummary = true;
+    /**
+     * The path to the suppression file.
+     */
+    private String suppressionFile;
+    /**
+     * The password to use when connecting to the database.
+     */
+    private String databasePassword;
+    /**
+     * Whether or not the Maven Central analyzer is enabled.
+     */
+    private boolean centralAnalyzerEnabled = true;
+    /**
+     * The URL of Maven Central.
+     */
+    private String centralUrl;
+    /**
+     * Whether or not the nexus analyzer is enabled.
+     */
+    private boolean nexusAnalyzerEnabled = true;
+    /**
+     * The URL of the Nexus server.
+     */
+    private String nexusUrl;
+    /**
+     * Whether or not the defined proxy should be used when connecting to Nexus.
+     */
+    private boolean nexusUsesProxy = true;
+    /**
+     * The database driver name; such as org.h2.Driver.
+     */
+    private String databaseDriverName;
+    /**
+     * The path to the database driver JAR file if it is not on the class path.
+     */
+    private String databaseDriverPath;
+    /**
+     * The database connection string.
+     */
+    private String connectionString;
+    /**
+     * The user name for connecting to the database.
+     */
+    private String databaseUser;
+    /**
+     * 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;
+    /**
+     * The url for the modified NVD CVE (1.2 schema).
+     */
+    private String cveUrl12Modified;
+    /**
+     * The url for the modified NVD CVE (2.0 schema).
+     */
+    private String cveUrl20Modified;
+    /**
+     * Base Data Mirror URL for CVE 1.2.
+     */
+    private String cveUrl12Base;
+    /**
+     * Data Mirror URL for CVE 2.0.
+     */
+    private String cveUrl20Base;
+    /**
+     * The path to Mono for .NET assembly analysis on non-windows systems.
+     */
+    private String pathToMono;
+    //</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="getters/setters">
 
     /**
      * Get the value of applicationName.
@@ -91,11 +231,6 @@ public class DependencyCheckScanAgent {
         this.applicationName = applicationName;
     }
 
-    /**
-     * The pre-determined dependencies to scan
-     */
-    private List<Dependency> dependencies;
-
     /**
      * Returns a list of pre-determined dependencies.
      *
@@ -114,11 +249,6 @@ public class DependencyCheckScanAgent {
         this.dependencies = dependencies;
     }
 
-    /**
-     * The location of the data directory that contains
-     */
-    private String dataDirectory = null;
-
     /**
      * Get the value of dataDirectory.
      *
@@ -137,11 +267,6 @@ public class DependencyCheckScanAgent {
         this.dataDirectory = dataDirectory;
     }
 
-    /**
-     * Specifies the destination directory for the generated Dependency-Check report.
-     */
-    private String reportOutputDirectory;
-
     /**
      * Get the value of reportOutputDirectory.
      *
@@ -160,13 +285,6 @@ public class DependencyCheckScanAgent {
         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.
      *
@@ -185,12 +303,6 @@ public class DependencyCheckScanAgent {
         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.
      *
@@ -209,11 +321,6 @@ public class DependencyCheckScanAgent {
         this.autoUpdate = autoUpdate;
     }
 
-    /**
-     * flag indicating whether or not to generate a report of findings.
-     */
-    private boolean generateReport = true;
-
     /**
      * Get the value of generateReport.
      *
@@ -232,12 +339,6 @@ public class DependencyCheckScanAgent {
         this.generateReport = generateReport;
     }
 
-    /**
-     * 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 ReportGenerator.Format reportFormat = ReportGenerator.Format.HTML;
-
     /**
      * Get the value of reportFormat.
      *
@@ -256,11 +357,6 @@ public class DependencyCheckScanAgent {
         this.reportFormat = reportFormat;
     }
 
-    /**
-     * The Proxy Server.
-     */
-    private String proxyServer;
-
     /**
      * Get the value of proxyServer.
      *
@@ -283,7 +379,9 @@ public class DependencyCheckScanAgent {
      * Get the value of proxyServer.
      *
      * @return the value of proxyServer
-     * @deprecated use {@link org.owasp.dependencycheck.agent.DependencyCheckScanAgent#getProxyServer()} instead
+     * @deprecated use
+     * {@link org.owasp.dependencycheck.agent.DependencyCheckScanAgent#getProxyServer()}
+     * instead
      */
     @Deprecated
     public String getProxyUrl() {
@@ -302,11 +400,6 @@ public class DependencyCheckScanAgent {
         this.proxyServer = proxyUrl;
     }
 
-    /**
-     * The Proxy Port.
-     */
-    private String proxyPort;
-
     /**
      * Get the value of proxyPort.
      *
@@ -325,11 +418,6 @@ public class DependencyCheckScanAgent {
         this.proxyPort = proxyPort;
     }
 
-    /**
-     * The Proxy username.
-     */
-    private String proxyUsername;
-
     /**
      * Get the value of proxyUsername.
      *
@@ -348,11 +436,6 @@ public class DependencyCheckScanAgent {
         this.proxyUsername = proxyUsername;
     }
 
-    /**
-     * The Proxy password.
-     */
-    private String proxyPassword;
-
     /**
      * Get the value of proxyPassword.
      *
@@ -371,11 +454,6 @@ public class DependencyCheckScanAgent {
         this.proxyPassword = proxyPassword;
     }
 
-    /**
-     * The Connection Timeout.
-     */
-    private String connectionTimeout;
-
     /**
      * Get the value of connectionTimeout.
      *
@@ -394,11 +472,6 @@ public class DependencyCheckScanAgent {
         this.connectionTimeout = connectionTimeout;
     }
 
-    /**
-     * The file path used for verbose logging.
-     */
-    private String logFile = null;
-
     /**
      * Get the value of logFile.
      *
@@ -417,11 +490,6 @@ public class DependencyCheckScanAgent {
         this.logFile = logFile;
     }
 
-    /**
-     * The path to the suppression file.
-     */
-    private String suppressionFile;
-
     /**
      * Get the value of suppressionFile.
      *
@@ -440,11 +508,6 @@ public class DependencyCheckScanAgent {
         this.suppressionFile = suppressionFile;
     }
 
-    /**
-     * flag indicating whether or not to show a summary of findings.
-     */
-    private boolean showSummary = true;
-
     /**
      * Get the value of showSummary.
      *
@@ -463,11 +526,6 @@ public class DependencyCheckScanAgent {
         this.showSummary = showSummary;
     }
 
-    /**
-     * Whether or not the Maven Central analyzer is enabled.
-     */
-    private boolean centralAnalyzerEnabled = true;
-
     /**
      * Get the value of centralAnalyzerEnabled.
      *
@@ -486,11 +544,6 @@ public class DependencyCheckScanAgent {
         this.centralAnalyzerEnabled = centralAnalyzerEnabled;
     }
 
-    /**
-     * The URL of Maven Central.
-     */
-    private String centralUrl;
-
     /**
      * Get the value of centralUrl.
      *
@@ -509,11 +562,6 @@ public class DependencyCheckScanAgent {
         this.centralUrl = centralUrl;
     }
 
-    /**
-     * Whether or not the nexus analyzer is enabled.
-     */
-    private boolean nexusAnalyzerEnabled = true;
-
     /**
      * Get the value of nexusAnalyzerEnabled.
      *
@@ -532,11 +580,6 @@ public class DependencyCheckScanAgent {
         this.nexusAnalyzerEnabled = nexusAnalyzerEnabled;
     }
 
-    /**
-     * The URL of the Nexus server.
-     */
-    private String nexusUrl;
-
     /**
      * Get the value of nexusUrl.
      *
@@ -555,11 +598,6 @@ public class DependencyCheckScanAgent {
         this.nexusUrl = nexusUrl;
     }
 
-    /**
-     * Whether or not the defined proxy should be used when connecting to Nexus.
-     */
-    private boolean nexusUsesProxy = true;
-
     /**
      * Get the value of nexusUsesProxy.
      *
@@ -578,11 +616,6 @@ public class DependencyCheckScanAgent {
         this.nexusUsesProxy = nexusUsesProxy;
     }
 
-    /**
-     * The database driver name; such as org.h2.Driver.
-     */
-    private String databaseDriverName;
-
     /**
      * Get the value of databaseDriverName.
      *
@@ -601,11 +634,6 @@ public class DependencyCheckScanAgent {
         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.
      *
@@ -624,11 +652,6 @@ public class DependencyCheckScanAgent {
         this.databaseDriverPath = databaseDriverPath;
     }
 
-    /**
-     * The database connection string.
-     */
-    private String connectionString;
-
     /**
      * Get the value of connectionString.
      *
@@ -647,11 +670,6 @@ public class DependencyCheckScanAgent {
         this.connectionString = connectionString;
     }
 
-    /**
-     * The user name for connecting to the database.
-     */
-    private String databaseUser;
-
     /**
      * Get the value of databaseUser.
      *
@@ -670,11 +688,6 @@ public class DependencyCheckScanAgent {
         this.databaseUser = databaseUser;
     }
 
-    /**
-     * The password to use when connecting to the database.
-     */
-    private String databasePassword;
-
     /**
      * Get the value of databasePassword.
      *
@@ -693,12 +706,6 @@ public class DependencyCheckScanAgent {
         this.databasePassword = databasePassword;
     }
 
-    /**
-     * 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.
      *
@@ -717,11 +724,6 @@ public class DependencyCheckScanAgent {
         this.zipExtensions = zipExtensions;
     }
 
-    /**
-     * The url for the modified NVD CVE (1.2 schema).
-     */
-    private String cveUrl12Modified;
-
     /**
      * Get the value of cveUrl12Modified.
      *
@@ -740,11 +742,6 @@ public class DependencyCheckScanAgent {
         this.cveUrl12Modified = cveUrl12Modified;
     }
 
-    /**
-     * The url for the modified NVD CVE (2.0 schema).
-     */
-    private String cveUrl20Modified;
-
     /**
      * Get the value of cveUrl20Modified.
      *
@@ -763,11 +760,6 @@ public class DependencyCheckScanAgent {
         this.cveUrl20Modified = cveUrl20Modified;
     }
 
-    /**
-     * Base Data Mirror URL for CVE 1.2.
-     */
-    private String cveUrl12Base;
-
     /**
      * Get the value of cveUrl12Base.
      *
@@ -786,11 +778,6 @@ public class DependencyCheckScanAgent {
         this.cveUrl12Base = cveUrl12Base;
     }
 
-    /**
-     * Data Mirror URL for CVE 2.0.
-     */
-    private String cveUrl20Base;
-
     /**
      * Get the value of cveUrl20Base.
      *
@@ -809,11 +796,6 @@ public class DependencyCheckScanAgent {
         this.cveUrl20Base = cveUrl20Base;
     }
 
-    /**
-     * The path to Mono for .NET assembly analysis on non-windows systems.
-     */
-    private String pathToMono;
-
     /**
      * Get the value of pathToMono.
      *
@@ -831,17 +813,23 @@ public class DependencyCheckScanAgent {
     public void setPathToMono(String pathToMono) {
         this.pathToMono = pathToMono;
     }
+    //</editor-fold>
 
     /**
      * Executes the Dependency-Check on the dependent libraries.
      *
      * @return the Engine used to scan the dependencies.
-     * @throws org.owasp.dependencycheck.data.nvdcve.DatabaseException thrown if there is an exception connecting to the database
+     * @throws ExceptionCollection a collection of one or more exceptions that
+     * occurred during analysis.
      */
-    private Engine executeDependencyCheck() throws DatabaseException {
+    private Engine executeDependencyCheck() throws ExceptionCollection {
         populateSettings();
-        Engine engine = null;
-        engine = new Engine();
+        final Engine engine;
+        try {
+            engine = new Engine();
+        } catch (DatabaseException ex) {
+            throw new ExceptionCollection(ex, true);
+        }
         engine.setDependencies(this.dependencies);
         engine.analyzeDependencies();
         return engine;
@@ -855,35 +843,25 @@ public class DependencyCheckScanAgent {
      */
     private void generateExternalReports(Engine engine, File outDirectory) {
         DatabaseProperties prop = null;
-        CveDB cve = null;
-        try {
-            cve = new CveDB();
-            cve.open();
+        try (CveDB cve = CveDB.getInstance()) {
             prop = cve.getDatabaseProperties();
         } catch (DatabaseException ex) {
+            //TODO shouldn't this be a fatal exception
             LOGGER.debug("Unable to retrieve DB Properties", ex);
-        } finally {
-            if (cve != null) {
-                cve.close();
-            }
         }
         final ReportGenerator r = new ReportGenerator(this.applicationName, engine.getDependencies(), engine.getAnalyzers(), prop);
         try {
             r.generateReports(outDirectory.getCanonicalPath(), this.reportFormat.name());
-        } catch (IOException ex) {
-            LOGGER.error(
-                    "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
-            LOGGER.debug("", ex);
-        } catch (Throwable ex) {
-            LOGGER.error(
-                    "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
+        } catch (IOException | ReportException ex) {
+            LOGGER.error("Unexpected exception occurred during analysis; please see the verbose error log for more details.");
             LOGGER.debug("", ex);
         }
     }
 
     /**
-     * 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.
+     * 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.
      */
     private void populateSettings() {
         Settings.initialize();
@@ -898,74 +876,36 @@ public class DependencyCheckScanAgent {
         }
 
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
-
-        if (proxyServer != null && !proxyServer.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_SERVER, proxyServer);
-        }
-        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);
-        }
-        if (suppressionFile != null && !suppressionFile.isEmpty()) {
-            Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
-        }
+        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.SUPPRESSION_FILE, suppressionFile);
         Settings.setBoolean(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, centralAnalyzerEnabled);
-        if (centralUrl != null && !centralUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.ANALYZER_CENTRAL_URL, centralUrl);
-        }
+        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_CENTRAL_URL, centralUrl);
         Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
-        if (nexusUrl != null && !nexusUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
-        }
-        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY, nexusUsesProxy);
-        if (databaseDriverName != null && !databaseDriverName.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
-        }
-        if (databaseDriverPath != null && !databaseDriverPath.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
-        }
-        if (connectionString != null && !connectionString.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
-        }
-        if (databaseUser != null && !databaseUser.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_USER, databaseUser);
-        }
-        if (databasePassword != null && !databasePassword.isEmpty()) {
-            Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
-        }
-        if (zipExtensions != null && !zipExtensions.isEmpty()) {
-            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
-        }
-        if (cveUrl12Modified != null && !cveUrl12Modified.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
-        }
-        if (cveUrl20Modified != null && !cveUrl20Modified.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
-        }
-        if (cveUrl12Base != null && !cveUrl12Base.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
-        }
-        if (cveUrl20Base != null && !cveUrl20Base.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
-        }
-        if (pathToMono != null && !pathToMono.isEmpty()) {
-            Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
-        }
+        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, zipExtensions);
+        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);
+        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
     }
 
     /**
      * Executes the dependency-check and generates the report.
      *
      * @return a reference to the engine used to perform the scan.
-     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if there is an exception executing the scan.
+     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if
+     * there is an exception executing the scan.
      */
     public Engine execute() throws ScanAgentException {
         Engine engine = null;
@@ -980,10 +920,12 @@ public class DependencyCheckScanAgent {
             if (this.failBuildOnCVSS <= 10) {
                 checkForFailure(engine.getDependencies());
             }
-        } catch (DatabaseException ex) {
-            LOGGER.error(
-                    "Unable to connect to the dependency-check database; analysis has stopped");
-            LOGGER.debug("", ex);
+        } catch (ExceptionCollection ex) {
+            if (ex.isFatal()) {
+                LOGGER.error("A fatal exception occurred during analysis; analysis has stopped. Please see the debug log for more details.");
+                LOGGER.debug("", ex);
+            }
+            throw new ScanAgentException("One or more exceptions occurred during analysis; please see the debug log for more details.", ex);
         } finally {
             Settings.cleanup(true);
             if (engine != null) {
@@ -994,11 +936,12 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Checks to see if a vulnerability has been identified with a CVSS score that is above the threshold set in the
-     * configuration.
+     * 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 org.owasp.dependencycheck.exception.ScanAgentException thrown if there is an exception executing the scan.
+     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if
+     * there is an exception executing the scan.
      */
     private void checkForFailure(List<Dependency> dependencies) throws ScanAgentException {
         final StringBuilder ids = new StringBuilder();
@@ -1018,7 +961,7 @@ public class DependencyCheckScanAgent {
         }
         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"
+                    + "One or more dependencies were identified with vulnerabilities that have a CVSS score greater than '%.1f': %s%n"
                     + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
 
             throw new ScanAgentException(msg);
@@ -1026,7 +969,8 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Generates a warning message listing a summary of dependencies and their associated CPE and CVE entries.
+     * Generates a warning message listing a summary of dependencies and their
+     * associated CPE and CVE entries.
      *
      * @param dependencies a list of dependency objects
      */
@@ -1063,5 +1007,4 @@ public class DependencyCheckScanAgent {
                     summary.toString());
         }
     }
-
 }

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

@@ -17,20 +17,125 @@
  */
 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.exception.InitializationException;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 /**
+ * Base class for analyzers to avoid code duplication of initialize and close as
+ * most analyzers do not need these methods.
  *
  * @author Jeremy Long
  */
 public abstract class AbstractAnalyzer implements Analyzer {
 
     /**
-     * The initialize method does nothing for this Analyzer.
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AbstractAnalyzer.class);
+    /**
+     * A flag indicating whether or not the analyzer is enabled.
+     */
+    private volatile boolean enabled = true;
+
+    /**
+     * Get the value of enabled.
+     *
+     * @return the value of enabled
+     */
+    @Override
+    public boolean isEnabled() {
+        return enabled;
+    }
+
+    /**
+     * Set the value of enabled.
+     *
+     * @param enabled new value of enabled
+     */
+    public void setEnabled(boolean enabled) {
+        this.enabled = enabled;
+    }
+
+    /**
+     * <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();
+
+    /**
+     * 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 analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException;
+
+    /**
+     * Initializes a given Analyzer. This will be skipped if the analyzer is
+     * disabled.
+     *
+     * @throws InitializationException thrown if there is an exception
+     */
+    protected void initializeAnalyzer() throws InitializationException {
+    }
+
+    /**
+     * Closes a given Analyzer. This will be skipped if the analyzer is
+     * disabled.
      *
      * @throws Exception thrown if there is an exception
      */
+    protected void closeAnalyzer() throws Exception {
+        // Intentionally empty, analyzer will override this if they must close a resource.
+    }
+
+    /**
+     * 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 initialize() throws Exception {
-        //do nothing
+    public final void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+        if (this.isEnabled()) {
+            analyzeDependency(dependency, engine);
+        }
+    }
+
+    /**
+     * The initialize method does nothing for this Analyzer.
+     *
+     * @throws InitializationException thrown if there is an exception
+     */
+    @Override
+    public final void initialize() throws InitializationException {
+        final String key = getAnalyzerEnabledSettingKey();
+        try {
+            this.setEnabled(Settings.getBoolean(key, true));
+        } catch (InvalidSettingException ex) {
+            LOGGER.warn("Invalid setting for property '{}'", key);
+            LOGGER.debug("", ex);
+        }
+
+        if (isEnabled()) {
+            initializeAnalyzer();
+        } else {
+            LOGGER.debug("{} has been disabled", getName());
+        }
     }
 
     /**
@@ -39,7 +144,19 @@ public abstract class AbstractAnalyzer implements Analyzer {
      * @throws Exception thrown if there is an exception
      */
     @Override
-    public void close() throws Exception {
-        //do nothing
+    public final void close() throws Exception {
+        if (isEnabled()) {
+            closeAnalyzer();
+        }
+    }
+
+    /**
+     * The default is to support parallel processing.
+     *
+     * @return true
+     */
+    @Override
+    public boolean supportsParallelProcessing() {
+        return true;
     }
 }

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

@@ -17,11 +17,6 @@
  */
 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;
 
@@ -30,24 +25,17 @@ import java.io.FileFilter;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
+import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
- * The base FileTypeAnalyzer that all analyzers that have specific file types they analyze should extend.
+ * 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">
+    //<editor-fold defaultstate="collapsed" desc="Field definitions, getters, and setters ">
     /**
      * The logger.
      */
@@ -58,7 +46,8 @@ public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implemen
     private boolean filesMatched = false;
 
     /**
-     * Get the value of filesMatched. A flag indicating whether the scan included any file types this analyzer supports.
+     * Get the value of filesMatched. A flag indicating whether the scan
+     * included any file types this analyzer supports.
      *
      * @return the value of filesMatched
      */
@@ -67,7 +56,8 @@ public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implemen
     }
 
     /**
-     * Set the value of filesMatched. A flag indicating whether the scan included any file types this analyzer supports.
+     * Set the value of filesMatched. A flag indicating whether the scan
+     * included any file types this analyzer supports.
      *
      * @param filesMatched new value of filesMatched
      */
@@ -75,122 +65,62 @@ public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implemen
         this.filesMatched = filesMatched;
     }
 
+    //</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="Final implementations for the Analyzer interface">
     /**
-     * A flag indicating whether or not the analyzer is enabled.
-     */
-    private boolean enabled = true;
-
-    /**
-     * Get the value of enabled.
+     * Initializes the analyzer.
      *
-     * @return the value of enabled
+     * @throws InitializationException thrown if there is an exception during
+     * initialization
      */
-    public boolean isEnabled() {
-        return enabled;
+    @Override
+    protected final void initializeAnalyzer() throws InitializationException {
+        if (filesMatched) {
+            initializeFileTypeAnalyzer();
+        } else {
+            this.setEnabled(false);
+        }
     }
 
-    /**
-     * Set the value of enabled.
-     *
-     * @param enabled new value of enabled
-     */
-    public void setEnabled(boolean enabled) {
-        this.enabled = enabled;
-    }
-//</editor-fold>
-
+    //</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>
+     * 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
-     * <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>
      */
     protected abstract FileFilter getFileFilter();
 
     /**
      * Initializes the file type analyzer.
      *
-     * @throws Exception thrown if there is an exception during initialization
+     * @throws InitializationException thrown if there is an exception during
+     * initialization
      */
-    protected abstract void initializeFileTypeAnalyzer() throws Exception;
+    protected abstract void initializeFileTypeAnalyzer() throws InitializationException;
 
+    //</editor-fold>
     /**
-     * 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.
+     * Determines if the file can be analyzed by the analyzer.
      *
-     * @param dependency the dependency to analyze
-     * @param engine the engine scanning
-     * @throws AnalysisException thrown if there is an analysis exception
+     * @param pathname the path to the file
+     * @return true if the file can be analyzed by the given analyzer; otherwise
+     * false
      */
-    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) {
+        } else if (this.isEnabled()) {
             accepted = filter.accept(pathname);
             if (accepted) {
                 filesMatched = true;
@@ -199,13 +129,10 @@ public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implemen
         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/>
+     * 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>
@@ -214,10 +141,8 @@ public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implemen
      * @return a Set of strings.
      */
     protected static Set<String> newHashSet(String... strings) {
-        final Set<String> set = new HashSet<String>();
+        final Set<String> set = new HashSet<>(strings.length);
         Collections.addAll(set, strings);
         return set;
     }
-
-//</editor-fold>
 }

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

@@ -25,18 +25,21 @@ 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.exception.InitializationException;
+import org.owasp.dependencycheck.xml.suppression.SuppressionParseException;
+import org.owasp.dependencycheck.xml.suppression.SuppressionParser;
+import org.owasp.dependencycheck.xml.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;
+import org.xml.sax.SAXException;
 
 /**
- * Abstract base suppression analyzer that contains methods for parsing the suppression xml file.
+ * Abstract base suppression analyzer that contains methods for parsing the
+ * suppression xml file.
  *
  * @author Jeremy Long
  */
@@ -61,12 +64,15 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
     /**
      * The initialize method loads the suppression XML file.
      *
-     * @throws Exception thrown if there is an exception
+     * @throws InitializationException thrown if there is an exception
      */
     @Override
-    public void initialize() throws Exception {
-        super.initialize();
-        loadSuppressionData();
+    public void initializeAnalyzer() throws InitializationException {
+        try {
+            loadSuppressionData();
+        } catch (SuppressionParseException ex) {
+            throw new InitializationException("Error initializing the suppression analyzer", ex);
+        }
     }
 
     /**
@@ -101,9 +107,10 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
         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 InputStream in = this.getClass().getClassLoader().getResourceAsStream("dependencycheck-base-suppression.xml");
+            rules = parser.parseSuppressionRules(in);
+        } catch (SAXException ex) {
+            throw new SuppressionParseException("Unable to parse the base suppression data file", ex);
         }
         final String suppressionFilePath = Settings.getString(Settings.KEYS.SUPPRESSION_FILE);
         if (suppressionFilePath == null) {
@@ -123,29 +130,33 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
                 }
             } 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);
+                    try (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) {
+                if (!file.exists()) {
+                    final String msg = String.format("Suppression file '%s' does not exists", file.getPath());
+                    LOGGER.warn(msg);
+                    throw new SuppressionParseException(msg);
+                }
                 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;
                 }
             }
@@ -153,6 +164,8 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
             throwSuppressionParseException("Unable to fetch the configured suppression file", ex);
         } catch (MalformedURLException ex) {
             throwSuppressionParseException("Configured suppression file has an invalid URL", ex);
+        } catch (SuppressionParseException ex) {
+            throw ex;
         } catch (IOException ex) {
             throwSuppressionParseException("Unable to create temp file for suppressions", ex);
         } finally {
@@ -167,7 +180,8 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
      *
      * @param message the exception message
      * @param exception the cause of the exception
-     * @throws SuppressionParseException throws the generated SuppressionParseException
+     * @throws SuppressionParseException throws the generated
+     * SuppressionParseException
      */
     private void throwSuppressionParseException(String message, Exception exception) throws SuppressionParseException {
         LOGGER.warn(message);

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

@@ -28,10 +28,18 @@ public enum AnalysisPhase {
      * Initialization phase.
      */
     INITIAL,
+    /**
+     * Pre information collection phase.
+     */
+    PRE_INFORMATION_COLLECTION,
     /**
      * Information collection phase.
      */
     INFORMATION_COLLECTION,
+    /**
+     * Post information collection phase.
+     */
+    POST_INFORMATION_COLLECTION,
     /**
      * Pre identifier analysis phase.
      */

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

@@ -20,24 +20,28 @@ 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.exception.InitializationException;
 
 /**
- * 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
  */
 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;
 
@@ -56,16 +60,33 @@ 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 InitializationException is thrown if an exception occurs
+     * initializing the analyzer.
      */
-    void initialize() throws Exception;
+    void initialize() throws InitializationException;
 
     /**
-     * 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.
      */
     void close() throws Exception;
+
+    /**
+     * Returns whether multiple instances of the same type of analyzer can run in parallel.
+     * Note that running analyzers of different types in parallel is not supported at all.
+     *
+     * @return {@code true} if the analyzer supports parallel processing, {@code false} else
+     */
+    boolean supportsParallelProcessing();
+    /**
+     * Get the value of enabled.
+     *
+     * @return the value of enabled
+     */
+    boolean isEnabled();
 }

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

@@ -17,8 +17,13 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
+import java.util.ArrayList;
 import java.util.Iterator;
+import java.util.List;
 import java.util.ServiceLoader;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.LoggerFactory;
 
 /**
  * The Analyzer Service Loader. This class loads all services that implement
@@ -27,11 +32,15 @@ import java.util.ServiceLoader;
  * @author Jeremy Long
  */
 public class AnalyzerService {
+    /**
+     * The Logger for use throughout the class.
+     */
+    private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(AnalyzerService.class);
 
     /**
      * The service loader for analyzers.
      */
-    private final ServiceLoader<Analyzer> loader;
+    private final ServiceLoader<Analyzer> service;
 
     /**
      * Creates a new instance of AnalyzerService.
@@ -39,15 +48,31 @@ public class AnalyzerService {
      * @param classLoader the ClassLoader to use when dynamically loading Analyzer and Update services
      */
     public AnalyzerService(ClassLoader classLoader) {
-        loader = ServiceLoader.load(Analyzer.class, classLoader);
+        service = ServiceLoader.load(Analyzer.class, classLoader);
     }
 
     /**
-     * Returns an Iterator for all instances of the Analyzer interface.
+     * Returns a list of all instances of the Analyzer interface.
      *
-     * @return an iterator of Analyzers.
+     * @return a list of Analyzers.
      */
-    public Iterator<Analyzer> getAnalyzers() {
-        return loader.iterator();
+    public List<Analyzer> getAnalyzers() {
+        final List<Analyzer> analyzers = new ArrayList<>();
+        final Iterator<Analyzer> iterator = service.iterator();
+        boolean experimentalEnabled = false;
+        try {
+            experimentalEnabled = Settings.getBoolean(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, false);
+        } catch (InvalidSettingException ex) {
+            LOGGER.error("invalid experimental setting", ex);
+        }
+        while (iterator.hasNext()) {
+            final Analyzer a = iterator.next();
+            if (!experimentalEnabled && a.getClass().isAnnotationPresent(Experimental.class)) {
+                continue;
+            }
+            LOGGER.debug("Loaded Analyzer {}", a.getName());
+            analyzers.add(a);
+        }
+        return analyzers;
     }
 }

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

@@ -18,17 +18,14 @@
 package org.owasp.dependencycheck.analyzer;
 
 import java.io.BufferedInputStream;
-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;
 
@@ -49,6 +46,7 @@ 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.exception.InitializationException;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
 import org.owasp.dependencycheck.utils.FileUtils;
 import org.owasp.dependencycheck.utils.Settings;
@@ -58,8 +56,8 @@ 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>
+ * 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
  */
@@ -70,7 +68,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      */
     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;
     /**
@@ -78,7 +77,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      */
     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);
     /**
@@ -98,43 +98,45 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * The set of things we can handle with Zip methods
      */
-    private static final Set<String> ZIPPABLES = newHashSet("zip", "ear", "war", "jar", "sar", "apk", "nupkg");
+    private static final Set<String> KNOWN_ZIP_EXT = 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)}.
+     * 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");
 
-    /**
-     * Detects files with extensions to remove from the engine's collection of dependencies.
-     */
-    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 Set<String> ext = new HashSet<String>(Collections.singletonList(additionalZipExt));
-            ZIPPABLES.addAll(ext);
+            final String[] ext = additionalZipExt.split("\\s*,\\s*");
+            Collections.addAll(KNOWN_ZIP_EXT, ext);
         }
-        EXTENSIONS.addAll(ZIPPABLES);
+        EXTENSIONS.addAll(KNOWN_ZIP_EXT);
     }
 
+    /**
+     * Detects files with extensions to remove from the engine's collection of
+     * dependencies.
+     */
+    private static final FileFilter REMOVE_FROM_ANALYSIS = FileFilterBuilder.newInstance()
+            .addExtensions("zip", "tar", "gz", "tgz", "bz2", "tbz2").build();
+
     /**
      * 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();
 
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
     /**
      * Returns the name of the analyzer.
      *
@@ -157,7 +159,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
     //</editor-fold>
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -169,72 +172,117 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * The initialize method does nothing for this Analyzer.
      *
-     * @throws Exception is thrown if there is an exception deleting or creating temporary files
+     * @throws InitializationException is thrown if there is an exception
+     * deleting or creating temporary files
      */
     @Override
-    public 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);
+    public void initializeFileTypeAnalyzer() throws InitializationException {
+        try {
+            final File baseDir = Settings.getTempDirectory();
+            tempFileLocation = File.createTempFile("check", "tmp", baseDir);
+            if (!tempFileLocation.delete()) {
+                setEnabled(false);
+                final String msg = String.format("Unable to delete temporary file '%s'.", tempFileLocation.getAbsolutePath());
+                throw new InitializationException(msg);
+            }
+            if (!tempFileLocation.mkdirs()) {
+                setEnabled(false);
+                final String msg = String.format("Unable to create directory '%s'.", tempFileLocation.getAbsolutePath());
+                throw new InitializationException(msg);
+            }
+        } catch (IOException ex) {
+            setEnabled(false);
+            throw new InitializationException("Unable to create a temporary file", ex);
         }
     }
 
