Added support for Java update version parsing.

Thanks for the PR!   Fix groovy script failure because of unescaped Windows File.separator.

.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

@@ -1,3 +1,5 @@
+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.
 

.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

@@ -1,6 +1,7 @@
 */target/**
 # IntelliJ test run side-effects
 dependency-check-core/data/
+dependency-check-ant/data/
 # Intellij project files
 *.iml
 *.ipr
@@ -15,6 +16,7 @@ maven-eclipse.xml
 .pmd
 # Netbeans configuration
 nb-configuration.xml
+**/nbproject/
 /target/
 #maven-shade-plugin generated pom
 dependency-reduced-pom.xml
@@ -27,4 +29,4 @@ _site/**
 #coverity
 /cov-int/
 /dependency-check-core/nbproject/
-cov-scan.bat
+cov-scan.bat

.travis.settings.xml

@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<settings xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.1.0 http://maven.apache.org/xsd/settings-1.1.0.xsd" xmlns="http://maven.apache.org/SETTINGS/1.1.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <servers>
+    <server>
+      <username>${env.JFROG_USER}</username>
+      <password>${env.JFROG_PASSWORD}</password>
+      <id>release</id>
+    </server>
+    <server>
+      <username>${env.JFROG_USER}</username>
+      <password>${env.JFROG_PASSWORD}</password>
+      <id>snapshot</id>
+    </server>
+    <server>
+      <username>${env.JFROG_USER}</username>
+      <password>${env.JFROG_PASSWORD}</password>
+      <id>plugins-release</id>
+    </server>
+    <server>
+      <username>${env.JFROG_USER}</username>
+      <password>${env.JFROG_PASSWORD}</password>
+      <id>plugins-snapshot</id>
+    </server>
+  </servers>
+  <profiles>
+    <profile>
+      <repositories>
+        <repository>
+          <snapshots>
+            <enabled>false</enabled>
+          </snapshots>
+          <id>release</id>
+          <name>libs-release</name>
+          <url>https://dependencycheck.jfrog.io/dependencycheck/libs-release</url>
+        </repository>
+        <repository>
+          <snapshots />
+          <id>snapshot</id>
+          <name>libs-snapshot</name>
+          <url>https://dependencycheck.jfrog.io/dependencycheck/libs-snapshot</url>
+        </repository>
+      </repositories>
+      <pluginRepositories>
+        <pluginRepository>
+          <snapshots>
+            <enabled>false</enabled>
+          </snapshots>
+          <id>plugins-release</id>
+          <name>plugins-release</name>
+          <url>https://dependencycheck.jfrog.io/dependencycheck/plugins-release</url>
+        </pluginRepository>
+        <pluginRepository>
+          <snapshots />
+          <id>plugins-snapshot</id>
+          <name>plugins-snapshot</name>
+          <url>https://dependencycheck.jfrog.io/dependencycheck/plugins-snapshot</url>
+        </pluginRepository>
+      </pluginRepositories>
+      <id>artifactory</id>
+    </profile>
+  </profiles>
+  <activeProfiles>
+    <activeProfile>artifactory</activeProfile>
+  </activeProfiles>
+</settings>

.travis.yml

@@ -1,2 +1,78 @@
 language: java
-jdk: oraclejdk7
+sudo: required
+group: deprecated-2017Q4
+
+env:
+  global:
+    - secure: "ZUzhWfpXJw/oAeDlUkDFkEJMT0T7kCN3d7ah8urkL2B0KFfKOqQagkbXkgvDa1SYud8VdcnoGa69LfkEr5IrdqW7R4bEYZAiN5swm4Z0iO8t53szVspm2f+O9jQ44O/sfOfpfLxWUUuhdc7Vbrszp+tSszxdPmssWL+f5a/mfWs="
+    - secure: "pmFymoI7qH0Kna3NkcHrqLiTVWKmrhwqA4Z9U6XLhWDQxcs5g94wCCKpGB6Lkz9mkvRxBRFpZZelnXJa9W9mnuVOMIa5tQfS5gBuaNXOe7AXXdc+Y2975OR9sSfvf16FxLFvNJILmZq+bpMLs+EXaQvjYQHW2O6OWZdLhAPVG6A="
+    - secure: "omj5HP2wKdegLYp8/a24Wsoryb92+XYWheEkxp7CzHGDJB1Y4SSr315n/na/mdgd7lr1Ac+m4stYfCrclG7be71xWs6ApF+6I5QSzplJ1fyIF5piHrmhgw6ymIf/HBdeevggJM8igD8agCOwEETYFKfPEj5wFWhNQfxYwANbpl0="
+    - secure: "FqPcda7a6rEvGVYEyWeaFP+mIhZeJ6FGSdHvVRlBL0H9I3bz6eZg50g6DH3yo1bkmTPQ94eXdDpoKihk9+CDLl0TS+Sg9W8HplG3B2U1/6Yi3vd0T8yjKZC7xf0VZO6t8AT9vpFvzQBRZe24n+6kDtp2OiBzawJhgU5t09zH6is="
+    - secure: "Bh5LAk8XQnJ885jc/Lli2fhPKDx0TNZRxcJMnNo96EgwOnD+Zhw+v3u/DMCgyyrRToM8Bkca/HktrlZaRTk2htsdKZZ3RHFMCXO0fXCgpcf+wkaSYDF/lnErpSJG3Lrz8ILxJPODsrGhjaIg2++79lwhsBYtpujc6UdxFhgpffc="
+
+addons:
+  sonarcloud:
+    organization: "odc"
+    token:
+      secure: "YVDnYmonPug885Hmr2pLWBko+rQ+oKyTUA95ry0PGGyfgs0z6kPCjmWBDVm7K4GM7NOluldWb5gLMf0QXoHGstdp9L6fQCQElt8hZMOwJf+IR3bWjiG3VfVyyB3gJWBWlcJFM9NVyfICidwBH5ZiJ0+LXhKUgnNqarTh/YmNj9w="
+
+cache:
+  directories:
+    - "$HOME/.m2/repository"
+    - "$HOME/.sonar/cache"
+
+before_install:
+  - sudo apt-get install jq
+  - wget -O ~/codacy-coverage-reporter-assembly-latest.jar $(curl https://api.github.com/repos/codacy/codacy-coverage-reporter/releases/latest | jq -r .assets[0].browser_download_url)
+
+matrix:
+  include:
+    - jdk: openjdk7
+      env:
+        - JDK="JDK7"
+      script:
+        - if [ ! -z "$TRAVIS_TAG" ]; then travis_wait 60 mvn install site site:stage -DreleaseTesting; else travis_wait 60 mvn install -DreleaseTesting; fi
+    - jdk: oraclejdk8
+      env:
+        - JDK="JDK8"
+      script:
+        - travis_wait 60 mvn install -DreleaseTesting
+
+after_success:
+  - if [ "$JDK" == "JDK8" ]; then 
+      java -cp ~/codacy-coverage-reporter-assembly-latest.jar com.codacy.CodacyCoverageReporter -l Java -r build-reporting/target/coverage-reports/jacoco.xml;
+      mvn sonar:sonar -Dsonar.java.coveragePlugin=jacoco -Dsonar.jacoco.reportPath=build-reporting/target/jacoco.xml;
+      ./coverity_scan.sh; 
+    fi;
+
+after_failure:
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/617-hierarchical-cross-deps/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/618-aggregator-purge/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/618-aggregator-update-only/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/629-jackson-dataformat/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/690-threadsafety/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/710-pom-parse-error/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/729-system-scope-resolved/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/729-system-scope-skipped/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/730-multiple-suppression-files/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/730-multiple-suppression-files-configs/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/815-broken-suppression-aggregate/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/846-site-plugin/build.log
+    - cat /home/travis/build/jeremylong/DependencyCheck/dependency-check-maven/target/it/false-positives/build.log
+
+deploy:
+  - provider: script
+    script: mvn --settings .travis.settings.xml source:jar javadoc:jar package deploy -DskipTests=true
+    skip_cleanup: true
+    on:
+      branch: master
+      jdk: openjdk7
+  - provider: pages
+    skip_cleanup: true
+    local_dir: target/staging
+    github_token: $GITHUB_TOKEN
+    on:
+      tags: true
+      branch: master
+      jdk: openjdk7
+ 

Dockerfile

@@ -1,14 +1,36 @@
-FROM java:8
+FROM openjdk:8-jre-slim
 
 MAINTAINER Timo Pagel <dependencycheckmaintainer@timo-pagel.de>
 
-RUN wget -O /tmp/current.txt http://jeremylong.github.io/DependencyCheck/current.txt && current=$(cat /tmp/current.txt) && wget https://dl.bintray.com/jeremy-long/owasp/dependency-check-$current-release.zip && unzip dependency-check-$current-release.zip && mv dependency-check /usr/share/
+ENV user=dependencycheck
+ENV version_url=https://jeremylong.github.io/DependencyCheck/current.txt
+ENV download_url=https://dl.bintray.com/jeremy-long/owasp
 
-RUN useradd -ms /bin/bash dockeruser && chown -R dockeruser:dockeruser /usr/share/dependency-check && mkdir /report && chown -R dockeruser:dockeruser /report
-USER dockeruser
+RUN apt-get update                                                          && \
+    apt-get install -y --no-install-recommends wget ruby mono-runtime       && \
+    gem install bundle-audit                                                && \
+    gem cleanup
 
-VOLUME "/src /usr/share/dependency-check/data /report"
+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/                                         && \
+    useradd -ms /bin/bash ${user}                                           && \
+    chown -R ${user}:${user} /usr/share/dependency-check                    && \
+    mkdir /report                                                           && \
+    chown -R ${user}:${user} /report                                        && \
+    apt-get remove --purge -y wget                                          && \
+    apt-get autoremove -y                                                   && \
+    rm -rf /var/lib/apt/lists/* /tmp/*
+ 
+USER ${user}
 
-WORKDIR /report
+VOLUME ["/src" "/usr/share/dependency-check/data" "/report"]
 
-ENTRYPOINT ["/usr/share/dependency-check/bin/dependency-check.sh", "--scan", "/src"]
+WORKDIR /src
+
+CMD ["--help"]
+ENTRYPOINT ["/usr/share/dependency-check/bin/dependency-check.sh"]

README.md

@@ -1,4 +1,6 @@
-[![Build Status](https://travis-ci.org/jeremylong/DependencyCheck.svg?branch=master)](https://travis-ci.org/jeremylong/DependencyCheck) [![Apache 2.0 License](https://img.shields.io/badge/license-Apache%202-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0.txt) [![Coverity Scan Build Status](https://scan.coverity.com/projects/1654/badge.svg)](https://scan.coverity.com/projects/dependencycheck)
+[![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) [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/843/badge)](https://bestpractices.coreinfrastructure.org/projects/843) [![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
 ================
@@ -27,8 +29,8 @@ $ ./bin/dependency-check.sh --project Testing --out . --scan [path to jar files
 ```
 On Windows
 ```
-> bin/dependency-check.bat -h
-> bin/dependency-check.bat --project 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)
 ```
@@ -40,7 +42,10 @@ $ dependency-check --project Testing --out . --scan [path to jar files to be sca
 ### Maven Plugin
 
 More detailed instructions can be found on the [dependency-check-maven github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-maven).
-The plugin can be configured using the following:
+By default, the plugin is tied to the `verify` phase (i.e. `mvn verify`). Alternatively,
+one can directly invoke the plugin via `mvn org.owasp:dependency-check-maven:check`.
+
+The dependency-check plugin can be configured using the following:
 
 ```xml
 <project>
@@ -91,43 +96,153 @@ $ ./dependency-check-cli/target/release/bin/dependency-check.sh --project Testin
 On Windows
 ```
 > mvn install
-> 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
+> .\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.
+Then load the resulting 'dependency-check-report.html' into your favorite browser.
 
 ### Docker
 
-In the following example it is assumed that the source to be checked is in the actual directory. A persistent data directory and a persistent report directory is used so that the container can be destroyed after running it to make sure that you use the newst version, always.
-```
-# After the first run, feel free to change the owner of the directories to the owner of the creted files and the permissions to 744
-DATA_DIRECTORY=$HOME/OWASP-Dependency-Check/data
-REPORT_DIRECTORY=/$HOME/OWASP-Dependency-Check/reports
+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.
 
-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 $REPORT_DIRECTORY
+```
+#!/bin/sh
+
+OWASPDC_DIRECTORY=$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
 
-docker pull owasp/dependency-check # Make sure it is the actual version
+# 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 \
-        --name dependency-check \
-        dc \
-        --suppression "/src/security/dependency-check-suppression.xml"\
-        --format "ALL" \
-        --project "My OWASP Dependency Check Projekt" \
+    --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"
+
 ```
 
 
+Upgrade Notes
+-------------
+
+### Upgrading from **1.x.x** to **2.x.x**
+
+Note that when upgrading from version 1.x.x that the following changes will need to be made to your configuration.
+
+#### Suppression file
+
+In order to support multiple suppression files, the mechanism for configuring suppression files has changed.
+As such, users that have defined a suppression file in their configuration will need to update.
+
+See the examples below:
+
+##### Ant
+
+Old:
+
+```xml
+<dependency-check
+  failBuildOnCVSS="3"
+  suppressionFile="suppression.xml">
+</dependency-check>
+```
+
+New:
+
+```xml
+<dependency-check
+  failBuildOnCVSS="3">
+  <suppressionFile path="suppression.xml" />
+</dependency-check>
+```
+
+##### Maven
+
+Old:
+
+```xml
+<plugin>
+  <groupId>org.owasp</groupId>
+  <artifactId>dependency-check-maven</artifactId>
+  <configuration>
+    <suppressionFile>suppression.xml</suppressionFile>
+  </configuration>
+</plugin>
+```
+
+New:
+
+```xml
+<plugin>
+  <groupId>org.owasp</groupId>
+  <artifactId>dependency-check-maven</artifactId>
+  <configuration>
+    <suppressionFiles>
+      <suppressionFile>suppression.xml</suppressionFile>
+    </suppressionFiles>
+  </configuration>
+</plugin>
+```
+
+### Gradle
+
+In addition to the changes to the suppression file, the task `dependencyCheck` has been
+renamed to `dependencyCheckAnalyze`.
+
+Old:
+
+```groovy
+buildscript {
+    repositories {
+		mavenLocal()
+    }
+    dependencies {
+        classpath 'org.owasp:dependency-check-gradle:2.0.1-SNAPSHOT'
+    }
+}
+apply plugin: 'org.owasp.dependencycheck'
+
+dependencyCheck {
+	suppressionFile='path/to/suppression.xml'
+}
+check.dependsOn dependencyCheckAnalyze
+```
+
+New:
+```groovy
+buildscript {
+    repositories {
+		mavenLocal()
+    }
+    dependencies {
+        classpath 'org.owasp:dependency-check-gradle:2.0.1-SNAPSHOT'
+    }
+}
+apply plugin: 'org.owasp.dependencycheck'
+
+dependencyCheck {
+	suppressionFiles = ['path/to/suppression1.xml', 'path/to/suppression2.xml']
+}
+check.dependsOn dependencyCheckAnalyze
+```
+
 Mailing List
 ------------
 