     /**
-     * The close method deletes any temporary files and directories created during analysis.
+     * 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 {
+    public void closeAnalyzer() throws Exception {
         if (tempFileLocation != null && tempFileLocation.exists()) {
             LOGGER.debug("Attempting to delete temporary files");
             final boolean success = FileUtils.delete(tempFileLocation);
-            if (!success && tempFileLocation.exists() && tempFileLocation.list().length > 0) {
-                LOGGER.warn("Failed to delete some temporary files, see the log for more details");
+            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.
+     * Does not support parallel processing as it both modifies and iterates
+     * over the engine's list of dependencies.
+     *
+     * @return <code>true</code> if the analyzer supports parallel processing;
+     * otherwise <code>false</code>
+     * @see #analyzeDependency(Dependency, Engine)
+     * @see #findMoreDependencies(Engine, File)
+     */
+    @Override
+    public boolean supportsParallelProcessing() {
+        return false;
+    }
+
+    /**
+     * 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 analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeDependency(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 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",
-                        dependency.getFileName(),
-                        d.getFileName());
-                d.setFilePath(displayPath);
-                d.setFileName(displayName);
+        final List<Dependency> dependencySet = findMoreDependencies(engine, tmpDir);
 
-                //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.accept(d.getActualFile()) && scanDepth < MAX_SCAN_DEPTH) {
-                    scanDepth += 1;
-                    analyze(d, engine);
-                    scanDepth -= 1;
+        if (dependencySet != null && !dependencySet.isEmpty()) {
+            for (Dependency d : dependencySet) {
+                if (d.getFilePath().startsWith(tmpDir.getAbsolutePath())) {
+                    //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",
+                            dependency.getFileName(),
+                            d.getFileName());
+                    d.setFilePath(displayPath);
+                    d.setFileName(displayName);
+                    d.setProjectReferences(dependency.getProjectReferences());
+
+                    //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.accept(d.getActualFile()) && scanDepth < MAX_SCAN_DEPTH) {
+                        scanDepth += 1;
+                        analyze(d, engine);
+                        scanDepth -= 1;
+                    }
+                } else {
+                    for (Dependency sub : dependencySet) {
+                        if (sub.getFilePath().startsWith(tmpDir.getAbsolutePath())) {
+                            final String displayPath = String.format("%s%s",
+                                    dependency.getFilePath(),
+                                    sub.getActualFilePath().substring(tmpDir.getAbsolutePath().length()));
+                            final String displayName = String.format("%s: %s",
+                                    dependency.getFileName(),
+                                    sub.getFileName());
+                            sub.setFilePath(displayPath);
+                            sub.setFileName(displayName);
+                        }
+                    }
                 }
             }
         }
@@ -246,7 +294,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * If a zip file was identified as a possible JAR, this method will add the zip to the list of dependencies.
+     * 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
@@ -254,34 +303,41 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private void addDisguisedJarsToDependencies(Dependency dependency, Engine engine) throws AnalysisException {
         if (ZIP_FILTER.accept(dependency.getActualFile()) && isZipFileActuallyJarFile(dependency)) {
-            final File tdir = getNextTempDirectory();
+            final File tempDir = 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");
+            final File tmpLoc = new File(tempDir, fileName.substring(0, fileName.length() - 3) + "jar");
+            //store the archives sha1 and change it so that the engine doesn't think the zip and jar file are the same
+            // and add it is a related dependency.
+            final String archiveSha1 = dependency.getSha1sum();
             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?");
-                    }
+                dependency.setSha1sum("");
+                org.apache.commons.io.FileUtils.copyFile(dependency.getActualFile(), tmpLoc);
+                final List<Dependency> dependencySet = findMoreDependencies(engine, tmpLoc);
+                if (dependencySet != null && !dependencySet.isEmpty()) {
                     for (Dependency d : dependencySet) {
                         //fix the dependency's display name and path
-                        d.setFilePath(dependency.getFilePath());
-                        d.setDisplayFileName(dependency.getFileName());
+                        if (d.getActualFile().equals(tmpLoc)) {
+                            d.setFilePath(dependency.getFilePath());
+                            d.setDisplayFileName(dependency.getFileName());
+                        } else {
+                            for (Dependency sub : d.getRelatedDependencies()) {
+                                if (sub.getActualFile().equals(tmpLoc)) {
+                                    sub.setFilePath(dependency.getFilePath());
+                                    sub.setDisplayFileName(dependency.getFileName());
+                                }
+                            }
+                        }
                     }
                 }
             } catch (IOException ex) {
                 LOGGER.debug("Unable to perform deep copy on '{}'", dependency.getActualFile().getPath(), ex);
+            } finally {
+                dependency.setSha1sum(archiveSha1);
             }
         }
     }
-    /**
-     * 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.
@@ -290,20 +346,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * @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;
+    private static List<Dependency> findMoreDependencies(Engine engine, File file) {
+        return engine.scan(file);
     }
 
     /**
@@ -336,30 +380,49 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private void extractFiles(File archive, File destination, Engine engine) throws AnalysisException {
         if (archive != null && destination != null) {
-            FileInputStream fis;
+            String archiveExt = FileUtils.getFileExtension(archive.getName());
+            if (archiveExt == null) {
+                return;
+            }
+            archiveExt = archiveExt.toLowerCase();
+
+            final FileInputStream fis;
             try {
                 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();
+            BufferedInputStream in = null;
+            ZipArchiveInputStream zin = null;
+            TarArchiveInputStream tin = null;
+            GzipCompressorInputStream gin = null;
+            BZip2CompressorInputStream bzin = null;
             try {
-                if (ZIPPABLES.contains(archiveExt)) {
-                    extractArchive(new ZipArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
+                if (KNOWN_ZIP_EXT.contains(archiveExt)) {
+                    in = new BufferedInputStream(fis);
+                    ensureReadableJar(archiveExt, in);
+                    zin = new ZipArchiveInputStream(in);
+                    extractArchive(zin, destination, engine);
                 } else if ("tar".equals(archiveExt)) {
-                    extractArchive(new TarArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
+                    in = new BufferedInputStream(fis);
+                    tin = new TarArchiveInputStream(in);
+                    extractArchive(tin, 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);
+                        in = new BufferedInputStream(fis);
+                        gin = new GzipCompressorInputStream(in);
+                        decompressFile(gin, 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);
+                        in = new BufferedInputStream(fis);
+                        bzin = new BZip2CompressorInputStream(in);
+                        decompressFile(bzin, f);
                     }
                 }
             } catch (ArchiveExtractionException ex) {
@@ -369,7 +432,66 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                 LOGGER.warn("Exception reading archive '{}'.", archive.getName());
                 LOGGER.debug("", ex);
             } finally {
-                close(fis);
+                //overly verbose and not needed... but keeping it anyway due to
+                //having issue with file handles being left open
+                FileUtils.close(fis);
+                FileUtils.close(in);
+                FileUtils.close(zin);
+                FileUtils.close(tin);
+                FileUtils.close(gin);
+                FileUtils.close(bzin);
+            }
+        }
+    }
+
+    /**
+     * Checks if the file being scanned is a JAR that begins with '#!/bin' which
+     * indicates it is a fully executable jar. If a fully executable JAR is
+     * identified the input stream will be advanced to the start of the actual
+     * JAR file ( skipping the script).
+     *
+     * @see
+     * <a href="http://docs.spring.io/spring-boot/docs/1.3.0.BUILD-SNAPSHOT/reference/htmlsingle/#deployment-install">Installing
+     * Spring Boot Applications</a>
+     * @param archiveExt the file extension
+     * @param in the input stream
+     * @throws IOException thrown if there is an error reading the stream
+     */
+    private void ensureReadableJar(final String archiveExt, BufferedInputStream in) throws IOException {
+        if ("jar".equals(archiveExt) && in.markSupported()) {
+            in.mark(7);
+            final byte[] b = new byte[7];
+            final int read = in.read(b);
+            if (read == 7
+                    && b[0] == '#'
+                    && b[1] == '!'
+                    && b[2] == '/'
+                    && b[3] == 'b'
+                    && b[4] == 'i'
+                    && b[5] == 'n'
+                    && b[6] == '/') {
+                boolean stillLooking = true;
+                int chr;
+                int nxtChr;
+                while (stillLooking && (chr = in.read()) != -1) {
+                    if (chr == '\n' || chr == '\r') {
+                        in.mark(4);
+                        if ((chr = in.read()) != -1) {
+                            if (chr == 'P' && (chr = in.read()) != -1) {
+                                if (chr == 'K' && (chr = in.read()) != -1) {
+                                    if ((chr == 3 || chr == 5 || chr == 7) && (nxtChr = in.read()) != -1) {
+                                        if (nxtChr == chr + 1) {
+                                            stillLooking = false;
+                                            in.reset();
+                                        }
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            } else {
+                in.reset();
             }
         }
     }
@@ -380,7 +502,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * @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;
@@ -396,10 +519,10 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                     extractAcceptedFile(input, file);
                 }
             }
-        } catch (Throwable ex) {
+        } catch (IOException | AnalysisException ex) {
             throw new ArchiveExtractionException(ex);
         } finally {
-            close(input);
+            FileUtils.close(input);
         }
     }
 
@@ -412,16 +535,12 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      */
     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()) {
-                if (!parent.mkdirs()) {
-                    final String msg = String.format("Unable to build directory '%s'.", parent.getAbsolutePath());
-                    throw new AnalysisException(msg);
-                }
-            }
-            fos = new FileOutputStream(file);
+        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);
+        }
+        try (FileOutputStream fos = new FileOutputStream(file)) {
             IOUtils.copy(input, fos);
         } catch (FileNotFoundException ex) {
             LOGGER.debug("", ex);
@@ -431,8 +550,6 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
             LOGGER.debug("", ex);
             final String msg = String.format("IO Exception while parsing file '%s'.", file.getName());
             throw new AnalysisException(msg, ex);
-        } finally {
-            close(fos);
         }
     }
 
@@ -441,37 +558,16 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      *
      * @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);
+        try (FileOutputStream out = new FileOutputStream(outputFile)) {
             IOUtils.copy(inputStream, out);
-        } catch (FileNotFoundException ex) {
-            LOGGER.debug("", ex);
-            throw new ArchiveExtractionException(ex);
         } catch (IOException ex) {
             LOGGER.debug("", ex);
             throw new ArchiveExtractionException(ex);
-        } finally {
-            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);
-            }
         }
     }
 
@@ -505,7 +601,6 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
         } finally {
             ZipFile.closeQuietly(zip);
         }
-
         return isJar;
     }
 }

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

@@ -17,13 +17,13 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileFilter;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.InputStreamReader;
+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;
@@ -37,15 +37,19 @@ 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;
+import javax.xml.parsers.ParserConfigurationException;
+import org.owasp.dependencycheck.exception.InitializationException;
+import org.apache.commons.lang3.SystemUtils;
+import org.owasp.dependencycheck.utils.XmlUtils;
 
 /**
- * Analyzer for getting company, product, and version information from a .NET assembly.
+ * Analyzer for getting company, product, and version information from a .NET
+ * assembly.
  *
  * @author colezlaw
  *
@@ -68,10 +72,6 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      * The temp value for GrokAssembly.exe
      */
     private File grokAssemblyExe = null;
-    /**
-     * The DocumentBuilder for parsing the XML
-     */
-    private DocumentBuilder builder;
     /**
      * Logger
      */
@@ -82,18 +82,19 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      *
      * @return the list of arguments to begin populating the ProcessBuilder
      */
-    private List<String> buildArgumentList() {
+    protected 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"))) {
+        final List<String> args = new ArrayList<>();
+        if (!SystemUtils.IS_OS_WINDOWS) {
             if (Settings.getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH) != null) {
                 args.add(Settings.getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH));
-            } else {
+            } else if (isInPath("mono")) {
                 args.add("mono");
+            } else {
+                return null;
             }
         }
         args.add(grokAssemblyExe.getPath());
-
         return args;
     }
 
@@ -105,7 +106,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws AnalysisException if anything goes sideways
      */
     @Override
-    public void analyzeFileType(Dependency dependency, Engine engine)
+    public void analyzeDependency(Dependency dependency, Engine engine)
             throws AnalysisException {
         if (grokAssemblyExe == null) {
             LOGGER.warn("GrokAssembly didn't get deployed");
@@ -113,23 +114,26 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
         }
 
         final List<String> args = buildArgumentList();
+        if (args == null) {
+            LOGGER.warn("Assembly Analyzer was unable to execute");
+            return;
+        }
         args.add(dependency.getActualFilePath());
         final ProcessBuilder pb = new ProcessBuilder(args);
-        BufferedReader rdr = null;
         Document doc = null;
         try {
             final Process proc = pb.start();
-            // Try evacuating the error stream
-            rdr = new BufferedReader(new InputStreamReader(proc.getErrorStream(), "UTF-8"));
-            String line = null;
-            // CHECKSTYLE:OFF
-            while (rdr.ready() && (line = rdr.readLine()) != null) {
-                LOGGER.warn("Error from GrokAssembly: {}", line);
-            }
-            // CHECKSTYLE:ON
-            int rc = 0;
+            final DocumentBuilder builder = XmlUtils.buildSecureDocumentBuilder();
+
             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) {
@@ -140,7 +144,9 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                         dependency.getActualFilePath());
                 return;
             } else if (rc != 0) {
-                LOGGER.warn("Return code {} from GrokAssembly", rc);
+                LOGGER.debug("Return code {} from GrokAssembly; dependency-check is unable to analyze the library: {}",
+                        rc, dependency.getActualFilePath());
+                return;
             }
 
             final XPath xpath = XPathFactory.newInstance().newXPath();
@@ -169,110 +175,99 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                         product, Confidence.HIGH));
             }
 
-        } catch (IOException ioe) {
+        } catch (ParserConfigurationException pce) {
+            throw new AnalysisException("Error initializing the assembly analyzer", pce);
+        } catch (IOException | XPathExpressionException 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);
-        } finally {
-            if (rdr != null) {
-                try {
-                    rdr.close();
-                } catch (IOException ex) {
-                    LOGGER.debug("ignore", ex);
-                }
-            }
+            LOGGER.error("----------------------------------------------------");
+            LOGGER.error("Failed to read the Assembly Analyzer results. "
+                    + "On some systems mono-runtime and mono-devel need to be installed.");
+            LOGGER.error("----------------------------------------------------");
+            throw new AnalysisException("Couldn't parse Assembly Analyzer results (GrokAssembly)", saxe);
         }
+        // This shouldn't happen
+
     }
 
     /**
-     * Initialize the analyzer. In this case, extract GrokAssembly.exe to a temporary location.
+     * Initialize the analyzer. In this case, extract GrokAssembly.exe to a
+     * temporary location.
      *
-     * @throws Exception if anything goes wrong
+     * @throws InitializationException thrown 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;
+    public void initializeFileTypeAnalyzer() throws InitializationException {
+        final File tempFile;
+        final String cfg;
         try {
-            fos = new FileOutputStream(tempFile);
-            is = AssemblyAnalyzer.class.getClassLoader().getResourceAsStream("GrokAssembly.exe");
-            final byte[] buff = new byte[4096];
-            int bread = -1;
-            while ((bread = is.read(buff)) >= 0) {
-                fos.write(buff, 0, bread);
-            }
+            tempFile = File.createTempFile("GKA", ".exe", Settings.getTempDirectory());
+            cfg = tempFile.getPath() + ".config";
+        } catch (IOException ex) {
+            setEnabled(false);
+            throw new InitializationException("Unable to create temporary file for the assembly analyzer", ex);
+        }
+        try (FileOutputStream fos = new FileOutputStream(tempFile);
+                InputStream is = AssemblyAnalyzer.class.getClassLoader().getResourceAsStream("GrokAssembly.exe");
+                FileOutputStream fosCfg = new FileOutputStream(cfg);
+                InputStream isCfg = AssemblyAnalyzer.class.getClassLoader().getResourceAsStream("GrokAssembly.exe.config")) {
+            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());
+            IOUtils.copy(isCfg, fosCfg);
+            LOGGER.debug("Extracted GrokAssembly.exe.config to {}", cfg);
         } 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");
-                }
-            }
+            throw new InitializationException("Could not extract GrokAssembly.exe", ioe);
         }
 
         // Now, need to see if GrokAssembly actually runs from this location.
         final List<String> args = buildArgumentList();
-        BufferedReader rdr = null;
+        //TODO this creates an "unreported" error - if someone doesn't look
+        // at the command output this could easily be missed (especially in an
+        // Ant or Maven build.
+        //
+        // We need to create a non-fatal warning error type that will
+        // get added to the report.
+        //TODO this idea needs to get replicated to the bundle audit analyzer.
+        if (args == null) {
+            setEnabled(false);
+            LOGGER.error("----------------------------------------------------");
+            LOGGER.error(".NET Assembly Analyzer could not be initialized and at least one "
+                    + "'exe' or 'dll' was scanned. The 'mono' executable could not be found on "
+                    + "the path; either disable the Assembly Analyzer or configure the path mono. "
+                    + "On some systems mono-runtime and mono-devel need to be installed.");
+            LOGGER.error("----------------------------------------------------");
+            return;
+        }
         try {
             final ProcessBuilder pb = new ProcessBuilder(args);
             final Process p = pb.start();
             // Try evacuating the error stream
-            rdr = new BufferedReader(new InputStreamReader(p.getErrorStream(), "UTF-8"));
-            // CHECKSTYLE:OFF
-            while (rdr.ready() && rdr.readLine() != null) {
-                // We expect this to complain
-            }
-            // CHECKSTYLE:ON
-            final Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(p.getInputStream());
+            IOUtils.copy(p.getErrorStream(), NullOutputStream.NULL_OUTPUT_STREAM);
+
+            final DocumentBuilder builder = XmlUtils.buildSecureDocumentBuilder();
+            final Document doc = builder.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 (Throwable e) {
-            if (e instanceof AnalysisException) {
-                throw (AnalysisException) e;
-            } else {
-                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 occured with the .NET AssemblyAnalyzer", e);
-            }
-        } finally {
-            if (rdr != null) {
-                try {
-                    rdr.close();
-                } catch (IOException ex) {
-                    LOGGER.trace("ignore", ex);
-                }
+                setEnabled(false);
+                throw new InitializationException("Could not execute .NET AssemblyAnalyzer");
             }
+        } catch (InitializationException e) {
+            setEnabled(false);
+            throw e;
+        } catch (IOException | ParserConfigurationException | SAXException | XPathExpressionException | InterruptedException 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());
+            setEnabled(false);
+            throw new InitializationException("An error occurred with the .NET AssemblyAnalyzer", e);
         }
-        builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
     }
 
     /**
@@ -281,14 +276,15 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws Exception thrown if there is a problem closing the analyzer
      */
     @Override
-    public void close() throws Exception {
-        super.close();
+    public void closeAnalyzer() throws Exception {
         try {
             if (grokAssemblyExe != null && !grokAssemblyExe.delete()) {
+                LOGGER.debug("Unable to delete temporary GrokAssembly.exe; attempting delete on exit");
                 grokAssemblyExe.deleteOnExit();
             }
         } catch (SecurityException se) {
             LOGGER.debug("Can't delete temporary GrokAssembly.exe");
+            grokAssemblyExe.deleteOnExit();
         }
     }
 
@@ -324,7 +320,8 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -332,4 +329,27 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
     protected String getAnalyzerEnabledSettingKey() {
         return Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED;
     }
+
+    /**
+     * Tests to see if a file is in the system path. <b>Note</b> - the current
+     * implementation only works on non-windows platforms. For purposes of the
+     * AssemblyAnalyzer this is okay as this is only needed on Mac/*nix.
+     *
+     * @param file the executable to look for
+     * @return <code>true</code> if the file exists; otherwise
+     * <code>false</code>
+     */
+    private boolean isInPath(String file) {
+        final ProcessBuilder pb = new ProcessBuilder("which", file);
+        try {
+            final Process proc = pb.start();
+            final int retCode = proc.waitFor();
+            if (retCode == 0) {
+                return true;
+            }
+        } catch (IOException | InterruptedException ex) {
+            LOGGER.debug("Path search failed for " + file, ex);
+        }
+        return false;
+    }
 }

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

@@ -30,18 +30,21 @@ 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.nio.charset.Charset;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
- * 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.
+ * 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 <dvisser@ida.org>
- * @see <a href="https://www.gnu.org/software/autoconf/">Autoconf - GNU Project - Free Software Foundation (FSF)</a>
+ * @author Dale Visser
+ * @see <a href="https://www.gnu.org/software/autoconf/">Autoconf - GNU Project
+ * - Free Software Foundation (FSF)</a>
  */
+@Experimental
 public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -140,7 +143,8 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -150,7 +154,7 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
+    protected void analyzeDependency(Dependency dependency, Engine engine)
             throws AnalysisException {
         final File actualFile = dependency.getActualFile();
         final String name = actualFile.getName();
@@ -172,11 +176,7 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
                 }
             }
         } 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);
+            engine.getDependencies().remove(dependency);
         }
     }
 
@@ -220,14 +220,12 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private String getFileContents(final File actualFile)
             throws AnalysisException {
-        String contents = "";
         try {
-            contents = FileUtils.readFileToString(actualFile).trim();
+            return FileUtils.readFileToString(actualFile, Charset.defaultCharset()).trim();
         } catch (IOException e) {
             throw new AnalysisException(
                     "Problem occurred while reading dependency file.", e);
         }
-        return contents;
     }
 
     /**
@@ -270,10 +268,11 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the file type analyzer.
      *
-     * @throws Exception thrown if there is an exception during initialization
+     * @throws InitializationException thrown if there is an exception during
+     * initialization
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws Exception {
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
         // No initialization needed.
     }
 }

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

@@ -32,23 +32,29 @@ import org.slf4j.LoggerFactory;
 import java.io.File;
 import java.io.FileFilter;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.nio.charset.Charset;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
  * <p>
- * Used to analyze CMake build files, and collect information that can be used to determine the associated CPE.</p>
- * <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
+ * 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 <dvisser@ida.org>
+ * @author Dale Visser
  */
+@Experimental
 public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -62,11 +68,19 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
     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);
 
-    // Group 1: Product
-    // Group 2: Version
+    /**
+     * 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\"]?\\)",
@@ -78,24 +92,10 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
     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() {
@@ -123,13 +123,19 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * No-op initializer implementation.
+     * Initializes the analyzer.
      *
-     * @throws Exception never thrown
+     * @throws InitializationException thrown if an exception occurs getting an
+     * instance of SHA1
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws Exception {
-        // Nothing to do here.
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
+        try {
+            getSha1MessageDigest();
+        } catch (IllegalStateException ex) {
+            setEnabled(false);
+            throw new InitializationException("Unable to create SHA1 MessageDigest", ex);
+        }
     }
 
     /**
@@ -137,10 +143,11 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
      *
      * @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
+     * @throws AnalysisException thrown if there is an unrecoverable error
+     * analyzing the dependency
      */
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
+    protected void analyzeDependency(Dependency dependency, Engine engine)
             throws AnalysisException {
         final File file = dependency.getActualFile();
         final String parentName = file.getParentFile().getName();
@@ -148,7 +155,7 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
         dependency.setDisplayFileName(String.format("%s%c%s", parentName, File.separatorChar, name));
         String contents;
         try {
-            contents = FileUtils.readFileToString(file).trim();
+            contents = FileUtils.readFileToString(file, Charset.defaultCharset()).trim();
         } catch (IOException e) {
             throw new AnalysisException(
                     "Problem occurred while reading dependency file.", e);
@@ -172,8 +179,21 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
         }
     }
 
+    /**
+     * 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
+     */
+    @edu.umd.cs.findbugs.annotations.SuppressFBWarnings(
+            value = "DM_DEFAULT_ENCODING",
+            justification = "Default encoding is only used if UTF-8 is not available")
     private void analyzeSetVersionCommand(Dependency dependency, Engine engine, String contents) {
-        final Dependency orig = dependency;
+        Dependency currentDep = dependency;
+
         final Matcher m = SET_VERSION.matcher(contents);
         int count = 0;
         while (m.find()) {
@@ -190,19 +210,25 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
             }
             if (count > 1) {
                 //TODO - refactor so we do not assign to the parameter (checkstyle)
-                dependency = new Dependency(orig.getActualFile());
-                dependency.setDisplayFileName(String.format("%s:%s", orig.getDisplayFileName(), product));
-                final String filePath = String.format("%s:%s", orig.getFilePath(), product);
-                dependency.setFilePath(filePath);
+                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);
 
-                // prevents coalescing into the dependency provided by engine
-                dependency.setSha1sum(Checksum.getHex(sha1.digest(filePath.getBytes())));
-                engine.getDependencies().add(dependency);
+                byte[] path;
+                try {
+                    path = filePath.getBytes("UTF-8");
+                } catch (UnsupportedEncodingException ex) {
+                    path = filePath.getBytes();
+                }
+                final MessageDigest sha1 = getSha1MessageDigest();
+                currentDep.setSha1sum(Checksum.getHex(sha1.digest(path)));
+                engine.getDependencies().add(currentDep);
             }
-            final String source = dependency.getDisplayFileName();
-            dependency.getProductEvidence().addEvidence(source, "Product",
+            final String source = currentDep.getDisplayFileName();
+            currentDep.getProductEvidence().addEvidence(source, "Product",
                     product, Confidence.MEDIUM);
-            dependency.getVersionEvidence().addEvidence(source, "Version",
+            currentDep.getVersionEvidence().addEvidence(source, "Version",
                     version, Confidence.MEDIUM);
         }
         LOGGER.debug(String.format("Found %d matches.", count));
@@ -212,4 +238,18 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
     protected String getAnalyzerEnabledSettingKey() {
         return Settings.KEYS.ANALYZER_CMAKE_ENABLED;
     }
+
+    /**
+     * Returns the sha1 message digest.
+     *
+     * @return the sha1 message digest
+     */
+    private MessageDigest getSha1MessageDigest() {
+        try {
+            return MessageDigest.getInstance("SHA1");
+        } catch (NoSuchAlgorithmException e) {
+            LOGGER.error(e.getMessage());
+            throw new IllegalStateException("Failed to obtain the SHA1 message digest.", e);
+        }
+    }
 }

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

@@ -25,6 +25,8 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 import java.util.StringTokenizer;
+import java.util.concurrent.TimeUnit;
+import org.apache.commons.lang3.builder.CompareToBuilder;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.index.CorruptIndexException;
 import org.apache.lucene.queryparser.classic.ParseException;
@@ -45,18 +47,21 @@ 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.exception.InitializationException;
 import org.owasp.dependencycheck.utils.DependencyVersion;
 import org.owasp.dependencycheck.utils.DependencyVersionUtil;
+import org.owasp.dependencycheck.utils.Settings;
 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
  */
-public class CPEAnalyzer implements Analyzer {
+public class CPEAnalyzer extends AbstractAnalyzer {
 
     /**
      * The Logger.
@@ -65,23 +70,26 @@ public class CPEAnalyzer implements Analyzer {
     /**
      * The maximum number of query results to return.
      */
-    static final int MAX_QUERY_RESULTS = 25;
+    private static final int MAX_QUERY_RESULTS = 25;
     /**
      * The weighting boost to give terms when constructing the Lucene query.
      */
-    static final String WEIGHTING_BOOST = "^5";
+    private 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 ._-]";
+    private 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]*";
+    private 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;
+    private static final int STRING_BUILDER_BUFFER = 20;
     /**
      * The CPE in memory index.
      */
@@ -117,34 +125,55 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * Creates the CPE Lucene Index.
+     * The default is to support parallel processing.
      *
-     * @throws Exception is thrown if there is an issue opening the index.
+     * @return false
      */
     @Override
-    public void initialize() throws Exception {
-        this.open();
+    public boolean supportsParallelProcessing() {
+        return false;
+    }
+
+    /**
+     * Creates the CPE Lucene Index.
+     *
+     * @throws InitializationException is thrown if there is an issue opening
+     * the index.
+     */
+    @Override
+    public void initializeAnalyzer() throws InitializationException {
+        try {
+            this.open();
+        } catch (IOException ex) {
+            LOGGER.debug("Exception initializing the Lucene Index", ex);
+            throw new InitializationException("An exception occurred initializing the Lucene Index", ex);
+        } catch (DatabaseException ex) {
+            LOGGER.debug("Exception accessing the database", ex);
+            throw new InitializationException("An exception occurred accessing the database", ex);
+        }
     }
 
     /**
      * 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 {
-        cve = new CveDB();
-        cve.open();
-        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);
+        if (!isOpen()) {
+            cve = CveDB.getInstance();
+            cpe = CpeMemoryIndex.getInstance();
+            try {
+                final long creationStart = System.currentTimeMillis();
+                cpe.open(cve);
+                final long creationSeconds = TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - creationStart);
+                LOGGER.info("Created CPE Index ({} seconds)", creationSeconds);
+            } catch (IndexException ex) {
+                LOGGER.debug("IndexException", ex);
+                throw new DatabaseException(ex);
+            }
         }
     }
 
@@ -152,24 +181,30 @@ public class CPEAnalyzer implements Analyzer {
      * Closes the data sources.
      */
     @Override
-    public void close() {
-        if (cpe != null) {
-            cpe.close();
-            cpe = null;
-        }
+    public void closeAnalyzer() {
         if (cve != null) {
             cve.close();
             cve = null;
         }
+        if (cpe != null) {
+            cpe.close();
+            cpe = null;
+        }
     }
 
+    /**
+     * Returns whether or not the analyzer is open.
+     *
+     * @return <code>true</code> if the analyzer is open
+     */
     public boolean isOpen() {
         return cpe != null && cpe.isOpen();
     }
 
     /**
-     * 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.
@@ -177,7 +212,7 @@ 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 {
-        //TODO test dojo-war against this. we shold get dojo-toolkit:dojo-toolkit AND dojo-toolkit:toolkit
+        //TODO test dojo-war against this. we should get dojo-toolkit:dojo-toolkit AND dojo-toolkit:toolkit
         String vendors = "";
         String products = "";
         for (Confidence confidence : Confidence.values()) {
@@ -190,8 +225,8 @@ public class CPEAnalyzer implements Analyzer {
                 LOGGER.debug("product search: {}", products);
             }
             if (!vendors.isEmpty() && !products.isEmpty()) {
-                final List<IndexEntry> entries = searchCPE(vendors, products, dependency.getProductEvidence().getWeighting(),
-                        dependency.getVendorEvidence().getWeighting());
+                final List<IndexEntry> entries = searchCPE(vendors, products, dependency.getVendorEvidence().getWeighting(),
+                        dependency.getProductEvidence().getWeighting());
                 if (entries == null) {
                     continue;
                 }
@@ -213,9 +248,10 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * 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
@@ -246,23 +282,25 @@ public class CPEAnalyzer implements Analyzer {
 
     /**
      * <p>
-     * Searches the Lucene CPE index to identify possible CPE entries associated with the supplied vendor, product, and
-     * version.</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>
+     * 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
      */
     protected List<IndexEntry> searchCPE(String vendor, String product,
             Set<String> vendorWeightings, Set<String> productWeightings) {
 
-        final List<IndexEntry> ret = new ArrayList<IndexEntry>(MAX_QUERY_RESULTS);
+        final List<IndexEntry> ret = new ArrayList<>(MAX_QUERY_RESULTS);
 
         final String searchString = buildSearch(vendor, product, vendorWeightings, productWeightings);
         if (searchString == null) {
@@ -284,10 +322,10 @@ public class CPEAnalyzer implements Analyzer {
             }
             return ret;
         } catch (ParseException ex) {
-            LOGGER.warn("An error occured querying the CPE data. See the log for more details.");
+            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 occured reading CPE data. See the log for more details.");
+            LOGGER.warn("An error occurred reading CPE data. See the log for more details.");
             LOGGER.info("IO Error with search string: {}", searchString, ex);
         }
         return null;
@@ -295,16 +333,20 @@ public class CPEAnalyzer implements Analyzer {
 
     /**
      * <p>
-     * Builds a Lucene search string by properly escaping data and constructing a valid search query.</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>
+     * 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,
@@ -325,17 +367,21 @@ 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);
 
@@ -349,20 +395,27 @@ 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(" ) ");
@@ -370,7 +423,8 @@ 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.
@@ -380,7 +434,8 @@ 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.
@@ -397,8 +452,9 @@ 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.
@@ -430,7 +486,7 @@ public class CPEAnalyzer implements Analyzer {
             return false;
         }
         final String[] words = text.split("[\\s_-]");
-        final List<String> list = new ArrayList<String>();
+        final List<String> list = new ArrayList<>();
         String tempWord = null;
         for (String word : words) {
             /*
@@ -465,14 +521,16 @@ 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 {
+    protected synchronized void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         try {
             determineCPE(dependency);
         } catch (CorruptIndexException ex) {
@@ -485,15 +543,19 @@ public class CPEAnalyzer implements Analyzer {
     }
 
     /**
-     * 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>
+     * @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
      */
     protected boolean determineIdentifiers(Dependency dependency, String vendor, String product,
@@ -502,11 +564,12 @@ public class CPEAnalyzer implements Analyzer {
         DependencyVersion bestGuess = new DependencyVersion("-");
         Confidence bestGuessConf = null;
         boolean hasBroadMatch = false;
-        final List<IdentifierMatch> collected = new ArrayList<IdentifierMatch>();
+        final List<IdentifierMatch> collected = new ArrayList<>();
+
+        //TODO the following algorithm incorrectly identifies things as a lower version
+        // if there lower confidence evidence when the current (highest) version number
+        // is newer then anything in the NVD.
         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) {
@@ -515,7 +578,7 @@ public class CPEAnalyzer implements Analyzer {
                 for (VulnerableSoftware vs : cpes) {
                     DependencyVersion dbVer;
                     if (vs.getUpdate() != null && !vs.getUpdate().isEmpty()) {
-                        dbVer = DependencyVersionUtil.parseVersion(vs.getVersion() + "." + vs.getUpdate());
+                        dbVer = DependencyVersionUtil.parseVersion(vs.getVersion() + '.' + vs.getUpdate());
                     } else {
                         dbVer = DependencyVersionUtil.parseVersion(vs.getVersion());
                     }
@@ -528,24 +591,22 @@ public class CPEAnalyzer implements Analyzer {
                         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 {
+
                         //TODO the following isn't quite right is it? need to think about this guessing game a bit more.
-                        if (evVer.getVersionParts().size() <= dbVer.getVersionParts().size()
-                                && evVer.matchesAtLeastThreeLevels(dbVer)) {
-                            if (bestGuessConf == null || bestGuessConf.compareTo(conf) > 0) {
-                                if (bestGuess.getVersionParts().size() < dbVer.getVersionParts().size()) {
-                                    bestGuess = dbVer;
-                                    bestGuessConf = conf;
-                                }
+                    } else if (evVer.getVersionParts().size() <= dbVer.getVersionParts().size()
+                            && evVer.matchesAtLeastThreeLevels(dbVer)) {
+                        if (bestGuessConf == null || bestGuessConf.compareTo(conf) > 0) {
+                            if (bestGuess.getVersionParts().size() < dbVer.getVersionParts().size()) {
+                                bestGuess = dbVer;
+                                bestGuessConf = conf;
                             }
                         }
                     }
                 }
-                if (bestGuessConf == null || bestGuessConf.compareTo(conf) > 0) {
-                    if (bestGuess.getVersionParts().size() < evVer.getVersionParts().size()) {
-                        bestGuess = evVer;
-                        bestGuessConf = conf;
-                    }
+                if ((bestGuessConf == null || bestGuessConf.compareTo(conf) > 0)
+                        && bestGuess.getVersionParts().size() < evVer.getVersionParts().size()) {
+                    bestGuess = evVer;
+                    bestGuessConf = conf;
                 }
             }
         }
@@ -555,10 +616,12 @@ public class CPEAnalyzer implements Analyzer {
             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) {
+        if (bestGuessConf
+                == null) {
             bestGuessConf = Confidence.LOW;
         }
         final IdentifierMatch match = new IdentifierMatch("cpe", cpeName, url, IdentifierConfidence.BEST_GUESS, bestGuessConf);
+
         collected.add(match);
 
         Collections.sort(collected);
@@ -581,6 +644,18 @@ public class CPEAnalyzer implements Analyzer {
         return identifierAdded;
     }
 
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_CPE_ENABLED;
+
+    }
+
     /**
      * The confidence whether the identifier is an exact match, or a best guess.
      */
@@ -595,37 +670,50 @@ public class CPEAnalyzer implements Analyzer {
          */
         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.
+         * 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> {
 
+        /**
+         * The confidence in the evidence used to identify this match.
+         */
+        private Confidence evidenceConfidence;
+        /**
+         * The confidence whether this is an exact match, or a best guess.
+         */
+        private IdentifierConfidence confidence;
+        /**
+         * The CPE identifier.
+         */
+        private Identifier identifier;
+
         /**
          * 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);
             this.confidence = identifierConfidence;
             this.evidenceConfidence = evidenceConfidence;
         }
-        //<editor-fold defaultstate="collapsed" desc="Property implementations: evidenceConfidence, confidence, identifier">
-        /**
-         * The confidence in the evidence used to identify this match.
-         */
-        private Confidence evidenceConfidence;
 
+        //<editor-fold defaultstate="collapsed" desc="Property implementations: evidenceConfidence, confidence, identifier">
         /**
          * Get the value of evidenceConfidence
          *
@@ -643,10 +731,6 @@ public class CPEAnalyzer implements Analyzer {
         public void setEvidenceConfidence(Confidence evidenceConfidence) {
             this.evidenceConfidence = evidenceConfidence;
         }
-        /**
-         * The confidence whether this is an exact match, or a best guess.
-         */
-        private IdentifierConfidence confidence;
 
         /**
          * Get the value of confidence.
@@ -665,10 +749,6 @@ public class CPEAnalyzer implements Analyzer {
         public void setConfidence(IdentifierConfidence confidence) {
             this.confidence = confidence;
         }
-        /**
-         * The CPE identifier.
-         */
-        private Identifier identifier;
 
         /**
          * Get the value of identifier.
@@ -736,29 +816,24 @@ public class CPEAnalyzer implements Analyzer {
             if (this.confidence != other.confidence) {
                 return false;
             }
-            if (this.identifier != other.identifier && (this.identifier == null || !this.identifier.equals(other.identifier))) {
-                return false;
-            }
-            return true;
+            return !(this.identifier != other.identifier && (this.identifier == null || !this.identifier.equals(other.identifier)));
         }
         //</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
          */
         @Override
         public int compareTo(IdentifierMatch o) {
-            int conf = this.confidence.compareTo(o.confidence);
-            if (conf == 0) {
-                conf = this.evidenceConfidence.compareTo(o.evidenceConfidence);
-                if (conf == 0) {
-                    conf = identifier.compareTo(o.identifier);
-                }
-            }
-            return conf;
+            return new CompareToBuilder()
+                    .append(confidence, o.confidence)
+                    .append(evidenceConfidence, o.evidenceConfidence)
+                    .append(identifier, o.identifier)
+                    .toComparison();
         }
     }
 }

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

@@ -33,8 +33,10 @@ 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 java.util.List;
+import org.owasp.dependencycheck.exception.InitializationException;
 import org.owasp.dependencycheck.utils.DownloadFailedException;
 import org.owasp.dependencycheck.utils.Downloader;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
@@ -42,8 +44,8 @@ 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.
+ * Analyzer which will attempt to locate a dependency, and the GAV information,
+ * by querying Central for the dependency's SHA-1 digest.
  *
  * @author colezlaw
  */
@@ -70,9 +72,10 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
     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.
+     * 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;
+    private volatile boolean errorFlag = false;
 
     /**
      * The searcher itself.
@@ -96,17 +99,18 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Determines if this analyzer is enabled.
      *
-     * @return <code>true</code> if the analyzer is enabled; otherwise <code>false</code>
+     * @return <code>true</code> if the analyzer is enabled; otherwise
+     * <code>false</code>
      */
     private boolean checkEnabled() {
-        boolean retval = false;
+        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;
+                    retVal = true;
                 } else {
                     LOGGER.info("Nexus analyzer is enabled, disabling the Central Analyzer");
                 }
@@ -116,22 +120,27 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
         } catch (InvalidSettingException ise) {
             LOGGER.warn("Invalid setting. Disabling the Central analyzer");
         }
-        return retval;
+        return retVal;
     }
 
     /**
      * Initializes the analyzer once before any analysis is performed.
      *
-     * @throws Exception if there's an error during initialization
+     * @throws InitializationException if there's an error during initialization
      */
     @Override
-    public void initializeFileTypeAnalyzer() throws Exception {
+    public void initializeFileTypeAnalyzer() throws InitializationException {
         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));
+            try {
+                searcher = new CentralSearch(new URL(searchUrl));
+            } catch (MalformedURLException ex) {
+                setEnabled(false);
+                throw new InitializationException("The configured URL to Maven Central is malformed: " + searchUrl, ex);
+            }
         }
     }
 
@@ -146,7 +155,8 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to to reference the
+     * analyzer's enabled property.
      *
      * @return the analyzer's enabled property setting key.
      */
@@ -183,7 +193,7 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws AnalysisException when there's an exception during analysis
      */
     @Override
-    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         if (errorFlag || !isEnabled()) {
             return;
         }
@@ -192,7 +202,7 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
             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.toString(), dependency.getFileName());
+                LOGGER.debug("Central analyzer found artifact ({}) for dependency ({})", ma, dependency.getFileName());
                 dependency.addAsEvidence("central", ma, confidence);
                 boolean pomAnalyzed = false;
                 for (Evidence e : dependency.getVendorEvidence()) {
@@ -219,7 +229,8 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
                         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)) {
+                        if (pomFile != null && pomFile.exists() && !FileUtils.deleteQuietly(pomFile)) {
+                            LOGGER.debug("Failed to delete temporary pom file {}", pomFile.toString());
                             pomFile.deleteOnExit();
                         }
                     }

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

@@ -0,0 +1,205 @@
+/*
+ * 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) 2016 IBM Corporation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+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;
+
+/**
+ * This analyzer is used to analyze SWIFT and Objective-C packages by collecting
+ * information from .podspec files. CocoaPods dependency manager see
+ * https://cocoapods.org/.
+ *
+ * @author Bianca Jiang (https://twitter.com/biancajiang)
+ */
+@Experimental
+public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+//    private static final Logger LOGGER = LoggerFactory.getLogger(CocoaPodsAnalyzer.class);
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "CocoaPods 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 PODSPEC = "podspec";
+    /**
+     * Filter that detects files named "*.podspec".
+     */
+    private static final FileFilter PODSPEC_FILTER = FileFilterBuilder.newInstance().addExtensions(PODSPEC).build();
+
+    /**
+     * The capture group #1 is the block variable. e.g. "Pod::Spec.new do
+     * |spec|"
+     */
+    private static final Pattern PODSPEC_BLOCK_PATTERN = Pattern.compile("Pod::Spec\\.new\\s+?do\\s+?\\|(.+?)\\|");
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return PODSPEC_FILTER;
+    }
+
+    @Override
+    protected void initializeFileTypeAnalyzer() {
+        // 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_COCOAPODS_ENABLED;
+    }
+
+    @Override
+    protected void analyzeDependency(Dependency dependency, Engine engine)
+            throws AnalysisException {
+
+        String contents;
+        try {
+            contents = FileUtils.readFileToString(dependency.getActualFile(), Charset.defaultCharset());
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+        final Matcher matcher = PODSPEC_BLOCK_PATTERN.matcher(contents);
+        if (matcher.find()) {
+            contents = contents.substring(matcher.end());
+            final String blockVariable = matcher.group(1);
+
+            final EvidenceCollection vendor = dependency.getVendorEvidence();
+            final EvidenceCollection product = dependency.getProductEvidence();
+            final EvidenceCollection version = dependency.getVersionEvidence();
+
+            final String name = addStringEvidence(product, contents, blockVariable, "name", "name", Confidence.HIGHEST);
+            if (!name.isEmpty()) {
+                vendor.addEvidence(PODSPEC, "name_project", name, Confidence.HIGHEST);
+            }
+            addStringEvidence(product, contents, blockVariable, "summary", "summary", Confidence.HIGHEST);
+
+            addStringEvidence(vendor, contents, blockVariable, "author", "authors?", Confidence.HIGHEST);
+            addStringEvidence(vendor, contents, blockVariable, "homepage", "homepage", Confidence.HIGHEST);
+            addStringEvidence(vendor, contents, blockVariable, "license", "licen[cs]es?", Confidence.HIGHEST);
+
+            addStringEvidence(version, contents, blockVariable, "version", "version", Confidence.HIGHEST);
+        }
+
+        setPackagePath(dependency);
+    }
+
+    /**
+     * Extracts evidence from the contents and adds it to the given evidence
+     * collection.
+     *
+     * @param evidences the evidence collection to update
+     * @param contents the text to extract evidence from
+     * @param blockVariable the block variable within the content to search for
+     * @param field the name of the field being searched for
+     * @param fieldPattern the field pattern within the contents to search for
+     * @param confidence the confidence level of the evidence if found
+     * @return the string that was added as evidence
+     */
+    private String addStringEvidence(EvidenceCollection evidences, String contents,
+            String blockVariable, String field, String fieldPattern, Confidence confidence) {
+        String value = "";
+
+        //capture array value between [ ]
+        final Matcher arrayMatcher = Pattern.compile(
+                String.format("\\s*?%s\\.%s\\s*?=\\s*?\\{\\s*?(.*?)\\s*?\\}", blockVariable, fieldPattern),
+                Pattern.CASE_INSENSITIVE).matcher(contents);
+        if (arrayMatcher.find()) {
+            value = arrayMatcher.group(1);
+        } else { //capture single value between quotes
+            final Matcher matcher = Pattern.compile(
+                    String.format("\\s*?%s\\.%s\\s*?=\\s*?(['\"])(.*?)\\1", blockVariable, fieldPattern),
+                    Pattern.CASE_INSENSITIVE).matcher(contents);
+            if (matcher.find()) {
+                value = matcher.group(2);
+            }
+        }
+        if (value.length() > 0) {
+            evidences.addEvidence(PODSPEC, field, value, confidence);
+        }
+        return value;
+    }
+
+    /**
+     * Sets the package path on the given dependency.
+     *
+     * @param dep the dependency to update
+     */
+    private void setPackagePath(Dependency dep) {
+        final File file = new File(dep.getFilePath());
+        final String parent = file.getParent();
+        if (parent != null) {
+            dep.setPackagePath(parent);
+        }
+    }
+}

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

@@ -24,6 +24,7 @@ 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.exception.InitializationException;
 import org.owasp.dependencycheck.utils.Checksum;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
 import org.owasp.dependencycheck.utils.Settings;
@@ -32,39 +33,41 @@ import org.slf4j.LoggerFactory;
 
 import java.io.FileFilter;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.charset.Charset;
 import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
 
 /**
  * Used to analyze a composer.lock file for a composer PHP app.
  *
  * @author colezlaw
  */
+@Experimental
 public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
-     * The logger
+     * The logger.
      */
     private static final Logger LOGGER = LoggerFactory.getLogger(ComposerLockAnalyzer.class);
 
     /**
-     * The analyzer name
+     * The analyzer name.
      */
     private static final String ANALYZER_NAME = "Composer.lock analyzer";
 
     /**
-     * composer.json
+     * composer.json.
      */
     private static final String COMPOSER_LOCK = "composer.lock";
 
     /**
-     * The FileFilter
+     * The FileFilter.
      */
     private static final FileFilter FILE_FILTER = FileFilterBuilder.newInstance().addFilenames(COMPOSER_LOCK).build();
 
     /**
-     * Returns the FileFilter
+     * Returns the FileFilter.
      *
      * @return the FileFilter
      */
@@ -74,20 +77,21 @@ public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Initializes the analyzer
+     * Initializes the analyzer.
      *
-     * @throws Exception
+     * @throws InitializationException thrown if an exception occurs getting an
+     * instance of SHA1
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws Exception {
-        sha1 = MessageDigest.getInstance("SHA1");
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
+        try {
+            getSha1MessageDigest();
+        } catch (IllegalStateException ex) {
+            setEnabled(false);
+            throw new InitializationException("Unable to create SHA1 MessageDigest", ex);
+        }
     }
 
-    /**
-     * The MessageDigest for calculating a new digest for the new dependencies added
-     */
-    private MessageDigest sha1 = null;
-
     /**
      * Entry point for the analyzer.
      *
@@ -96,10 +100,8 @@ public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
      * @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());
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
+        try (FileInputStream fis = new FileInputStream(dependency.getActualFile())) {
             final ComposerLockParser clp = new ComposerLockParser(fis);
             LOGGER.info("Checking composer.lock file {}", dependency.getActualFilePath());
             clp.process();
@@ -107,6 +109,7 @@ public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
                 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());
+                final MessageDigest sha1 = getSha1MessageDigest();
                 d.setFilePath(filePath);
                 d.setSha1sum(Checksum.getHex(sha1.digest(filePath.getBytes(Charset.defaultCharset()))));
                 d.getVendorEvidence().addEvidence(COMPOSER_LOCK, "vendor", dep.getGroup(), Confidence.HIGHEST);
@@ -115,18 +118,10 @@ public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
                 LOGGER.info("Adding dependency {}", d);
                 engine.getDependencies().add(d);
             }
-        } catch (FileNotFoundException fnfe) {
+        } catch (IOException ex) {
             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);
-                }
-            }
         }
     }
 
@@ -159,4 +154,18 @@ public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
     public AnalysisPhase getAnalysisPhase() {
         return AnalysisPhase.INFORMATION_COLLECTION;
     }
+
+    /**
+     * Returns the sha1 message digest.
+     *
+     * @return the sha1 message digest
+     */
+    private MessageDigest getSha1MessageDigest() {
+        try {
+            return MessageDigest.getInstance("SHA1");
+        } catch (NoSuchAlgorithmException e) {
+            LOGGER.error(e.getMessage());
+            throw new IllegalStateException("Failed to obtain the SHA1 message digest.", e);
+        }
+    }
 }

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

@@ -20,7 +20,8 @@ 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;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.xml.suppression.SuppressionRule;
 
 /**
  * The suppression analyzer processes an externally defined XML document that complies with the suppressions.xsd schema.
@@ -62,7 +63,7 @@ public class CpeSuppressionAnalyzer extends AbstractSuppressionAnalyzer {
     //</editor-fold>
 
     @Override
-    public void analyze(final Dependency dependency, final Engine engine) throws AnalysisException {
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
 
         if (getRules() == null || getRules().size() <= 0) {
             return;
@@ -72,4 +73,15 @@ public class CpeSuppressionAnalyzer extends AbstractSuppressionAnalyzer {
             rule.process(dependency);
         }
     }
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_CPE_SUPPRESSION_ENABLED;
+    }
 }

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

@@ -30,20 +30,24 @@ 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.Settings;
 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>
+ * 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>
+ * Note, this grouping only works on dependencies with identified CVE
+ * entries</p>
  *
  * @author Jeremy Long
  */
-public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Analyzer {
+public class DependencyBundlingAnalyzer extends AbstractAnalyzer {
 
     /**
      * The Logger.
@@ -55,10 +59,23 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
      * A pattern for obtaining the first part of a filename.
      */
     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;
+
+    /**
+     * Returns a flag indicating if this analyzer has run. This analyzer only
+     * runs once. Note this is currently only used in the unit tests.
+     *
+     * @return a flag indicating if this analyzer has run. This analyzer only
+     * runs once
+     */
+    protected synchronized boolean getAnalyzed() {
+        return analyzed;
+    }
+
     //</editor-fold>
     //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
@@ -68,7 +85,7 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     /**
      * The phase that this analyzer is intended to run in.
      */
-    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.PRE_FINDING_ANALYSIS;
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.FINAL;
 
     /**
      * Returns the name of the analyzer.
@@ -92,18 +109,43 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     //</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.
+     * Does not support parallel processing as it only runs once and then
+     * operates on <em>all</em> dependencies.
+     *
+     * @return whether or not parallel processing is enabled
+     * @see #analyze(Dependency, Engine)
+     */
+    @Override
+    public boolean supportsParallelProcessing() {
+        return false;
+    }
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_DEPENDENCY_BUNDLING_ENABLED;
+    }
+
+    /**
+     * 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 {
+    protected synchronized void analyzeDependency(Dependency ignore, Engine engine) throws AnalysisException {
         if (!analyzed) {
             analyzed = true;
-            final Set<Dependency> dependenciesToRemove = new HashSet<Dependency>();
+            final Set<Dependency> dependenciesToRemove = new HashSet<>();
             final ListIterator<Dependency> mainIterator = engine.getDependencies().listIterator();
             //for (Dependency nextDependency : engine.getDependencies()) {
             while (mainIterator.hasNext()) {
@@ -112,13 +154,15 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
                     final ListIterator<Dependency> subIterator = engine.getDependencies().listIterator(mainIterator.nextIndex());
                     while (subIterator.hasNext()) {
                         final Dependency nextDependency = subIterator.next();
-                        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
+                        if (hashesMatch(dependency, nextDependency)) {
+                            if (!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")) {
@@ -131,6 +175,7 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
                             }
                         } else if (cpeIdentifiersMatch(dependency, nextDependency)
                                 && hasSameBasePath(dependency, nextDependency)
+                                && vulnCountMatches(dependency, nextDependency)
                                 && fileNameMatch(dependency, nextDependency)) {
                             if (isCore(dependency, nextDependency)) {
                                 mergeDependencies(dependency, nextDependency, dependenciesToRemove);
@@ -152,10 +197,11 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
      * 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
+     * @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);
@@ -171,13 +217,19 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * Attempts to trim a maven repo to a common base path. This is typically [drive]\[repo_location]\repository\[path1]\[path2].
+     * 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.
      */
     private String getBaseRepoPath(final String path) {
-        int pos = path.indexOf("repository" + File.separator) + 11;
+        int pos;
+        if (path.contains("local-repo")) {
+            pos = path.indexOf("local-repo" + File.separator) + 11;
+        } else {
+            pos = path.indexOf("repository" + File.separator) + 11;
+        }
         if (pos < 0) {
             return path;
         }
@@ -196,11 +248,13 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * Returns true if the file names (and version if it exists) of the two dependencies are sufficiently similar.
+     * 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
@@ -213,10 +267,8 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
         //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
@@ -230,11 +282,13 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * Returns true if the CPE 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 cpeIdentifiersMatch(Dependency dependency1, Dependency dependency2) {
         if (dependency1 == null || dependency1.getIdentifiers() == null
@@ -268,6 +322,19 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
         return matches;
     }
 
+    /**
+     * Returns true if the two dependencies have the same vulnerability count.
+     *
+     * @param dependency1 a dependency2 to compare
+     * @param dependency2 a dependency2 to compare
+     * @return true if the two dependencies have the same vulnerability count
+     */
+    private boolean vulnCountMatches(Dependency dependency1, Dependency dependency2) {
+        return dependency1.getVulnerabilities() != null && dependency2.getVulnerabilities() != null
+                && dependency1.getVulnerabilities().size() == dependency2.getVulnerabilities().size();
+
+    }
+
     /**
      * Determines if the two dependencies have the same base path.
      *
@@ -285,11 +352,14 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
         String right = rFile.getParent();
         if (left == null) {
             return right == null;
+        } else if (right == null) {
+            return false;
         }
         if (left.equalsIgnoreCase(right)) {
             return true;
         }
-        if (left.matches(".*[/\\\\]repository[/\\\\].*") && right.matches(".*[/\\\\]repository[/\\\\].*")) {
+
+        if (left.matches(".*[/\\\\](repository|local-repo)[/\\\\].*") && right.matches(".*[/\\\\](repository|local-repo)[/\\\\].*")) {
             left = getBaseRepoPath(left);
             right = getBaseRepoPath(right);
         }
@@ -306,14 +376,15 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * 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.
      */
-    boolean isCore(Dependency left, Dependency right) {
+    protected boolean isCore(Dependency left, Dependency right) {
         final String leftName = left.getFileName().toLowerCase();
         final String rightName = right.getFileName().toLowerCase();
 
@@ -326,10 +397,6 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
                 || !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,
@@ -347,11 +414,13 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * Compares the SHA1 hashes of two dependencies to determine if they are equal.
+     * 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
+     * @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) {
@@ -361,12 +430,13 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * 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.
+     * 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
+     * @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();
@@ -380,14 +450,18 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     }
 
     /**
-     * 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.
+     * 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>
+     * @return <code>true</code> if the leftPath is the shortest; otherwise
+     * <code>false</code>
      */
     protected boolean firstPathIsShortest(String left, String right) {
+        if (left.contains("dctemp")) {
+            return false;
+        }
         final String leftPath = left.replace('\\', '/');
         final String rightPath = right.replace('\\', '/');
 
@@ -425,6 +499,7 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
      * @return true if the path contains '.war\' or '.ear\'.
      */
     private boolean containedInWar(String filePath) {
-        return filePath == null ? false : filePath.matches(".*\\.(ear|war)[\\\\/].*");
+        return filePath != null && filePath.matches(".*\\.(ear|war)[\\\\/].*");
     }
+
 }

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

@@ -0,0 +1,283 @@
+/*
+ * 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.util.HashSet;
+import java.util.Iterator;
+import java.util.ListIterator;
+import java.util.Set;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * <p>
+ * This analyzer will merge dependencies, created from different source, into a
+ * single dependency.</p>
+ *
+ * @author Jeremy Long
+ */
+public class DependencyMergingAnalyzer extends AbstractAnalyzer {
+
+    //<editor-fold defaultstate="collapsed" desc="Constants and Member Variables">
+    /**
+     * The Logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(DependencyMergingAnalyzer.class);
+    /**
+     * a flag indicating if this analyzer has run. This analyzer only runs once.
+     */
+    private boolean analyzed = false;
+
+    /**
+     * Returns a flag indicating if this analyzer has run. This analyzer only
+     * runs once. Note this is currently only used in the unit tests.
+     *
+     * @return a flag indicating if this analyzer has run. This analyzer only
+     * runs once
+     */
+    protected synchronized boolean getAnalyzed() {
+        return analyzed;
+    }
+
+    //</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Dependency Merging Analyzer";
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.POST_INFORMATION_COLLECTION;
+
+    /**
+     * 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;
+    }
+
+    /**
+     * Does not support parallel processing as it only runs once and then
+     * operates on <em>all</em> dependencies.
+     *
+     * @return whether or not parallel processing is enabled
+     * @see #analyze(Dependency, Engine)
+     */
+    @Override
+    public boolean supportsParallelProcessing() {
+        return false;
+    }
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_DEPENDENCY_MERGING_ENABLED;
+    }
+    //</editor-fold>
+
+    /**
+     * Analyzes a set of dependencies. If they have been found to be the same
+     * dependency created by more multiple FileTypeAnalyzers (i.e. a gemspec
+     * dependency and a dependency from the Bundle Audit Analyzer. The
+     * dependencies are then merged 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.
+     */
+    @Override
+    protected synchronized void analyzeDependency(Dependency ignore, Engine engine) throws AnalysisException {
+        if (!analyzed) {
+            analyzed = true;
+            final Set<Dependency> dependenciesToRemove = new HashSet<>();
+            final ListIterator<Dependency> mainIterator = engine.getDependencies().listIterator();
+            //for (Dependency nextDependency : engine.getDependencies()) {
+            while (mainIterator.hasNext()) {
+                final Dependency dependency = mainIterator.next();
+                if (mainIterator.hasNext() && !dependenciesToRemove.contains(dependency)) {
+                    final ListIterator<Dependency> subIterator = engine.getDependencies().listIterator(mainIterator.nextIndex());
+                    while (subIterator.hasNext()) {
+                        final Dependency nextDependency = subIterator.next();
+                        Dependency main;
+                        if ((main = getMainGemspecDependency(dependency, nextDependency)) != null) {
+                            if (main == dependency) {
+                                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 ((main = getMainSwiftDependency(dependency, nextDependency)) != null) {
+                            if (main == dependency) {
+                                mergeDependencies(dependency, nextDependency, dependenciesToRemove);
+                            } else {
+                                mergeDependencies(nextDependency, dependency, dependenciesToRemove);
+                                break; //since we merged into the next dependency - skip forward to the next in mainIterator
+                            }
+                        }
+                    }
+                }
+            }
+            //removing dependencies here as ensuring correctness and avoiding ConcurrentUpdateExceptions
+            // was difficult because of the inner iterator.
+            engine.getDependencies().removeAll(dependenciesToRemove);
+        }
+    }
+
+    /**
+     * 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) {
+        LOGGER.debug("Merging '{}' into '{}'", relatedDependency.getFilePath(), dependency.getFilePath());
+        dependency.addRelatedDependency(relatedDependency);
+        dependency.getVendorEvidence().getEvidence().addAll(relatedDependency.getVendorEvidence().getEvidence());
+        dependency.getProductEvidence().getEvidence().addAll(relatedDependency.getProductEvidence().getEvidence());
+        dependency.getVersionEvidence().getEvidence().addAll(relatedDependency.getVersionEvidence().getEvidence());
+
+        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);
+    }
+
+    /**
+     * Bundling Ruby gems that are identified from different .gemspec files but
+     * denote the same package path. This happens when Ruby bundler installs an
+     * application's dependencies by running "bundle install".
+     *
+     * @param dependency1 dependency to compare
+     * @param dependency2 dependency to compare
+     * @return true if the the dependencies being analyzed appear to be the
+     * same; otherwise false
+     */
+    private boolean isSameRubyGem(Dependency dependency1, Dependency dependency2) {
+        if (dependency1 == null || dependency2 == null
+                || !dependency1.getFileName().endsWith(".gemspec")
+                || !dependency2.getFileName().endsWith(".gemspec")
+                || dependency1.getPackagePath() == null
+                || dependency2.getPackagePath() == null) {
+            return false;
+        }
+        return dependency1.getPackagePath().equalsIgnoreCase(dependency2.getPackagePath());
+    }
+
+    /**
+     * Ruby gems installed by "bundle install" can have zero or more *.gemspec
+     * files, all of which have the same packagePath and should be grouped. If
+     * one of these gemspec is from <parent>/specifications/*.gemspec, because
+     * it is a stub with fully resolved gem meta-data created by Ruby bundler,
+     * this dependency should be the main one. Otherwise, use dependency2 as
+     * main.
+     *
+     * This method returns null if any dependency is not from *.gemspec, or the
+     * two do not have the same packagePath. In this case, they should not be
+     * grouped.
+     *
+     * @param dependency1 dependency to compare
+     * @param dependency2 dependency to compare
+     * @return the main dependency; or null if a gemspec is not included in the
+     * analysis
+     */
+    private Dependency getMainGemspecDependency(Dependency dependency1, Dependency dependency2) {
+        if (isSameRubyGem(dependency1, dependency2)) {
+            final File lFile = dependency1.getActualFile();
+            final File left = lFile.getParentFile();
+            if (left != null && left.getName().equalsIgnoreCase("specifications")) {
+                return dependency1;
+            }
+            return dependency2;
+        }
+        return null;
+    }
+
+    /**
+     * Bundling same swift dependencies with the same packagePath but identified
+     * by different file type analyzers.
+     *
+     * @param dependency1 dependency to test
+     * @param dependency2 dependency to test
+     * @return <code>true</code> if the dependencies appear to be the same;
+     * otherwise <code>false</code>
+     */
+    private boolean isSameSwiftPackage(Dependency dependency1, Dependency dependency2) {
+        if (dependency1 == null || dependency2 == null
+                || (!dependency1.getFileName().endsWith(".podspec")
+                && !dependency1.getFileName().equals("Package.swift"))
+                || (!dependency2.getFileName().endsWith(".podspec")
+                && !dependency2.getFileName().equals("Package.swift"))
+                || dependency1.getPackagePath() == null
+                || dependency2.getPackagePath() == null) {
+            return false;
+        }
+        return dependency1.getPackagePath().equalsIgnoreCase(dependency2.getPackagePath());
+    }
+
+    /**
+     * Determines which of the swift dependencies should be considered the
+     * primary.
+     *
+     * @param dependency1 the first swift dependency to compare
+     * @param dependency2 the second swift dependency to compare
+     * @return the primary swift dependency
+     */
+    private Dependency getMainSwiftDependency(Dependency dependency1, Dependency dependency2) {
+        if (isSameSwiftPackage(dependency1, dependency2)) {
+            if (dependency1.getFileName().endsWith(".podspec")) {
+                return dependency1;
+            }
+            return dependency2;
+        }
+        return null;
+    }
+}