@@ -140,11 +255,11 @@ Archive: [google group](https://groups.google.com/forum/#!forum/dependency-check
 Copyright & License
 -
 
-Dependency-Check is Copyright (c) 2012-2016 Jeremy Long. All Rights Reserved.
+Dependency-Check is Copyright (c) 2012-2017 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

RELEASE_NOTES.md

@@ -0,0 +1,61 @@
+# Release Notes
+
+Please see the [dependency-check google group](https://groups.google.com/forum/#!forum/dependency-check) for the release notes on versions not listed below.
+
+## [Version 3.1.1](https://github.com/jeremylong/DependencyCheck/releases/tag/v3.1.1) (2018-01-29)
+
+### Bug fixes
+
+- Fixed the Central Analyzer to use the updated SHA1 query syntax.
+- Reverted change that broke Maven 3.1.0 compatability; Maven 3.1.0 and beyond is once again supported.
+- False positive reduction.
+- Minor documentation cleanup.
+
+
+## [Version 3.1.0](https://github.com/jeremylong/DependencyCheck/releases/tag/v3.1.0) (2018-01-02)
+
+### Enhancements
+
+- Major enhancements to the Node and NSP analyzer - the analyzers are now considered
+  production ready and should be used in combination.
+- Added a shutdown hook so that if the update process is interrupted while using an H2
+  database the lock files will be properly removed allowing future executions of ODC to
+  succeed.
+- UNC paths can now be scanned using the CLI.
+- Batch updates are now used which may help with the update speed when using some DBMS
+  instead of the embedded H2.
+- Upgrade Lucene to 5.5.5, the highest version that will allow us to maintain Java 7 support
+
+### Bug fixes
+
+- Fixed the CSV report output to correctly list all fields.
+- Invalid suppression files will now break the build instead of causing ODC to
+  skip the usage of the suppression analyzer.
+- Fixed bug in Lucene query where LARGE entries in the pom.xml or manifest caused
+  the query to break.
+- General cleanup, false positive, and false negative reduction. 
+
+## [Version 3.0.2](https://github.com/jeremylong/DependencyCheck/releases/tag/v3.0.2) (2017-11-13)
+
+### Bug fixes
+
+- Updated the query format for the CentralAnalyzer; the old format caused the CentralAnalyzer to fail
+
+## [Version 3.0.1](https://github.com/jeremylong/DependencyCheck/releases/tag/v3.0.1) (2017-10-20)
+
+### Bug fixes
+
+- Fixed a database connection issue that affected some usages.
+
+## [Version 3.0.0](https://github.com/jeremylong/DependencyCheck/releases/tag/v3.0.0) (2017-10-16)
+
+- Several bug fixes and false positive reduction
+  - The 2.x branch introduced several new false positives – but also reduced the false negatives
+- Java 9 compatibility update
+- Stability issues with the Central Analyzer resolved
+  - This comes at a cost of a longer analysis time
+- The CSV report now includes the GAV and CPE
+- The Hint Analyzer now supports regular expressions
+- If show summary is disabled and vulnerable libraries are found that fail the build details are no longer displayed in the console – only that vulnerable libraries were identified
+- Resolved issues with threading and multiple connections to the embedded H2 database
+  - This allows the Jenkins pipeline, Maven Plugin, etc. to safely run parallel executions of 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>1.4.4</version>
+        <version>3.1.2-SNAPSHOT</version>
     </parent>
 
     <artifactId>dependency-check-ant</artifactId>
@@ -28,15 +28,6 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
 
     <name>Dependency-Check Ant Task</name>
     <description>dependency-check-ant is an Ant Task that uses dependency-check-core to detect publicly disclosed vulnerabilities associated with the project's dependencies. The task will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.</description>
-    <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
-    <distributionManagement>
-        <site>
-            <id>github-pages-site</id>
-            <name>Deployment through GitHub's site deployment plugin</name>
-            <url>${basedir}/../target/site/${project.version}/dependency-check-ant</url>
-        </site>
-    </distributionManagement>
-    <!-- end copy -->
     <build>
         <resources>
             <resource>
@@ -223,86 +214,8 @@ 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>
-                    <argLine>-Dfile.encoding=UTF-8</argLine>
-                    <systemProperties>
-                        <property>
-                            <name>data.directory</name>
-                            <value>${project.build.directory}/dependency-check-data</value>
-                        </property>
-                    </systemProperties>
-                </configuration>
-            </plugin>
         </plugins>
     </build>
-    <reporting>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-checkstyle-plugin</artifactId>
-                <version>${reporting.checkstyle-plugin.version}</version>
-                <configuration>
-                    <enableRulesSummary>false</enableRulesSummary>
-                    <enableFilesSummary>false</enableFilesSummary>
-                    <configLocation>${basedir}/../src/main/config/checkstyle-checks.xml</configLocation>
-                    <headerLocation>${basedir}/../src/main/config/checkstyle-header.txt</headerLocation>
-                    <suppressionsLocation>${basedir}/../src/main/config/checkstyle-suppressions.xml</suppressionsLocation>
-                    <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-pmd-plugin</artifactId>
-                <version>${reporting.pmd-plugin.version}</version>
-                <configuration>
-                    <targetJdk>1.6</targetJdk>
-                    <linkXref>true</linkXref>
-                    <sourceEncoding>utf-8</sourceEncoding>
-                    <excludes>
-                        <exclude>**/generated/*.java</exclude>
-                    </excludes>
-                    <rulesets>
-                        <ruleset>../src/main/config/dcrules.xml</ruleset>
-                        <ruleset>/rulesets/java/basic.xml</ruleset>
-                        <ruleset>/rulesets/java/imports.xml</ruleset>
-                        <ruleset>/rulesets/java/unusedcode.xml</ruleset>
-                    </rulesets>
-                </configuration>
-            </plugin>
-        </plugins>
-    </reporting>
     <dependencies>
         <dependency>
             <groupId>org.owasp</groupId>

ant/src/main/java/org/owasp/dependencycheck/taskdefs/Check.java

@@ -18,7 +18,10 @@
 package org.owasp.dependencycheck.taskdefs;
 
 import java.io.File;
+import java.util.ArrayList;
 import java.util.List;
+import javax.annotation.concurrent.NotThreadSafe;
+
 import org.apache.tools.ant.BuildException;
 import org.apache.tools.ant.Project;
 import org.apache.tools.ant.types.EnumeratedAttribute;
@@ -28,16 +31,13 @@ import org.apache.tools.ant.types.ResourceCollection;
 import org.apache.tools.ant.types.resources.FileProvider;
 import org.apache.tools.ant.types.resources.Resources;
 import org.owasp.dependencycheck.Engine;
-import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
-import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.data.update.exception.UpdateException;
 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.reporting.ReportGenerator;
 import org.owasp.dependencycheck.reporting.ReportGenerator.Format;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.impl.StaticLoggerBinder;
@@ -47,22 +47,179 @@ import org.slf4j.impl.StaticLoggerBinder;
  *
  * @author Jeremy Long
  */
+@NotThreadSafe
 public class Check extends Update {
 
     /**
      * System specific new line character.
      */
     private static final String NEW_LINE = System.getProperty("line.separator", "\n").intern();
+    /**
+     * Whether the ruby gemspec analyzer should be enabled.
+     */
+    private Boolean rubygemsAnalyzerEnabled;
+    /**
+     * Whether or not the Node.js Analyzer is enabled.
+     */
+    private Boolean nodeAnalyzerEnabled;
+    /**
+     * Whether or not the NSP Analyzer is enabled.
+     */
+    private Boolean nspAnalyzerEnabled;
 
     /**
-     * Construct a new DependencyCheckTask.
+     * Whether or not the Ruby Bundle Audit Analyzer is enabled.
      */
-    public Check() {
-        super();
-        // Call this before Dependency Check Core starts logging anything - this way, all SLF4J messages from
-        // core end up coming through this tasks logger
-        StaticLoggerBinder.getSingleton().setTask(this);
-    }
+    private Boolean bundleAuditAnalyzerEnabled;
+    /**
+     * Whether the CMake analyzer should be enabled.
+     */
+    private Boolean cmakeAnalyzerEnabled;
+    /**
+     * Whether or not the Open SSL analyzer is enabled.
+     */
+    private Boolean opensslAnalyzerEnabled;
+    /**
+     * Whether the python package analyzer should be enabled.
+     */
+    private Boolean pyPackageAnalyzerEnabled;
+    /**
+     * Whether the python distribution analyzer should be enabled.
+     */
+    private Boolean pyDistributionAnalyzerEnabled;
+    /**
+     * Whether or not the central analyzer is enabled.
+     */
+    private Boolean centralAnalyzerEnabled;
+    /**
+     * Whether or not the nexus analyzer is enabled.
+     */
+    private Boolean nexusAnalyzerEnabled;
+    /**
+     * The URL of a Nexus server's REST API end point
+     * (http://domain/nexus/service/local).
+     */
+    private String nexusUrl;
+    /**
+     * Whether or not the defined proxy should be used when connecting to Nexus.
+     */
+    private Boolean nexusUsesProxy;
+    /**
+     * Additional ZIP File extensions to add analyze. This should be a
+     * comma-separated list of file extensions to treat like ZIP files.
+     */
+    private String zipExtensions;
+    /**
+     * The path to Mono for .NET assembly analysis on non-windows systems.
+     */
+    private String pathToMono;
+
+    /**
+     * The application name for the report.
+     *
+     * @deprecated use projectName instead.
+     */
+    @Deprecated
+    private String applicationName = null;
+    /**
+     * The name of the project being analyzed.
+     */
+    private String projectName = "dependency-check";
+    /**
+     * 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;
+    /**
+     * Whether only the update phase should be executed.
+     *
+     * @deprecated Use the update task instead
+     */
+    @Deprecated
+    private boolean updateOnly = false;
+
+    /**
+     * The report format to be generated (HTML, XML, VULN, CSV, JSON, ALL).
+     * Default is HTML.
+     */
+    private String reportFormat = "HTML";
+    /**
+     * Suppression file path.
+     */
+    private String suppressionFile = null;
+    /**
+     * Suppression file paths.
+     */
+    @SuppressWarnings("CanBeFinal")
+    private List<String> suppressionFiles = new ArrayList<>();
+
+    /**
+     * The path to the suppression file.
+     */
+    private String hintsFile;
+    /**
+     * flag indicating whether or not to show a summary of findings.
+     */
+    private boolean showSummary = true;
+    /**
+     * Whether experimental analyzers are enabled.
+     */
+    private Boolean enableExperimental;
+    /**
+     * Whether retired analyzers are enabled.
+     */
+    private Boolean enableRetired;
+    /**
+     * Whether or not the Jar Analyzer is enabled.
+     */
+    private Boolean jarAnalyzerEnabled;
+    /**
+     * Whether or not the Archive Analyzer is enabled.
+     */
+    private Boolean archiveAnalyzerEnabled;
+    /**
+     * Whether or not the .NET Nuspec Analyzer is enabled.
+     */
+    private Boolean nuspecAnalyzerEnabled;
+    /**
+     * Whether or not the PHP Composer Analyzer is enabled.
+     */
+    private Boolean composerAnalyzerEnabled;
+
+    /**
+     * Whether or not the .NET Assembly Analyzer is enabled.
+     */
+    private Boolean assemblyAnalyzerEnabled;
+    /**
+     * Whether the autoconf analyzer should be enabled.
+     */
+    private Boolean autoconfAnalyzerEnabled;
+    /**
+     * Sets the path for the bundle-audit binary.
+     */
+    private String bundleAuditPath;
+    /**
+     * Whether or not the CocoaPods Analyzer is enabled.
+     */
+    private Boolean cocoapodsAnalyzerEnabled;
+
+    /**
+     * Whether or not the Swift package Analyzer is enabled.
+     */
+    private Boolean swiftPackageManagerAnalyzerEnabled;
     //The following code was copied Apache Ant PathConvert
     //BEGIN COPY from org.apache.tools.ant.taskdefs.PathConvert
     /**
@@ -70,9 +227,9 @@ public class Check extends Update {
      */
     private Resources path = null;
     /**
-     * Reference to path/fileset to convert
+     * Reference to path/file set to convert
      */
-    private Reference refid = null;
+    private Reference refId = null;
 
     /**
      * Add an arbitrary ResourceCollection.
@@ -82,11 +239,22 @@ public class Check extends Update {
      */
     public void add(ResourceCollection rc) {
         if (isReference()) {
-            throw new BuildException("Nested elements are not allowed when using the refid attribute.");
+            throw new BuildException("Nested elements are not allowed when using the refId attribute.");
         }
         getPath().add(rc);
     }
 
+    /**
+     * Add a suppression file.
+     *
+     * This is called by Ant with the configured {@link SuppressionFile}.
+     *
+     * @param suppressionFile the suppression file to add.
+     */
+    public void addConfiguredSuppressionFile(final SuppressionFile suppressionFile) {
+        suppressionFiles.add(suppressionFile.getPath());
+    }
+
     /**
      * Returns the path. If the path has not been initialized yet, this class is
      * synchronized, and will instantiate the path object.
@@ -102,12 +270,12 @@ public class Check extends Update {
     }
 
     /**
-     * Learn whether the refid attribute of this element been set.
+     * Learn whether the refId attribute of this element been set.
      *
-     * @return true if refid is valid.
+     * @return true if refId is valid.
      */
     public boolean isReference() {
-        return refid != null;
+        return refId != null;
     }
 