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

@@ -1,5 +1,5 @@
 /*
- * This file is part of dependency-check-gradle.
+ * 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.
@@ -13,15 +13,22 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *
- * Copyright (c) 2015 Wei Ma. All Rights Reserved.
+ * Copyright (c) 2016 Jeremy Long. All Rights Reserved.
  */
+package org.owasp.dependencycheck.analyzer;
 
-package com.tools.security.extension
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
 
-class DependencyCheckExtension {
-    ProxyExtension proxyExtension
-    CveExtension cveExtension
+/**
+ * Annotation used to flag an analyzer as experimental.
+ *
+ * @author jeremy long
+ */
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
+public @interface Experimental {
 
-    String outputDirectory = "./reports"
-    Boolean quickQueryTimestamp;
 }

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

@@ -34,11 +34,13 @@ 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.owasp.dependencycheck.utils.Settings;
 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
  */
@@ -83,17 +85,30 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_FALSE_POSITIVE_ENABLED;
+    }
     //</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 {
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         removeJreEntries(dependency);
         removeBadMatches(dependency);
         removeBadSpringMatches(dependency);
@@ -106,22 +121,23 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     /**
      * Removes inaccurate matches on springframework CPEs.
      *
-     * @param dependency the dependency to test for and remove known inaccurate CPE matches
+     * @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 ("maven".contains(i.getType())
+                    && 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) {
+        if (mustContain
+                != null) {
             final Iterator<Identifier> itr = dependency.getIdentifiers().iterator();
             while (itr.hasNext()) {
                 final Identifier i = itr.next();
@@ -138,7 +154,8 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
 
     /**
      * <p>
-     * Intended to remove spurious CPE entries. By spurious we mean duplicate, less specific CPE entries.</p>
+     * Intended to remove spurious CPE entries. By spurious we mean duplicate,
+     * less specific CPE entries.</p>
      * <p>
      * Example:</p>
      * <code>
@@ -156,7 +173,7 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
      */
     @SuppressWarnings("null")
     private void removeSpuriousCPE(Dependency dependency) {
-        final List<Identifier> ids = new ArrayList<Identifier>(dependency.getIdentifiers());
+        final List<Identifier> ids = new ArrayList<>(dependency.getIdentifiers());
         Collections.sort(ids);
         final ListIterator<Identifier> mainItr = ids.listIterator();
         while (mainItr.hasNext()) {
@@ -189,10 +206,8 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
                             if (nextVersion.startsWith(currentVersion) || "-".equals(currentVersion)) {
                                 dependency.getIdentifiers().remove(currentId);
                             }
-                        } else {
-                            if (currentVersion.startsWith(nextVersion) || "-".equals(nextVersion)) {
-                                dependency.getIdentifiers().remove(nextId);
-                            }
+                        } else if (currentVersion.startsWith(nextVersion) || "-".equals(nextVersion)) {
+                            dependency.getIdentifiers().remove(nextId);
                         }
                     }
                 }
@@ -200,7 +215,8 @@ 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(_platform_micro_edition|_runtime_environment|_se|virtual_machine|se_development_kit|fx)?|"
@@ -215,12 +231,14 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
      */
     public static final Pattern CORE_FILES = Pattern.compile("(^|/)((alt[-])?rt|jsse|jfxrt|jfr|jce|javaws|deploy|charsets)\\.jar$");
     /**
-     * Regex to identify core jsf java library files. This is currently incomplete.
+     * Regex to identify core jsf java library files. This is currently
+     * incomplete.
      */
     public static final Pattern CORE_JSF_FILES = Pattern.compile("(^|/)jsf[-][^/]*\\.jar$");
 
     /**
-     * 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
      */
@@ -264,8 +282,9 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     }
 
     /**
-     * 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
      */
@@ -340,7 +359,8 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     }
 
     /**
-     * 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
      */
@@ -373,8 +393,10 @@ 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
      */
@@ -411,19 +433,21 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     }
 
     /**
-     * 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.
+     * 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) {
+    private synchronized 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());
+                final List<Dependency> dependencies = engine.getDependencies();
+                final Dependency parent = findDependency(parentPath, dependencies);
                 if (parent != null) {
                     boolean remove = false;
                     for (Identifier i : dependency.getIdentifiers()) {
@@ -440,16 +464,16 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
                         }
                     }
                     if (remove) {
-                        engine.getDependencies().remove(dependency);
+                        dependencies.remove(dependency);
                     }
                 }
             }
-
         }
     }
 
     /**
-     * Retrieves a given dependency, based on a given path, from a list of dependencies.
+     * 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
@@ -465,15 +489,16 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     }
 
     /**
-     * Takes a full CPE and returns the CPE trimmed to include only vendor and product.
+     * 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
+        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 {

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

@@ -18,12 +18,16 @@
 package org.owasp.dependencycheck.analyzer;
 
 import java.io.File;
+
+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;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  *
@@ -31,7 +35,7 @@ import org.owasp.dependencycheck.utils.DependencyVersionUtil;
  *
  * @author Jeremy Long
  */
-public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
+public class FileNameAnalyzer extends AbstractAnalyzer {
 
     //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
@@ -62,56 +66,66 @@ public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_FILE_NAME_ENABLED;
+    }
     //</editor-fold>
 
+    /**
+     * Python init files
+     */
+    //CSOFF: WhitespaceAfter
+    private static final NameFileFilter IGNORED_FILES = new NameFileFilter(new String[]{
+        "__init__.py",
+        "__init__.pyc",
+        "__init__.pyo",});
+    //CSON: WhitespaceAfter
+
     /**
      * 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 {
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
 
         //strip any path information that may get added by ArchiveAnalyzer, etc.
         final File f = dependency.getActualFile();
-        String fileName = f.getName();
-
-        //remove file extension
-        final int pos = fileName.lastIndexOf(".");
-        if (pos > 0) {
-            fileName = fileName.substring(0, pos);
-        }
+        final String fileName = FilenameUtils.removeExtension(f.getName());
 
         //add version evidence
         final DependencyVersion version = DependencyVersionUtil.parseVersion(fileName);
+        final String packageName = DependencyVersionUtil.parsePreVersion(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",
+                dependency.getVersionEvidence().addEvidence("file", "version",
                         version.toString(), Confidence.MEDIUM);
             } else {
-                dependency.getVersionEvidence().addEvidence("file", "name",
+                dependency.getVersionEvidence().addEvidence("file", "version",
                         version.toString(), Confidence.HIGHEST);
             }
             dependency.getVersionEvidence().addEvidence("file", "name",
-                    fileName, Confidence.MEDIUM);
+                    packageName, Confidence.MEDIUM);
         }
 
-        //add as vendor and product evidence
-        if (fileName.contains("-")) {
+        if (!IGNORED_FILES.accept(f)) {
             dependency.getProductEvidence().addEvidence("file", "name",
-                    fileName, Confidence.HIGHEST);
+                    packageName, Confidence.HIGH);
             dependency.getVendorEvidence().addEvidence("file", "name",
-                    fileName, Confidence.HIGHEST);
-        } else {
-            dependency.getProductEvidence().addEvidence("file", "name",
-                    fileName, Confidence.HIGH);
-            dependency.getVendorEvidence().addEvidence("file", "name",
-                    fileName, Confidence.HIGH);
+                    packageName, Confidence.HIGH);
         }
     }
 }

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

@@ -26,8 +26,4 @@ import java.io.FileFilter;
  */
 public interface FileTypeAnalyzer extends Analyzer, FileFilter {
 
-    /**
-     * Resets the analyzers state.
-     */
-    void reset();
 }

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

@@ -17,21 +17,54 @@
  */
 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.ArrayList;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Set;
+import java.util.regex.Pattern;
 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.exception.InitializationException;
+import org.owasp.dependencycheck.xml.suppression.PropertyType;
+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.owasp.dependencycheck.xml.hints.VendorDuplicatingHintRule;
+import org.owasp.dependencycheck.xml.hints.HintParseException;
+import org.owasp.dependencycheck.xml.hints.HintParser;
+import org.owasp.dependencycheck.xml.hints.HintRule;
+import org.owasp.dependencycheck.xml.hints.Hints;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.xml.sax.SAXException;
 
 /**
+ * This analyzer adds evidence to dependencies to enhance the accuracy of
+ * library identification.
  *
  * @author Jeremy Long
  */
-public class HintAnalyzer extends AbstractAnalyzer implements Analyzer {
+public class HintAnalyzer extends AbstractAnalyzer {
+
+    /**
+     * The Logger for use throughout the class
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(HintAnalyzer.class);
+    /**
+     * The name of the hint rule file
+     */
+    private static final String HINT_RULE_FILE_NAME = "dependencycheck-base-hint.xml";
+    /**
+     * The collection of hints.
+     */
+    private Hints hints;
 
     //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
@@ -62,115 +95,192 @@ public class HintAnalyzer extends AbstractAnalyzer implements Analyzer {
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_HINT_ENABLED;
+    }
+
+    /**
+     * The initialize method does nothing for this Analyzer.
+     *
+     * @throws InitializationException thrown if there is an exception
+     */
+    @Override
+    public void initializeAnalyzer() throws InitializationException {
+        try {
+            loadHintRules();
+        } catch (HintParseException ex) {
+            LOGGER.debug("Unable to parse hint file", ex);
+            throw new InitializationException("Unable to parse the hint file", ex);
+        }
+    }
     //</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",
-                Confidence.HIGH);
-
-        final Evidence springTest2 = new Evidence("Manifest",
-                "Implementation-Title",
-                "org.springframework.core",
-                Confidence.HIGH);
-
-        final Evidence springTest3 = new Evidence("Manifest",
-                "Implementation-Title",
-                "spring-core",
-                Confidence.HIGH);
-
-        final Evidence springTest4 = new Evidence("jar",
-                "package name",
-                "springframework",
-                Confidence.LOW);
-
-        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);
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
+        for (HintRule hint : hints.getHintRules()) {
+            boolean matchFound = false;
+            for (Evidence given : hint.getGivenVendor()) {
+                if (dependency.getVendorEvidence().getEvidence().contains(given)) {
+                    matchFound = true;
+                    break;
+                }
+            }
+            if (!matchFound) {
+                for (Evidence given : hint.getGivenProduct()) {
+                    if (dependency.getProductEvidence().getEvidence().contains(given)) {
+                        matchFound = true;
+                        break;
+                    }
+                }
+            }
+            if (!matchFound) {
+                for (Evidence given : hint.getGivenVersion()) {
+                    if (dependency.getVersionEvidence().getEvidence().contains(given)) {
+                        matchFound = true;
+                        break;
+                    }
+                }
+            }
+            if (!matchFound) {
+                for (PropertyType pt : hint.getFilenames()) {
+                    if (pt.matches(dependency.getFileName())) {
+                        matchFound = true;
+                        break;
+                    }
+                }
+            }
+            if (matchFound) {
+                for (Evidence e : hint.getAddVendor()) {
+                    dependency.getVendorEvidence().addEvidence(e);
+                }
+                for (Evidence e : hint.getAddProduct()) {
+                    dependency.getProductEvidence().addEvidence(e);
+                }
+                for (Evidence e : hint.getAddVersion()) {
+                    dependency.getVersionEvidence().addEvidence(e);
+                }
+                for (Evidence e : hint.getRemoveVendor()) {
+                    if (dependency.getVendorEvidence().getEvidence().contains(e)) {
+                        dependency.getVendorEvidence().getEvidence().remove(e);
+                    }
+                }
+                for (Evidence e : hint.getRemoveProduct()) {
+                    if (dependency.getProductEvidence().getEvidence().contains(e)) {
+                        dependency.getProductEvidence().getEvidence().remove(e);
+                    }
+                }
+                for (Evidence e : hint.getRemoveVersion()) {
+                    if (dependency.getVersionEvidence().getEvidence().contains(e)) {
+                        dependency.getVersionEvidence().getEvidence().remove(e);
+                    }
+                }
+            }
         }
 
-        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 List<Evidence> newEntries = new ArrayList<Evidence>();
+        final List<Evidence> newEntries = new ArrayList<>();
         while (itr.hasNext()) {
             final Evidence e = itr.next();
-            if ("sun".equalsIgnoreCase(e.getValue(false))) {
-                final Evidence newEvidence = new Evidence(e.getSource() + " (hint)", e.getName(), "oracle", e.getConfidence());
-                newEntries.add(newEvidence);
-            } else if ("oracle".equalsIgnoreCase(e.getValue(false))) {
-                final Evidence newEvidence = new Evidence(e.getSource() + " (hint)", e.getName(), "sun", e.getConfidence());
-                newEntries.add(newEvidence);
+            for (VendorDuplicatingHintRule dhr : hints.getVendorDuplicatingHintRules()) {
+                if (dhr.getValue().equalsIgnoreCase(e.getValue(false))) {
+                    newEntries.add(new Evidence(e.getSource() + " (hint)",
+                            e.getName(), dhr.getDuplicate(), e.getConfidence()));
+                }
             }
         }
         for (Evidence e : newEntries) {
             dependency.getVendorEvidence().addEvidence(e);
         }
+    }
 
+    /**
+     * Loads the hint rules file.
+     *
+     * @throws HintParseException thrown if the XML cannot be parsed.
+     */
+    private void loadHintRules() throws HintParseException {
+        final HintParser parser = new HintParser();
+        File file = null;
+        try {
+            hints = parser.parseHints(this.getClass().getClassLoader().getResourceAsStream(HINT_RULE_FILE_NAME));
+        } catch (HintParseException | SAXException ex) {
+            LOGGER.error("Unable to parse the base hint data file");
+            LOGGER.debug("Unable to parse the base hint data file", ex);
+        }
+        final String filePath = Settings.getString(Settings.KEYS.HINTS_FILE);
+        if (filePath == null) {
+            return;
+        }
+        boolean deleteTempFile = false;
+        try {
+            final Pattern uriRx = Pattern.compile("^(https?|file)\\:.*", Pattern.CASE_INSENSITIVE);
+            if (uriRx.matcher(filePath).matches()) {
+                deleteTempFile = true;
+                file = FileUtils.getTempFile("hint", "xml");
+                final URL url = new URL(filePath);
+                try {
+                    Downloader.fetchFile(url, file, false);
+                } catch (DownloadFailedException ex) {
+                    Downloader.fetchFile(url, file, true);
+                }
+            } else {
+                file = new File(filePath);
+                if (!file.exists()) {
+                    try (InputStream fromClasspath = this.getClass().getClassLoader().getResourceAsStream(filePath)) {
+                        if (fromClasspath != null) {
+                            deleteTempFile = true;
+                            file = FileUtils.getTempFile("hint", "xml");
+                            try {
+                                org.apache.commons.io.FileUtils.copyInputStreamToFile(fromClasspath, file);
+                            } catch (IOException ex) {
+                                throw new HintParseException("Unable to locate hints file in classpath", ex);
+                            }
+                        }
+                    }
+                }
+            }
+
+            if (file != null) {
+                try {
+                    final Hints newHints = parser.parseHints(file);
+                    hints.getHintRules().addAll(newHints.getHintRules());
+                    hints.getVendorDuplicatingHintRules().addAll(newHints.getVendorDuplicatingHintRules());
+                    LOGGER.debug("{} hint rules were loaded.", hints.getHintRules().size());
+                    LOGGER.debug("{} duplicating hint rules were loaded.", hints.getVendorDuplicatingHintRules().size());
+                } catch (HintParseException ex) {
+                    LOGGER.warn("Unable to parse hint rule xml file '{}'", file.getPath());
+                    LOGGER.warn(ex.getMessage());
+                    LOGGER.debug("", ex);
+                    throw ex;
+                }
+            }
+        } catch (DownloadFailedException ex) {
+            throw new HintParseException("Unable to fetch the configured hint file", ex);
+        } catch (MalformedURLException ex) {
+            throw new HintParseException("Configured hint file has an invalid URL", ex);
+        } catch (IOException ex) {
+            throw new HintParseException("Unable to create temp file for hints", ex);
+        } finally {
+            if (deleteTempFile && file != null) {
+                FileUtils.delete(file);
+            }
+        }
     }
 }

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

@@ -23,10 +23,10 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.io.OutputStream;
 import java.io.Reader;
+import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
-import java.util.Collections;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.List;
@@ -35,6 +35,7 @@ import java.util.Map.Entry;
 import java.util.Properties;
 import java.util.Set;
 import java.util.StringTokenizer;
+import java.util.concurrent.atomic.AtomicInteger;
 import java.util.jar.Attributes;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
@@ -42,12 +43,15 @@ import java.util.jar.Manifest;
 import java.util.regex.Pattern;
 import java.util.zip.ZipEntry;
 import org.apache.commons.compress.utils.IOUtils;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.jsoup.Jsoup;
 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.exception.InitializationException;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
 import org.owasp.dependencycheck.xml.pom.License;
 import org.owasp.dependencycheck.xml.pom.PomUtils;
@@ -58,7 +62,8 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * Used to load a JAR file and collect information that can be used to determine the associated CPE.
+ * Used to load a JAR file and collect information that can be used to determine
+ * the associated CPE.
  *
  * @author Jeremy Long
  */
@@ -70,15 +75,17 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private static final Logger LOGGER = LoggerFactory.getLogger(JarAnalyzer.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;
+    private static final AtomicInteger DIR_COUNT = new AtomicInteger(0);
     /**
      * The system independent newline character.
      */
     private static final String NEWLINE = System.getProperty("line.separator");
     /**
-     * A list of values in the manifest to ignore as they only result in false positives.
+     * A list of values in the manifest to ignore as they only result in false
+     * positives.
      */
     private static final Set<String> IGNORE_VALUES = newHashSet(
             "Sun Java System Application Server");
@@ -121,7 +128,8 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             "ipojo-extension",
             "eclipse-sourcereferences");
     /**
-     * Deprecated Jar manifest attribute, that is, nonetheless, useful for analysis.
+     * Deprecated Jar manifest attribute, that is, nonetheless, useful for
+     * analysis.
      */
     @SuppressWarnings("deprecation")
     private static final String IMPLEMENTATION_VENDOR_ID = Attributes.Name.IMPLEMENTATION_VENDOR_ID
@@ -142,15 +150,6 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      * A pattern to detect HTML within text.
      */
     private static final Pattern HTML_DETECTION_PATTERN = Pattern.compile("\\<[a-z]+.*/?\\>", Pattern.CASE_INSENSITIVE);
-
-    //</editor-fold>
-    /**
-     * Constructs a new JarAnalyzer.
-     */
-    public JarAnalyzer() {
-    }
-
-    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
     /**
      * The name of the analyzer.
      */
@@ -169,6 +168,8 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(EXTENSIONS).build();
 
+    //</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
     /**
      * Returns the FileFilter.
      *
@@ -201,7 +202,8 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     //</editor-fold>
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -211,15 +213,16 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Loads a specified JAR file and collects information from the manifest and checksums to identify the correct CPE
-     * information.
+     * 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.
+     * @throws AnalysisException is thrown if there is an error reading the JAR
+     * file.
      */
     @Override
-    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         try {
             final List<ClassNameInformation> classNames = collectClassNames(dependency);
             final String fileName = dependency.getFileName().toLowerCase();
@@ -235,65 +238,58 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             final boolean addPackagesAsEvidence = !(hasManifest && hasPOM);
             analyzePackageNames(classNames, dependency, addPackagesAsEvidence);
         } catch (IOException ex) {
-            throw new AnalysisException("Exception occurred reading the JAR file.", ex);
+            throw new AnalysisException("Exception occurred reading the JAR file (" + dependency.getFileName() + ").", ex);
         }
     }
 
     /**
-     * Attempts to find a pom.xml within the JAR file. If found it extracts information and adds it to the evidence. This will
-     * attempt to interpolate the strings contained within the pom.properties if one exists.
+     * Attempts to find a pom.xml within the JAR file. If found it extracts
+     * information and adds it to the evidence. This will attempt to interpolate
+     * the strings contained within the pom.properties if one exists.
      *
      * @param dependency the dependency being analyzed
      * @param classes a collection of class name information
      * @param engine the analysis engine, used to add additional dependencies
-     * @throws AnalysisException is thrown if there is an exception parsing the pom
+     * @throws AnalysisException is thrown if there is an exception parsing the
+     * pom
      * @return whether or not evidence was added to the dependency
      */
     protected boolean analyzePOM(Dependency dependency, List<ClassNameInformation> classes, Engine engine) throws AnalysisException {
-        boolean foundSomething = false;
-        final JarFile jar;
-        try {
-            jar = new JarFile(dependency.getActualFilePath());
-        } catch (IOException ex) {
-            LOGGER.warn("Unable to read JarFile '{}'.", dependency.getActualFilePath());
-            LOGGER.trace("", ex);
-            return false;
-        }
-        List<String> pomEntries;
-        try {
-            pomEntries = retrievePomListing(jar);
-        } catch (IOException ex) {
-            LOGGER.warn("Unable to read Jar file entries in '{}'.", dependency.getActualFilePath());
-            LOGGER.trace("", ex);
-            return false;
-        }
-        File externalPom = null;
-        if (pomEntries.isEmpty()) {
-            String pomPath = dependency.getActualFilePath();
-            pomPath = pomPath.substring(0, pomPath.lastIndexOf('.')) + ".pom";
-            externalPom = new File(pomPath);
-            if (externalPom.isFile()) {
-                pomEntries.add(pomPath);
-            } else {
-                return false;
-            }
-        }
-        for (String path : pomEntries) {
-            LOGGER.debug("Reading pom entry: {}", path);
-            Properties pomProperties = null;
-            try {
-                if (externalPom == null) {
+        try (JarFile jar = new JarFile(dependency.getActualFilePath())) {
+            final List<String> pomEntries = retrievePomListing(jar);
+            if (pomEntries != null && pomEntries.size() <= 1) {
+                String path;
+                File pomFile;
+                Properties pomProperties = null;
+                if (pomEntries.size() == 1) {
+                    path = pomEntries.get(0);
+                    pomFile = extractPom(path, jar);
                     pomProperties = retrievePomProperties(path, jar);
+                } else {
+                    path = FilenameUtils.removeExtension(dependency.getActualFilePath()) + ".pom";
+                    pomFile = new File(path);
+                }
+                if (pomFile.isFile()) {
+                    final Model pom = PomUtils.readPom(pomFile);
+                    if (pom != null && pomProperties != null) {
+                        pom.processProperties(pomProperties);
+                    }
+                    return pom != null && setPomEvidence(dependency, pom, classes);
+                } else {
+                    return false;
                 }
-            } catch (IOException ex) {
-                LOGGER.trace("ignore this, failed reading a non-existent pom.properties", ex);
             }
-            Model pom = null;
-            try {
-                if (pomEntries.size() > 1) {
+
+            //reported possible null dereference on pomEntries is on a non-feasible path
+            for (String path : pomEntries) {
+                //TODO - one of these is likely the pom for the main JAR we are analyzing
+                LOGGER.debug("Reading pom entry: {}", path);
+                try {
                     //extract POM to its own directory and add it as its own dependency
-                    final Dependency newDependency = new Dependency();
-                    pom = extractPom(path, jar, newDependency);
+                    final Properties pomProperties = retrievePomProperties(path, jar);
+                    final File pomFile = extractPom(path, jar);
+                    final Model pom = PomUtils.readPom(pomFile);
+                    pom.processProperties(pomProperties);
 
                     final String displayPath = String.format("%s%s%s",
                             dependency.getFilePath(),
@@ -303,71 +299,60 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                             dependency.getFileName(),
                             File.separator,
                             path);
-
+                    final Dependency newDependency = new Dependency();
+                    newDependency.setActualFilePath(pomFile.getAbsolutePath());
                     newDependency.setFileName(displayName);
                     newDependency.setFilePath(displayPath);
-                    pom.processProperties(pomProperties);
                     setPomEvidence(newDependency, pom, null);
                     engine.getDependencies().add(newDependency);
-                    Collections.sort(engine.getDependencies());
-                } else {
-                    if (externalPom == null) {
-                        pom = PomUtils.readPom(path, jar);
-                    } else {
-                        pom = PomUtils.readPom(externalPom);
-                    }
-                    pom.processProperties(pomProperties);
-                    foundSomething |= setPomEvidence(dependency, pom, classes);
+                } catch (AnalysisException ex) {
+                    LOGGER.warn("An error occurred while analyzing '{}'.", dependency.getActualFilePath());
+                    LOGGER.trace("", ex);
                 }
-            } catch (AnalysisException ex) {
-                LOGGER.warn("An error occured while analyzing '{}'.", dependency.getActualFilePath());
-                LOGGER.trace("", ex);
             }
+        } catch (IOException ex) {
+            LOGGER.warn("Unable to read JarFile '{}'.", dependency.getActualFilePath());
+            LOGGER.trace("", ex);
         }
-        return foundSomething;
+        return false;
     }
 
     /**
-     * Given a path to a pom.xml within a JarFile, this method attempts to load a sibling pom.properties if one exists.
+     * Given a path to a pom.xml within a JarFile, this method attempts to load
+     * a sibling pom.properties if one exists.
      *
      * @param path the path to the pom.xml within the JarFile
      * @param jar the JarFile to load the pom.properties from
      * @return a Properties object or null if no pom.properties was found
-     * @throws IOException thrown if there is an exception reading the pom.properties
      */
-    private Properties retrievePomProperties(String path, final JarFile jar) throws IOException {
+    private Properties retrievePomProperties(String path, final JarFile jar) {
         Properties pomProperties = null;
         final String propPath = path.substring(0, path.length() - 7) + "pom.properies";
         final ZipEntry propEntry = jar.getEntry(propPath);
         if (propEntry != null) {
-            Reader reader = null;
-            try {
-                reader = new InputStreamReader(jar.getInputStream(propEntry), "UTF-8");
+            try (Reader reader = new InputStreamReader(jar.getInputStream(propEntry), "UTF-8")) {
                 pomProperties = new Properties();
                 pomProperties.load(reader);
                 LOGGER.debug("Read pom.properties: {}", propPath);
-            } finally {
-                if (reader != null) {
-                    try {
-                        reader.close();
-                    } catch (IOException ex) {
-                        LOGGER.trace("close error", ex);
-                    }
-                }
+            } catch (UnsupportedEncodingException ex) {
+                LOGGER.trace("UTF-8 is not supported", ex);
+            } catch (IOException ex) {
+                LOGGER.trace("Unable to read the POM properties", ex);
             }
         }
         return pomProperties;
     }
 
     /**
-     * Searches a JarFile for pom.xml entries and returns a listing of these entries.
+     * Searches a JarFile for pom.xml entries and returns a listing of these
+     * entries.
      *
      * @param jar the JarFile to search
      * @return a list of pom.xml entries
      * @throws IOException thrown if there is an exception reading a JarEntry
      */
     private List<String> retrievePomListing(final JarFile jar) throws IOException {
-        final List<String> pomEntries = new ArrayList<String>();
+        final List<String> pomEntries = new ArrayList<>();
         final Enumeration<JarEntry> entries = jar.entries();
         while (entries.hasMoreElements()) {
             final JarEntry entry = entries.nextElement();
@@ -381,64 +366,29 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Retrieves the specified POM from a jar file and converts it to a Model.
+     * Retrieves the specified POM from a jar.
      *
      * @param path the path to the pom.xml file within the jar file
      * @param jar the jar file to extract the pom from
-     * @param dependency the dependency being analyzed
-     * @return returns the POM object
-     * @throws AnalysisException is thrown if there is an exception extracting or parsing the POM
-     * {@link org.owasp.dependencycheck.xml.pom.Model} object
+     * @return returns the POM file
+     * @throws AnalysisException is thrown if there is an exception extracting
+     * the file
      */
-    private Model extractPom(String path, JarFile jar, Dependency dependency) throws AnalysisException {
-        InputStream input = null;
-        FileOutputStream fos = null;
+    private File extractPom(String path, JarFile jar) throws AnalysisException {
         final File tmpDir = getNextTempDirectory();
         final File file = new File(tmpDir, "pom.xml");
-        try {
-            final ZipEntry entry = jar.getEntry(path);
-            input = jar.getInputStream(entry);
-            fos = new FileOutputStream(file);
+        final ZipEntry entry = jar.getEntry(path);
+        if (entry == null) {
+            throw new AnalysisException(String.format("Pom (%s) does not exist in %s", path, jar.getName()));
+        }
+        try (InputStream input = jar.getInputStream(entry);
+                FileOutputStream fos = new FileOutputStream(file)) {
             IOUtils.copy(input, fos);
-            dependency.setActualFilePath(file.getAbsolutePath());
         } catch (IOException ex) {
-            LOGGER.warn("An error occurred reading '{}' from '{}'.", path, dependency.getFilePath());
+            LOGGER.warn("An error occurred reading '{}' from '{}'.", path, jar.getName());
             LOGGER.error("", ex);
-        } finally {
-            closeStream(fos);
-            closeStream(input);
-        }
-        return PomUtils.readPom(file);
-    }
-
-    /**
-     * Silently closes an input stream ignoring errors.
-     *
-     * @param stream an input stream to close
-     */
-    private void closeStream(InputStream stream) {
-        if (stream != null) {
-            try {
-                stream.close();
-            } catch (IOException ex) {
-                LOGGER.trace("", ex);
-            }
-        }
-    }
-
-    /**
-     * Silently closes an output stream ignoring errors.
-     *
-     * @param stream an output stream to close
-     */
-    private void closeStream(OutputStream stream) {
-        if (stream != null) {
-            try {
-                stream.close();
-            } catch (IOException ex) {
-                LOGGER.trace("", ex);
-            }
         }
+        return file;
     }
 
     /**
@@ -446,16 +396,17 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      *
      * @param dependency the dependency to set data on
      * @param pom the information from the pom
-     * @param classes a collection of ClassNameInformation - containing data about the fully qualified class names within the JAR
-     * file being analyzed
-     * @return true if there was evidence within the pom that we could use; otherwise false
+     * @param classes a collection of ClassNameInformation - containing data
+     * about the fully qualified class names within the JAR file being analyzed
+     * @return true if there was evidence within the pom that we could use;
+     * otherwise false
      */
     public static boolean setPomEvidence(Dependency dependency, Model pom, List<ClassNameInformation> classes) {
+        if (pom == null) {
+            return false;
+        }
         boolean foundSomething = false;
         boolean addAsIdentifier = true;
-        if (pom == null) {
-            return foundSomething;
-        }
         String groupid = pom.getGroupId();
         String parentGroupId = pom.getParentGroupId();
         String artifactid = pom.getArtifactId();
@@ -474,7 +425,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
         }
 
         final String originalGroupID = groupid;
-        if (groupid.startsWith("org.") || groupid.startsWith("com.")) {
+        if (groupid != null && (groupid.startsWith("org.") || groupid.startsWith("com."))) {
             groupid = groupid.substring(4);
         }
 
@@ -483,7 +434,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
         }
 
         final String originalArtifactID = artifactid;
-        if (artifactid.startsWith("org.") || artifactid.startsWith("com.")) {
+        if (artifactid != null && (artifactid.startsWith("org.") || artifactid.startsWith("com."))) {
             artifactid = artifactid.substring(4);
         }
 
@@ -545,6 +496,12 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             addMatchingValues(classes, org, dependency.getVendorEvidence());
             addMatchingValues(classes, org, dependency.getProductEvidence());
         }
+        // org name
+        final String orgUrl = pom.getOrganizationUrl();
+        if (orgUrl != null && !orgUrl.isEmpty()) {
+            dependency.getVendorEvidence().addEvidence("pom", "organization url", orgUrl, Confidence.MEDIUM);
+            dependency.getProductEvidence().addEvidence("pom", "organization url", orgUrl, Confidence.LOW);
+        }
         //pom name
         final String pomName = pom.getName();
         if (pomName
@@ -565,22 +522,30 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             addMatchingValues(classes, trimmedDescription, dependency.getProductEvidence());
         }
 
+        final String projectURL = pom.getProjectURL();
+        if (projectURL != null && !projectURL.trim().isEmpty()) {
+            dependency.getVendorEvidence().addEvidence("pom", "url", projectURL, Confidence.HIGHEST);
+        }
+
         extractLicense(pom, dependency);
         return foundSomething;
     }
 
     /**
-     * Analyzes the path information of the classes contained within the JarAnalyzer to try and determine possible vendor or
-     * product names. If any are found they are stored in the packageVendor and packageProduct hashSets.
+     * Analyzes the path information of the classes contained within the
+     * JarAnalyzer to try and determine possible vendor or product names. If any
+     * are found they are stored in the packageVendor and packageProduct
+     * hashSets.
      *
      * @param classNames a list of class names
      * @param dependency a dependency to analyze
-     * @param addPackagesAsEvidence a flag indicating whether or not package names should be added as evidence.
+     * @param addPackagesAsEvidence a flag indicating whether or not package
+     * names should be added as evidence.
      */
     protected void analyzePackageNames(List<ClassNameInformation> classNames,
             Dependency dependency, boolean addPackagesAsEvidence) {
-        final Map<String, Integer> vendorIdentifiers = new HashMap<String, Integer>();
-        final Map<String, Integer> productIdentifiers = new HashMap<String, Integer>();
+        final Map<String, Integer> vendorIdentifiers = new HashMap<>();
+        final Map<String, Integer> productIdentifiers = new HashMap<>();
         analyzeFullyQualifiedClassNames(classNames, vendorIdentifiers, productIdentifiers);
 
         final int classCount = classNames.size();
@@ -610,11 +575,13 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
      * <p>
-     * Reads the manifest from the JAR file and collects the entries. Some vendorKey entries are:</p>
+     * Reads the manifest from the JAR file and collects the entries. Some
+     * vendorKey entries are:</p>
      * <ul><li>Implementation Title</li>
      * <li>Implementation Version</li> <li>Implementation Vendor</li>
-     * <li>Implementation VendorId</li> <li>Bundle Name</li> <li>Bundle Version</li> <li>Bundle Vendor</li> <li>Bundle
-     * Description</li> <li>Main Class</li> </ul>
+     * <li>Implementation VendorId</li> <li>Bundle Name</li> <li>Bundle
+     * Version</li> <li>Bundle Vendor</li> <li>Bundle Description</li> <li>Main
+     * Class</li> </ul>
      * However, all but a handful of specific entries are read in.
      *
      * @param dependency A reference to the dependency
@@ -622,16 +589,12 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      * @return whether evidence was identified parsing the manifest
      * @throws IOException if there is an issue reading the JAR file
      */
-    protected boolean parseManifest(Dependency dependency, List<ClassNameInformation> classInformation) throws IOException {
+    protected boolean parseManifest(Dependency dependency, List<ClassNameInformation> classInformation)
+            throws IOException {
         boolean foundSomething = false;
-        JarFile jar = null;
-        try {
-            jar = new JarFile(dependency.getActualFilePath());
-
+        try (JarFile jar = new JarFile(dependency.getActualFilePath())) {
             final Manifest manifest = jar.getManifest();
-
             if (manifest == null) {
-                //don't log this for javadoc or sources jar files
                 if (!dependency.getFileName().toLowerCase().endsWith("-sources.jar")
                         && !dependency.getFileName().toLowerCase().endsWith("-javadoc.jar")
                         && !dependency.getFileName().toLowerCase().endsWith("-src.jar")
@@ -641,17 +604,13 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                 }
                 return false;
             }
-            final Attributes atts = manifest.getMainAttributes();
-
             final EvidenceCollection vendorEvidence = dependency.getVendorEvidence();
             final EvidenceCollection productEvidence = dependency.getProductEvidence();
             final EvidenceCollection versionEvidence = dependency.getVersionEvidence();
-
-            final String source = "Manifest";
-
+            String source = "Manifest";
             String specificationVersion = null;
             boolean hasImplementationVersion = false;
-
+            Attributes atts = manifest.getMainAttributes();
             for (Entry<Object, Object> entry : atts.entrySet()) {
                 String key = entry.getKey().toString();
                 String value = atts.getValue(key);
@@ -669,7 +628,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                     foundSomething = true;
                     versionEvidence.addEvidence(source, key, value, Confidence.HIGH);
                 } else if ("specification-version".equalsIgnoreCase(key)) {
-                    specificationVersion = key;
+                    specificationVersion = value;
                 } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VENDOR.toString())) {
                     foundSomething = true;
                     vendorEvidence.addEvidence(source, key, value, Confidence.HIGH);
@@ -681,7 +640,6 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                 } else if (key.equalsIgnoreCase(BUNDLE_DESCRIPTION)) {
                     foundSomething = true;
                     addDescription(dependency, value, "manifest", key);
-                    //productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                     addMatchingValues(classInformation, value, productEvidence);
                 } else if (key.equalsIgnoreCase(BUNDLE_NAME)) {
                     foundSomething = true;
@@ -689,25 +647,14 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                     addMatchingValues(classInformation, value, productEvidence);
 //                //the following caused false positives.
 //                } else if (key.equalsIgnoreCase(BUNDLE_VENDOR)) {
-//                    foundSomething = true;
-//                    vendorEvidence.addEvidence(source, key, value, Confidence.HIGH);
-//                    addMatchingValues(classInformation, value, vendorEvidence);
                 } else if (key.equalsIgnoreCase(BUNDLE_VERSION)) {
                     foundSomething = true;
                     versionEvidence.addEvidence(source, key, value, Confidence.HIGH);
                 } else if (key.equalsIgnoreCase(Attributes.Name.MAIN_CLASS.toString())) {
                     continue;
-                    //skipping main class as if this has important information to add
-                    // it will be added during class name analysis...  if other fields
-                    // have the information from the class name then they will get added...
-//                    foundSomething = true;
-//                    productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
-//                    vendorEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
-//                    addMatchingValues(classInformation, value, vendorEvidence);
-//                    addMatchingValues(classInformation, value, productEvidence);
+                    //skipping main class as if this has important information to add it will be added during class name analysis...
                 } else {
                     key = key.toLowerCase();
-
                     if (!IGNORE_KEYS.contains(key)
                             && !key.endsWith("jdk")
                             && !key.contains("lastmodified")
@@ -719,21 +666,18 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                             && !value.trim().startsWith("scm:")
                             && !isImportPackage(key, value)
                             && !isPackage(key, value)) {
-
                         foundSomething = true;
                         if (key.contains("version")) {
                             if (!key.contains("specification")) {
-                                //versionEvidence.addEvidence(source, key, value, Confidence.LOW);
-                                //} else {
                                 versionEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                             }
                         } else if ("build-id".equals(key)) {
                             int pos = value.indexOf('(');
-                            if (pos >= 0) {
+                            if (pos > 0) {
                                 value = value.substring(0, pos - 1);
                             }
                             pos = value.indexOf('[');
-                            if (pos >= 0) {
+                            if (pos > 0) {
                                 value = value.substring(0, pos - 1);
                             }
                             versionEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
@@ -754,21 +698,19 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                             addMatchingValues(classInformation, value, productEvidence);
                         } else if (key.contains("license")) {
                             addLicense(dependency, value);
+                        } else if (key.contains("description")) {
+                            addDescription(dependency, value, "manifest", key);
                         } else {
-                            if (key.contains("description")) {
-                                addDescription(dependency, value, "manifest", key);
-                            } else {
-                                productEvidence.addEvidence(source, key, value, Confidence.LOW);
-                                vendorEvidence.addEvidence(source, key, value, Confidence.LOW);
-                                addMatchingValues(classInformation, value, vendorEvidence);
-                                addMatchingValues(classInformation, value, productEvidence);
-                                if (value.matches(".*\\d.*")) {
-                                    final StringTokenizer tokenizer = new StringTokenizer(value, " ");
-                                    while (tokenizer.hasMoreElements()) {
-                                        final String s = tokenizer.nextToken();
-                                        if (s.matches("^[0-9.]+$")) {
-                                            versionEvidence.addEvidence(source, key, s, Confidence.LOW);
-                                        }
+                            productEvidence.addEvidence(source, key, value, Confidence.LOW);
+                            vendorEvidence.addEvidence(source, key, value, Confidence.LOW);
+                            addMatchingValues(classInformation, value, vendorEvidence);
+                            addMatchingValues(classInformation, value, productEvidence);
+                            if (value.matches(".*\\d.*")) {
+                                final StringTokenizer tokenizer = new StringTokenizer(value, " ");
+                                while (tokenizer.hasMoreElements()) {
+                                    final String s = tokenizer.nextToken();
+                                    if (s.matches("^[0-9.]+$")) {
+                                        versionEvidence.addEvidence(source, key, s, Confidence.LOW);
                                     }
                                 }
                             }
@@ -776,28 +718,52 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                     }
                 }
             }
+            for (Map.Entry<String, Attributes> item : manifest.getEntries().entrySet()) {
+                final String name = item.getKey();
+                source = "manifest: " + name;
+                atts = item.getValue();
+                for (Entry<Object, Object> entry : atts.entrySet()) {
+                    final String key = entry.getKey().toString();
+                    final String value = atts.getValue(key);
+                    if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_TITLE.toString())) {
+                        foundSomething = true;
+                        productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
+                        addMatchingValues(classInformation, value, productEvidence);
+                    } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VERSION.toString())) {
+                        foundSomething = true;
+                        versionEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
+                    } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VENDOR.toString())) {
+                        foundSomething = true;
+                        vendorEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
+                        addMatchingValues(classInformation, value, vendorEvidence);
+                    } else if (key.equalsIgnoreCase(Attributes.Name.SPECIFICATION_TITLE.toString())) {
+                        foundSomething = true;
+                        productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
+                        addMatchingValues(classInformation, value, productEvidence);
+                    }
+                }
+            }
             if (specificationVersion != null && !hasImplementationVersion) {
                 foundSomething = true;
-                versionEvidence.addEvidence(source, "specificationn-version", specificationVersion, Confidence.HIGH);
-            }
-        } finally {
-            if (jar != null) {
-                jar.close();
+                versionEvidence.addEvidence(source, "specification-version", specificationVersion, Confidence.HIGH);
             }
         }
         return foundSomething;
     }
 
     /**
-     * Adds a description to the given dependency. If the description contains one of the following strings beyond 100 characters,
-     * then the description used will be trimmed to that position:
-     * <ul><li>"such as"</li><li>"like "</li><li>"will use "</li><li>"* uses "</li></ul>
+     * Adds a description to the given dependency. If the description contains
+     * one of the following strings beyond 100 characters, then the description
+     * used will be trimmed to that position:
+     * <ul><li>"such as"</li><li>"like "</li><li>"will use "</li><li>"* uses
+     * "</li></ul>
      *
      * @param dependency a dependency
      * @param description the description
      * @param source the source of the evidence
      * @param key the "name" of the evidence
-     * @return if the description is trimmed, the trimmed version is returned; otherwise the original description is returned
+     * @return if the description is trimmed, the trimmed version is returned;
+     * otherwise the original description is returned
      */
     public static String addDescription(Dependency dependency, String description, String source, String key) {
         if (dependency.getDescription() == null) {
@@ -835,10 +801,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             }
 
             if (pos > 0) {
-                final StringBuilder sb = new StringBuilder(pos + 3);
-                sb.append(desc.substring(0, pos));
-                sb.append("...");
-                desc = sb.toString();
+                desc = desc.substring(0, pos) + "...";
             }
             dependency.getProductEvidence().addEvidence(source, key, desc, Confidence.LOW);
             dependency.getVendorEvidence().addEvidence(source, key, desc, Confidence.LOW);
@@ -871,19 +834,27 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the JarAnalyzer.
      *
-     * @throws Exception is thrown if there is an exception creating a temporary directory
+     * @throws InitializationException is thrown if there is an exception
+     * creating a temporary directory
      */
     @Override
-    public 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);
+    public void initializeFileTypeAnalyzer() throws InitializationException {
+        try {
+            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());
+                setEnabled(false);
+                throw new InitializationException(msg);
+            }
+            if (!tempFileLocation.mkdirs()) {
+                final String msg = String.format("Unable to create directory '%s'.", tempFileLocation.getAbsolutePath());
+                setEnabled(false);
+                throw new InitializationException(msg);
+            }
+        } catch (IOException ex) {
+            setEnabled(false);
+            throw new InitializationException("Unable to create a temporary file", ex);
         }
     }
 
@@ -891,22 +862,27 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      * Deletes any files extracted from the JAR during analysis.
      */
     @Override
-    public void close() {
+    public void closeAnalyzer() {
         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");
+            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");
+                }
             }
         }
     }
 
     /**
-     * Determines if the key value pair from the manifest is for an "import" type entry for package names.
+     * Determines if the key value pair from the manifest is for an "import"
+     * type entry for package names.
      *
      * @param key the key from the manifest
      * @param value the value from the manifest
-     * @return true or false depending on if it is believed the entry is an "import" entry
+     * @return true or false depending on if it is believed the entry is an
+     * "import" entry
      */
     private boolean isImportPackage(String key, String value) {
         final Pattern packageRx = Pattern.compile("^([a-zA-Z0-9_#\\$\\*\\.]+\\s*[,;]\\s*)+([a-zA-Z0-9_#\\$\\*\\.]+\\s*)?$");
@@ -915,17 +891,16 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Cycles through an enumeration of JarEntries, contained within the dependency, and returns a list of the class names. This
-     * does not include core Java package names (i.e. java.* or javax.*).
+     * Cycles through an enumeration of JarEntries, contained within the
+     * dependency, and returns a list of the class names. This does not include
+     * core Java package names (i.e. java.* or javax.*).
      *
      * @param dependency the dependency being analyzed
      * @return an list of fully qualified class names
      */
     private List<ClassNameInformation> collectClassNames(Dependency dependency) {
-        final List<ClassNameInformation> classNames = new ArrayList<ClassNameInformation>();
-        JarFile jar = null;
-        try {
-            jar = new JarFile(dependency.getActualFilePath());
+        final List<ClassNameInformation> classNames = new ArrayList<>();
+        try (JarFile jar = new JarFile(dependency.getActualFilePath())) {
             final Enumeration<JarEntry> entries = jar.entries();
             while (entries.hasMoreElements()) {
                 final JarEntry entry = entries.nextElement();
@@ -939,25 +914,21 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
         } catch (IOException ex) {
             LOGGER.warn("Unable to open jar file '{}'.", dependency.getFileName());
             LOGGER.debug("", ex);
-        } finally {
-            if (jar != null) {
-                try {
-                    jar.close();
-                } catch (IOException ex) {
-                    LOGGER.trace("", ex);
-                }
-            }
         }
         return classNames;
     }
 
     /**
-     * Cycles through the list of class names and places the package levels 0-3 into the provided maps for vendor and product.
-     * This is helpful when analyzing vendor/product as many times this is included in the package name.
+     * Cycles through the list of class names and places the package levels 0-3
+     * into the provided maps for vendor and product. This is helpful when
+     * analyzing vendor/product as many times this is included in the package
+     * name.
      *
      * @param classNames a list of class names
-     * @param vendor HashMap of possible vendor names from package names (e.g. owasp)
-     * @param product HashMap of possible product names from package names (e.g. dependencycheck)
+     * @param vendor HashMap of possible vendor names from package names (e.g.
+     * owasp)
+     * @param product HashMap of possible product names from package names (e.g.
+     * dependencycheck)
      */
     private void analyzeFullyQualifiedClassNames(List<ClassNameInformation> classNames,
             Map<String, Integer> vendor, Map<String, Integer> product) {
@@ -967,13 +938,11 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
 
             if (list.size() == 2) {
                 addEntry(product, list.get(1));
-            }
-            if (list.size() == 3) {
+            } else if (list.size() == 3) {
                 addEntry(vendor, list.get(1));
                 addEntry(product, list.get(1));
                 addEntry(product, list.get(2));
-            }
-            if (list.size() >= 4) {
+            } else if (list.size() >= 4) {
                 addEntry(vendor, list.get(1));
                 addEntry(vendor, list.get(2));
                 addEntry(product, list.get(1));
@@ -984,8 +953,9 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Adds an entry to the specified collection and sets the Integer (e.g. the count) to 1. If the entry already exists in the
-     * collection then the Integer is incremented by 1.
+     * Adds an entry to the specified collection and sets the Integer (e.g. the
+     * count) to 1. If the entry already exists in the collection then the
+     * Integer is incremented by 1.
      *
      * @param collection a collection of strings and their occurrence count
      * @param key the key to add to the collection
@@ -999,9 +969,10 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Cycles through the collection of class name information to see if parts of the package names are contained in the provided
-     * value. If found, it will be added as the HIGHEST confidence evidence because we have more then one source corroborating the
-     * value.
+     * Cycles through the collection of class name information to see if parts
+     * of the package names are contained in the provided value. If found, it
+     * will be added as the HIGHEST confidence evidence because we have more
+     * then one source corroborating the value.
      *
      * @param classes a collection of class name information
      * @param value the value to check to see if it contains a package name
@@ -1014,7 +985,9 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
         final String text = value.toLowerCase();
         for (ClassNameInformation cni : classes) {
             for (String key : cni.getPackageStructure()) {
-                if (text.contains(key)) { //note, package structure elements are already lowercase.
+                final Pattern p = Pattern.compile("\b" + key + "\b");
+                if (p.matcher(text).find()) {
+                    //if (text.contains(key)) { //note, package structure elements are already lowercase.
                     evidence.addEvidence("jar", "package name", key, Confidence.HIGHEST);
                 }
             }
@@ -1022,7 +995,8 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Simple check to see if the attribute from a manifest is just a package name.
+     * Simple check to see if the attribute from a manifest is just a package
+     * name.
      *
      * @param key the key of the value to check
      * @param value the value to check
@@ -1036,7 +1010,8 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Extracts the license information from the pom and adds it to the dependency.
+     * Extracts the license information from the pom and adds it to the
+     * dependency.
      *
      * @param pom the pom object
      * @param dependency the dependency to add license information too
@@ -1081,12 +1056,24 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      */
     protected static class ClassNameInformation {
 
+        /**
+         * The fully qualified class name.
+         */
+        private String name;
+        /**
+         * Up to the first four levels of the package structure, excluding a
+         * leading "org" or "com".
+         */
+        private final ArrayList<String> packageStructure = new ArrayList<>();
+
         /**
          * <p>
-         * Stores information about a given class name. This class will keep the fully qualified class name and a list of the
-         * important parts of the package structure. Up to the first four levels of the package structure are stored, excluding a
-         * leading "org" or "com". Example:</p>
-         * <code>ClassNameInformation obj = new ClassNameInformation("org.owasp.dependencycheck.analyzer.JarAnalyzer");
+         * Stores information about a given class name. This class will keep the
+         * fully qualified class name and a list of the important parts of the
+         * package structure. Up to the first four levels of the package
+         * structure are stored, excluding a leading "org" or "com".
+         * Example:</p>
+         * <code>ClassNameInformation obj = new ClassNameInformation("org/owasp/dependencycheck/analyzer/JarAnalyzer");
          * System.out.println(obj.getName());
          * for (String p : obj.getPackageStructure())
          *     System.out.println(p);
@@ -1104,7 +1091,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
         ClassNameInformation(String className) {
             name = className;
             if (name.contains("/")) {
-                final String[] tmp = className.toLowerCase().split("/");
+                final String[] tmp = StringUtils.split(className.toLowerCase(), '/');
                 int start = 0;
                 int end = 3;
                 if ("com".equals(tmp[0]) || "org".equals(tmp[0])) {
@@ -1114,17 +1101,11 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                 if (tmp.length <= end) {
                     end = tmp.length - 1;
                 }
-                for (int i = start; i <= end; i++) {
-                    packageStructure.add(tmp[i]);
-                }
+                packageStructure.addAll(Arrays.asList(tmp).subList(start, end + 1));
             } else {
                 packageStructure.add(name);
             }
         }
-        /**
-         * The fully qualified class name.
-         */
-        private String name;
 
         /**
          * Get the value of name
@@ -1143,10 +1124,6 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
         public void setName(String name) {
             this.name = name;
         }
-        /**
-         * Up to the first four levels of the package structure, excluding a leading "org" or "com".
-         */
-        private final ArrayList<String> packageStructure = new ArrayList<String>();
 
         /**
          * Get the value of packageStructure
@@ -1165,7 +1142,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws AnalysisException thrown if unable to create temporary directory
      */
     private File getNextTempDirectory() throws AnalysisException {
-        dirCount += 1;
+        final int dirCount = DIR_COUNT.incrementAndGet();
         final File directory = new File(tempFileLocation, String.valueOf(dirCount));
         //getting an exception for some directories not being able to be created; might be because the directory already exists?
         if (directory.exists()) {

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

@@ -35,6 +35,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
+import org.owasp.dependencycheck.exception.InitializationException;
 import org.owasp.dependencycheck.utils.DownloadFailedException;
 import org.owasp.dependencycheck.utils.Downloader;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
@@ -42,15 +43,18 @@ 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.
+ * 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>
+ * <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
@@ -58,7 +62,8 @@ import org.owasp.dependencycheck.utils.Settings;
 public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
-     * The default URL - this will be used by the CentralAnalyzer to determine whether to enable this.
+     * 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/";
 
@@ -95,7 +100,8 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Determines if this analyzer is enabled
      *
-     * @return <code>true</code> if the analyzer is enabled; otherwise <code>false</code>
+     * @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
@@ -104,7 +110,7 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
          */
         boolean retval = false;
         try {
-            if ((!DEFAULT_URL.equals(Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL)))
+            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;
@@ -131,26 +137,25 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the analyzer once before any analysis is performed.
      *
-     * @throws Exception if there's an error during initialization
+     * @throws InitializationException if there's an error during initialization
      */
     @Override
-    public void initializeFileTypeAnalyzer() throws Exception {
+    public void initializeFileTypeAnalyzer() throws InitializationException {
         LOGGER.debug("Initializing Nexus Analyzer");
         LOGGER.debug("Nexus Analyzer enabled: {}", isEnabled());
         if (isEnabled()) {
+            final boolean useProxy = useProxy();
             final String searchUrl = Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL);
             LOGGER.debug("Nexus Analyzer URL: {}", searchUrl);
             try {
-                searcher = new NexusSearch(new URL(searchUrl));
+                searcher = new NexusSearch(new URL(searchUrl), useProxy);
                 if (!searcher.preflightRequest()) {
-                    LOGGER.warn("There was an issue getting Nexus status. Disabling analyzer.");
                     setEnabled(false);
+                    throw new InitializationException("There was an issue getting Nexus status. Disabling analyzer.");
                 }
             } 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);
+                throw new InitializationException("Malformed URL to Nexus: " + searchUrl, mue);
             }
         }
     }
@@ -166,7 +171,8 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -208,7 +214,7 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws AnalysisException when there's an exception during analysis
      */
     @Override
-    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         if (!isEnabled()) {
             return;
         }
@@ -240,7 +246,8 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
                     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)) {
+                    if (pomFile != null && pomFile.exists() && !FileUtils.deleteQuietly(pomFile)) {
+                        LOGGER.debug("Failed to delete temporary pom file {}", pomFile.toString());
                         pomFile.deleteOnExit();
                     }
                 }
@@ -257,4 +264,19 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
             LOGGER.debug("Could not connect to nexus repository", ioe);
         }
     }
+
+    /**
+     * Determine if a proxy should be used.
+     *
+     * @return {@code true} if a proxy should be used
+     */
+    public static boolean useProxy() {
+        try {
+            return Settings.getString(Settings.KEYS.PROXY_SERVER) != null
+                    && Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY);
+        } catch (InvalidSettingException ise) {
+            LOGGER.warn("Failed to parse proxy settings.", ise);
+            return false;
+        }
+    }
 }

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

@@ -38,13 +38,15 @@ import javax.json.JsonObject;
 import javax.json.JsonReader;
 import javax.json.JsonString;
 import javax.json.JsonValue;
+import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
- * Used to analyze Node Package Manager (npm) package.json files, and collect information that can be used to determine the
- * associated CPE.
+ * 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 <dvisser@ida.org>
+ * @author Dale Visser
  */
+@Experimental
 public class NodePackageAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -83,7 +85,7 @@ public class NodePackageAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     @Override
-    protected void initializeFileTypeAnalyzer() throws Exception {
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
         // NO-OP
     }
 
@@ -108,7 +110,8 @@ public class NodePackageAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -118,17 +121,9 @@ public class NodePackageAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
-            throws AnalysisException {
+    protected void analyzeDependency(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 {
+        try (JsonReader jsonReader = Json.createReader(FileUtils.openInputStream(file))) {
             final JsonObject json = jsonReader.readObject();
             final EvidenceCollection productEvidence = dependency.getProductEvidence();
             final EvidenceCollection vendorEvidence = dependency.getVendorEvidence();
@@ -148,13 +143,14 @@ public class NodePackageAnalyzer extends AbstractFileTypeAnalyzer {
             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();
+        } catch (IOException e) {
+            throw new AnalysisException("Problem occurred while reading dependency file.", e);
         }
     }
 
     /**
-     * Adds information to an evidence collection from the node json configuration.
+     * 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

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

@@ -33,7 +33,7 @@ import org.slf4j.LoggerFactory;
 import java.io.FileFilter;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.IOException;
+import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
  * Analyzer which will parse a Nuspec file to gather module information.
@@ -65,10 +65,10 @@ public class NuspecAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the analyzer once before any analysis is performed.
      *
-     * @throws Exception if there's an error during initialization
+     * @throws InitializationException if there's an error during initialization
      */
     @Override
-    public void initializeFileTypeAnalyzer() throws Exception {
+    public void initializeFileTypeAnalyzer() throws InitializationException {
     }
 
     /**
@@ -82,7 +82,8 @@ public class NuspecAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -125,27 +126,15 @@ public class NuspecAnalyzer extends AbstractFileTypeAnalyzer {
      * @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.toString());
+    public void analyzeDependency(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());
+            try (FileInputStream fis = new FileInputStream(dependency.getActualFilePath())) {
                 np = parser.parse(fis);
-            } catch (NuspecParseException ex) {
+            } catch (NuspecParseException | FileNotFoundException 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-check-core/src/main/java/org/owasp/dependencycheck/analyzer/NvdCveAnalyzer.java

@@ -27,19 +27,24 @@ 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;
+import org.owasp.dependencycheck.exception.InitializationException;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.LoggerFactory;
 
 /**
- * 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
  */
-public class NvdCveAnalyzer implements Analyzer {
+public class NvdCveAnalyzer extends AbstractAnalyzer {
 
     /**
-     * The maximum number of query results to return.
+     * The Logger for use throughout the class
      */
-    static final int MAX_QUERY_RESULTS = 100;
+    private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(NvdCveAnalyzer.class);
+
     /**
      * The CVE Index.
      */
@@ -51,18 +56,18 @@ 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();
-        cveDB.open();
+        cveDB = CveDB.getInstance();
     }
 
     /**
      * Closes the data source.
      */
     @Override
-    public void close() {
+    public void closeAnalyzer() {
         cveDB.close();
         cveDB = null;
     }
@@ -73,31 +78,20 @@ public class NvdCveAnalyzer implements Analyzer {
      * @return true or false.
      */
     public boolean isOpen() {
-        return (cveDB != null);
+        return cveDB != null;
     }
 
     /**
-     * Ensures that the CVE Database is closed.
-     *
-     * @throws Throwable when a throwable is thrown.
-     */
-    @Override
-    protected void finalize() throws Throwable {
-        super.finalize();
-        if (isOpen()) {
-            close();
-        }
-    }
-
-    /**
-     * 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 thrown if there is an issue analyzing the
+     * dependency
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         for (Identifier id : dependency.getIdentifiers()) {
             if ("cpe".equals(id.getType())) {
                 try {
@@ -143,12 +137,38 @@ public class NvdCveAnalyzer implements Analyzer {
     }
 
     /**
-     * Opens the database used to gather NVD CVE data.
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
      *
-     * @throws Exception is thrown if there is an issue opening the index.
+     * @return the key for the analyzer's enabled property
      */
     @Override
-    public void initialize() throws Exception {
-        this.open();
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_NVD_CVE_ENABLED;
+    }
+
+    /**
+     * Opens the database used to gather NVD CVE data.
+     *
+     * @throws InitializationException is thrown if there is an issue opening
+     * the index.
+     */
+    @Override
+    public void initializeAnalyzer() throws InitializationException {
+        try {
+            this.open();
+        } catch (SQLException ex) {
+            LOGGER.debug("SQL Exception initializing NvdCveAnalyzer", ex);
+            throw new InitializationException(ex);
+        } catch (IOException ex) {
+            LOGGER.debug("IO Exception initializing NvdCveAnalyzer", ex);
+            throw new InitializationException(ex);
+        } catch (DatabaseException ex) {
+            LOGGER.debug("Database Exception initializing NvdCveAnalyzer", ex);
+            throw new InitializationException(ex);
+        } catch (ClassNotFoundException ex) {
+            LOGGER.debug("Exception initializing NvdCveAnalyzer", ex);
+            throw new InitializationException(ex);
+        }
     }
 }

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

@@ -28,16 +28,21 @@ import org.owasp.dependencycheck.utils.Settings;
 import java.io.File;
 import java.io.FileFilter;
 import java.io.IOException;
+import java.nio.charset.Charset;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
  * Used to analyze OpenSSL source code present in the file system.
  *
- * @author Dale Visser <dvisser@ida.org>
+ * @author Dale Visser
  */
 public class OpenSSLAnalyzer extends AbstractFileTypeAnalyzer {
 