     /**
@@ -116,11 +284,11 @@ public class Check extends Update {
      *
      * @param r the reference to a path, fileset, dirset or filelist.
      */
-    public void setRefid(Reference r) {
+    public synchronized void setRefId(Reference r) {
         if (path != null) {
-            throw new BuildException("Nested elements are not allowed when using the refid attribute.");
+            throw new BuildException("Nested elements are not allowed when using the refId attribute.");
         }
-        refid = r;
+        refId = r;
     }
 
     /**
@@ -131,22 +299,25 @@ public class Check extends Update {
      */
     private void dealWithReferences() throws BuildException {
         if (isReference()) {
-            final Object o = refid.getReferencedObject(getProject());
+            final Object o = refId.getReferencedObject(getProject());
             if (!(o instanceof ResourceCollection)) {
-                throw new BuildException("refid '" + refid.getRefId()
+                throw new BuildException("refId '" + refId.getRefId()
                         + "' does not refer to a resource collection.");
             }
             getPath().add((ResourceCollection) o);
         }
     }
     // END COPY from org.apache.tools.ant.taskdefs
+
     /**
-     * The application name for the report.
-     *
-     * @deprecated use projectName instead.
+     * Construct a new DependencyCheckTask.
      */
-    @Deprecated
-    private String applicationName = null;
+    public Check() {
+        super();
+        // Call this before Dependency Check Core starts logging anything - this way, all SLF4J messages from
+        // core end up coming through this tasks logger
+        StaticLoggerBinder.getSingleton().setTask(this);
+    }
 
     /**
      * Get the value of applicationName.
@@ -170,10 +341,6 @@ public class Check extends Update {
     public void setApplicationName(String applicationName) {
         this.applicationName = applicationName;
     }
-    /**
-     * The name of the project being analyzed.
-     */
-    private String projectName = "dependency-check";
 
     /**
      * Get the value of projectName.
@@ -199,12 +366,6 @@ public class Check extends Update {
         this.projectName = projectName;
     }
 
-    /**
-     * Specifies the destination directory for the generated Dependency-Check
-     * report.
-     */
-    private String reportOutputDirectory = ".";
-
     /**
      * Get the value of reportOutputDirectory.
      *
@@ -222,14 +383,6 @@ public class Check extends Update {
     public void setReportOutputDirectory(String reportOutputDirectory) {
         this.reportOutputDirectory = reportOutputDirectory;
     }
-    /**
-     * Specifies if the build should be failed if a CVSS score above a specified
-     * level is identified. The default is 11 which means since the CVSS scores
-     * are 0-10, by default the build will never fail and the CVSS score is set
-     * to 11. The valid range for the fail build on CVSS is 0 to 11, where
-     * anything above 10 will not cause the build to fail.
-     */
-    private float failBuildOnCVSS = 11;
 
     /**
      * Get the value of failBuildOnCVSS.
@@ -248,11 +401,6 @@ public class Check extends Update {
     public void setFailBuildOnCVSS(float failBuildOnCVSS) {
         this.failBuildOnCVSS = failBuildOnCVSS;
     }
-    /**
-     * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not
-     * recommended that this be turned to false. Default is true.
-     */
-    private Boolean autoUpdate;
 
     /**
      * Get the value of autoUpdate.
@@ -271,13 +419,6 @@ public class Check extends Update {
     public void setAutoUpdate(Boolean autoUpdate) {
         this.autoUpdate = autoUpdate;
     }
-    /**
-     * Whether only the update phase should be executed.
-     *
-     * @deprecated Use the update task instead
-     */
-    @Deprecated
-    private boolean updateOnly = false;
 
     /**
      * Get the value of updateOnly.
@@ -301,12 +442,6 @@ public class Check extends Update {
         this.updateOnly = updateOnly;
     }
 
-    /**
-     * The report format to be generated (HTML, XML, VULN, ALL). Default is
-     * HTML.
-     */
-    private String reportFormat = "HTML";
-
     /**
      * Get the value of reportFormat.
      *
@@ -324,18 +459,14 @@ public class Check extends Update {
     public void setReportFormat(ReportFormats reportFormat) {
         this.reportFormat = reportFormat.getValue();
     }
-    /**
-     * The path to the suppression file.
-     */
-    private String suppressionFile;
 
     /**
-     * Get the value of suppressionFile.
+     * Gets suppression file paths.
      *
-     * @return the value of suppressionFile
+     * @return the suppression files.
      */
-    public String getSuppressionFile() {
-        return suppressionFile;
+    public List<String> getSuppressionFiles() {
+        return suppressionFiles;
     }
 
     /**
@@ -345,11 +476,8 @@ public class Check extends Update {
      */
     public void setSuppressionFile(String suppressionFile) {
         this.suppressionFile = suppressionFile;
+        suppressionFiles.add(suppressionFile);
     }
-    /**
-     * The path to the suppression file.
-     */
-    private String hintsFile;
 
     /**
      * Get the value of hintsFile.
@@ -368,10 +496,6 @@ public class Check extends Update {
     public void setHintsFile(String hintsFile) {
         this.hintsFile = hintsFile;
     }
-    /**
-     * flag indicating whether or not to show a summary of findings.
-     */
-    private boolean showSummary = true;
 
     /**
      * Get the value of showSummary.
@@ -391,11 +515,6 @@ public class Check extends Update {
         this.showSummary = showSummary;
     }
 
-    /**
-     * Whether experimental analyzers are enabled.
-     */
-    private Boolean enableExperimental;
-
     /**
      * Get the value of enableExperimental.
      *
@@ -415,9 +534,22 @@ public class Check extends Update {
     }
 
     /**
-     * Whether or not the Jar Analyzer is enabled.
+     * Get the value of enableRetired.
+     *
+     * @return the value of enableRetired
      */
-    private Boolean jarAnalyzerEnabled;
+    public Boolean isEnableRetired() {
+        return enableRetired;
+    }
+
+    /**
+     * Set the value of enableRetired.
+     *
+     * @param enableRetired new value of enableRetired
+     */
+    public void setEnableRetired(Boolean enableRetired) {
+        this.enableRetired = enableRetired;
+    }
 
     /**
      * Returns whether or not the analyzer is enabled.
@@ -436,10 +568,6 @@ public class Check extends Update {
     public void setJarAnalyzerEnabled(Boolean jarAnalyzerEnabled) {
         this.jarAnalyzerEnabled = jarAnalyzerEnabled;
     }
-    /**
-     * Whether or not the Archive Analyzer is enabled.
-     */
-    private Boolean archiveAnalyzerEnabled;
 
     /**
      * Returns whether or not the analyzer is enabled.
@@ -449,10 +577,6 @@ public class Check extends Update {
     public Boolean isArchiveAnalyzerEnabled() {
         return archiveAnalyzerEnabled;
     }
-    /**
-     * Whether or not the .NET Assembly Analyzer is enabled.
-     */
-    private Boolean assemblyAnalyzerEnabled;
 
     /**
      * Sets whether or not the analyzer is enabled.
@@ -480,10 +604,6 @@ public class Check extends Update {
     public void setAssemblyAnalyzerEnabled(Boolean assemblyAnalyzerEnabled) {
         this.assemblyAnalyzerEnabled = assemblyAnalyzerEnabled;
     }
-    /**
-     * Whether or not the .NET Nuspec Analyzer is enabled.
-     */
-    private Boolean nuspecAnalyzerEnabled;
 
     /**
      * Returns whether or not the analyzer is enabled.
@@ -502,10 +622,6 @@ public class Check extends Update {
     public void setNuspecAnalyzerEnabled(Boolean nuspecAnalyzerEnabled) {
         this.nuspecAnalyzerEnabled = nuspecAnalyzerEnabled;
     }
-    /**
-     * Whether or not the PHP Composer Analyzer is enabled.
-     */
-    private Boolean composerAnalyzerEnabled;
 
     /**
      * Get the value of composerAnalyzerEnabled.
@@ -524,10 +640,6 @@ public class Check extends Update {
     public void setComposerAnalyzerEnabled(Boolean composerAnalyzerEnabled) {
         this.composerAnalyzerEnabled = composerAnalyzerEnabled;
     }
-    /**
-     * Whether the autoconf analyzer should be enabled.
-     */
-    private Boolean autoconfAnalyzerEnabled;
 
     /**
      * Get the value of autoconfAnalyzerEnabled.
@@ -546,10 +658,6 @@ public class Check extends Update {
     public void setAutoconfAnalyzerEnabled(Boolean autoconfAnalyzerEnabled) {
         this.autoconfAnalyzerEnabled = autoconfAnalyzerEnabled;
     }
-    /**
-     * Whether the CMake analyzer should be enabled.
-     */
-    private Boolean cmakeAnalyzerEnabled;
 
     /**
      * Get the value of cmakeAnalyzerEnabled.
@@ -568,10 +676,80 @@ public class Check extends Update {
     public void setCMakeAnalyzerEnabled(Boolean cmakeAnalyzerEnabled) {
         this.cmakeAnalyzerEnabled = cmakeAnalyzerEnabled;
     }
+
     /**
-     * Whether or not the openssl analyzer is enabled.
+     * Returns if the Bundle Audit Analyzer is enabled.
+     *
+     * @return if the Bundle Audit Analyzer is enabled.
      */
-    private Boolean opensslAnalyzerEnabled;
+    public Boolean isBundleAuditAnalyzerEnabled() {
+        return bundleAuditAnalyzerEnabled;
+    }
+
+    /**
+     * Sets if the Bundle Audit Analyzer is enabled.
+     *
+     * @param bundleAuditAnalyzerEnabled whether or not the analyzer should be
+     * enabled
+     */
+    public void setBundleAuditAnalyzerEnabled(Boolean bundleAuditAnalyzerEnabled) {
+        this.bundleAuditAnalyzerEnabled = bundleAuditAnalyzerEnabled;
+    }
+
+    /**
+     * Returns the path to the bundle audit executable.
+     *
+     * @return the path to the bundle audit executable
+     */
+    public String getBundleAuditPath() {
+        return bundleAuditPath;
+    }
+
+    /**
+     * Sets the path to the bundle audit executable.
+     *
+     * @param bundleAuditPath the path to the bundle audit executable
+     */
+    public void setBundleAuditPath(String bundleAuditPath) {
+        this.bundleAuditPath = bundleAuditPath;
+    }
+
+    /**
+     * Returns if the cocoapods analyzer is enabled.
+     *
+     * @return if the cocoapods analyzer is enabled
+     */
+    public boolean isCocoapodsAnalyzerEnabled() {
+        return cocoapodsAnalyzerEnabled;
+    }
+
+    /**
+     * Sets whether or not the cocoapods analyzer is enabled.
+     *
+     * @param cocoapodsAnalyzerEnabled the state of the cocoapods analyzer
+     */
+    public void setCocoapodsAnalyzerEnabled(Boolean cocoapodsAnalyzerEnabled) {
+        this.cocoapodsAnalyzerEnabled = cocoapodsAnalyzerEnabled;
+    }
+
+    /**
+     * Returns whether or not the Swift package Analyzer is enabled.
+     *
+     * @return whether or not the Swift package Analyzer is enabled
+     */
+    public Boolean isSwiftPackageManagerAnalyzerEnabled() {
+        return swiftPackageManagerAnalyzerEnabled;
+    }
+
+    /**
+     * Sets the enabled state of the swift package manager analyzer.
+     *
+     * @param swiftPackageManagerAnalyzerEnabled the enabled state of the swift
+     * package manager
+     */
+    public void setSwiftPackageManagerAnalyzerEnabled(Boolean swiftPackageManagerAnalyzerEnabled) {
+        this.swiftPackageManagerAnalyzerEnabled = swiftPackageManagerAnalyzerEnabled;
+    }
 
     /**
      * Get the value of opensslAnalyzerEnabled.
@@ -590,10 +768,6 @@ public class Check extends Update {
     public void setOpensslAnalyzerEnabled(Boolean opensslAnalyzerEnabled) {
         this.opensslAnalyzerEnabled = opensslAnalyzerEnabled;
     }
-    /**
-     * Whether or not the Node.js Analyzer is enabled.
-     */
-    private Boolean nodeAnalyzerEnabled;
 
     /**
      * Get the value of nodeAnalyzerEnabled.
@@ -612,10 +786,24 @@ public class Check extends Update {
     public void setNodeAnalyzerEnabled(Boolean nodeAnalyzerEnabled) {
         this.nodeAnalyzerEnabled = nodeAnalyzerEnabled;
     }
+
     /**
-     * Whether the ruby gemspec analyzer should be enabled.
+     * Get the value of nspAnalyzerEnabled.
+     *
+     * @return the value of nspAnalyzerEnabled
      */
-    private Boolean rubygemsAnalyzerEnabled;
+    public Boolean isNspAnalyzerEnabled() {
+        return nspAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of nspAnalyzerEnabled.
+     *
+     * @param nspAnalyzerEnabled new value of nspAnalyzerEnabled
+     */
+    public void setNspAnalyzerEnabled(Boolean nspAnalyzerEnabled) {
+        this.nspAnalyzerEnabled = nspAnalyzerEnabled;
+    }
 
     /**
      * Get the value of rubygemsAnalyzerEnabled.
@@ -634,10 +822,6 @@ public class Check extends Update {
     public void setRubygemsAnalyzerEnabled(Boolean rubygemsAnalyzerEnabled) {
         this.rubygemsAnalyzerEnabled = rubygemsAnalyzerEnabled;
     }
-    /**
-     * Whether the python package analyzer should be enabled.
-     */
-    private Boolean pyPackageAnalyzerEnabled;
 
     /**
      * Get the value of pyPackageAnalyzerEnabled.
@@ -657,11 +841,6 @@ public class Check extends Update {
         this.pyPackageAnalyzerEnabled = pyPackageAnalyzerEnabled;
     }
 
-    /**
-     * Whether the python distribution analyzer should be enabled.
-     */
-    private Boolean pyDistributionAnalyzerEnabled;
-
     /**
      * Get the value of pyDistributionAnalyzerEnabled.
      *
@@ -681,11 +860,6 @@ public class Check extends Update {
         this.pyDistributionAnalyzerEnabled = pyDistributionAnalyzerEnabled;
     }
 
-    /**
-     * Whether or not the central analyzer is enabled.
-     */
-    private Boolean centralAnalyzerEnabled;
-
     /**
      * Get the value of centralAnalyzerEnabled.
      *
@@ -704,11 +878,6 @@ public class Check extends Update {
         this.centralAnalyzerEnabled = centralAnalyzerEnabled;
     }
 