+    /**
+     * Hexadecimal.
+     */
     private static final int HEXADECIMAL = 16;
     /**
      * Filename to analyze. All other .h files get removed from consideration.
@@ -48,17 +53,47 @@ public class OpenSSLAnalyzer extends AbstractFileTypeAnalyzer {
      * Filter that detects files named "__init__.py".
      */
     private static final FileFilter OPENSSLV_FILTER = FileFilterBuilder.newInstance().addFilenames(OPENSSLV_H).build();
+    /**
+     * Open SSL Version number pattern.
+     */
     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);
+    /**
+     * The offset of the major version number.
+     */
     private static final int MAJOR_OFFSET = 28;
+    /**
+     * The mask for the minor version number.
+     */
     private static final long MINOR_MASK = 0x0ff00000L;
+    /**
+     * The offset of the minor version number.
+     */
     private static final int MINOR_OFFSET = 20;
+    /**
+     * The max for the fix version.
+     */
     private static final long FIX_MASK = 0x000ff000L;
+    /**
+     * The offset for the fix version.
+     */
     private static final int FIX_OFFSET = 12;
+    /**
+     * The mask for the patch version.
+     */
     private static final long PATCH_MASK = 0x00000ff0L;
+    /**
+     * The offset for the patch version.
+     */
     private static final int PATCH_OFFSET = 4;
+    /**
+     * Number of letters.
+     */
     private static final int NUM_LETTERS = 26;
+    /**
+     * The status mask.
+     */
     private static final int STATUS_MASK = 0x0000000f;
 
     /**
@@ -67,7 +102,7 @@ public class OpenSSLAnalyzer extends AbstractFileTypeAnalyzer {
      * @param openSSLVersionConstant The open SSL version
      * @return the version of openssl
      */
-    static String getOpenSSLVersion(long openSSLVersionConstant) {
+    protected 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;
@@ -111,10 +146,10 @@ public class OpenSSLAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * No-op initializer implementation.
      *
-     * @throws Exception never thrown
+     * @throws InitializationException never thrown
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws Exception {
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
         // Nothing to do here.
     }
 
@@ -123,10 +158,11 @@ public class OpenSSLAnalyzer extends AbstractFileTypeAnalyzer {
      *
      * @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
+     * @throws AnalysisException thrown if there is an unrecoverable error
+     * analyzing the dependency
      */
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
+    protected void analyzeDependency(Dependency dependency, Engine engine)
             throws AnalysisException {
         final File file = dependency.getActualFile();
         final String parentName = file.getParentFile().getName();
@@ -158,16 +194,19 @@ public class OpenSSLAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private String getFileContents(final File actualFile)
             throws AnalysisException {
-        String contents;
         try {
-            contents = FileUtils.readFileToString(actualFile).trim();
+            return FileUtils.readFileToString(actualFile, Charset.defaultCharset()).trim();
         } catch (IOException e) {
             throw new AnalysisException(
                     "Problem occurred while reading dependency file.", e);
         }
-        return contents;
     }
 
+    /**
+     * Returns the setting for the analyzer enabled setting key.
+     *
+     * @return the setting for the analyzer enabled setting key
+     */
     @Override
     protected String getAnalyzerEnabledSettingKey() {
         return Settings.KEYS.ANALYZER_OPENSSL_ENABLED;

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

@@ -23,9 +23,10 @@ import java.io.FileFilter;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FilenameFilter;
+import java.io.IOException;
+import java.io.InputStream;
 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;
@@ -37,19 +38,23 @@ import org.slf4j.LoggerFactory;
 
 import javax.mail.MessagingException;
 import javax.mail.internet.InternetHeaders;
+import org.owasp.dependencycheck.exception.InitializationException;
 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;
+import java.util.concurrent.atomic.AtomicInteger;
 
 /**
- * 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.
+ * 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 <dvisser@ida.org>
+ * @author Dale Visser
  */
+@Experimental
 public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -69,9 +74,10 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
             .getLogger(PythonDistributionAnalyzer.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;
+    private static final AtomicInteger DIR_COUNT = new AtomicInteger(0);
 
     /**
      * The name of the analyzer.
@@ -103,7 +109,8 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
     private File tempFileLocation;
 
     /**
-     * Filter that detects *.dist-info files (but doesn't verify they are directories.
+     * Filter that detects *.dist-info files (but doesn't verify they are
+     * directories.
      */
     private static final FilenameFilter DIST_INFO_FILTER = new SuffixFileFilter(
             ".dist-info");
@@ -163,7 +170,8 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -173,7 +181,7 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
+    protected void analyzeDependency(Dependency dependency, Engine engine)
             throws AnalysisException {
         final File actualFile = dependency.getActualFile();
         if (WHL_FILTER.accept(actualFile)) {
@@ -205,7 +213,8 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
      * @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
+     * @throws AnalysisException thrown when there is a problem analyzing the
+     * dependency
      */
     private void collectMetadataFromArchiveFormat(Dependency dependency,
             FilenameFilter folderFilter, FilenameFilter metadataFilter)
@@ -220,32 +229,43 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
             throw new AnalysisException(ex);
         }
 
-        collectWheelMetadata(
-                dependency,
-                getMatchingFile(getMatchingFile(temp, folderFilter),
-                        metadataFilter));
+        File matchingFile = getMatchingFile(temp, folderFilter);
+        if (matchingFile != null) {
+            matchingFile = getMatchingFile(matchingFile, metadataFilter);
+            if (matchingFile != null) {
+                collectWheelMetadata(dependency, matchingFile);
+            }
+        }
     }
 
     /**
      * Makes sure a usable temporary directory is available.
      *
-     * @throws Exception an AnalyzeException is thrown when the temp directory cannot be created
+     * @throws InitializationException 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);
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
+        try {
+            final File baseDir = Settings.getTempDirectory();
+            tempFileLocation = File.createTempFile("check", "tmp", baseDir);
+            if (!tempFileLocation.delete()) {
+                setEnabled(false);
+                final String msg = String.format(
+                        "Unable to delete temporary file '%s'.",
+                        tempFileLocation.getAbsolutePath());
+                throw new InitializationException(msg);
+            }
+            if (!tempFileLocation.mkdirs()) {
+                setEnabled(false);
+                final String msg = String.format(
+                        "Unable to create directory '%s'.",
+                        tempFileLocation.getAbsolutePath());
+                throw new InitializationException(msg);
+            }
+        } catch (IOException ex) {
+            setEnabled(false);
+            throw new InitializationException("Unable to create a temporary file", ex);
         }
     }
 
@@ -253,13 +273,15 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
      * Deletes any files extracted from the Wheel during analysis.
      */
     @Override
-    public void close() {
+    public void closeAnalyzer() {
         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");
+            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");
+                }
             }
         }
     }
@@ -311,7 +333,8 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns a list of files that match the given filter, this does not recursively scan the directory.
+     * 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
@@ -337,20 +360,20 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
         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) {
+            try (InputStream in = new BufferedInputStream(new FileInputStream(manifest))) {
+                result.load(in);
+            } catch (MessagingException | FileNotFoundException e) {
                 LOGGER.warn(e.getMessage(), e);
+            } catch (IOException ex) {
+                LOGGER.warn(ex.getMessage(), ex);
             }
         }
         return result;
     }
 
     /**
-     * Retrieves the next temporary destination directory for extracting an archive.
+     * Retrieves the next temporary destination directory for extracting an
+     * archive.
      *
      * @return a directory
      * @throws AnalysisException thrown if unable to create temporary directory
@@ -361,7 +384,7 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
         // getting an exception for some directories not being able to be
         // created; might be because the directory already exists?
         do {
-            dirCount += 1;
+            final int dirCount = DIR_COUNT.incrementAndGet();
             directory = new File(tempFileLocation, String.valueOf(dirCount));
         } while (directory.exists());
         if (!directory.mkdirs()) {

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

@@ -32,16 +32,18 @@ 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.nio.charset.Charset;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
- * Used to analyze a Python package, and collect information that can be used to determine the associated CPE.
+ * Used to analyze a Python package, and collect information that can be used to
+ * determine the associated CPE.
  *
- * @author Dale Visser <dvisser@ida.org>
+ * @author Dale Visser
  */
+@Experimental
 public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -141,10 +143,10 @@ public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * No-op initializer implementation.
      *
-     * @throws Exception never thrown
+     * @throws InitializationException never thrown
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws Exception {
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
         // Nothing to do here.
     }
 
@@ -164,40 +166,42 @@ public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
      * 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
+     * @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)
+    protected void analyzeDependency(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)) {
-            for (final File sourceFile : parent.listFiles(PY_FILTER)) {
-                found |= analyzeFileContents(dependency, sourceFile);
-            }
-        }
-        if (found) {
+            //by definition, the containing folder of __init__.py is considered the package, even the file is empty:
+            //"The __init__.py files are required to make Python treat the directories as containing packages"
+            //see section "6.4 Packages" from https://docs.python.org/2/tutorial/modules.html;
             dependency.setDisplayFileName(parentName + "/__init__.py");
             dependency.getProductEvidence().addEvidence(file.getName(),
-                    "PackageName", parentName, Confidence.MEDIUM);
+                    "PackageName", parentName, Confidence.HIGHEST);
+
+            final File[] fileList = parent.listFiles(PY_FILTER);
+            if (fileList != null) {
+                for (final File sourceFile : fileList) {
+                    analyzeFileContents(dependency, sourceFile);
+                }
+            }
         } 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);
+            engine.getDependencies().remove(dependency);
         }
     }
 
     /**
-     * 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.
+     * 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
+     * @param file the file name to analyze
      * @return whether evidence was found
      * @throws AnalysisException thrown if there is an unrecoverable error
      */
@@ -205,7 +209,7 @@ public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
             throws AnalysisException {
         String contents;
         try {
-            contents = FileUtils.readFileToString(file).trim();
+            contents = FileUtils.readFileToString(file, Charset.defaultCharset()).trim();
         } catch (IOException e) {
             throw new AnalysisException(
                     "Problem occurred while reading dependency file.", e);
@@ -241,15 +245,15 @@ public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
      * 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
+     * @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) {
+            int group, String contents, String source, String key) {
         final Matcher matcher = pattern.matcher(contents);
         final boolean found = matcher.find();
         if (found) {
@@ -262,16 +266,16 @@ public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Collects evidence from the home page URL.
      *
-     * @param pattern  the pattern to match
+     * @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 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) {
+            EvidenceCollection evidence, String source, String name,
+            String contents) {
         final Matcher matcher = pattern.matcher(contents);
         boolean found = false;
         if (matcher.find()) {
@@ -285,19 +289,20 @@ public class PythonPackageAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Gather evidence from a Python source file using the given string assignment regex pattern.
+     * 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 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) {
+            String source, EvidenceCollection evidence, String name,
+            Confidence confidence) {
         final Matcher matcher = pattern.matcher(contents);
         final boolean found = matcher.find();
         if (found) {

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

@@ -0,0 +1,494 @@
+/*
+ * 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.BufferedReader;
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.io.FileUtils;
+import org.owasp.dependencycheck.Engine;
+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.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Reference;
+import org.owasp.dependencycheck.dependency.Vulnerability;
+import org.owasp.dependencycheck.exception.InitializationException;
+import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Used to analyze Ruby Bundler Gemspec.lock files utilizing the 3rd party
+ * bundle-audit tool.
+ *
+ * @author Dale Visser
+ */
+@Experimental
+public class RubyBundleAuditAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    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;
+    /**
+     * The filter defining which files will be analyzed.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addFilenames("Gemfile.lock").build();
+    /**
+     * Name.
+     */
+    public static final String NAME = "Name: ";
+    /**
+     * Version.
+     */
+    public static final String VERSION = "Version: ";
+    /**
+     * Advisory.
+     */
+    public static final String ADVISORY = "Advisory: ";
+    /**
+     * Criticality.
+     */
+    public static final String CRITICALITY = "Criticality: ";
+
+    /**
+     * The DAL.
+     */
+    private CveDB cvedb;
+
+    /**
+     * @return a filter that accepts files named Gemfile.lock
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return FILTER;
+    }
+
+    /**
+     * Launch bundle-audit.
+     *
+     * @param folder directory that contains bundle audit
+     * @return a handle to the process
+     * @throws AnalysisException thrown when there is an issue launching bundle
+     * audit
+     */
+    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<>();
+        final String bundleAuditPath = Settings.getString(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_PATH);
+        File bundleAudit = null;
+        if (bundleAuditPath != null) {
+            bundleAudit = new File(bundleAuditPath);
+            if (!bundleAudit.isFile()) {
+                LOGGER.warn("Supplied `bundleAudit` path is incorrect: " + bundleAuditPath);
+                bundleAudit = null;
+            }
+        }
+        args.add(bundleAudit != null && bundleAudit.isFile() ? bundleAudit.getAbsolutePath() : "bundle-audit");
+        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 initialization failure; this error can be ignored if you are not analyzing Ruby. "
+                    + "Otherwise ensure that bundle-audit is installed and the path to bundle audit is correctly specified", ioe);
+        }
+    }
+
+    /**
+     * Initialize the analyzer. In this case, extract GrokAssembly.exe to a
+     * temporary location.
+     *
+     * @throws InitializationException if anything goes wrong
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws InitializationException {
+        try {
+            cvedb = CveDB.getInstance();
+        } catch (DatabaseException ex) {
+            LOGGER.warn("Exception opening the database");
+            LOGGER.debug("error", ex);
+            setEnabled(false);
+            throw new InitializationException("Error connecting to the database", ex);
+        }
+        // Now, need to see if bundle-audit actually runs from this location.
+        Process process = null;
+        try {
+            process = launchBundleAudit(Settings.getTempDirectory());
+        } catch (AnalysisException ae) {
+
+            setEnabled(false);
+            final String msg = String.format("Exception from bundle-audit process: %s. Disabling %s", ae.getCause(), ANALYZER_NAME);
+            throw new InitializationException(msg, ae);
+        } catch (IOException ex) {
+            setEnabled(false);
+            throw new InitializationException("Unable to create temporary file, the Ruby Bundle Audit Analyzer will be disabled", ex);
+        }
+
+        final int exitValue;
+        try {
+            exitValue = process.waitFor();
+        } catch (InterruptedException ex) {
+            setEnabled(false);
+            final String msg = String.format("Bundle-audit process was interrupted. Disabling %s", ANALYZER_NAME);
+            throw new InitializationException(msg);
+        }
+        if (0 == exitValue) {
+            setEnabled(false);
+            final String msg = String.format("Unexpected exit code from bundle-audit process. Disabling %s: %s", ANALYZER_NAME, exitValue);
+            throw new InitializationException(msg);
+        } else {
+            try (BufferedReader 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 InitializationException("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 InitializationException("Unexpected bundle-audit output.");
+                    }
+                }
+            } catch (UnsupportedEncodingException ex) {
+                setEnabled(false);
+                throw new InitializationException("Unexpected bundle-audit encoding.", ex);
+            } catch (IOException ex) {
+                setEnabled(false);
+                throw new InitializationException("Unable to read bundle-audit output.", ex);
+            }
+        }
+
+        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.");
+        }
+    }
+
+    /**
+     * Closes the data source.
+     */
+    @Override
+    public void closeAnalyzer() {
+        if (cvedb != null) {
+            cvedb.close();
+            cvedb = null;
+        }
+    }
+
+    /**
+     * 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 #analyzeDependency(Dependency, Engine)} is called, then we have
+     * successfully initialized, and it will be necessary to disable
+     * {@link RubyGemspecAnalyzer}.
+     */
+    private boolean needToDisableGemspecAnalyzer = true;
+
+    /**
+     * Determines if the analyzer can analyze the given file type.
+     *
+     * @param dependency the dependency to determine if it can analyze
+     * @param engine the dependency-check engine
+     * @throws AnalysisException thrown if there is an analysis exception.
+     */
+    @Override
+    protected void analyzeDependency(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 RubyBundlerAnalyzer) {
+                    ((RubyBundlerAnalyzer) analyzer).setEnabled(false);
+                    LOGGER.info("Disabled " + RubyBundlerAnalyzer.class.getName() + " to avoid noisy duplicate results.");
+                } else 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);
+        final int exitValue;
+        try {
+            exitValue = process.waitFor();
+        } catch (InterruptedException ie) {
+            throw new AnalysisException("bundle-audit process interrupted", ie);
+        }
+        if (exitValue < 0 || exitValue > 1) {
+            final String msg = String.format("Unexpected exit code from bundle-audit process; exit code: %s", exitValue);
+            throw new AnalysisException(msg);
+        }
+        try {
+            try (BufferedReader errReader = new BufferedReader(new InputStreamReader(process.getErrorStream(), "UTF-8"))) {
+                while (errReader.ready()) {
+                    final String error = errReader.readLine();
+                    LOGGER.warn(error);
+                }
+            }
+            try (BufferedReader rdr = new BufferedReader(new InputStreamReader(process.getInputStream(), "UTF-8"))) {
+                processBundlerAuditOutput(dependency, engine, rdr);
+            }
+        } catch (IOException ioe) {
+            LOGGER.warn("bundle-audit failure", ioe);
+        }
+    }
+
+    /**
+     * Processes the bundler audit output.
+     *
+     * @param original the dependency
+     * @param engine the dependency-check engine
+     * @param rdr the reader of the report
+     * @throws IOException thrown if the report cannot be read.
+     */
+    private void processBundlerAuditOutput(Dependency original, Engine engine, BufferedReader rdr) throws IOException {
+        final String parentName = original.getActualFile().getParentFile().getName();
+        final String fileName = original.getFileName();
+        final String filePath = original.getFilePath();
+        Dependency dependency = null;
+        Vulnerability vulnerability = null;
+        String gem = null;
+        final Map<String, Dependency> map = new HashMap<>();
+        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, filePath, gem));
+                }
+                dependency = map.get(gem);
+                LOGGER.debug(String.format("bundle-audit (%s): %s", parentName, nextLine));
+            } else if (nextLine.startsWith(VERSION)) {
+                vulnerability = createVulnerability(parentName, dependency, 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 && null != vulnerability) {
+                vulnerability.setDescription(vulnerability.getDescription() + nextLine + "\n");
+            }
+        }
+    }
+
+    /**
+     * Sets the vulnerability name.
+     *
+     * @param parentName the parent name
+     * @param dependency the dependency
+     * @param vulnerability the vulnerability
+     * @param nextLine the line to parse
+     */
+    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));
+    }
+
+    /**
+     * Adds a reference to the vulnerability.
+     *
+     * @param parentName the parent name
+     * @param vulnerability the vulnerability
+     * @param nextLine the line to parse
+     */
+    private void addReferenceToVulnerability(String parentName, Vulnerability vulnerability, String nextLine) {
+        final String url = nextLine.substring(("URL: ").length());
+        if (null != vulnerability) {
+            final 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));
+    }
+
+    /**
+     * Adds the criticality to the vulnerability
+     *
+     * @param parentName the parent name
+     * @param vulnerability the vulnerability
+     * @param nextLine the line to parse
+     */
+    private void addCriticalityToVulnerability(String parentName, Vulnerability vulnerability, String nextLine) {
+        if (null != vulnerability) {
+            final String criticality = nextLine.substring(CRITICALITY.length()).trim();
+            float score = -1.0f;
+            Vulnerability v = null;
+            try {
+                v = cvedb.getVulnerability(vulnerability.getName());
+            } catch (DatabaseException ex) {
+                LOGGER.debug("Unable to look up vulnerability {}", vulnerability.getName());
+            }
+            if (v != null) {
+                score = v.getCvssScore();
+            } else if ("High".equalsIgnoreCase(criticality)) {
+                score = 8.5f;
+            } else if ("Medium".equalsIgnoreCase(criticality)) {
+                score = 5.5f;
+            } else if ("Low".equalsIgnoreCase(criticality)) {
+                score = 2.0f;
+            }
+            vulnerability.setCvssScore(score);
+        }
+        LOGGER.debug(String.format("bundle-audit (%s): %s", parentName, nextLine));
+    }
+
+    /**
+     * Creates a vulnerability.
+     *
+     * @param parentName the parent name
+     * @param dependency the dependency
+     * @param gem the gem name
+     * @param nextLine the line to parse
+     * @return the vulnerability
+     */
+    private Vulnerability createVulnerability(String parentName, Dependency dependency, String gem, String nextLine) {
+        Vulnerability vulnerability = null;
+        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;
+    }
+
+    /**
+     * Creates the dependency based off of the gem.
+     *
+     * @param engine the engine used for scanning
+     * @param parentName the gem parent
+     * @param fileName the file name
+     * @param filePath the file path
+     * @param gem the gem name
+     * @return the dependency to add
+     * @throws IOException thrown if a temporary gem file could not be written
+     */
+    private Dependency createDependencyForGem(Engine engine, String parentName, String fileName, String filePath, String gem) throws IOException {
+        final File gemFile = new File(Settings.getTempDirectory(), gem + "_Gemfile.lock");
+        if (!gemFile.createNewFile()) {
+            throw new IOException("Unable to create temporary gem file");
+        }
+        final String displayFileName = String.format("%s%c%s:%s", parentName, File.separatorChar, fileName, gem);
+
+        FileUtils.write(gemFile, displayFileName, Charset.defaultCharset()); // unique contents to avoid dependency bundling
+        final Dependency dependency = new Dependency(gemFile);
+        dependency.getProductEvidence().addEvidence("bundler-audit", "Name", gem, Confidence.HIGHEST);
+        dependency.setDisplayFileName(displayFileName);
+        dependency.setFileName(fileName);
+        dependency.setFilePath(filePath);
+        engine.getDependencies().add(dependency);
+        return dependency;
+    }
+}

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

@@ -0,0 +1,141 @@
+/*
+ * 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) 2016 IBM Corporation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.File;
+import java.io.FilenameFilter;
+
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+
+/**
+ * This analyzer accepts the fully resolved .gemspec created by the Ruby bundler
+ * (http://bundler.io) for better evidence results. It also tries to resolve the
+ * dependency packagePath to where the gem is actually installed. Then during
+ * the {@link org.owasp.dependencycheck.analyzer.AnalysisPhase#PRE_FINDING_ANALYSIS}
+ * {@link DependencyMergingAnalyzer} will merge two .gemspec dependencies
+ * together if <code>Dependency.getPackagePath()</code> are the same.
+ *
+ * Ruby bundler creates new .gemspec files under a folder called
+ * "specifications" at deploy time, in addition to the original .gemspec files
+ * from source. The bundler generated .gemspec files always contain fully
+ * resolved attributes thus provide more accurate evidences, whereas the
+ * original .gemspec from source often contain variables for attributes that
+ * can't be used for evidences.
+ *
+ * Note this analyzer share the same
+ * {@link org.owasp.dependencycheck.utils.Settings.KEYS#ANALYZER_RUBY_GEMSPEC_ENABLED}
+ * as {@link RubyGemspecAnalyzer}, so it will enabled/disabled with
+ * {@link RubyGemspecAnalyzer}.
+ *
+ * @author Bianca Jiang (https://twitter.com/biancajiang)
+ */
+@Experimental
+public class RubyBundlerAnalyzer extends RubyGemspecAnalyzer {
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Ruby Bundler Analyzer";
+
+    /**
+     * Folder name that contains .gemspec files created by "bundle install"
+     */
+    private static final String SPECIFICATIONS = "specifications";
+
+    /**
+     * Folder name that contains the gems by "bundle install"
+     */
+    private static final String GEMS = "gems";
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Only accept *.gemspec files generated by "bundle install --deployment"
+     * under "specifications" folder.
+     *
+     * @param pathname the path name to test
+     * @return true if the analyzer can process the given file; otherwise false
+     */
+    @Override
+    public boolean accept(File pathname) {
+
+        boolean accepted = super.accept(pathname);
+        if (accepted) {
+            final File parentDir = pathname.getParentFile();
+            accepted = parentDir != null && parentDir.getName().equals(SPECIFICATIONS);
+        }
+
+        return accepted;
+    }
+
+    @Override
+    protected void analyzeDependency(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        super.analyzeDependency(dependency, engine);
+
+        //find the corresponding gem folder for this .gemspec stub by "bundle install --deployment"
+        final File gemspecFile = dependency.getActualFile();
+        final String gemFileName = gemspecFile.getName();
+        final String gemName = gemFileName.substring(0, gemFileName.lastIndexOf(".gemspec"));
+        final File specificationsDir = gemspecFile.getParentFile();
+        if (specificationsDir != null && specificationsDir.getName().equals(SPECIFICATIONS) && specificationsDir.exists()) {
+            final File parentDir = specificationsDir.getParentFile();
+            if (parentDir != null && parentDir.exists()) {
+                final File gemsDir = new File(parentDir, GEMS);
+                if (gemsDir.exists()) {
+                    final File[] matchingFiles = gemsDir.listFiles(new FilenameFilter() {
+                        @Override
+                        public boolean accept(File dir, String name) {
+                            return name.equals(gemName);
+                        }
+                    });
+
+                    if (matchingFiles != null && matchingFiles.length > 0) {
+                        final String gemPath = matchingFiles[0].getAbsolutePath();
+                        if (dependency.getActualFilePath().equals(dependency.getFilePath())) {
+                            if (gemPath != null) {
+                                dependency.setPackagePath(gemPath);
+                            }
+                        } else {
+                            //.gemspec's actualFilePath and filePath are different when it's from a compressed file
+                            //in which case actualFilePath is the temp directory used by decompression.
+                            //packagePath should use the filePath of the identified gem file in "gems" folder
+                            final File gemspecStub = new File(dependency.getFilePath());
+                            final File specDir = gemspecStub.getParentFile();
+                            if (specDir != null && specDir.getName().equals(SPECIFICATIONS)) {
+                                final File gemsDir2 = new File(specDir.getParentFile(), GEMS);
+                                final File packageDir = new File(gemsDir2, gemName);
+                                dependency.setPackagePath(packageDir.getAbsolutePath());
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

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

@@ -17,28 +17,41 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
 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.exception.InitializationException;
 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;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
- * 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.
+ * 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 <dvisser@ida.org>
+ * @author Dale Visser
  */
+@Experimental
 public class RubyGemspecAnalyzer extends AbstractFileTypeAnalyzer {
 
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(RubyGemspecAnalyzer.class);
     /**
      * The name of the analyzer.
      */
@@ -49,14 +62,26 @@ public class RubyGemspecAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
 
-    private static final FileFilter FILTER =
-            FileFilterBuilder.newInstance().addExtensions("gemspec").addFilenames("Rakefile").build();
-
-    private static final String EMAIL = "email";
+    /**
+     * The gemspec file extension.
+     */
     private static final String GEMSPEC = "gemspec";
 
     /**
-     * @return a filter that accepts files named Rakefile or matching the glob pattern, *.gemspec
+     * The file filter containing the list of file extensions that can be
+     * analyzed.
+     */
+    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(GEMSPEC).build();
+    //TODO: support Rakefile
+    //= FileFilterBuilder.newInstance().addExtensions(GEMSPEC).addFilenames("Rakefile").build();
+
+    /**
+     * The name of the version file.
+     */
+    private static final String VERSION_FILE_NAME = "VERSION";
+
+    /**
+     * @return a filter that accepts files matching the glob pattern, *.gemspec
      */
     @Override
     protected FileFilter getFileFilter() {
@@ -64,7 +89,7 @@ public class RubyGemspecAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     @Override
-    protected void initializeFileTypeAnalyzer() throws Exception {
+    protected void initializeFileTypeAnalyzer() throws InitializationException {
         // NO-OP
     }
 
@@ -89,7 +114,8 @@ public class RubyGemspecAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     * Returns the key used in the properties file to reference the analyzer's
+     * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -101,15 +127,14 @@ public class RubyGemspecAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * The capture group #1 is the block variable.
      */
-    private static final Pattern GEMSPEC_BLOCK_INIT =
-            Pattern.compile("Gem::Specification\\.new\\s+?do\\s+?\\|(.+?)\\|");
+    private static final Pattern GEMSPEC_BLOCK_INIT = Pattern.compile("Gem::Specification\\.new\\s+?do\\s+?\\|(.+?)\\|");
 
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
+    protected void analyzeDependency(Dependency dependency, Engine engine)
             throws AnalysisException {
         String contents;
         try {
-            contents = FileUtils.readFileToString(dependency.getActualFile());
+            contents = FileUtils.readFileToString(dependency.getActualFile(), Charset.defaultCharset());
         } catch (IOException e) {
             throw new AnalysisException(
                     "Problem occurred while reading dependency file.", e);
@@ -118,43 +143,107 @@ public class RubyGemspecAnalyzer extends AbstractFileTypeAnalyzer {
         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);
+            final String name = addStringEvidence(product, contents, blockVariable, "name", "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);
+            addStringEvidence(product, contents, blockVariable, "summary", "summary", Confidence.LOW);
+
+            addStringEvidence(vendor, contents, blockVariable, "author", "authors?", Confidence.HIGHEST);
+            addStringEvidence(vendor, contents, blockVariable, "email", "emails?", Confidence.MEDIUM);
+            addStringEvidence(vendor, contents, blockVariable, "homepage", "homepage", Confidence.HIGHEST);
+            addStringEvidence(vendor, contents, blockVariable, "license", "licen[cs]es?", Confidence.HIGHEST);
+
+            final String value = addStringEvidence(dependency.getVersionEvidence(), contents,
+                    blockVariable, "version", "version", Confidence.HIGHEST);
+            if (value.length() < 1) {
+                addEvidenceFromVersionFile(dependency.getActualFile(), dependency.getVersionEvidence());
+            }
         }
+
+        setPackagePath(dependency);
     }
 
+    /**
+     * Adds the specified evidence to the given evidence collection.
+     *
+     * @param evidences the collection to add the evidence to
+     * @param contents the evidence contents
+     * @param blockVariable the variable
+     * @param field the field
+     * @param fieldPattern the field pattern
+     * @param confidence the confidence of the evidence
+     * @return the evidence string value added
+     */
     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 blockVariable, String field, String fieldPattern, Confidence confidence) {
         String value = "";
-        if (matcher.find()) {
-            value = matcher.group(2);
+
+        //capture array value between [ ]
+        final Matcher arrayMatcher = Pattern.compile(
+                String.format("\\s*?%s\\.%s\\s*?=\\s*?\\[(.*?)\\]", blockVariable, fieldPattern), Pattern.CASE_INSENSITIVE).matcher(contents);
+        if (arrayMatcher.find()) {
+            final String arrayValue = arrayMatcher.group(1);
+            value = arrayValue.replaceAll("['\"]", "").trim(); //strip quotes
+        } else { //capture single value between quotes
+            final Matcher matcher = Pattern.compile(
+                    String.format("\\s*?%s\\.%s\\s*?=\\s*?(['\"])(.*?)\\1", blockVariable, fieldPattern), Pattern.CASE_INSENSITIVE).matcher(contents);
+            if (matcher.find()) {
+                value = matcher.group(2);
+            }
+        }
+        if (value.length() > 0) {
             evidences.addEvidence(GEMSPEC, field, value, confidence);
         }
+
         return value;
     }
+
+    /**
+     * Adds evidence from the version file.
+     *
+     * @param dependencyFile the dependency being analyzed
+     * @param versionEvidences the version evidence
+     */
+    private void addEvidenceFromVersionFile(File dependencyFile, EvidenceCollection versionEvidences) {
+        final File parentDir = dependencyFile.getParentFile();
+        if (parentDir != null) {
+            final File[] matchingFiles = parentDir.listFiles(new FilenameFilter() {
+                @Override
+                public boolean accept(File dir, String name) {
+                    return name.contains(VERSION_FILE_NAME);
+                }
+            });
+            if (matchingFiles == null) {
+                return;
+            }
+            for (File f : matchingFiles) {
+                try {
+                    final List<String> lines = FileUtils.readLines(f, Charset.defaultCharset());
+                    if (lines.size() == 1) { //TODO other checking?
+                        final String value = lines.get(0).trim();
+                        versionEvidences.addEvidence(GEMSPEC, "version", value, Confidence.HIGH);
+                    }
+                } catch (IOException e) {
+                    LOGGER.debug("Error reading gemspec", e);
+                }
+            }
+        }
+    }
+
+    /**
+     * Sets the package path on the dependency.
+     *
+     * @param dep the dependency to alter
+     */
+    private void setPackagePath(Dependency dep) {
+        final File file = new File(dep.getFilePath());
+        final String parent = file.getParent();
+        if (parent != null) {
+            dep.setPackagePath(parent);
+        }
+    }
 }