-    /**
-     * Whether or not the nexus analyzer is enabled.
-     */
-    private Boolean nexusAnalyzerEnabled;
-
     /**
      * Get the value of nexusAnalyzerEnabled.
      *
@@ -727,12 +896,6 @@ public class Check extends Update {
         this.nexusAnalyzerEnabled = nexusAnalyzerEnabled;
     }
 
-    /**
-     * The URL of a Nexus server's REST API end point
-     * (http://domain/nexus/service/local).
-     */
-    private String nexusUrl;
-
     /**
      * Get the value of nexusUrl.
      *
@@ -750,10 +913,6 @@ public class Check extends Update {
     public void setNexusUrl(String nexusUrl) {
         this.nexusUrl = nexusUrl;
     }
-    /**
-     * Whether or not the defined proxy should be used when connecting to Nexus.
-     */
-    private Boolean nexusUsesProxy;
 
     /**
      * Get the value of nexusUsesProxy.
@@ -773,12 +932,6 @@ public class Check extends Update {
         this.nexusUsesProxy = nexusUsesProxy;
     }
 
-    /**
-     * Additional ZIP File extensions to add analyze. This should be a
-     * comma-separated list of file extensions to treat like ZIP files.
-     */
-    private String zipExtensions;
-
     /**
      * Get the value of zipExtensions.
      *
@@ -797,11 +950,6 @@ public class Check extends Update {
         this.zipExtensions = zipExtensions;
     }
 
-    /**
-     * The path to Mono for .NET assembly analysis on non-windows systems.
-     */
-    private String pathToMono;
-
     /**
      * Get the value of pathToMono.
      *
@@ -825,9 +973,7 @@ public class Check extends Update {
         dealWithReferences();
         validateConfiguration();
         populateSettings();
-        Engine engine = null;
-        try {
-            engine = new Engine(Check.class.getClassLoader());
+        try (Engine engine = new Engine(Check.class.getClassLoader(), getSettings())) {
             if (isUpdateOnly()) {
                 log("Deprecated 'UpdateOnly' property set; please use the UpdateTask instead", Project.MSG_WARN);
                 try {
@@ -839,7 +985,7 @@ public class Check extends Update {
                     log(ex.getMessage(), Project.MSG_ERR);
                 }
             } else {
-                for (Resource resource : path) {
+                for (Resource resource : getPath()) {
                     final FileProvider provider = resource.as(FileProvider.class);
                     if (provider != null) {
                         final File file = provider.getFile();
@@ -856,21 +1002,7 @@ public class Check extends Update {
                         throw new BuildException(ex);
                     }
                 }
-                DatabaseProperties prop = null;
-                CveDB cve = null;
-                try {
-                    cve = new CveDB();
-                    cve.open();
-                    prop = cve.getDatabaseProperties();
-                } catch (DatabaseException ex) {
-                    log("Unable to retrieve DB Properties", ex, Project.MSG_DEBUG);
-                } finally {
-                    if (cve != null) {
-                        cve.close();
-                    }
-                }
-                final ReportGenerator reporter = new ReportGenerator(getProjectName(), engine.getDependencies(), engine.getAnalyzers(), prop);
-                reporter.generateReports(reportOutputDirectory, reportFormat);
+                engine.writeReports(getProjectName(), new File(reportOutputDirectory), reportFormat);
 
                 if (this.failBuildOnCVSS <= 10) {
                     checkForFailure(engine.getDependencies());
@@ -891,11 +1023,6 @@ public class Check extends Update {
                 throw new BuildException(msg, ex);
             }
             log(msg, ex, Project.MSG_ERR);
-        } finally {
-            Settings.cleanup(true);
-            if (engine != null) {
-                engine.cleanup();
-            }
         }
     }
 
@@ -905,7 +1032,7 @@ public class Check extends Update {
      *
      * @throws BuildException if the task was not configured correctly.
      */
-    private void validateConfiguration() throws BuildException {
+    private synchronized void validateConfiguration() throws BuildException {
         if (path == null) {
             throw new BuildException("No project dependencies have been defined to analyze.");
         }
@@ -924,28 +1051,34 @@ public class Check extends Update {
     @Override
     protected void populateSettings() throws BuildException {
         super.populateSettings();
-        Settings.setBooleanIfNotNull(Settings.KEYS.AUTO_UPDATE, autoUpdate);
-        Settings.setStringIfNotEmpty(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
-        Settings.setStringIfNotEmpty(Settings.KEYS.HINTS_FILE, hintsFile);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, enableExperimental);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_JAR_ENABLED, jarAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED, pyDistributionAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED, pyPackageAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED, rubygemsAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_OPENSSL_ENABLED, opensslAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_CMAKE_ENABLED, cmakeAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_AUTOCONF_ENABLED, autoconfAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED, composerAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED, nodeAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, nuspecAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, centralAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, archiveAnalyzerEnabled);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, assemblyAnalyzerEnabled);
-        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
-        Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY, nexusUsesProxy);
-        Settings.setStringIfNotEmpty(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
-        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.AUTO_UPDATE, autoUpdate);
+        getSettings().setArrayIfNotEmpty(Settings.KEYS.SUPPRESSION_FILE, suppressionFiles.toArray(new String[suppressionFiles.size()]));
+        getSettings().setStringIfNotEmpty(Settings.KEYS.HINTS_FILE, hintsFile);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, enableExperimental);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_RETIRED_ENABLED, enableRetired);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_JAR_ENABLED, jarAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED, pyDistributionAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED, pyPackageAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED, rubygemsAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_OPENSSL_ENABLED, opensslAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_CMAKE_ENABLED, cmakeAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_SWIFT_PACKAGE_MANAGER_ENABLED, swiftPackageManagerAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_COCOAPODS_ENABLED, cocoapodsAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_ENABLED, bundleAuditAnalyzerEnabled);
+        getSettings().setStringIfNotNull(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_PATH, bundleAuditPath);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_AUTOCONF_ENABLED, autoconfAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED, composerAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED, nodeAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_NSP_PACKAGE_ENABLED, nspAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, nuspecAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, centralAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, archiveAnalyzerEnabled);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, assemblyAnalyzerEnabled);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
+        getSettings().setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY, nexusUsesProxy);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
     }
 
     /**
@@ -954,9 +1087,9 @@ public class Check extends Update {
      *
      * @param dependencies the list of dependency objects
      * @throws BuildException thrown if a CVSS score is found that is higher
-     * then the threshold set
+     * than the threshold set
      */
-    private void checkForFailure(List<Dependency> dependencies) throws BuildException {
+    private void checkForFailure(Dependency[] dependencies) throws BuildException {
         final StringBuilder ids = new StringBuilder();
         for (Dependency d : dependencies) {
             for (Vulnerability v : d.getVulnerabilities()) {
@@ -970,9 +1103,16 @@ public class Check extends Update {
             }
         }
         if (ids.length() > 0) {
-            final String msg = String.format("%n%nDependency-Check Failure:%n"
-                    + "One or more dependencies were identified with vulnerabilities that have a CVSS score greater then '%.1f': %s%n"
-                    + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
+            final String msg;
+            if (showSummary) {
+                msg = String.format("%n%nDependency-Check Failure:%n"
+                        + "One or more dependencies were identified with vulnerabilities that have a CVSS score greater than or equal to '%.1f': %s%n"
+                        + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
+            } else {
+                msg = String.format("%n%nDependency-Check Failure:%n"
+                        + "One or more dependencies were identified with vulnerabilities.%n%n"
+                        + "See the dependency-check report for more details.%n%n");
+            }
             throw new BuildException(msg);
         }
     }
@@ -983,12 +1123,12 @@ public class Check extends Update {
      *
      * @param dependencies a list of dependency objects
      */
-    private void showSummary(List<Dependency> dependencies) {
+    private void showSummary(Dependency[] dependencies) {
         final StringBuilder summary = new StringBuilder();
         for (Dependency d : dependencies) {
             boolean firstEntry = true;
             final StringBuilder ids = new StringBuilder();
-            for (Vulnerability v : d.getVulnerabilities()) {
+            for (Vulnerability v : d.getVulnerabilities(true)) {
                 if (firstEntry) {
                     firstEntry = false;
                 } else {
@@ -1019,8 +1159,8 @@ public class Check extends Update {
     }
 
     /**
-     * An enumeration of supported report formats: "ALL", "HTML", "XML", "VULN",
-     * etc..
+     * An enumeration of supported report formats: "ALL", "HTML", "XML", "CSV",
+     * "JSON", "VULN", etc..
      */
     public static class ReportFormats extends EnumeratedAttribute {
 

ant/src/main/java/org/owasp/dependencycheck/taskdefs/Purge.java

@@ -37,21 +37,35 @@ public class Purge extends Task {
      * The properties file location.
      */
     private static final String PROPERTIES_FILE = "task.properties";
+    /**
+     * The configured settings.
+     */
+    private Settings settings;
+
+    /**
+     * The location of the data directory that contains
+     */
+    private String dataDirectory = null;
+    /**
+     * Indicates if dependency-check should fail the build if an exception
+     * occurs.
+     */
+    private boolean failOnError = true;
 
     /**
      * Construct a new DependencyCheckTask.
      */
     public Purge() {
         super();
+
         // Call this before Dependency Check Core starts logging anything - this way, all SLF4J messages from
         // core end up coming through this tasks logger
         StaticLoggerBinder.getSingleton().setTask(this);
     }
 
-    /**
-     * The location of the data directory that contains
-     */
-    private String dataDirectory = null;
+    public Settings getSettings() {
+        return settings;
+    }
 
     /**
      * Get the value of dataDirectory.
@@ -71,12 +85,6 @@ 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.
      *
@@ -95,12 +103,18 @@ public class Purge extends Task {
         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();
         File db;
         try {
-            db = new File(Settings.getDataDirectory(), "dc.h2.db");
+            db = new File(settings.getDataDirectory(), "dc.h2.db");
             if (db.exists()) {
                 if (db.delete()) {
                     log("Database file purged; local copy of the NVD has been removed", Project.MSG_INFO);
@@ -112,7 +126,7 @@ public class Purge extends Task {
                     log(msg, Project.MSG_ERR);
                 }
             } else {
-                final String msg = String.format("Unable to purge database; the database file does not exists: %s", db.getAbsolutePath());
+                final String msg = String.format("Unable to purge database; the database file does not exist: %s", db.getAbsolutePath());
                 if (this.failOnError) {
                     throw new BuildException(msg);
                 }
@@ -125,7 +139,7 @@ public class Purge extends Task {
             }
             log(msg, Project.MSG_ERR);
         } finally {
-            Settings.cleanup(true);
+            settings.cleanup(true);
         }
     }
 
@@ -137,34 +151,24 @@ public class Purge extends Task {
      * @throws BuildException thrown if the properties file cannot be read.
      */
     protected void populateSettings() throws BuildException {
-        Settings.initialize();
-        InputStream taskProperties = null;
-        try {
-            taskProperties = this.getClass().getClassLoader().getResourceAsStream(PROPERTIES_FILE);
-            Settings.mergeProperties(taskProperties);
+        settings = new Settings();
+        try (InputStream taskProperties = this.getClass().getClassLoader().getResourceAsStream(PROPERTIES_FILE)) {
+            settings.mergeProperties(taskProperties);
         } catch (IOException ex) {
             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);
-        } finally {
-            if (taskProperties != null) {
-                try {
-                    taskProperties.close();
-                } catch (IOException ex) {
-                    log("", ex, Project.MSG_DEBUG);
-                }
-            }
         }
         if (dataDirectory != null) {
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
+            settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
         } else {
             final File jarPath = new File(Purge.class.getProtectionDomain().getCodeSource().getLocation().getPath());
             final File base = jarPath.getParentFile();
-            final String sub = Settings.getString(Settings.KEYS.DATA_DIRECTORY);
+            final String sub = settings.getString(Settings.KEYS.DATA_DIRECTORY);
             final File dataDir = new File(base, sub);
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
+            settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
         }
     }
 }

ant/src/main/java/org/owasp/dependencycheck/taskdefs/SuppressionFile.java

@@ -0,0 +1,51 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2017 The OWASP Foundation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.taskdefs;
+
+/**
+ * Class : {@link SuppressionFile} Responsibility : Models a suppression file
+ * nested XML element where the simple content is its location.
+ *
+ * @author Phillip Whittlesea
+ */
+public class SuppressionFile {
+
+    /**
+     * The path to the suppression file.
+     */
+    private String path;
+
+    /**
+     * Sets the path to the suppression file.
+     *
+     * @param path the path to the suppression file
+     */
+    public void setPath(String path) {
+        this.path = path;
+    }
+
+    /**
+     * Gets the path to the suppression file.
+     *
+     * @return the path
+     */
+    public String getPath() {
+        return path;
+    }
+
+}

ant/src/main/java/org/owasp/dependencycheck/taskdefs/Update.java

@@ -34,6 +34,67 @@ import org.slf4j.impl.StaticLoggerBinder;
  */
 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.
      */
@@ -44,11 +105,6 @@ public class Update extends Purge {
         StaticLoggerBinder.getSingleton().setTask(this);
     }
 
-    /**
-     * The Proxy Server.
-     */
-    private String proxyServer;
-
     /**
      * Get the value of proxyServer.
      *
@@ -67,11 +123,6 @@ public class Update extends Purge {
         this.proxyServer = server;
     }
 
-    /**
-     * The Proxy Port.
-     */
-    private String proxyPort;
-
     /**
      * Get the value of proxyPort.
      *
@@ -89,10 +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.
@@ -111,10 +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.
@@ -133,10 +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.
@@ -155,10 +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.
@@ -178,11 +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.
      *
@@ -200,10 +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.
@@ -222,10 +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.
@@ -245,11 +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.
      *
@@ -268,11 +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.
      *
@@ -291,11 +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.
      *
@@ -314,11 +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.
      *
@@ -337,11 +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.
      *
@@ -360,11 +357,6 @@ public class Update extends Purge {
         this.cveUrl20Base = cveUrl20Base;
     }
 