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

@@ -0,0 +1,192 @@
+/*
+ * 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) 2016 IBM Corporation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+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;
+
+/**
+ * This analyzer is used to analyze the SWIFT Package Manager
+ * (https://swift.org/package-manager/). It collects information about a package
+ * from Package.swift files.
+ *
+ * @author Bianca Jiang (https://twitter.com/biancajiang)
+ */
+@Experimental
+public class SwiftPackageManagerAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "SWIFT Package Manager 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 SPM_FILE_NAME = "Package.swift";
+
+    /**
+     * Filter that detects files named "package.json".
+     */
+    private static final FileFilter SPM_FILE_FILTER = FileFilterBuilder.newInstance().addFilenames(SPM_FILE_NAME).build();
+
+    /**
+     * The capture group #1 is the block variable. e.g. "import
+     * PackageDescription let package = Package( name: "Gloss" )"
+     */
+    private static final Pattern SPM_BLOCK_PATTERN = Pattern.compile("let[^=]+=\\s*Package\\s*\\(\\s*([^)]*)\\s*\\)", Pattern.DOTALL);
+
+    /**
+     * Returns the FileFilter
+     *
+     * @return the FileFilter
+     */
+    @Override
+    protected FileFilter getFileFilter() {
+        return SPM_FILE_FILTER;
+    }
+
+    @Override
+    protected void initializeFileTypeAnalyzer() {
+        // 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_SWIFT_PACKAGE_MANAGER_ENABLED;
+    }
+
+    @Override
+    protected void analyzeDependency(Dependency dependency, Engine engine)
+            throws AnalysisException {
+
+        String contents;
+        try {
+            contents = FileUtils.readFileToString(dependency.getActualFile(), Charset.defaultCharset());
+        } catch (IOException e) {
+            throw new AnalysisException(
+                    "Problem occurred while reading dependency file.", e);
+        }
+        final Matcher matcher = SPM_BLOCK_PATTERN.matcher(contents);
+        if (matcher.find()) {
+            final String packageDescription = matcher.group(1);
+            if (packageDescription.isEmpty()) {
+                return;
+            }
+
+            final EvidenceCollection product = dependency.getProductEvidence();
+            final EvidenceCollection vendor = dependency.getVendorEvidence();
+
+            //SPM is currently under development for SWIFT 3. Its current metadata includes package name and dependencies.
+            //Future interesting metadata: version, license, homepage, author, summary, etc.
+            final String name = addStringEvidence(product, packageDescription, "name", "name", Confidence.HIGHEST);
+            if (name != null && !name.isEmpty()) {
+                vendor.addEvidence(SPM_FILE_NAME, "name_project", name, Confidence.HIGHEST);
+            }
+        }
+        setPackagePath(dependency);
+    }
+
+    /**
+     * Extracts evidence from the package description and adds it to the given
+     * evidence collection.
+     *
+     * @param evidences the evidence collection to update
+     * @param packageDescription the text to extract evidence from
+     * @param field the name of the field being searched for
+     * @param fieldPattern the field pattern within the contents to search for
+     * @param confidence the confidence level of the evidence if found
+     * @return the string that was added as evidence
+     */
+    private String addStringEvidence(EvidenceCollection evidences,
+            String packageDescription, String field, String fieldPattern, Confidence confidence) {
+        String value = "";
+
+        final Matcher matcher = Pattern.compile(
+                String.format("%s *:\\s*\"([^\"]*)", fieldPattern), Pattern.DOTALL).matcher(packageDescription);
+        if (matcher.find()) {
+            value = matcher.group(1);
+        }
+
+        if (value != null) {
+            value = value.trim();
+            if (value.length() > 0) {
+                evidences.addEvidence(SPM_FILE_NAME, field, value, confidence);
+            }
+        }
+
+        return value;
+    }
+
+    /**
+     * Sets the package path on the given dependency.
+     *
+     * @param dep the dependency to update
+     */
+    private void setPackagePath(Dependency dep) {
+        final File file = new File(dep.getFilePath());
+        final String parent = file.getParent();
+        if (parent != null) {
+            dep.setPackagePath(parent);
+        }
+    }
+}

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

@@ -0,0 +1,167 @@
+/*
+ * 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) 2017 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.util.Iterator;
+import java.util.Objects;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.dependency.EvidenceCollection;
+import org.owasp.dependencycheck.utils.DependencyVersion;
+import org.owasp.dependencycheck.utils.Settings;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * This analyzer attempts to filter out erroneous version numbers collected.
+ * Initially, this will focus on JAR files that contain a POM version number
+ * that matches the file name - if identified all other version information will
+ * be removed.
+ *
+ * @author Jeremy Long
+ */
+public class VersionFilterAnalyzer extends AbstractAnalyzer {
+
+    //<editor-fold defaultstate="collapsed" desc="Constants">
+    /**
+     * Evidence source.
+     */
+    private static final String FILE = "file";
+    /**
+     * Evidence source.
+     */
+    private static final String POM = "pom";
+    /**
+     * Evidence source.
+     */
+    private static final String NEXUS = "nexus";
+    /**
+     * Evidence source.
+     */
+    private static final String CENTRAL = "central";
+    /**
+     * Evidence source.
+     */
+    private static final String MANIFEST = "Manifest";
+    /**
+     * Evidence name.
+     */
+    private static final String VERSION = "version";
+    /**
+     * Evidence name.
+     */
+    private static final String IMPLEMENTATION_VERSION = "Implementation-Version";
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Version Filter Analyzer";
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.POST_INFORMATION_COLLECTION;
+
+    //</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="Standard implementation of Analyzer">
+    /**
+     * 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 setting key to determine if the analyzer is enabled.
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_VERSION_FILTER_ENABLED;
+    }
+    //</editor-fold>
+
+    /**
+     * The Logger for use throughout the class
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(VersionFilterAnalyzer.class);
+
+    /**
+     * 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.
+     */
+    @Override
+    protected synchronized void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
+        String fileVersion = null;
+        String pomVersion = null;
+        String manifestVersion = null;
+        for (Evidence e : dependency.getVersionEvidence()) {
+            if (FILE.equals(e.getSource()) && VERSION.equals(e.getName())) {
+                fileVersion = e.getValue(Boolean.FALSE);
+            } else if ((NEXUS.equals(e.getSource()) || CENTRAL.equals(e.getSource())
+                    || POM.equals(e.getSource())) && VERSION.equals(e.getName())) {
+                pomVersion = e.getValue(Boolean.FALSE);
+            } else if (MANIFEST.equals(e.getSource()) && IMPLEMENTATION_VERSION.equals(e.getName())) {
+                manifestVersion = e.getValue(Boolean.FALSE);
+            }
+        }
+        //ensure we have at least two not null
+        if (((fileVersion == null ? 0 : 1) + (pomVersion == null ? 0 : 1) + (manifestVersion == null ? 0 : 1)) > 1) {
+            final DependencyVersion dvFile = new DependencyVersion(fileVersion);
+            final DependencyVersion dvPom = new DependencyVersion(pomVersion);
+            final DependencyVersion dvManifest = new DependencyVersion(manifestVersion);
+            final boolean fileMatch = Objects.equals(dvFile, dvPom) || Objects.equals(dvFile, dvManifest);
+            final boolean manifestMatch = Objects.equals(dvManifest, dvPom) || Objects.equals(dvManifest, dvFile);
+            final boolean pomMatch = Objects.equals(dvPom, dvFile) || Objects.equals(dvPom, dvManifest);
+            if (fileMatch || manifestMatch || pomMatch) {
+                LOGGER.debug("filtering evidence from {}", dependency.getFileName());
+                final EvidenceCollection versionEvidence = dependency.getVersionEvidence();
+                final Iterator<Evidence> itr = versionEvidence.iterator();
+                while (itr.hasNext()) {
+                    final Evidence e = itr.next();
+                    if (!(pomMatch && VERSION.equals(e.getName())
+                            && (NEXUS.equals(e.getSource()) || CENTRAL.equals(e.getSource()) || POM.equals(e.getSource())))
+                            && !(fileMatch && VERSION.equals(e.getName()) && FILE.equals(e.getSource()))
+                            && !(manifestMatch && MANIFEST.equals(e.getSource()) && IMPLEMENTATION_VERSION.equals(e.getName()))) {
+                        itr.remove();
+                    }
+                }
+            }
+        }
+    }
+}

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

@@ -20,11 +20,13 @@ 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;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.xml.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.
+ * 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
  */
@@ -59,10 +61,29 @@ public class VulnerabilitySuppressionAnalyzer extends AbstractSuppressionAnalyze
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_VULNERABILITY_SUPPRESSION_ENABLED;
+    }
     //</editor-fold>
 
+    /**
+     * Analyzes a dependency's vulnerabilities against the configured CVE
+     * suppressions.
+     *
+     * @param dependency the dependency being analyzed
+     * @param engine a reference to the engine orchestrating the analysis
+     * @throws AnalysisException thrown if there is an error during analysis
+     */
     @Override
-    public void analyze(final Dependency dependency, final Engine engine) throws AnalysisException {
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
 
         if (getRules() == null || getRules().size() <= 0) {
             return;

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/central/CentralSearch.java

@@ -24,17 +24,20 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.xpath.XPath;
 import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpressionException;
 import javax.xml.xpath.XPathFactory;
 import org.owasp.dependencycheck.data.nexus.MavenArtifact;
 import org.owasp.dependencycheck.utils.Settings;
 import org.owasp.dependencycheck.utils.URLConnectionFactory;
+import org.owasp.dependencycheck.utils.XmlUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
 import org.w3c.dom.NodeList;
+import org.xml.sax.SAXException;
 
 /**
  * Class of methods to search Maven Central via Central.
@@ -51,7 +54,7 @@ public class CentralSearch {
     /**
      * Whether to use the Proxy when making requests
      */
-    private boolean useProxy;
+    private final boolean useProxy;
 
     /**
      * Used for logging.
@@ -61,8 +64,8 @@ public class CentralSearch {
     /**
      * Creates a NexusSearch for the given repository URL.
      *
-     * @param rootURL the URL of the repository on which searches should execute. Only parameters are added to this (so it should
-     * end in /select)
+     * @param rootURL the URL of the repository on which searches should
+     * execute. Only parameters are added to this (so it should end in /select)
      */
     public CentralSearch(URL rootURL) {
         this.rootURL = rootURL;
@@ -76,21 +79,23 @@ public class CentralSearch {
     }
 
     /**
-     * Searches the configured Central URL for the given sha1 hash. If the artifact is found, a <code>MavenArtifact</code> is
-     * populated with the GAV.
+     * Searches the configured Central URL for the given sha1 hash. If the
+     * artifact is found, a <code>MavenArtifact</code> is populated with the
+     * GAV.
      *
      * @param sha1 the SHA-1 hash string for which to search
      * @return the populated Maven GAV.
-     * @throws IOException if it's unable to connect to the specified repository or if the specified artifact is not found.
+     * @throws IOException if it's unable to connect to the specified repository
+     * or if the specified artifact is not found.
      */
     public List<MavenArtifact> searchSha1(String sha1) throws IOException {
         if (null == sha1 || !sha1.matches("^[0-9A-Fa-f]{40}$")) {
             throw new IllegalArgumentException("Invalid SHA1 format");
         }
-
+        List<MavenArtifact> result = null;
         final URL url = new URL(rootURL + String.format("?q=1:\"%s\"&wt=xml", sha1));
 
-        LOGGER.debug("Searching Central url {}", url.toString());
+        LOGGER.debug("Searching Central url {}", url);
 
         // Determine if we need to use a proxy. The rules:
         // 1) If the proxy is set, AND the setting is set to true, use the proxy
@@ -108,15 +113,14 @@ public class CentralSearch {
         if (conn.getResponseCode() == 200) {
             boolean missing = false;
             try {
-                final DocumentBuilder builder = DocumentBuilderFactory
-                        .newInstance().newDocumentBuilder();
+                final DocumentBuilder builder = XmlUtils.buildSecureDocumentBuilder();
                 final Document doc = builder.parse(conn.getInputStream());
                 final XPath xpath = XPathFactory.newInstance().newXPath();
                 final String numFound = xpath.evaluate("/response/result/@numFound", doc);
                 if ("0".equals(numFound)) {
                     missing = true;
                 } else {
-                    final List<MavenArtifact> result = new ArrayList<MavenArtifact>();
+                    result = new ArrayList<>();
                     final NodeList docs = (NodeList) xpath.evaluate("/response/result/doc", doc, XPathConstants.NODESET);
                     for (int i = 0; i < docs.getLength(); i++) {
                         final String g = xpath.evaluate("./str[@name='g']", docs.item(i));
@@ -124,11 +128,11 @@ public class CentralSearch {
                         final String a = xpath.evaluate("./str[@name='a']", docs.item(i));
                         LOGGER.trace("ArtifactId: {}", a);
                         final String v = xpath.evaluate("./str[@name='v']", docs.item(i));
-                        NodeList atts = (NodeList) xpath.evaluate("./arr[@name='ec']/str", docs.item(i), XPathConstants.NODESET);
+                        NodeList attributes = (NodeList) xpath.evaluate("./arr[@name='ec']/str", docs.item(i), XPathConstants.NODESET);
                         boolean pomAvailable = false;
                         boolean jarAvailable = false;
-                        for (int x = 0; x < atts.getLength(); x++) {
-                            final String tmp = xpath.evaluate(".", atts.item(x));
+                        for (int x = 0; x < attributes.getLength(); x++) {
+                            final String tmp = xpath.evaluate(".", attributes.item(x));
                             if (".pom".equals(tmp)) {
                                 pomAvailable = true;
                             } else if (".jar".equals(tmp)) {
@@ -136,24 +140,20 @@ public class CentralSearch {
                             }
                         }
 
-                        atts = (NodeList) xpath.evaluate("./arr[@name='tags']/str", docs.item(i), XPathConstants.NODESET);
+                        attributes = (NodeList) xpath.evaluate("./arr[@name='tags']/str", docs.item(i), XPathConstants.NODESET);
                         boolean useHTTPS = false;
-                        for (int x = 0; x < atts.getLength(); x++) {
-                            final String tmp = xpath.evaluate(".", atts.item(x));
+                        for (int x = 0; x < attributes.getLength(); x++) {
+                            final String tmp = xpath.evaluate(".", attributes.item(x));
                             if ("https".equals(tmp)) {
                                 useHTTPS = true;
                             }
                         }
-
                         LOGGER.trace("Version: {}", v);
                         result.add(new MavenArtifact(g, a, v, jarAvailable, pomAvailable, useHTTPS));
                     }
-
-                    return result;
                 }
-            } catch (Throwable e) {
-                // Anything else is jacked up XML stuff that we really can't recover
-                // from well
+            } catch (ParserConfigurationException | IOException | SAXException | XPathExpressionException e) {
+                // Anything else is jacked up XML stuff that we really can't recover from well
                 throw new IOException(e.getMessage(), e);
             }
 
@@ -162,10 +162,9 @@ public class CentralSearch {
             }
         } else {
             LOGGER.debug("Could not connect to Central received response code: {} {}",
-                conn.getResponseCode(), conn.getResponseMessage());
+                    conn.getResponseCode(), conn.getResponseMessage());
             throw new IOException("Could not connect to Central");
         }
-
-        return null;
+        return result;
     }
 }

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

@@ -1,6 +1,6 @@
 /**
  *
- * Contains classes related to searching Maven Central.<br/><br/>
+ * Contains classes related to searching Maven Central.<br><br>
  *
  * These are used to abstract Maven Central searching away from OWASP Dependency Check so they can be reused elsewhere.
  */

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/composer/ComposerDependency.java

@@ -18,7 +18,7 @@
 package org.owasp.dependencycheck.data.composer;
 
 /**
- * Reperesents a dependency (GAV, right now) from a Composer dependency.
+ * Represents a dependency (GAV, right now) from a Composer dependency.
  *
  * @author colezlaw
  */

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/composer/ComposerException.java

@@ -24,6 +24,11 @@ package org.owasp.dependencycheck.data.composer;
  */
 public class ComposerException extends RuntimeException {
 
+    /**
+     * The serial version UID for serialization.
+     */
+    private static final long serialVersionUID = 1L;
+
     /**
      * Creates a ComposerException with default message.
      */

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/composer/ComposerLockParser.java

@@ -42,11 +42,6 @@ public class ComposerLockParser {
      */
     private final JsonReader jsonReader;
 
-    /**
-     * The input stream we'll read
-     */
-    private final InputStream inputStream; // NOPMD - it gets set in the constructor, read later
-
     /**
      * The List of ComposerDependencies found
      */
@@ -58,15 +53,14 @@ public class ComposerLockParser {
     private static final Logger LOGGER = LoggerFactory.getLogger(ComposerLockParser.class);
 
     /**
-     * Createas a ComposerLockParser from a JsonReader and an InputStream.
+     * Creates a ComposerLockParser from a JsonReader and an InputStream.
      *
      * @param inputStream the InputStream to parse
      */
     public ComposerLockParser(InputStream inputStream) {
         LOGGER.info("Creating a ComposerLockParser");
-        this.inputStream = inputStream;
         this.jsonReader = Json.createReader(inputStream);
-        this.composerDependencies = new ArrayList<ComposerDependency>();
+        this.composerDependencies = new ArrayList<>();
     }
 
     /**
@@ -87,7 +81,7 @@ public class ComposerLockParser {
                                 final String group = groupName.substring(0, groupName.indexOf('/'));
                                 final String project = groupName.substring(groupName.indexOf('/') + 1);
                                 String version = pkg.getString("version");
-                                // Some version nubmers begin with v - which doesn't end up matching CPE's
+                                // Some version numbers begin with v - which doesn't end up matching CPE's
                                 if (version.startsWith("v")) {
                                     version = version.substring(1);
                                 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/cpe/CpeMemoryIndex.java

@@ -38,7 +38,6 @@ import org.apache.lucene.search.IndexSearcher;
 import org.apache.lucene.search.Query;
 import org.apache.lucene.search.TopDocs;
 import org.apache.lucene.store.RAMDirectory;
-import org.owasp.dependencycheck.data.lucene.FieldAnalyzer;
 import org.owasp.dependencycheck.data.lucene.LuceneUtils;
 import org.owasp.dependencycheck.data.lucene.SearchFieldAnalyzer;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
@@ -48,8 +47,8 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * An in memory lucene index that contains the vendor/product combinations from the CPE (application) identifiers within the NVD
- * CVE data.
+ * An in memory lucene index that contains the vendor/product combinations from
+ * the CPE (application) identifiers within the NVD CVE data.
  *
  * @author Jeremy Long
  */
@@ -63,21 +62,6 @@ public final class CpeMemoryIndex {
      * singleton instance.
      */
     private static final CpeMemoryIndex INSTANCE = new CpeMemoryIndex();
-
-    /**
-     * private constructor for singleton.
-     */
-    private CpeMemoryIndex() {
-    }
-
-    /**
-     * Gets the singleton instance of the CpeMemoryIndex.
-     *
-     * @return the instance of the CpeMemoryIndex
-     */
-    public static CpeMemoryIndex getInstance() {
-        return INSTANCE;
-    }
     /**
      * The in memory Lucene index.
      */
@@ -101,11 +85,30 @@ public final class CpeMemoryIndex {
     /**
      * The search field analyzer for the product field.
      */
-    private SearchFieldAnalyzer productSearchFieldAnalyzer;
+    private SearchFieldAnalyzer productFieldAnalyzer;
     /**
      * The search field analyzer for the vendor field.
      */
-    private SearchFieldAnalyzer vendorSearchFieldAnalyzer;
+    private SearchFieldAnalyzer vendorFieldAnalyzer;
+    /**
+     * A flag indicating whether or not the index is open.
+     */
+    private boolean openState = false;
+
+    /**
+     * private constructor for singleton.
+     */
+    private CpeMemoryIndex() {
+    }
+
+    /**
+     * Gets the singleton instance of the CpeMemoryIndex.
+     *
+     * @return the instance of the CpeMemoryIndex
+     */
+    public static CpeMemoryIndex getInstance() {
+        return INSTANCE;
+    }
 
     /**
      * Creates and loads data into an in memory index.
@@ -130,10 +133,6 @@ public final class CpeMemoryIndex {
             }
         }
     }
-    /**
-     * A flag indicating whether or not the index is open.
-     */
-    private boolean openState = false;
 
     /**
      * returns whether or not the index is open.
@@ -144,51 +143,20 @@ public final class CpeMemoryIndex {
         return openState;
     }
 
-    /**
-     * Creates the indexing analyzer for the CPE Index.
-     *
-     * @return the CPE Analyzer.
-     */
-    @SuppressWarnings("unchecked")
-    private Analyzer createIndexingAnalyzer() {
-        final Map<String, Analyzer> fieldAnalyzers = new HashMap<String, Analyzer>();
-        fieldAnalyzers.put(Fields.DOCUMENT_KEY, new KeywordAnalyzer());
-        return new PerFieldAnalyzerWrapper(new FieldAnalyzer(LuceneUtils.CURRENT_VERSION), fieldAnalyzers);
-    }
-
     /**
      * Creates an Analyzer for searching the CPE Index.
      *
      * @return the CPE Analyzer.
      */
-    @SuppressWarnings("unchecked")
     private Analyzer createSearchingAnalyzer() {
-        final Map<String, Analyzer> fieldAnalyzers = new HashMap<String, Analyzer>();
+        final Map<String, Analyzer> fieldAnalyzers = new HashMap<>();
         fieldAnalyzers.put(Fields.DOCUMENT_KEY, new KeywordAnalyzer());
-        productSearchFieldAnalyzer = new SearchFieldAnalyzer(LuceneUtils.CURRENT_VERSION);
-        vendorSearchFieldAnalyzer = new SearchFieldAnalyzer(LuceneUtils.CURRENT_VERSION);
-        fieldAnalyzers.put(Fields.PRODUCT, productSearchFieldAnalyzer);
-        fieldAnalyzers.put(Fields.VENDOR, vendorSearchFieldAnalyzer);
+        productFieldAnalyzer = new SearchFieldAnalyzer(LuceneUtils.CURRENT_VERSION);
+        vendorFieldAnalyzer = new SearchFieldAnalyzer(LuceneUtils.CURRENT_VERSION);
+        fieldAnalyzers.put(Fields.PRODUCT, productFieldAnalyzer);
+        fieldAnalyzers.put(Fields.VENDOR, vendorFieldAnalyzer);
 
-        return new PerFieldAnalyzerWrapper(new FieldAnalyzer(LuceneUtils.CURRENT_VERSION), fieldAnalyzers);
-    }
-
-    /**
-     * Saves a CPE IndexEntry into the Lucene index.
-     *
-     * @param vendor the vendor to index
-     * @param product the product to index
-     * @param indexWriter the index writer to write the entry into
-     * @throws CorruptIndexException is thrown if the index is corrupt
-     * @throws IOException is thrown if an IOException occurs
-     */
-    public void saveEntry(String vendor, String product, IndexWriter indexWriter) throws CorruptIndexException, IOException {
-        final Document doc = new Document();
-        final Field v = new TextField(Fields.VENDOR, vendor, Field.Store.YES);
-        final Field p = new TextField(Fields.PRODUCT, product, Field.Store.YES);
-        doc.add(v);
-        doc.add(p);
-        indexWriter.addDocument(doc);
+        return new PerFieldAnalyzerWrapper(new KeywordAnalyzer(), fieldAnalyzers);
     }
 
     /**
@@ -223,54 +191,47 @@ public final class CpeMemoryIndex {
      * @throws IndexException thrown if there is an issue creating the index
      */
     private void buildIndex(CveDB cve) throws IndexException {
-        Analyzer analyzer = null;
-        IndexWriter indexWriter = null;
-        try {
-            analyzer = createIndexingAnalyzer();
-            final IndexWriterConfig conf = new IndexWriterConfig(LuceneUtils.CURRENT_VERSION, analyzer);
-            indexWriter = new IndexWriter(index, conf);
-            try {
-                final Set<Pair<String, String>> data = cve.getVendorProductList();
-                for (Pair<String, String> pair : data) {
-                    saveEntry(pair.getLeft(), pair.getRight(), indexWriter);
+        try (Analyzer analyzer = createSearchingAnalyzer();
+                IndexWriter indexWriter = new IndexWriter(index, new IndexWriterConfig(LuceneUtils.CURRENT_VERSION, analyzer))) {
+            // Tip: reuse the Document and Fields for performance...
+            // See "Re-use Document and Field instances" from
+            // http://wiki.apache.org/lucene-java/ImproveIndexingSpeed
+            final Document doc = new Document();
+            final Field v = new TextField(Fields.VENDOR, Fields.VENDOR, Field.Store.YES);
+            final Field p = new TextField(Fields.PRODUCT, Fields.PRODUCT, Field.Store.YES);
+            doc.add(v);
+            doc.add(p);
+
+            final Set<Pair<String, String>> data = cve.getVendorProductList();
+            for (Pair<String, String> pair : data) {
+                if (pair.getLeft() != null && pair.getRight() != null) {
+                    v.setStringValue(pair.getLeft());
+                    p.setStringValue(pair.getRight());
+                    indexWriter.addDocument(doc);
+                    resetFieldAnalyzer();
                 }
-            } catch (DatabaseException ex) {
-                LOGGER.debug("", ex);
-                throw new IndexException("Error reading CPE data", ex);
             }
+            indexWriter.commit();
+            indexWriter.close(true);
+        } catch (DatabaseException ex) {
+            LOGGER.debug("", ex);
+            throw new IndexException("Error reading CPE data", ex);
         } catch (CorruptIndexException ex) {
             throw new IndexException("Unable to close an in-memory index", ex);
         } catch (IOException ex) {
             throw new IndexException("Unable to close an in-memory index", ex);
-        } finally {
-            if (indexWriter != null) {
-                try {
-                    try {
-                        indexWriter.commit();
-                    } finally {
-                        indexWriter.close(true);
-                    }
-                } catch (CorruptIndexException ex) {
-                    throw new IndexException("Unable to close an in-memory index", ex);
-                } catch (IOException ex) {
-                    throw new IndexException("Unable to close an in-memory index", ex);
-                }
-                if (analyzer != null) {
-                    analyzer.close();
-                }
-            }
         }
     }
 
     /**
-     * Resets the searching analyzers
+     * Resets the product and vendor field analyzers.
      */
-    private void resetSearchingAnalyzer() {
-        if (productSearchFieldAnalyzer != null) {
-            productSearchFieldAnalyzer.clear();
+    private void resetFieldAnalyzer() {
+        if (productFieldAnalyzer != null) {
+            productFieldAnalyzer.clear();
         }
-        if (vendorSearchFieldAnalyzer != null) {
-            vendorSearchFieldAnalyzer.clear();
+        if (vendorFieldAnalyzer != null) {
+            vendorFieldAnalyzer.clear();
         }
     }
 
@@ -281,14 +242,17 @@ public final class CpeMemoryIndex {
      * @param maxQueryResults the maximum number of documents to return
      * @return the TopDocs found by the search
      * @throws ParseException thrown when the searchString is invalid
-     * @throws IOException is thrown if there is an issue with the underlying Index
+     * @throws IOException is thrown if there is an issue with the underlying
+     * Index
      */
-    public TopDocs search(String searchString, int maxQueryResults) throws ParseException, IOException {
+    public synchronized TopDocs search(String searchString, int maxQueryResults) throws ParseException, IOException {
         if (searchString == null || searchString.trim().isEmpty()) {
             throw new ParseException("Query is null or empty");
         }
+        LOGGER.debug(searchString);
+        resetFieldAnalyzer();
         final Query query = queryParser.parse(searchString);
-        return indexSearcher.search(query, maxQueryResults);
+        return search(query, maxQueryResults);
     }
 
     /**
@@ -300,8 +264,8 @@ public final class CpeMemoryIndex {
      * @throws CorruptIndexException thrown if the Index is corrupt
      * @throws IOException thrown if there is an IOException
      */
-    public TopDocs search(Query query, int maxQueryResults) throws CorruptIndexException, IOException {
-        resetSearchingAnalyzer();
+    public synchronized TopDocs search(Query query, int maxQueryResults) throws CorruptIndexException, IOException {
+        resetFieldAnalyzer();
         return indexSearcher.search(query, maxQueryResults);
     }
 

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/cpe/IndexEntry.java

@@ -20,6 +20,7 @@ package org.owasp.dependencycheck.data.cpe;
 import java.io.Serializable;
 import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
+import org.apache.commons.lang3.StringUtils;
 
 /**
  * A CPE entry containing the name, vendor, product, and version.
@@ -31,7 +32,7 @@ public class IndexEntry implements Serializable {
     /**
      * the serial version uid.
      */
-    static final long serialVersionUID = 8011924485946326934L;
+    private static final long serialVersionUID = 8011924485946326934L;
     /**
      * The vendor name.
      */
@@ -48,7 +49,7 @@ public class IndexEntry implements Serializable {
      */
     public String getDocumentId() {
         if (documentId == null && vendor != null && product != null) {
-            documentId = vendor + ":" + product;
+            documentId = vendor + ':' + product;
         }
         return documentId;
     }
@@ -143,7 +144,8 @@ public class IndexEntry implements Serializable {
      */
     public void parseName(String cpeName) throws UnsupportedEncodingException {
         if (cpeName != null && cpeName.length() > 7) {
-            final String[] data = cpeName.substring(7).split(":");
+            final String cpeNameWithoutPrefix = cpeName.substring(7);
+            final String[] data = StringUtils.split(cpeNameWithoutPrefix, ':');
             if (data.length >= 1) {
                 vendor = URLDecoder.decode(data[0].replace("+", "%2B"), "UTF-8");
                 if (data.length >= 2) {
@@ -172,10 +174,7 @@ public class IndexEntry implements Serializable {
         if ((this.vendor == null) ? (other.vendor != null) : !this.vendor.equals(other.vendor)) {
             return false;
         }
-        if ((this.product == null) ? (other.product != null) : !this.product.equals(other.product)) {
-            return false;
-        }
-        return true;
+        return !((this.product == null) ? (other.product != null) : !this.product.equals(other.product));
     }
 
     /**

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/cwe/CweDB.java

@@ -54,12 +54,10 @@ public final class CweDB {
      * @return a HashMap of CWE data
      */
     private static Map<String, String> loadData() {
-        ObjectInputStream oin = null;
-        try {
-            final String filePath = "data/cwe.hashmap.serialized";
-            final InputStream input = CweDB.class.getClassLoader().getResourceAsStream(filePath);
-            oin = new ObjectInputStream(input);
-            @SuppressWarnings("unchecked")
+        final String filePath = "data/cwe.hashmap.serialized";
+        try (InputStream input = CweDB.class.getClassLoader().getResourceAsStream(filePath);
+                ObjectInputStream oin = new ObjectInputStream(input)) {
+
             final Map<String, String> ret = (HashMap<String, String>) oin.readObject();
             return ret;
         } catch (ClassNotFoundException ex) {
@@ -68,14 +66,6 @@ public final class CweDB {
         } catch (IOException ex) {
             LOGGER.warn("Unable to load CWE data due to an IO Error. This should not be an issue.");
             LOGGER.debug("", ex);
-        } finally {
-            if (oin != null) {
-                try {
-                    oin.close();
-                } catch (IOException ex) {
-                    LOGGER.trace("", ex);
-                }
-            }
         }
         return null;
     }