-    /**
-     * The number of hours to wait before re-checking for updates.
-     */
-    private Integer cveValidForHours;
-
     /**
      * Get the value of cveValidForHours.
      *
@@ -393,9 +385,7 @@ public class Update extends Purge {
     @Override
     public void execute() throws BuildException {
         populateSettings();
-        Engine engine = null;
-        try {
-            engine = new Engine(Update.class.getClassLoader());
+        try (Engine engine = new Engine(Update.class.getClassLoader(), getSettings())) {
             try {
                 engine.doUpdates();
             } catch (UpdateException ex) {
@@ -410,11 +400,6 @@ public class Update extends Purge {
                 throw new BuildException(msg, ex);
             }
             log(msg, Project.MSG_ERR);
-        } finally {
-            Settings.cleanup(true);
-            if (engine != null) {
-                engine.cleanup();
-            }
         }
     }
 
@@ -428,23 +413,23 @@ public class Update extends Purge {
     @Override
     protected void populateSettings() throws BuildException {
         super.populateSettings();
-        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_SERVER, proxyServer);
-        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_PORT, proxyPort);
-        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_USERNAME, proxyUsername);
-        Settings.setStringIfNotEmpty(Settings.KEYS.PROXY_PASSWORD, proxyPassword);
-        Settings.setStringIfNotEmpty(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
-        Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
-        Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
-        Settings.setStringIfNotEmpty(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
-        Settings.setStringIfNotEmpty(Settings.KEYS.DB_USER, databaseUser);
-        Settings.setStringIfNotEmpty(Settings.KEYS.DB_PASSWORD, databasePassword);
-        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
-        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
-        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
-        Settings.setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.PROXY_SERVER, proxyServer);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.PROXY_PORT, proxyPort);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.PROXY_USERNAME, proxyUsername);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.PROXY_PASSWORD, proxyPassword);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.DB_USER, databaseUser);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.DB_PASSWORD, databasePassword);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
+        getSettings().setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
         if (cveValidForHours != null) {
             if (cveValidForHours >= 0) {
-                Settings.setInt(Settings.KEYS.CVE_CHECK_VALID_FOR_HOURS, cveValidForHours);
+                getSettings().setInt(Settings.KEYS.CVE_CHECK_VALID_FOR_HOURS, cveValidForHours);
             } else {
                 throw new BuildException("Invalid setting: `cpeValidForHours` must be 0 or greater");
             }

ant/src/main/java/org/slf4j/impl/StaticLoggerBinder.java

@@ -37,22 +37,21 @@ public class StaticLoggerBinder implements LoggerFactoryBinder {
      * 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.
      *
      * @return the StaticLoggerBinder singleton
      */
-    public static final StaticLoggerBinder getSingleton() {
+    public static StaticLoggerBinder getSingleton() {
         return SINGLETON;
     }
 
-    /**
-     * Ant tasks have the log method we actually want to call. So we hang onto
-     * the task as a delegate
-     */
-    private Task task = null;
-
     /**
      * Set the Task which will this is to log through.
      *

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.
 

ant/src/site/markdown/configuration.md

@@ -17,7 +17,7 @@ the project's dependencies.
     <dependency-check projectname="Hello World"
                       reportoutputdirectory="${basedir}"
                       reportformat="ALL">
-
+        <suppressionfile path="${basedir}/path/to/suppression.xml" />
         <fileset dir="lib">
             <include name="**/*.jar"/>
         </fileset>
@@ -33,19 +33,26 @@ Property              | Description
 ----------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------
 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
+failBuildOnCVSS       | Specifies if the build should be failed if a CVSS score equal to or 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, VULN, ALL). This configuration option has no affect if using this within the Site plugin unless the externalReport is set to true.                   | HTML
+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)                                                                                       | &nbsp;
-hintsFile             | The file path to the XML hints file \- used to resolve [false negatives](../general/hints.html)                                                                                       | &nbsp;
-proxyServer           | The Proxy Server; see the [proxy configuration](../data/proxy.html) page for more information.                                                                                                                        | &nbsp;
+hintsFile             | The file path to the XML hints file \- used to resolve [false negatives](../general/hints.html)                                                                                                    | &nbsp;
+proxyServer           | The Proxy Server; see the [proxy configuration](../data/proxy.html) page for more information.                                                                                                     | &nbsp;
 proxyPort             | The Proxy Port.                                                                                                                                                                                    | &nbsp;
 proxyUsername         | Defines the proxy user name.                                                                                                                                                                       | &nbsp;
 proxyPassword         | Defines the proxy password.                                                                                                                                                                        | &nbsp;
 connectionTimeout     | The URL Connection Timeout.                                                                                                                                                                        | &nbsp;
-enableExperimental    | Enable the [experimental analyzers](../analyzers/index.html). If not enabled the experimental analyzers (see below) will not be loaded or used.                                                                             | false
+enableExperimental    | Enable the [experimental analyzers](../analyzers/index.html). If not enabled the experimental analyzers (see below) will not be loaded or used.                                                    | false
+enableRetired         | Enable the [retired analyzers](../analyzers/index.html). If not enabled the retired analyzers (see below) will not be loaded or used.                                                              | false
+suppressionFile       | The file path to the XML suppression file \- used to suppress [false positives](../general/suppression.html).                                                                                      | &nbsp;
+
+The following nested elements can be set on the dependency-check task.
+
+Element           | Property | Description                                                                                                                                                                                        | Default Value
+------------------|----------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------
+suppressionFile   | path     | The file path to the XML suppression file \- used to suppress [false positives](../general/suppression.html). Element can be specified multiple times.                                             | &nbsp;
 
 Analyzer Configuration
 ====================
@@ -55,26 +62,31 @@ 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. | &nbsp;
-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
+nexusAnalyzerEnabled          | Sets whether Nexus Analyzer will be used (requires Nexus Pro). This analyzer is superceded by the Central Analyzer; however, you can configure this to run against a Nexus Pro installation. | true
 nexusUrl                      | Defines the Nexus web service endpoint (example http://domain.enterprise/nexus/service/local/). If not set the Nexus Analyzer will be disabled. | &nbsp;
-nexusUsesProxy                | Whether or not the defined proxy should be used when connecting to Nexus.         | true
+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
+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
-assemblyAnalyzerEnabled       | Sets whether the .NET Assembly Analyzer should be used.                           | true
-pathToMono                    | The path to Mono for .NET assembly analysis on non-windows systems.               | &nbsp;
+nodeAnalyzerEnabled           | Sets whether the [retired](../analyzers/index.html) Node.js Analyzer should be used.                  | true
+nspAnalyzerEnabled            | Sets whether the NSP 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.  | &nbsp;
+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.                                        | &nbsp;
 
 Advanced Configuration
 ====================
@@ -88,8 +100,8 @@ cveUrl20Modified     | URL for the modified CVE 2.0.
 cveUrl12Base         | Base URL for each year's CVE 1.2, the %d will be replaced with the year. | http://nvd.nist.gov/download/nvdcve-%d.xml
 cveUrl20Base         | Base URL for each year's CVE 2.0, the %d will be replaced with the year. | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
 dataDirectory        | Data directory that is used to store the local copy of the NVD. This should generally not be changed. | data
-databaseDriverName   | The name of the database driver. Example: org.h2.Driver.                                    | &nbsp;
+databaseDriverName   | The name of the database driver. Example: org.h2.Driver.                 | &nbsp;
 databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path. | &nbsp;
-connectionString     | The connection string used to connect to the database.                                      | &nbsp;
-databaseUser         | The username used when connecting to the database.                                          | &nbsp;
-databasePassword     | The password used when connecting to the database.                                          | &nbsp;
+connectionString     | The connection string used to connect to the database.                   | &nbsp;
+databaseUser         | The username used when connecting to the database.                       | &nbsp;
+databasePassword     | The password used when connecting to the database.                       | &nbsp;

ant/src/test/java/org/owasp/dependencycheck/taskdefs/DependencyCheckTaskTest.java

@@ -0,0 +1,171 @@
+/*
+ * This file is part of dependency-check-ant.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.taskdefs;
+
+import java.io.File;
+
+import org.apache.tools.ant.BuildException;
+import org.apache.tools.ant.BuildFileRule;
+import org.apache.tools.ant.types.LogLevel;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.ExpectedException;
+import org.owasp.dependencycheck.BaseDBTestCase;
+
+import static org.junit.Assert.assertTrue;
+
+/**
+ *
+ * @author Jeremy Long
+ */
+public class DependencyCheckTaskTest extends BaseDBTestCase {
+
+    @Rule
+    public BuildFileRule buildFileRule = new BuildFileRule();
+
+    @Rule
+    public ExpectedException expectedException = ExpectedException.none();
+
+    @Before
+    @Override
+    public void setUp() throws Exception {
+        super.setUp();
+        final String buildFile = this.getClass().getClassLoader().getResource("build.xml").getPath();
+        buildFileRule.configureProject(buildFile, LogLevel.VERBOSE.getLevel());
+    }
+
+    /**
+     * Test of addFileSet method, of class DependencyCheckTask.
+     */
+    @Test
+    public void testAddFileSet() throws Exception {
+        File report = new File("target/dependency-check-report.html");
+        if (report.exists() && !report.delete()) {
+            throw new Exception("Unable to delete 'target/dependency-check-report.html' prior to test.");
+        }
+        buildFileRule.executeTarget("test.fileset");
+        assertTrue("DependencyCheck report was not generated", report.exists());
+    }
+
+    /**
+     * Test of addFileList method, of class DependencyCheckTask.
+     *
+     * @throws Exception
+     */
+    @Test
+    public void testAddFileList() throws Exception {
+        File report = new File("target/dependency-check-report.xml");
+        if (report.exists()) {
+            if (!report.delete()) {
+                throw new Exception("Unable to delete 'target/DependencyCheck-Report.xml' prior to test.");
+            }
+        }
+        buildFileRule.executeTarget("test.filelist");
+
+        assertTrue("DependencyCheck report was not generated", report.exists());
+    }
+
+    /**
+     * Test of addDirSet method, of class DependencyCheckTask.
+     *
+     * @throws Exception
+     */
+    @Test
+    public void testAddDirSet() throws Exception {
+        File report = new File("target/dependency-check-vulnerability.html");
+        if (report.exists()) {
+            if (!report.delete()) {
+                throw new Exception("Unable to delete 'target/DependencyCheck-Vulnerability.html' prior to test.");
+            }
+        }
+        buildFileRule.executeTarget("test.dirset");
+        assertTrue("DependencyCheck report was not generated", report.exists());
+    }
+
+    /**
+     * Test of getFailBuildOnCVSS method, of class DependencyCheckTask.
+     */
+    @Test
+    public void testGetFailBuildOnCVSS() {
+        expectedException.expect(BuildException.class);
+        buildFileRule.executeTarget("failCVSS");
+    }
+
+    /**
+     * Test the DependencyCheckTask where a CVE is suppressed.
+     */
+    @Test
+    public void testSuppressingCVE() {
+        // GIVEN an ant task with a vulnerability
+        final String antTaskName = "suppression";
+
+        // WHEN executing the ant task
+        buildFileRule.executeTarget(antTaskName);
+        System.out.println("----------------------------------------------------------");
+        System.out.println("----------------------------------------------------------");
+        System.out.println("----------------------------------------------------------");
+        System.out.println("----------------------------------------------------------");
+        System.out.println(buildFileRule.getError());
+        System.out.println("----------------------------------------------------------");
+        System.out.println("----------------------------------------------------------");
+        System.out.println(buildFileRule.getFullLog());
+        System.out.println("----------------------------------------------------------");
+        System.out.println("----------------------------------------------------------");
+        System.out.println("----------------------------------------------------------");
+        System.out.println("----------------------------------------------------------");
+
+        // THEN the ant task executed without error
+        final File report = new File("target/suppression-report.html");
+        assertTrue("Expected the DependencyCheck report to be generated", report.exists());
+    }
+
+    /**
+     * Test the DependencyCheckTask deprecated suppression property throws an
+     * exception with a warning.
+     */
+    @Test
+    public void testSuppressingSingle() {
+        // GIVEN an ant task with a vulnerability using the legacy property
+        final String antTaskName = "suppression-single";
+
+        // WHEN executing the ant task
+        buildFileRule.executeTarget(antTaskName);
+
+        // THEN the ant task executed without error
+        final File report = new File("target/suppression-single-report.html");
+        assertTrue("Expected the DependencyCheck report to be generated", report.exists());
+    }
+
+    /**
+     * Test the DependencyCheckTask deprecated suppression property throws an
+     * exception with a warning.
+     */
+    @Test
+    public void testSuppressingMultiple() {
+        // GIVEN an ant task with a vulnerability using multiple was to configure the suppression file
+        final String antTaskName = "suppression-multiple";
+
+        // WHEN executing the ant task
+        buildFileRule.executeTarget(antTaskName);
+
+        // THEN the ant task executed without error
+        final File report = new File("target/suppression-multiple-report.html");
+        assertTrue("Expected the DependencyCheck report to be generated", report.exists());
+    }
+}

ant/src/test/resources/build.xml

@@ -61,11 +61,57 @@
 
     <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>
+
+    <target name="suppression">
+        <dependency-check
+            applicationName="test suppression"
+            reportOutputDirectory="${project.build.directory}/suppression-report.html"
+            autoupdate="false"
+            failBuildOnCVSS="3">
+            <suppressionfile path="${project.build.directory}/test-classes/test-suppression1.xml" />
+            <suppressionfile path="${project.build.directory}/test-classes/test-suppression2.xml" />
+            <fileset dir="${project.build.directory}/test-classes/jars">
+                <include name="axis-1.4.jar"/>
+            </fileset>
+            <filelist
+                dir="${project.build.directory}/test-classes/list"
+                files="jetty-6.1.0.jar,org.mortbay.jetty.jar"/>
+        </dependency-check>
+    </target>
+    <target name="suppression-single">
+        <dependency-check
+            applicationName="test suppression"
+            reportOutputDirectory="${project.build.directory}/suppression-single-report.html"
+            autoupdate="false"
+            failBuildOnCVSS="3"
+            suppressionFile="${project.build.directory}/test-classes/test-suppression.xml">
+            <fileset dir="${project.build.directory}/test-classes/jars">
+                <include name="axis-1.4.jar"/>
+            </fileset>
+        </dependency-check>
+    </target>
+    <target name="suppression-multiple">
+        <dependency-check
+            applicationName="test suppression"
+            reportOutputDirectory="${project.build.directory}/suppression-multiple-report.html"
+            autoupdate="false"
+            failBuildOnCVSS="3"
+            suppressionFile="${project.build.directory}/test-classes/test-suppression1.xml">
+            <suppressionfile path="${project.build.directory}/test-classes/test-suppression2.xml"/>
+            <fileset dir="${project.build.directory}/test-classes/jars">
+                <include name="axis-1.4.jar"/>
+            </fileset>
+        </dependency-check>
+    </target>
+    
 </project>