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/cwe/CweHandler.java

@@ -32,12 +32,12 @@ public class CweHandler extends DefaultHandler {
     /**
      * a HashMap containing the CWE data.
      */
-    private final HashMap<String, String> cwe = new HashMap<String, String>();
+    private final HashMap<String, String> cwe = new HashMap<>();
 
     /**
      * Returns the HashMap of CWE entries (CWE-ID, Full CWE Name).
      *
-     * @return a HashMap of CWE entries <String, String>
+     * @return a HashMap of CWE entries &lt;String, String&gt;
      */
     public HashMap<String, String> getCwe() {
         return cwe;

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/lucene/AbstractTokenizingFilter.java

@@ -63,7 +63,7 @@ public abstract class AbstractTokenizingFilter extends TokenFilter {
      */
     public AbstractTokenizingFilter(TokenStream stream) {
         super(stream);
-        tokens = new LinkedList<String>();
+        tokens = new LinkedList<>();
     }
 
     /**

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/lucene/FieldAnalyzer.java

@@ -29,11 +29,15 @@ import org.apache.lucene.util.Version;
 
 /**
  * <p>
- * A Lucene Analyzer that utilizes the WhitespaceTokenizer, WordDelimiterFilter, LowerCaseFilter, and StopFilter. The intended
- * purpose of this Analyzer is to index the CPE fields vendor and product.</p>
+ * A Lucene Analyzer that utilizes the WhitespaceTokenizer, WordDelimiterFilter,
+ * LowerCaseFilter, and StopFilter. The intended purpose of this Analyzer is to
+ * index the CPE fields vendor and product.</p>
  *
  * @author Jeremy Long
+ * @deprecated the field analyzer should not be used, instead use the
+ * SearchFieldAnalyzer so that the token analyzing filter is used.
  */
+@Deprecated
 public class FieldAnalyzer extends Analyzer {
 
     /**

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/lucene/LuceneUtils.java

@@ -77,6 +77,7 @@ public final class LuceneUtils {
                 case '*':
                 case '?':
                 case ':':
+                case '/':
                 case '\\': //it is supposed to fall through here
                     buf.append('\\');
                 default:

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/lucene/TokenPairConcatenatingFilter.java

@@ -27,7 +27,7 @@ import org.apache.lucene.analysis.tokenattributes.CharTermAttribute;
  * <p>
  * Takes a TokenStream and adds additional tokens by concatenating pairs of words.</p>
  * <p>
- * <b>Example:</b> "Spring Framework Core" -> "Spring SpringFramework Framework FrameworkCore Core".</p>
+ * <b>Example:</b> "Spring Framework Core" -&gt; "Spring SpringFramework Framework FrameworkCore Core".</p>
  *
  * @author Jeremy Long
  */
@@ -71,7 +71,7 @@ public final class TokenPairConcatenatingFilter extends TokenFilter {
      */
     public TokenPairConcatenatingFilter(TokenStream stream) {
         super(stream);
-        words = new LinkedList<String>();
+        words = new LinkedList<>();
     }
 
     /**
@@ -156,10 +156,7 @@ public final class TokenPairConcatenatingFilter extends TokenFilter {
         if ((this.previousWord == null) ? (other.previousWord != null) : !this.previousWord.equals(other.previousWord)) {
             return false;
         }
-        if (this.words != other.words && (this.words == null || !this.words.equals(other.words))) {
-            return false;
-        }
-        return true;
+        return !(this.words != other.words && (this.words == null || !this.words.equals(other.words)));
     }
 
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/lucene/UrlTokenizingFilter.java

@@ -31,15 +31,17 @@ import org.slf4j.LoggerFactory;
  * <p>
  * Takes a TokenStream and splits or adds tokens to correctly index version numbers.</p>
  * <p>
- * <b>Example:</b> "3.0.0.RELEASE" -> "3 3.0 3.0.0 RELEASE 3.0.0.RELEASE".</p>
+ * <b>Example:</b> "3.0.0.RELEASE" -&gt; "3 3.0 3.0.0 RELEASE 3.0.0.RELEASE".</p>
  *
  * @author Jeremy Long
  */
 public final class UrlTokenizingFilter extends AbstractTokenizingFilter {
+
     /**
      * The logger.
      */
     private static final Logger LOGGER = LoggerFactory.getLogger(UrlTokenizingFilter.class);
+
     /**
      * Constructs a new VersionTokenizingFilter.
      *
@@ -50,8 +52,8 @@ public final class UrlTokenizingFilter extends AbstractTokenizingFilter {
     }
 
     /**
-     * Increments the underlying TokenStream and sets CharTermAttributes to construct an expanded set of tokens by
-     * concatenating tokens with the previous token.
+     * Increments the underlying TokenStream and sets CharTermAttributes to construct an expanded set of tokens by concatenating
+     * tokens with the previous token.
      *
      * @return whether or not we have hit the end of the TokenStream
      * @throws IOException is thrown when an IOException occurs

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/nexus/MavenArtifact.java

@@ -94,13 +94,13 @@ public class MavenArtifact {
         }
         if (jarAvailable) {
             //org/springframework/spring-core/3.2.0.RELEASE/spring-core-3.2.0.RELEASE.pom
-            this.artifactUrl = base + groupId.replace('.', '/') + "/" + artifactId + "/"
-                    + version + "/" + artifactId + "-" + version + ".jar";
+            this.artifactUrl = base + groupId.replace('.', '/') + '/' + artifactId + '/'
+                    + version + '/' + artifactId + '-' + version + ".jar";
         }
         if (pomAvailable) {
             //org/springframework/spring-core/3.2.0.RELEASE/spring-core-3.2.0.RELEASE.pom
-            this.pomUrl = base + groupId.replace('.', '/') + "/" + artifactId + "/"
-                    + version + "/" + artifactId + "-" + version + ".pom";
+            this.pomUrl = base + groupId.replace('.', '/') + '/' + artifactId + '/'
+                    + version + '/' + artifactId + '-' + version + ".pom";
         }
     }
 

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/nexus/NexusSearch.java

@@ -22,15 +22,17 @@ import java.io.IOException;
 import java.net.HttpURLConnection;
 import java.net.URL;
 import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathExpressionException;
 import javax.xml.xpath.XPathFactory;
-import org.owasp.dependencycheck.utils.InvalidSettingException;
-import org.owasp.dependencycheck.utils.Settings;
+
 import org.owasp.dependencycheck.utils.URLConnectionFactory;
+import org.owasp.dependencycheck.utils.XmlUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
+import org.xml.sax.SAXException;
 
 /**
  * Class of methods to search Nexus repositories.
@@ -47,7 +49,7 @@ public class NexusSearch {
     /**
      * Whether to use the Proxy when making requests.
      */
-    private boolean useProxy;
+    private final boolean useProxy;
     /**
      * Used for logging.
      */
@@ -56,32 +58,26 @@ public class NexusSearch {
     /**
      * Creates a NexusSearch for the given repository URL.
      *
-     * @param rootURL the root URL of the repository on which searches should execute. full URL's are calculated relative to this
-     * URL, so it should end with a /
+     * @param rootURL the root URL of the repository on which searches should
+     * execute. full URL's are calculated relative to this URL, so it should end
+     * with a /
+     * @param useProxy flag indicating if the proxy settings should be used
      */
-    public NexusSearch(URL rootURL) {
+    public NexusSearch(URL rootURL, boolean useProxy) {
         this.rootURL = rootURL;
-        try {
-            if (null != Settings.getString(Settings.KEYS.PROXY_SERVER)
-                    && Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY)) {
-                useProxy = true;
-                LOGGER.debug("Using proxy");
-            } else {
-                useProxy = false;
-                LOGGER.debug("Not using proxy");
-            }
-        } catch (InvalidSettingException ise) {
-            useProxy = false;
-        }
+        this.useProxy = useProxy;
+        LOGGER.debug("Using proxy: {}", useProxy);
     }
 
     /**
-     * Searches the configured Nexus repository for the given sha1 hash. If the artifact is found, a <code>MavenArtifact</code> is
-     * populated with the coordinate information.
+     * Searches the configured Nexus repository for the given sha1 hash. If the
+     * artifact is found, a <code>MavenArtifact</code> is populated with the
+     * coordinate information.
      *
      * @param sha1 The SHA-1 hash string for which to search
      * @return the populated Maven coordinates
-     * @throws IOException if it's unable to connect to the specified repository or if the specified artifact is not found.
+     * @throws IOException if it's unable to connect to the specified repository
+     * or if the specified artifact is not found.
      */
     public MavenArtifact searchSha1(String sha1) throws IOException {
         if (null == sha1 || !sha1.matches("^[0-9A-Fa-f]{40}$")) {
@@ -106,57 +102,58 @@ public class NexusSearch {
         conn.addRequestProperty("Accept", "application/xml");
         conn.connect();
 
-        if (conn.getResponseCode() == 200) {
-            try {
-                final DocumentBuilder builder = DocumentBuilderFactory
-                        .newInstance().newDocumentBuilder();
-                final Document doc = builder.parse(conn.getInputStream());
-                final XPath xpath = XPathFactory.newInstance().newXPath();
-                final String groupId = xpath
-                        .evaluate(
-                                "/org.sonatype.nexus.rest.model.NexusArtifact/groupId",
-                                doc);
-                final String artifactId = xpath.evaluate(
-                        "/org.sonatype.nexus.rest.model.NexusArtifact/artifactId",
-                        doc);
-                final String version = xpath
-                        .evaluate(
-                                "/org.sonatype.nexus.rest.model.NexusArtifact/version",
-                                doc);
-                final String link = xpath
-                        .evaluate(
-                                "/org.sonatype.nexus.rest.model.NexusArtifact/artifactLink",
-                                doc);
-                final String pomLink = xpath
-                        .evaluate(
-                                "/org.sonatype.nexus.rest.model.NexusArtifact/pomLink",
-                                doc);
-                final MavenArtifact ma = new MavenArtifact(groupId, artifactId, version);
-                if (link != null && !link.isEmpty()) {
-                    ma.setArtifactUrl(link);
+        switch (conn.getResponseCode()) {
+            case 200:
+                try {
+                    final DocumentBuilder builder = XmlUtils.buildSecureDocumentBuilder();
+                    final Document doc = builder.parse(conn.getInputStream());
+                    final XPath xpath = XPathFactory.newInstance().newXPath();
+                    final String groupId = xpath
+                            .evaluate(
+                                    "/org.sonatype.nexus.rest.model.NexusArtifact/groupId",
+                                    doc);
+                    final String artifactId = xpath.evaluate(
+                            "/org.sonatype.nexus.rest.model.NexusArtifact/artifactId",
+                            doc);
+                    final String version = xpath
+                            .evaluate(
+                                    "/org.sonatype.nexus.rest.model.NexusArtifact/version",
+                                    doc);
+                    final String link = xpath
+                            .evaluate(
+                                    "/org.sonatype.nexus.rest.model.NexusArtifact/artifactLink",
+                                    doc);
+                    final String pomLink = xpath
+                            .evaluate(
+                                    "/org.sonatype.nexus.rest.model.NexusArtifact/pomLink",
+                                    doc);
+                    final MavenArtifact ma = new MavenArtifact(groupId, artifactId, version);
+                    if (link != null && !link.isEmpty()) {
+                        ma.setArtifactUrl(link);
+                    }
+                    if (pomLink != null && !pomLink.isEmpty()) {
+                        ma.setPomUrl(pomLink);
+                    }
+                    return ma;
+                } catch (ParserConfigurationException | IOException | SAXException | XPathExpressionException e) {
+                    // Anything else is jacked-up XML stuff that we really can't recover
+                    // from well
+                    throw new IOException(e.getMessage(), e);
                 }
-                if (pomLink != null && !pomLink.isEmpty()) {
-                    ma.setPomUrl(pomLink);
-                }
-                return ma;
-            } catch (Throwable e) {
-                // Anything else is jacked-up XML stuff that we really can't recover
-                // from well
-                throw new IOException(e.getMessage(), e);
-            }
-        } else if (conn.getResponseCode() == 404) {
-            throw new FileNotFoundException("Artifact not found in Nexus");
-        } else {
-            LOGGER.debug("Could not connect to Nexus received response code: {} {}",
-                    conn.getResponseCode(), conn.getResponseMessage());
-            throw new IOException("Could not connect to Nexus");
+            case 404:
+                throw new FileNotFoundException("Artifact not found in Nexus");
+            default:
+                LOGGER.debug("Could not connect to Nexus received response code: {} {}",
+                        conn.getResponseCode(), conn.getResponseMessage());
+                throw new IOException("Could not connect to Nexus");
         }
     }
 
     /**
      * Do a preflight request to see if the repository is actually working.
      *
-     * @return whether the repository is listening and returns the /status URL correctly
+     * @return whether the repository is listening and returns the /status URL
+     * correctly
      */
     public boolean preflightRequest() {
         HttpURLConnection conn;
@@ -169,13 +166,14 @@ public class NexusSearch {
                 LOGGER.warn("Expected 200 result from Nexus, got {}", conn.getResponseCode());
                 return false;
             }
-            final DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+            final DocumentBuilder builder = XmlUtils.buildSecureDocumentBuilder();
+
             final Document doc = builder.parse(conn.getInputStream());
             if (!"status".equals(doc.getDocumentElement().getNodeName())) {
                 LOGGER.warn("Expected root node name of status, got {}", doc.getDocumentElement().getNodeName());
                 return false;
             }
-        } catch (Throwable e) {
+        } catch (IOException | ParserConfigurationException | SAXException e) {
             return false;
         }
 

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

@@ -1,5 +1,5 @@
 /**
- * Contains classes related to searching a Nexus repository.<br/><br/>
+ * Contains classes related to searching a Nexus repository.<br><br>
  *
  * These are used to abstract Nexus searching away from OWASP Dependency Check so they can be reused elsewhere.
  */

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/nuget/NugetPackage.java

@@ -53,12 +53,6 @@ public class NugetPackage {
      */
     private String licenseUrl;
 
-    /**
-     * Creates an empty NugetPackage.
-     */
-    public NugetPackage() {
-    }
-
     /**
      * Sets the id.
      * @param id the id

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/nuget/XPathNuspecParser.java

@@ -17,13 +17,18 @@
  */
 package org.owasp.dependencycheck.data.nuget;
 
+import java.io.IOException;
 import java.io.InputStream;
-import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.xpath.XPath;
 import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpressionException;
 import javax.xml.xpath.XPathFactory;
+import org.owasp.dependencycheck.utils.XmlUtils;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
+import org.xml.sax.SAXException;
 
 /**
  * Parse a Nuspec file using XPath.
@@ -36,7 +41,8 @@ public class XPathNuspecParser implements NuspecParser {
      * Gets the string value of a node or null if it's not present
      *
      * @param n the node to test
-     * @return the string content of the node, or null if the node itself is null
+     * @return the string content of the node, or null if the node itself is
+     * null
      */
     private String getOrNull(Node n) {
         if (n != null) {
@@ -56,7 +62,9 @@ public class XPathNuspecParser implements NuspecParser {
     @Override
     public NugetPackage parse(InputStream stream) throws NuspecParseException {
         try {
-            final Document d = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(stream);
+            final DocumentBuilder db = XmlUtils.buildSecureDocumentBuilder();
+            final Document d = db.parse(stream);
+
             final XPath xpath = XPathFactory.newInstance().newXPath();
             final NugetPackage nuspec = new NugetPackage();
 
@@ -74,7 +82,7 @@ public class XPathNuspecParser implements NuspecParser {
             nuspec.setLicenseUrl(getOrNull((Node) xpath.evaluate("/package/metadata/licenseUrl", d, XPathConstants.NODE)));
             nuspec.setTitle(getOrNull((Node) xpath.evaluate("/package/metadata/title", d, XPathConstants.NODE)));
             return nuspec;
-        } catch (Throwable e) {
+        } catch (ParserConfigurationException | SAXException | IOException | XPathExpressionException | NuspecParseException e) {
             throw new NuspecParseException("Unable to parse nuspec", e);
         }
     }

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

@@ -1,5 +1,5 @@
 /**
- * Contains classes related to parsing Nuget related files<br/><br/>
+ * Contains classes related to parsing Nuget related files<br><br>
  * These are used to abstract away Nuget-related handling from Dependency Check so they can be used elsewhere.
  */
 package org.owasp.dependencycheck.data.nuget;

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/nvdcve/ConnectionFactory.java

@@ -17,26 +17,29 @@
  */
 package org.owasp.dependencycheck.data.nvdcve;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.sql.CallableStatement;
+import java.sql.PreparedStatement;
 import java.sql.Connection;
 import java.sql.Driver;
 import java.sql.DriverManager;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Statement;
+import org.apache.commons.io.IOUtils;
 import org.owasp.dependencycheck.utils.DBUtils;
+import org.owasp.dependencycheck.utils.DependencyVersion;
+import org.owasp.dependencycheck.utils.DependencyVersionUtil;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * Loads the configured database driver and returns the database connection. If the embedded H2 database is used obtaining a
- * connection will ensure the database file exists and that the appropriate table structure has been created.
+ * Loads the configured database driver and returns the database connection. If
+ * the embedded H2 database is used obtaining a connection will ensure the
+ * database file exists and that the appropriate table structure has been
+ * created.
  *
  * @author Jeremy Long
  */
@@ -58,6 +61,10 @@ public final class ConnectionFactory {
      * Resource location for SQL file used to create the database schema.
      */
     public static final String DB_STRUCTURE_UPDATE_RESOURCE = "data/upgrade_%s.sql";
+    /**
+     * The URL that discusses upgrading non-H2 databases.
+     */
+    public static final String UPGRADE_HELP_URL = "http://jeremylong.github.io/DependencyCheck/data/upgrade.html";
     /**
      * The database driver used to connect to the database.
      */
@@ -82,12 +89,13 @@ public final class ConnectionFactory {
     }
 
     /**
-     * Initializes the connection factory. Ensuring that the appropriate drivers are loaded and that a connection can be made
-     * successfully.
+     * Initializes the connection factory. Ensuring that the appropriate drivers
+     * are loaded and that a connection can be made successfully.
      *
-     * @throws DatabaseException thrown if we are unable to connect to the database
+     * @throws DatabaseException thrown if we are unable to connect to the
+     * database
      */
-    public static synchronized void initialize() throws DatabaseException {
+    public static void initialize() throws DatabaseException {
         //this only needs to be called once.
         if (connectionString != null) {
             return;
@@ -183,11 +191,12 @@ public final class ConnectionFactory {
     }
 
     /**
-     * Cleans up resources and unloads any registered database drivers. This needs to be called to ensure the driver is
-     * unregistered prior to the finalize method being called as during shutdown the class loader used to load the driver may be
-     * unloaded prior to the driver being de-registered.
+     * Cleans up resources and unloads any registered database drivers. This
+     * needs to be called to ensure the driver is unregistered prior to the
+     * finalize method being called as during shutdown the class loader used to
+     * load the driver may be unloaded prior to the driver being de-registered.
      */
-    public static synchronized void cleanup() {
+    public static void cleanup() {
         if (driver != null) {
             try {
                 DriverManager.deregisterDriver(driver);
@@ -205,10 +214,12 @@ public final class ConnectionFactory {
     }
 
     /**
-     * Constructs a new database connection object per the database configuration.
+     * Constructs a new database connection object per the database
+     * configuration.
      *
      * @return a database connection object
-     * @throws DatabaseException thrown if there is an exception loading the database connection
+     * @throws DatabaseException thrown if there is an exception loading the
+     * database connection
      */
     public static Connection getConnection() throws DatabaseException {
         initialize();
@@ -223,12 +234,14 @@ public final class ConnectionFactory {
     }
 
     /**
-     * Determines if the H2 database file exists. If it does not exist then the data structure will need to be created.
+     * Determines if the H2 database file exists. If it does not exist then the
+     * data structure will need to be created.
      *
      * @return true if the H2 database file does not exist; otherwise false
-     * @throws IOException thrown if the data directory does not exist and cannot be created
+     * @throws IOException thrown if the data directory does not exist and
+     * cannot be created
      */
-    private static boolean h2DataFileExists() throws IOException {
+    public static boolean h2DataFileExists() throws IOException {
         final File dir = Settings.getDataDirectory();
         final String fileName = Settings.getString(Settings.KEYS.DB_FILE_NAME);
         final File file = new File(dir, fileName);
@@ -236,29 +249,41 @@ public final class ConnectionFactory {
     }
 
     /**
-     * Creates the database structure (tables and indexes) to store the CVE data.
+     * Determines if the connection string is for an H2 database.
+     *
+     * @return true if the connection string is for an H2 database
+     */
+    public static boolean isH2Connection() {
+        String connStr;
+        try {
+            connStr = Settings.getConnectionString(
+                    Settings.KEYS.DB_CONNECTION_STRING,
+                    Settings.KEYS.DB_FILE_NAME);
+        } catch (IOException ex) {
+            LOGGER.debug("Unable to get connectionn string", ex);
+            return false;
+        }
+        return connStr.startsWith("jdbc:h2:file:");
+    }
+
+    /**
+     * Creates the database structure (tables and indexes) to store the CVE
+     * data.
      *
      * @param conn the database connection
      * @throws DatabaseException thrown if there is a Database Exception
      */
     private static void createTables(Connection conn) throws DatabaseException {
         LOGGER.debug("Creating database structure");
-        InputStream is;
-        InputStreamReader reader;
-        BufferedReader in = null;
+        InputStream is = null;
         try {
             is = ConnectionFactory.class.getClassLoader().getResourceAsStream(DB_STRUCTURE_RESOURCE);
-            reader = new InputStreamReader(is, "UTF-8");
-            in = new BufferedReader(reader);
-            final StringBuilder sb = new StringBuilder(2110);
-            String tmp;
-            while ((tmp = in.readLine()) != null) {
-                sb.append(tmp);
-            }
+            final String dbStructure = IOUtils.toString(is, "UTF-8");
+
             Statement statement = null;
             try {
                 statement = conn.createStatement();
-                statement.execute(sb.toString());
+                statement.execute(dbStructure);
             } catch (SQLException ex) {
                 LOGGER.debug("", ex);
                 throw new DatabaseException("Unable to create database statement", ex);
@@ -268,86 +293,119 @@ public final class ConnectionFactory {
         } catch (IOException ex) {
             throw new DatabaseException("Unable to create database schema", ex);
         } finally {
-            if (in != null) {
-                try {
-                    in.close();
-                } catch (IOException ex) {
-                    LOGGER.trace("", ex);
-                }
-            }
+            IOUtils.closeQuietly(is);
         }
     }
 
     /**
-     * Updates the database schema by loading the upgrade script for the version specified. The intended use is that if the
-     * current schema version is 2.9 then we would call updateSchema(conn, "2.9"). This would load the upgrade_2.9.sql file and
-     * execute it against the database. The upgrade script must update the 'version' in the properties table.
+     * Updates the database schema by loading the upgrade script for the version
+     * specified. The intended use is that if the current schema version is 2.9
+     * then we would call updateSchema(conn, "2.9"). This would load the
+     * upgrade_2.9.sql file and execute it against the database. The upgrade
+     * script must update the 'version' in the properties table.
      *
      * @param conn the database connection object
-     * @param schema the current schema version that is being upgraded
-     * @throws DatabaseException thrown if there is an exception upgrading the database schema
+     * @param appExpectedVersion the schema version that the application expects
+     * @param currentDbVersion the current schema version of the database
+     * @throws DatabaseException thrown if there is an exception upgrading the
+     * database schema
      */
-    private static void updateSchema(Connection conn, String schema) throws DatabaseException {
-        LOGGER.debug("Updating database structure");
-        InputStream is;
-        InputStreamReader reader;
-        BufferedReader in = null;
-        String updateFile = null;
+    private static void updateSchema(Connection conn, DependencyVersion appExpectedVersion, DependencyVersion currentDbVersion)
+            throws DatabaseException {
+
+        final String databaseProductName;
         try {
-            updateFile = String.format(DB_STRUCTURE_UPDATE_RESOURCE, schema);
-            is = ConnectionFactory.class.getClassLoader().getResourceAsStream(updateFile);
-            if (is == null) {
-                throw new DatabaseException(String.format("Unable to load update file '%s'", updateFile));
-            }
-            reader = new InputStreamReader(is, "UTF-8");
-            in = new BufferedReader(reader);
-            final StringBuilder sb = new StringBuilder(2110);
-            String tmp;
-            while ((tmp = in.readLine()) != null) {
-                sb.append(tmp);
-            }
-            Statement statement = null;
+            databaseProductName = conn.getMetaData().getDatabaseProductName();
+        } catch (SQLException ex) {
+            throw new DatabaseException("Unable to get the database product name");
+        }
+        if ("h2".equalsIgnoreCase(databaseProductName)) {
+            LOGGER.debug("Updating database structure");
+            InputStream is = null;
+            String updateFile = null;
             try {
-                statement = conn.createStatement();
-                statement.execute(sb.toString());
-            } catch (SQLException ex) {
-                LOGGER.debug("", ex);
-                throw new DatabaseException("Unable to update database schema", ex);
-            } finally {
-                DBUtils.closeStatement(statement);
-            }
-        } catch (IOException ex) {
-            final String msg = String.format("Upgrade SQL file does not exist: %s", updateFile);
-            throw new DatabaseException(msg, ex);
-        } finally {
-            if (in != null) {
-                try {
-                    in.close();
-                } catch (IOException ex) {
-                    LOGGER.trace("", ex);
+                updateFile = String.format(DB_STRUCTURE_UPDATE_RESOURCE, currentDbVersion.toString());
+                is = ConnectionFactory.class.getClassLoader().getResourceAsStream(updateFile);
+                if (is == null) {
+                    throw new DatabaseException(String.format("Unable to load update file '%s'", updateFile));
                 }
+                final String dbStructureUpdate = IOUtils.toString(is, "UTF-8");
+
+                Statement statement = null;
+                try {
+                    statement = conn.createStatement();
+                    final boolean success = statement.execute(dbStructureUpdate);
+                    if (!success && statement.getUpdateCount() <= 0) {
+                        throw new DatabaseException(String.format("Unable to upgrade the database schema to %s",
+                                currentDbVersion.toString()));
+                    }
+                } catch (SQLException ex) {
+                    LOGGER.debug("", ex);
+                    throw new DatabaseException("Unable to update database schema", ex);
+                } finally {
+                    DBUtils.closeStatement(statement);
+                }
+            } catch (IOException ex) {
+                final String msg = String.format("Upgrade SQL file does not exist: %s", updateFile);
+                throw new DatabaseException(msg, ex);
+            } finally {
+                IOUtils.closeQuietly(is);
+            }
+        } else {
+            final int e0 = Integer.parseInt(appExpectedVersion.getVersionParts().get(0));
+            final int c0 = Integer.parseInt(currentDbVersion.getVersionParts().get(0));
+            final int e1 = Integer.parseInt(appExpectedVersion.getVersionParts().get(1));
+            final int c1 = Integer.parseInt(currentDbVersion.getVersionParts().get(1));
+            if (e0 == c0 && e1 < c1) {
+                LOGGER.warn("A new version of dependency-check is available; consider upgrading");
+                Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+            } else if (e0 == c0 && e1 == c1) {
+                //do nothing - not sure how we got here, but just in case...
+            } else {
+                LOGGER.error("The database schema must be upgraded to use this version of dependency-check. Please see {} for more information.",
+                        UPGRADE_HELP_URL);
+                throw new DatabaseException("Database schema is out of date");
             }
         }
     }
 
     /**
-     * Uses the provided connection to check the specified schema version within the database.
+     * Counter to ensure that calls to ensureSchemaVersion does not end up in an
+     * endless loop.
+     */
+    private static int callDepth = 0;
+
+    /**
+     * Uses the provided connection to check the specified schema version within
+     * the database.
      *
      * @param conn the database connection object
-     * @throws DatabaseException thrown if the schema version is not compatible with this version of dependency-check
+     * @throws DatabaseException thrown if the schema version is not compatible
+     * with this version of dependency-check
      */
     private static void ensureSchemaVersion(Connection conn) throws DatabaseException {
         ResultSet rs = null;
-        CallableStatement cs = null;
+        PreparedStatement ps = null;
         try {
             //TODO convert this to use DatabaseProperties
-            cs = conn.prepareCall("SELECT value FROM properties WHERE id = 'version'");
-            rs = cs.executeQuery();
+            ps = conn.prepareStatement("SELECT value FROM properties WHERE id = 'version'");
+            rs = ps.executeQuery();
             if (rs.next()) {
-                if (!DB_SCHEMA_VERSION.equals(rs.getString(1))) {
-                    LOGGER.debug("Current Schema: " + DB_SCHEMA_VERSION);
-                    LOGGER.debug("DB Schema: " + rs.getString(1));
-                    updateSchema(conn, rs.getString(1));
+                final DependencyVersion appDbVersion = DependencyVersionUtil.parseVersion(DB_SCHEMA_VERSION);
+                if (appDbVersion == null) {
+                    throw new DatabaseException("Invalid application database schema");
+                }
+                final DependencyVersion db = DependencyVersionUtil.parseVersion(rs.getString(1));
+                if (db == null) {
+                    throw new DatabaseException("Invalid database schema");
+                }
+                if (appDbVersion.compareTo(db) > 0) {
+                    LOGGER.debug("Current Schema: {}", DB_SCHEMA_VERSION);
+                    LOGGER.debug("DB Schema: {}", rs.getString(1));
+                    updateSchema(conn, appDbVersion, db);
+                    if (++callDepth < 10) {
+                        ensureSchemaVersion(conn);
+                    }
                 }
             } else {
                 throw new DatabaseException("Database schema is missing");
@@ -357,7 +415,7 @@ public final class ConnectionFactory {
             throw new DatabaseException("Unable to check the database schema version");
         } finally {
             DBUtils.closeResultSet(rs);
-            DBUtils.closeStatement(cs);
+            DBUtils.closeStatement(ps);
         }
     }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/nvdcve/CorruptDatabaseException.java

@@ -18,12 +18,11 @@
 package org.owasp.dependencycheck.data.nvdcve;
 
 /**
- * An exception used to indicate the db4o database is corrupt. This could be due to invalid data or a complete failure
- * of the db.
+ * An exception used to indicate the db4o database is corrupt. This could be due to invalid data or a complete failure of the db.
  *
  * @author Jeremy Long
  */
-class CorruptDatabaseException extends DatabaseException {
+public class CorruptDatabaseException extends DatabaseException {
 
     /**
      * the serial version uid.
@@ -31,7 +30,7 @@ class CorruptDatabaseException extends DatabaseException {
     private static final long serialVersionUID = 1L;
 
     /**
-     * Creates an CorruptDatabaseException
+     * Creates an CorruptDatabaseException.
      *
      * @param msg the exception message
      */
@@ -40,7 +39,7 @@ class CorruptDatabaseException extends DatabaseException {
     }
 
     /**
-     * Creates an CorruptDatabaseException
+     * Creates an CorruptDatabaseException.
      *
      * @param msg the exception message
      * @param ex the cause of the exception