ant/src/test/resources/test-suppression.xml

@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+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 The OWASP Foundation. All Rights Reserved.
+-->
+<suppressions xmlns="https://jeremylong.github.io/DependencyCheck/dependency-suppression.1.1.xsd">
+    <suppress>
+        <notes><![CDATA[
+            file name: axis-1.4.jar
+        ]]></notes>
+        <gav regex="true">^org\.apache\.axis:axis:.*$</gav>
+        <cpe>cpe:/a:apache:axis</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+            file name: org.mortbay.jetty.jar
+        ]]></notes>
+        <gav regex="true">^jetty:org\.mortbay\.jetty:.*$</gav>
+        <cpe>cpe:/a:jetty:jetty</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+         file name: org.mortbay.jetty.jar
+         ]]></notes>
+        <gav regex="true">^jetty:org\.mortbay\.jetty:.*$</gav>
+        <cpe>cpe:/a:mortbay:jetty</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+            file name: org.mortbay.jetty.jar
+        ]]></notes>
+        <gav regex="true">^jetty:org\.mortbay\.jetty:.*$</gav>
+        <cpe>cpe:/a:mortbay_jetty:jetty</cpe>
+    </suppress>
+</suppressions>

ant/src/test/resources/test-suppression1.xml

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+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 The OWASP Foundation. All Rights Reserved.
+-->
+<suppressions xmlns="https://jeremylong.github.io/DependencyCheck/dependency-suppression.1.1.xsd">
+    <suppress>
+        <notes><![CDATA[
+            file name: axis-1.4.jar
+        ]]></notes>
+        <gav regex="true">^org\.apache\.axis:axis:.*$</gav>
+        <cpe>cpe:/a:apache:axis</cpe>
+    </suppress>
+</suppressions>

ant/src/test/resources/test-suppression2.xml

@@ -0,0 +1,41 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+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 The OWASP Foundation. All Rights Reserved.
+-->
+<suppressions xmlns="https://jeremylong.github.io/DependencyCheck/dependency-suppression.1.1.xsd">
+    <suppress>
+        <notes><![CDATA[
+            file name: org.mortbay.jetty.jar
+        ]]></notes>
+        <gav regex="true">^jetty:org\.mortbay\.jetty:.*$</gav>
+        <cpe>cpe:/a:jetty:jetty</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+            file name: org.mortbay.jetty.jar
+        ]]></notes>
+        <gav regex="true">^jetty:org\.mortbay\.jetty:.*$</gav>
+        <cpe>cpe:/a:mortbay:jetty</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+            file name: org.mortbay.jetty.jar
+        ]]></notes>
+        <gav regex="true">^jetty:org\.mortbay\.jetty:.*$</gav>
+        <cpe>cpe:/a:mortbay_jetty:jetty</cpe>
+    </suppress>
+</suppressions>

archetype/pom.xml

@@ -0,0 +1,57 @@
+<!--
+This file is part of dependency-check-maven.
+
+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 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>org.owasp</groupId>
+        <artifactId>dependency-check-parent</artifactId>
+        <version>3.1.2-SNAPSHOT</version>
+    </parent>
+    <groupId>org.owasp</groupId>
+    <artifactId>dependency-check-plugin</artifactId>
+    <name>Dependency-Check Plugin Archetype</name>
+    <packaging>jar</packaging>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <configuration>
+                    <escapeString>\</escapeString>
+                </configuration>
+            </plugin>
+        </plugins>
+        <resources>
+            <resource>
+                <directory>src/main/resources</directory>
+                <filtering>true</filtering>
+                <includes>
+                    <include>archetype-resources/pom.xml</include>
+                </includes>
+            </resource>
+            <resource>
+                <directory>src/main/resources</directory>
+                <filtering>false</filtering>
+                <excludes>
+                    <exclude>archetype-resources/pom.xml</exclude>
+                </excludes>
+            </resource>
+        </resources>
+    </build>
+</project>

archetype/src/main/resources/META-INF/maven/archetype-metadata.xml

@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<archetype-descriptor name="dependency-check-plugin"
+    xsi:schemaLocation="http://maven.apache.org/plugins/maven-archetype-plugin/archetype-descriptor/1.0.0 http://maven.apache.org/xsd/archetype-descriptor-1.0.0.xsd" 
+    xmlns="http://maven.apache.org/plugins/maven-archetype-plugin/archetype-descriptor/1.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <requiredProperties>
+    <requiredProperty key="analyzerName">
+      <defaultValue>CustomAnalyzer</defaultValue>
+    </requiredProperty>
+  </requiredProperties>
+  <fileSets>
+    <fileSet filtered="true" packaged="true" encoding="UTF-8">
+      <directory>src/main/java</directory>
+      <includes>
+        <include>**/*.java</include>
+      </includes>
+    </fileSet>
+    <fileSet filtered="true" encoding="UTF-8">
+      <directory>src/main/resources</directory>
+      <includes>
+        <include>**/*</include>
+      </includes>
+    </fileSet>
+	<fileSet filtered="true" packaged="true" encoding="UTF-8">
+      <directory>src/test/java</directory>
+      <includes>
+        <include>**/*.java</include>
+      </includes>
+    </fileSet>
+    <fileSet filtered="true" encoding="UTF-8">
+      <directory>src/test/resources</directory>
+      <includes>
+        <include>**/*</include>
+      </includes>
+    </fileSet>
+  </fileSets>
+</archetype-descriptor>

archetype/src/main/resources/archetype-resources/pom.xml

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>\${groupId}</groupId>
+    <artifactId>\${artifactId}</artifactId>
+    <version>\${version}</version>
+    
+    <name>\${artifactId}</name>
+    <packaging>jar</packaging>
+    
+    <licenses>
+        <license>
+            <name>The Apache Software License, Version 2.0</name>
+            <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
+        </license>
+    </licenses>
+    
+    <dependencies>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-core</artifactId>
+            <version>${project.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+            <version>${slf4j.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>       
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+</project>

archetype/src/main/resources/archetype-resources/src/main/java/__analyzerName__.java

@@ -0,0 +1,155 @@
+/*
+ * 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.
+ */
+package ${package};
+
+import java.io.File;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.AnalysisPhase;
+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.exception.InitializationException;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * An OWASP dependency-check plug-in example. If you are not implementing a
+ * FileTypeAnalyzer, simple remove the annotation and the accept() method.
+ */
+public class ${analyzerName} implements Analyzer, FileTypeAnalyzer {
+
+    /**
+     * The Logger for use throughout the ${analyzerName}.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(${analyzerName}.class);
+
+    /**
+     * <p>
+     * Method implementation for the FileTypeAnalyzer; if not implementing a
+     * file type analyzer this method can be removed.</p>
+     * <p>
+     * Determines if the analyzer can process the given file.</p>
+     *
+     * @param pathname the path to the file
+     * @return <code>true</code> if the analyzer can process the file; otherwise
+     * <code>false</code>
+     */
+    @Override
+    public boolean accept(File pathname) {
+        return true;
+    }
+
+    /**
+     * 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
+     */
+    @Override
+    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+        if (enabled) {
+            //TODO implement analyze
+        }
+    }
+
+    /**
+     * Returns the name of the analyzer.
+     *
+     * @return the name of the analyzer.
+     */
+    @Override
+    public String getName() {
+        return "${analyzerName}";
+    }
+
+    /**
+     * 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 AnalysisPhase.INFORMATION_COLLECTION;
+    }
+
+    /**
+     * The initialize method is called just after instantiation of the object.
+     *
+     * @param settings a reference to the configured settings
+     */
+    @Override
+    public void initialize(Settings settings) {
+        //TODO implement initialize
+    }
+
+    /**
+     * The prepare method is called once just prior to repeated calls to
+     * analyze.
+     *
+     * @param engine a reference to the engine
+     * @throws InitializationException thrown when the analyzer cannot be
+     * initialized
+     */
+    @Override
+    public void prepare(Engine engine) throws InitializationException {
+        //TODO implement prepare
+    }
+
+    /**
+     * The close method is called after all of the dependencies have been
+     * analyzed.
+     *
+     * @throws Exception is thrown if an exception occurs closing the analyzer.
+     */
+    @Override
+    public void close() throws Exception {
+
+    }
+
+    /**
+     * Returns whether multiple instances of the same type of analyzer can run
+     * in parallel. If the analyzer does not support parallel processing it is
+     * generally best to also mark the analyze(Dependency,Engine) as synchronized.
+     *
+     * @return {@code true} if the analyzer supports parallel processing,
+     * {@code false} else
+     */
+    @Override
+    public boolean supportsParallelProcessing() {
+        return true;
+    }
+
+    /**
+     * Flag indicating whether or not the analyzer is enabled.
+     */
+    private boolean enabled = true;
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return whether or not the analyzer is enabled
+     */
+    @Override
+    public boolean isEnabled() {
+        return enabled;
+    }
+}

archetype/src/main/resources/archetype-resources/src/main/resources/META-INF/services/org.owasp.dependencycheck.analyzer.Analyzer

@@ -0,0 +1 @@
+${package}.${analyzerName}

archetype/src/main/resources/archetype-resources/src/test/java/__analyzerName__Test.java

@@ -0,0 +1,147 @@
+/*
+ * 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.
+ */
+package ${package};
+
+import java.io.File;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import static org.junit.Assert.*;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.AnalysisPhase;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * Test cases for ${analyzerName}
+ */
+public class ${analyzerName}Test {
+    
+    Settings settings = null;
+	
+    public ${analyzerName}Test() {
+    }
+    
+    @BeforeClass
+    public static void setUpClass() {
+    }
+    
+    @AfterClass
+    public static void tearDownClass() {
+    }
+    
+    @Before
+    public void setUp() {
+        settings = new Settings();
+    }
+
+    @After
+    public void tearDown() {
+        settings.cleanup();
+    }
+
+    /**
+     * Test of accept method, of class ${analyzerName}.
+     */
+    @Test
+    public void testAccept() {
+        File pathname = new File("test.file");
+        ${analyzerName} instance = new ${analyzerName}();
+        boolean expResult = true;
+        boolean result = instance.accept(pathname);
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of analyze method, of class ${analyzerName}.
+     */
+    @Test
+    public void testAnalyze() throws Exception {
+        //The engine is generally null for most analyzer test cases but can be instantiated if needed.
+        Engine engine = null;
+        ${analyzerName} instance = new ${analyzerName}();
+        instance.initialize(settings);
+        instance.prepare(engine);
+		
+        File file = new File(${analyzerName}.class.getClassLoader().getResource("test.file").toURI().getPath());
+        Dependency dependency = new Dependency(file);
+
+        //TODO uncomment the following line and add assertions against the dependency.
+        //instance.analyze(dependency, engine);
+    }
+
+    /**
+     * Test of getName method, of class ${analyzerName}.
+     */
+    @Test
+    public void testGetName() {
+        ${analyzerName} instance = new ${analyzerName}();
+        String expResult = "${analyzerName}";
+        String result = instance.getName();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of getAnalysisPhase method, of class ${analyzerName}.
+     */
+    @Test
+    public void testGetAnalysisPhase() {
+        ${analyzerName} instance = new ${analyzerName}();
+        AnalysisPhase expResult = AnalysisPhase.INFORMATION_COLLECTION;
+        AnalysisPhase result = instance.getAnalysisPhase();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of initialize method, of class ${analyzerName}.
+     */
+    @Test
+    public void testInitialize() throws Exception {
+        ${analyzerName} instance = new ${analyzerName}();
+        instance.initialize(settings);
+    }
+
+    /**
+     * Test of close method, of class ${analyzerName}.
+     */
+    @Test
+    public void testClose() throws Exception {
+        ${analyzerName} instance = new ${analyzerName}();
+        instance.close();
+    }
+
+    /**
+     * Test of supportsParallelProcessing method, of class ${analyzerName}.
+     */
+    @Test
+    public void testSupportsParallelProcessing() {
+        ${analyzerName} instance = new ${analyzerName}();
+        boolean expResult = true;
+        boolean result = instance.supportsParallelProcessing();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of isEnabled method, of class ${analyzerName}.
+     */
+    @Test
+    public void testIsEnabled() {
+        ${analyzerName} instance = new ${analyzerName}();
+        boolean expResult = true;
+        boolean result = instance.isEnabled();
+        assertEquals(expResult, result);
+    }
+}

archetype/src/site/markdown/index.md.vm

@@ -0,0 +1,10 @@
+About
+=====
+OWASP dependency-check-plugin is a maven archetype for generating a maven project for
+a dependency-check plugin (i.e. a project containing one or more analyzers).
+
+Usage
+=====
+```bash
+mvn archetype:generate -DarchetypeGroupId=org.owasp -DarchetypeArtifactId=dependency-check-plugin -DarchetypeVersion=${project.version}
+```

archetype/src/site/site.xml

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!--
+This file is part of dependency-check-plugin.
+
+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 name="dependency-check-plugin">
+	<bannerLeft>
+        <name>OWASP dependency-check-plugin</name>
+        <alt>OWASP dependency-check-plugin</alt>
+        <src>/images/dc.svg</src>
+    </bannerLeft>
+    <body>
+        <breadcrumbs>
+            <item name="dependency-check" href="../index.html"/>
+        </breadcrumbs>
+        <menu name="Getting Started">
+            <item name="Usage" href="index.html"/>
+        </menu>
+		<menu ref="reports"/>
+    </body>
+</project>

build-reporting/pom.xml

@@ -0,0 +1,114 @@
+<!--
+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>3.1.2-SNAPSHOT</version>
+    </parent>
+    <name>Dependency-Check Build-Reporting</name>
+    <artifactId>build-reporting</artifactId>
+    <packaging>pom</packaging>
+    <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>${project.version}</version>
+        </dependency>
+    </dependencies>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-deploy-plugin</artifactId>
+                <configuration>
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-enforcer-plugin</artifactId>
+                <configuration>
+                    <skip>true</skip>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>report-merge</id>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>merge</goal>
+                        </goals>
+                        <configuration>
+                            <fileSets>
+                                <fileSet implementation="org.apache.maven.shared.model.fileset.FileSet">
+                                    <directory>${project.basedir}/../</directory>
+                                    <includes>
+                                        <include>utils/target/coverage-reports/*.exec</include>
+                                        <include>core/target/coverage-reports/*.exec</include>
+                                        <include>cli/target/coverage-reports/*.exec</include>
+                                        <include>ant/target/coverage-reports/*.exec</include>
+                                        <include>maven/target/coverage-reports/*.exec</include>
+                                    </includes>
+                                </fileSet>
+                            </fileSets>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>report-aggregate</id>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>report-aggregate</goal>
+                        </goals>
+                        <configuration>
+                            <outputDirectory>target/coverage-reports/</outputDirectory>
+                            <dataFileIncludes>
+                                <dataFileInclude>target/coverage-reports/jacoco-ut.exec</dataFileInclude>
+                                <dataFileInclude>target/coverage-reports/jacoco-it.exec</dataFileInclude>
+                            </dataFileIncludes>
+                        </configuration>
+                    </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

@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!--
+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 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>

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>1.4.4</version>
+        <version>3.1.2-SNAPSHOT</version>
     </parent>
 
     <artifactId>dependency-check-cli</artifactId>
@@ -28,15 +28,6 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
 
     <name>Dependency-Check Command Line</name>
     <description>dependency-check-cli is an command line tool that uses dependency-check-core to detect publicly disclosed vulnerabilities associated with the scanned project dependencies. The tool will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.</description>
-    <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
-    <distributionManagement>
-        <site>
-            <id>github-pages-site</id>
-            <name>Deployment through GitHub's site deployment plugin</name>
-            <url>${basedir}/../target/site/${project.version}/dependency-check-cli</url>
-        </site>
-    </distributionManagement>
-    <!-- end copy -->
     <build>
         <finalName>dependency-check-${project.version}</finalName>
         <resources>
@@ -69,62 +60,6 @@ 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>
-                    <argLine>-Dfile.encoding=UTF-8</argLine>
-                    <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>
@@ -140,6 +75,8 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                     <binFileExtensions>
                         <unix>.sh</unix>
                     </binFileExtensions>
+                    <configurationDirectory>plugins/*</configurationDirectory>
+                    <includeConfigurationDirectoryInClasspath>true</includeConfigurationDirectoryInClasspath>
                 </configuration>
                 <executions>
                     <execution>
@@ -173,42 +110,6 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
             </plugin>
         </plugins>
     </build>
-    <reporting>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-checkstyle-plugin</artifactId>
-                <version>${reporting.checkstyle-plugin.version}</version>
-                <configuration>
-                    <enableRulesSummary>false</enableRulesSummary>
-                    <enableFilesSummary>false</enableFilesSummary>
-                    <configLocation>${basedir}/../src/main/config/checkstyle-checks.xml</configLocation>
-                    <headerLocation>${basedir}/../src/main/config/checkstyle-header.txt</headerLocation>
-                    <suppressionsLocation>${basedir}/../src/main/config/checkstyle-suppressions.xml</suppressionsLocation>
-                    <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-pmd-plugin</artifactId>
-                <version>${reporting.pmd-plugin.version}</version>
-                <configuration>
-                    <targetJdk>1.6</targetJdk>
-                    <linkXref>true</linkXref>
-                    <sourceEncoding>utf-8</sourceEncoding>
-                    <excludes>
-                        <exclude>**/generated/*.java</exclude>
-                    </excludes>
-                    <rulesets>
-                        <ruleset>../src/main/config/dcrules.xml</ruleset>
-                        <ruleset>/rulesets/java/basic.xml</ruleset>
-                        <ruleset>/rulesets/java/imports.xml</ruleset>
-                        <ruleset>/rulesets/java/unusedcode.xml</ruleset>
-                    </rulesets>
-                </configuration>
-            </plugin>
-        </plugins>
-    </reporting>
     <dependencies>
         <dependency>
             <groupId>commons-cli</groupId>

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>

cli/src/main/java/org/owasp/dependencycheck/App.java

@@ -28,12 +28,10 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import org.apache.commons.cli.ParseException;
-import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
-import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.apache.tools.ant.DirectoryScanner;
-import org.owasp.dependencycheck.reporting.ReportGenerator;
+import org.owasp.dependencycheck.dependency.Vulnerability;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -55,6 +53,10 @@ public class App {
      * The logger.
      */
     private static final Logger LOGGER = LoggerFactory.getLogger(App.class);
+    /**
+     * The configured settings.
+     */
+    private Settings settings = null;
 
     /**
      * The main method for the application.
@@ -63,17 +65,28 @@ public class App {
      */
     public static void main(String[] args) {
         int exitCode = 0;
-        try {
-            Settings.initialize();
-            final App app = new App();
-            exitCode = app.run(args);
-            LOGGER.debug("Exit code: " + exitCode);
-        } finally {
-            Settings.cleanup(true);
-        }
+        final App app = new App();
+        exitCode = app.run(args);
+        LOGGER.debug("Exit code: {}", exitCode);
         System.exit(exitCode);
     }
 
+    /**
+     * Builds the App object.
+     */
+    public App() {
+        settings = new Settings();
+    }
+
+    /**
+     * Builds the App object; this method is used for testing.
+     *
+     * @param settings the configured settings
+     */
+    protected App(Settings settings) {
+        this.settings = settings;
+    }
+
     /**
      * Main CLI entry-point into the application.
      *
@@ -82,7 +95,7 @@ public class App {
      */
     public int run(String[] args) {
         int exitCode = 0;
-        final CliParser cli = new CliParser();
+        final CliParser cli = new CliParser(settings);
 
         try {
             cli.parse(args);
@@ -111,10 +124,11 @@ public class App {
                     LOGGER.error(ex.getMessage());
                     LOGGER.debug("Error loading properties file", ex);
                     exitCode = -4;
+                    return exitCode;
                 }
                 File db;
                 try {
-                    db = new File(Settings.getDataDirectory(), "dc.h2.db");
+                    db = new File(settings.getDataDirectory(), settings.getString(Settings.KEYS.DB_FILE_NAME, "dc.h2.db"));
                     if (db.exists()) {
                         if (db.delete()) {
                             LOGGER.info("Database file purged; local copy of the NVD has been removed");
@@ -123,12 +137,14 @@ public class App {
                             exitCode = -5;
                         }
                     } else {
-                        LOGGER.error("Unable to purge database; the database file does not exists: {}", db.getAbsolutePath());
+                        LOGGER.error("Unable to purge database; the database file does not exist: {}", db.getAbsolutePath());
                         exitCode = -6;
                     }
                 } catch (IOException ex) {
                     LOGGER.error("Unable to delete the database");
                     exitCode = -7;
+                } finally {
+                    settings.cleanup();
                 }
             }
         } else if (cli.isGetVersion()) {
@@ -140,6 +156,7 @@ public class App {
                 LOGGER.error(ex.getMessage());
                 LOGGER.debug("Error loading properties file", ex);
                 exitCode = -4;
+                return exitCode;
             }
             try {
                 runUpdateOnly();
@@ -149,6 +166,8 @@ public class App {
             } catch (DatabaseException ex) {
                 LOGGER.error(ex.getMessage());
                 exitCode = -9;
+            } finally {
+                settings.cleanup();
             }
         } else if (cli.isRunScan()) {
             try {
@@ -157,12 +176,13 @@ public class App {
                 LOGGER.error(ex.getMessage());
                 LOGGER.debug("Error loading properties file", ex);
                 exitCode = -4;
+                return exitCode;
             }
             try {
                 final String[] scanFiles = cli.getScanFiles();
                 if (scanFiles != null) {
-                    runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getProjectName(), scanFiles,
-                            cli.getExcludeList(), cli.getSymLinkDepth());
+                    exitCode = runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getProjectName(), scanFiles,
+                            cli.getExcludeList(), cli.getSymLinkDepth(), cli.getFailOnCVSS());
                 } else {
                     LOGGER.error("No scan files configured");
                 }
@@ -183,8 +203,12 @@ public class App {
                     exitCode = -14;
                 }
                 for (Throwable e : ex.getExceptions()) {
-                    LOGGER.error(e.getMessage());
+                    if (e.getMessage() != null) {
+                        LOGGER.error(e.getMessage());
+                    }
                 }
+            } finally {
+                settings.cleanup();
             }
         } else {
             cli.printHelp();
@@ -203,6 +227,8 @@ public class App {
      * @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
      * "//"
@@ -213,58 +239,15 @@ public class App {
      * 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, DatabaseException, ExceptionCollection, ReportException {
+    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;
         try {
-            engine = new Engine();
-            final List<String> antStylePaths = new ArrayList<String>();
-            for (String file : files) {
-                final String antPath = ensureCanonicalPath(file);
-                antStylePaths.add(antPath);
-            }
+            final List<String> antStylePaths = getPaths(files);
+            final Set<File> paths = scanAntStylePaths(antStylePaths, symLinkDepth, excludes);
 
-            final Set<File> paths = new HashSet<File>();
-            for (String file : antStylePaths) {
-                LOGGER.debug("Scanning {}", file);
-                final DirectoryScanner scanner = new DirectoryScanner();
-                String include = file.replace('\\', '/');
-                File baseDir;
-
-                if (include.startsWith("//")) {
-                    throw new InvalidScanPathException("Unable to scan paths specified by //");
-                } else {
-                    final int pos = getLastFileSeparator(include);
-                    final String tmpBase = include.substring(0, pos);
-                    final String tmpInclude = include.substring(pos + 1);
-                    if (tmpInclude.indexOf('*') >= 0 || tmpInclude.indexOf('?') >= 0
-                            || (new File(include)).isFile()) {
-                        baseDir = new File(tmpBase);
-                        include = tmpInclude;
-                    } else {
-                        baseDir = new File(tmpBase, tmpInclude);
-                        include = "**/*";
-                    }
-                }
-                scanner.setBasedir(baseDir);
-                final String[] includes = {include};
-                scanner.setIncludes(includes);
-                scanner.setMaxLevelsOfSymlinks(symLinkDepth);
-                if (symLinkDepth <= 0) {
-                    scanner.setFollowSymlinks(false);
-                }
-                if (excludes != null && excludes.length > 0) {
-                    scanner.addExcludes(excludes);
-                }
-                scanner.scan();
-                if (scanner.getIncludedFilesCount() > 0) {
-                    for (String s : scanner.getIncludedFiles()) {
-                        final File f = new File(baseDir, s);
-                        LOGGER.debug("Found file {}", f.toString());
-                        paths.add(f);
-                    }
-                }
-            }
+            engine = new Engine(settings);
             engine.scan(paths);
 
             ExceptionCollection exCol = null;
@@ -276,21 +259,9 @@ public class App {
                 }
                 exCol = ex;
             }
-            final List<Dependency> dependencies = engine.getDependencies();
-            DatabaseProperties prop = null;
-            CveDB cve = null;
+
             try {
-                cve = new CveDB();
-                cve.open();
-                prop = cve.getDatabaseProperties();
-            } finally {
-                if (cve != null) {
-                    cve.close();
-                }
-            }
-            final ReportGenerator report = new ReportGenerator(applicationName, dependencies, engine.getAnalyzers(), prop);
-            try {
-                report.generateReports(reportDirectory, outputFormat);
+                engine.writeReports(applicationName, new File(reportDirectory), outputFormat);
             } catch (ReportException ex) {
                 if (exCol != null) {
                     exCol.addException(ex);
@@ -299,15 +270,110 @@ public class App {
                     throw ex;
                 }
             }
-            if (exCol != null && exCol.getExceptions().size() > 0) {
+            if (exCol != null && !exCol.getExceptions().isEmpty()) {
                 throw exCol;
             }
+            return determineReturnCode(engine, cvssFailScore);
         } finally {
             if (engine != null) {
-                engine.cleanup();
+                engine.close();
             }
         }
+    }
 
+    /**
+     * Determines the return code based on if one of the dependencies scanned
+     * has a vulnerability with a CVSS score above the cvssFailScore.
+     *
+     * @param engine the engine used during analysis
+     * @param cvssFailScore the max allowed CVSS score
+     * @return returns <code>1</code> if a severe enough vulnerability is
+     * identified; otherwise <code>0</code>
+     */
+    private int determineReturnCode(Engine engine, int cvssFailScore) {
+        int retCode = 0;
+        //Set the exit code based on whether we found a high enough vulnerability
+        for (Dependency dep : engine.getDependencies()) {
+            if (!dep.getVulnerabilities().isEmpty()) {
+                for (Vulnerability vuln : dep.getVulnerabilities()) {
+                    LOGGER.debug("VULNERABILITY FOUND {}", dep.getDisplayFileName());
+                    if (vuln.getCvssScore() > cvssFailScore) {
+                        retCode = 1;
+                    }
+                }
+            }
+        }
+        return retCode;
+    }
+
+    /**
+     * Scans the give Ant Style paths and collects the actual files.
+     *
+     * @param antStylePaths a list of ant style paths to scan for actual files
+     * @param symLinkDepth the depth to traverse symbolic links
+     * @param excludes an array of ant style excludes
+     * @return returns the set of identified files
+     * @throws InvalidScanPathException thrown when the scan path is invalid
+     */
+    private Set<File> scanAntStylePaths(List<String> antStylePaths, int symLinkDepth, String[] excludes)
+            throws InvalidScanPathException {
+        final Set<File> paths = new HashSet<>();
+        for (String file : antStylePaths) {
+            LOGGER.debug("Scanning {}", file);
+            final DirectoryScanner scanner = new DirectoryScanner();
+            String include = file.replace('\\', '/');
+            File baseDir;
+
+            if (include.startsWith("//")) {
+                throw new InvalidScanPathException("Unable to scan paths specified by //");
+            } else {
+                final int pos = getLastFileSeparator(include);
+                final String tmpBase = include.substring(0, pos);
+                final String tmpInclude = include.substring(pos + 1);
+                if (tmpInclude.indexOf('*') >= 0 || tmpInclude.indexOf('?') >= 0
+                        || (new File(include)).isFile()) {
+                    baseDir = new File(tmpBase);
+                    include = tmpInclude;
+                } else {
+                    baseDir = new File(tmpBase, tmpInclude);
+                    include = "**/*";
+                }
+            }
+            scanner.setBasedir(baseDir);
+            final String[] includes = {include};
+            scanner.setIncludes(includes);
+            scanner.setMaxLevelsOfSymlinks(symLinkDepth);
+            if (symLinkDepth <= 0) {
+                scanner.setFollowSymlinks(false);
+            }
+            if (excludes != null && excludes.length > 0) {
+                scanner.addExcludes(excludes);
+            }
+            scanner.scan();
+            if (scanner.getIncludedFilesCount() > 0) {
+                for (String s : scanner.getIncludedFiles()) {
+                    final File f = new File(baseDir, s);
+                    LOGGER.debug("Found file {}", f.toString());
+                    paths.add(f);
+                }
+            }
+        }
+        return paths;
+    }
+
+    /**
+     * Determines the ant style paths from the given array of files.
+     *
+     * @param files an array of file paths
+     * @return a list containing ant style paths
+     */
+    private List<String> getPaths(String[] files) {
+        final List<String> antStylePaths = new ArrayList<>();
+        for (String file : files) {
+            final String antPath = ensureCanonicalPath(file);
+            antStylePaths.add(antPath);
+        }
+        return antStylePaths;
     }
 
     /**
@@ -318,14 +384,8 @@ public class App {
      * connection to the database could not be established
      */
     private void runUpdateOnly() throws UpdateException, DatabaseException {
-        Engine engine = null;
-        try {
-            engine = new Engine();
+        try (Engine engine = new Engine(settings)) {
             engine.doUpdates();
-        } finally {
-            if (engine != null) {
-                engine.cleanup();
-            }
         }
     }
 
@@ -338,8 +398,7 @@ public class App {
      * @throws InvalidSettingException thrown when a user defined properties
      * file is unable to be loaded.
      */
-    private void populateSettings(CliParser cli) throws InvalidSettingException {
-        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();
@@ -347,7 +406,7 @@ public class App {
         final String proxyPass = cli.getProxyPassword();
         final String dataDirectory = cli.getDataDirectory();
         final File propertiesFile = cli.getPropertiesFile();
-        final String suppressionFile = cli.getSuppressionFile();
+        final String[] suppressionFiles = cli.getSuppressionFiles();
         final String hintsFile = cli.getHintsFile();
         final String nexusUrl = cli.getNexusUrl();
         final String databaseDriverName = cli.getDatabaseDriverName();
@@ -362,11 +421,13 @@ public class App {
         final String cveBase12 = cli.getBaseCve12Url();
         final String cveBase20 = cli.getBaseCve20Url();
         final Integer cveValidForHours = cli.getCveValidForHours();
-        final boolean experimentalEnabled = cli.isExperimentalEnabled();
+        final Boolean autoUpdate = cli.isAutoUpdate();
+        final Boolean experimentalEnabled = cli.isExperimentalEnabled();
+        final Boolean retiredEnabled = cli.isRetiredEnabled();
 
         if (propertiesFile != null) {
             try {
-                Settings.mergeProperties(propertiesFile);
+                settings.mergeProperties(propertiesFile);
             } catch (FileNotFoundException ex) {
                 throw new InvalidSettingException("Unable to find properties file '" + propertiesFile.getPath() + "'", ex);
             } catch (IOException ex) {
@@ -375,63 +436,69 @@ public class App {
         }
         // 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);
+            settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
         } else if (System.getProperty("basedir") != null) {
             final File dataDir = new File(System.getProperty("basedir"), "data");
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
+            settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
         } else {
             final File jarPath = new File(App.class.getProtectionDomain().getCodeSource().getLocation().getPath());
             final File base = jarPath.getParentFile();
-            final String sub = Settings.getString(Settings.KEYS.DATA_DIRECTORY);
+            final String sub = settings.getString(Settings.KEYS.DATA_DIRECTORY);
             final File dataDir = new File(base, sub);
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
+            settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
         }
-        Settings.setBoolean(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);
+        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.HINTS_FILE, hintsFile);
+        settings.setIntIfNotNull(Settings.KEYS.CVE_CHECK_VALID_FOR_HOURS, cveValidForHours);
+
+        settings.setArrayIfNotEmpty(Settings.KEYS.SUPPRESSION_FILE, suppressionFiles);
 
         //File Type Analyzer Settings
-        Settings.setBoolean(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());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED, !cli.isPythonPackageDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_AUTOCONF_ENABLED, !cli.isAutoconfDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_CMAKE_ENABLED, !cli.isCmakeDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, !cli.isNuspecDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, !cli.isAssemblyDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_ENABLED, !cli.isBundleAuditDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_OPENSSL_ENABLED, !cli.isOpenSSLDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED, !cli.isComposerDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED, !cli.isNodeJsDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED, !cli.isRubyGemspecDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, !cli.isCentralDisabled());
-        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, !cli.isNexusDisabled());
+        settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, experimentalEnabled);
+        settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_RETIRED_ENABLED, retiredEnabled);
 
-        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);
+        settings.setBoolean(Settings.KEYS.ANALYZER_JAR_ENABLED, !cli.isJarDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, !cli.isArchiveDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED, !cli.isPythonDistributionDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED, !cli.isPythonPackageDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_AUTOCONF_ENABLED, !cli.isAutoconfDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_CMAKE_ENABLED, !cli.isCmakeDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, !cli.isNuspecDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, !cli.isAssemblyDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_ENABLED, !cli.isBundleAuditDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_OPENSSL_ENABLED, !cli.isOpenSSLDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED, !cli.isComposerDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED, !cli.isNodeJsDisabled());
+        settings.setBoolean(Settings.KEYS.ANALYZER_NSP_PACKAGE_ENABLED, !cli.isNspDisabled());
+        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());
+
+        settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_BUNDLE_AUDIT_PATH, cli.getPathToBundleAudit());
+        settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
+        settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY, nexusUsesProxy);
+        settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
+        settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
+        settings.setStringIfNotEmpty(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
+        settings.setStringIfNotEmpty(Settings.KEYS.DB_USER, databaseUser);
+        settings.setStringIfNotEmpty(Settings.KEYS.DB_PASSWORD, databasePassword);
+        settings.setStringIfNotEmpty(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, additionalZipExtensions);
+        settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
         if (cveBase12 != null && !cveBase12.isEmpty()) {
-            Settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, cveBase12);
-            Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveBase20);
-            Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveMod12);
-            Settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, cveMod20);
+            settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, cveBase12);
+            settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveBase20);
+            settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveMod12);
+            settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, cveMod20);
         }
     }
 
@@ -448,7 +515,7 @@ public class App {
         encoder.setPattern("%d %C:%L%n%-5level - %msg%n");
         encoder.setContext(context);
         encoder.start();
-        final FileAppender<ILoggingEvent> fa = new FileAppender<ILoggingEvent>();
+        final FileAppender<ILoggingEvent> fa = new FileAppender<>();
         fa.setAppend(true);
         fa.setEncoder(encoder);
         fa.setContext(context);

cli/src/main/java/org/owasp/dependencycheck/CliParser.java

@@ -53,6 +53,19 @@ public final class CliParser {
      * Indicates whether the arguments are valid.
      */
     private boolean isValid = true;
+    /**
+     * The configured settings.
+     */
+    private final Settings settings;
+
+    /**
+     * Constructs a new CLI Parser object with the configured settings.
+     *
+     * @param settings the configured settings
+     */
+    public CliParser(Settings settings) {
+        this.settings = settings;
+    }
 
     /**
      * Parses the arguments passed in and captures the results for later use.
@@ -120,7 +133,7 @@ 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);
                 }
             }
@@ -192,14 +205,13 @@ public final class CliParser {
                 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.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; "
+            LOGGER.warn("Possibly incorrect path '{}' from argument '{}' because it ends with a slash star; "
                     + "dependency-check uses ant-style paths", path, argumentName);
-            LOGGER.warn(msg);
         }
     }
 
@@ -222,10 +234,9 @@ public final class CliParser {
      * Adds the standard command line options to the given options collection.
      *
      * @param options a collection of command line arguments
-     * @throws IllegalArgumentException thrown if there is an exception
      */
     @SuppressWarnings("static-access")
-    private void addStandardOptions(final Options options) throws IllegalArgumentException {
+    private void addStandardOptions(final Options options) {
         final Option help = new Option(ARGUMENT.HELP_SHORT, ARGUMENT.HELP, false,
                 "Print this message.");
 
@@ -249,7 +260,7 @@ 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)
@@ -262,7 +273,7 @@ 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)
@@ -273,8 +284,9 @@ public final class CliParser {
                 .desc("Sets how deep nested symbolic links will be followed; 0 indicates symbolic links will not be followed.")
                 .build();
 
-        final Option suppressionFile = Option.builder().argName("file").hasArg().longOpt(ARGUMENT.SUPPRESSION_FILE)
-                .desc("The file path to the suppression XML file.")
+        final Option suppressionFile = Option.builder().argName("file").hasArgs().longOpt(ARGUMENT.SUPPRESSION_FILES)
+                .desc("The file path to the suppression XML file. This can be specified more then once to utilize multiple "
+                        + "suppression files")
                 .build();
 
         final Option hintsFile = Option.builder().argName("file").hasArg().longOpt(ARGUMENT.HINTS_FILE)
@@ -286,7 +298,16 @@ public final class CliParser {
                 .build();
 
         final Option experimentalEnabled = Option.builder().longOpt(ARGUMENT.EXPERIMENTAL)
-                .desc("Enables the experimental analzers.")
+                .desc("Enables the experimental analyzers.")
+                .build();
+
+        final Option retiredEnabled = Option.builder().longOpt(ARGUMENT.RETIRED)
+                .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.
@@ -311,7 +332,9 @@ public final class CliParser {
                 .addOption(suppressionFile)
                 .addOption(hintsFile)
                 .addOption(cveValidForHours)
-                .addOption(experimentalEnabled);
+                .addOption(experimentalEnabled)
+                .addOption(retiredEnabled)
+                .addOption(failOnCVSS);
     }
 
     /**
@@ -320,10 +343,9 @@ public final class CliParser {
      * help messages.
      *
      * @param options a collection of command line arguments
-     * @throws IllegalArgumentException thrown if there is an exception
      */
     @SuppressWarnings("static-access")
-    private void addAdvancedOptions(final Options options) throws IllegalArgumentException {
+    private void addAdvancedOptions(final Options options) {
 
         final Option cve12Base = Option.builder().argName("url").hasArg().longOpt(ARGUMENT.CVE_BASE_12)
                 .desc("Base URL for each year’s CVE 1.2, the %d will be replaced with the year. ")
@@ -431,6 +453,11 @@ 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();
@@ -475,8 +502,12 @@ public final class CliParser {
                 .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(Option.builder().longOpt(ARGUMENT.DISABLE_NSP)
+                        .desc("Disable the NSP Package Analyzer.").build())
                 .addOption(nexusUrl)
                 .addOption(nexusUsesProxy)
                 .addOption(additionalZipExtensions)
@@ -492,10 +523,9 @@ public final class CliParser {
      * existing scripts.
      *
      * @param options a collection of command line arguments
-     * @throws IllegalArgumentException thrown if there is an exception
      */
     @SuppressWarnings({"static-access", "deprecation"})
-    private void addDeprecatedOptions(final Options options) throws IllegalArgumentException {
+    private void addDeprecatedOptions(final Options options) {
 
         final Option proxyServer = Option.builder().argName("url").hasArg().longOpt(ARGUMENT.PROXY_URL)
                 .desc("The proxy url argument is deprecated, use proxyserver instead.")
@@ -554,6 +584,32 @@ 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.
      *
@@ -561,7 +617,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isJarDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_JAR);
+        return hasDisableOption(ARGUMENT.DISABLE_JAR, Settings.KEYS.ANALYZER_JAR_ENABLED);
     }
 
     /**
@@ -571,7 +627,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isArchiveDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_ARCHIVE);
+        return hasDisableOption(ARGUMENT.DISABLE_ARCHIVE, Settings.KEYS.ANALYZER_ARCHIVE_ENABLED);
     }
 
     /**
@@ -581,7 +637,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isNuspecDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_NUSPEC);
+        return hasDisableOption(ARGUMENT.DISABLE_NUSPEC, Settings.KEYS.ANALYZER_NUSPEC_ENABLED);
     }
 
     /**
@@ -591,7 +647,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isAssemblyDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_ASSEMBLY);
+        return hasDisableOption(ARGUMENT.DISABLE_ASSEMBLY, Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED);
     }
 
     /**
@@ -602,7 +658,7 @@ public final class CliParser {
      * specified; otherwise false
      */
     public boolean isBundleAuditDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_BUNDLE_AUDIT);
+        return hasDisableOption(ARGUMENT.DISABLE_BUNDLE_AUDIT, Settings.KEYS.ANALYZER_BUNDLE_AUDIT_ENABLED);
     }
 
     /**
@@ -612,7 +668,7 @@ public final class CliParser {
      * 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);
     }
 
     /**
@@ -622,7 +678,7 @@ public final class CliParser {
      * 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);
     }
 
     /**
@@ -632,7 +688,7 @@ public final class CliParser {
      * 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);
     }
 
     /**
@@ -642,7 +698,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isCmakeDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_CMAKE);
+        return hasDisableOption(ARGUMENT.DISABLE_CMAKE, Settings.KEYS.ANALYZER_CMAKE_ENABLED);
     }
 
     /**
@@ -652,7 +708,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isAutoconfDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_AUTOCONF);
+        return hasDisableOption(ARGUMENT.DISABLE_AUTOCONF, Settings.KEYS.ANALYZER_AUTOCONF_ENABLED);
     }
 
     /**
@@ -662,7 +718,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isComposerDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_COMPOSER);
+        return hasDisableOption(ARGUMENT.DISABLE_COMPOSER, Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED);
     }
 
     /**
@@ -672,7 +728,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isNexusDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_NEXUS);
+        return hasDisableOption(ARGUMENT.DISABLE_NEXUS, Settings.KEYS.ANALYZER_NEXUS_ENABLED);
     }
 
     /**
@@ -682,7 +738,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isOpenSSLDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_OPENSSL);
+        return hasDisableOption(ARGUMENT.DISABLE_OPENSSL, Settings.KEYS.ANALYZER_OPENSSL_ENABLED);
     }
 
     /**
@@ -692,7 +748,39 @@ public final class CliParser {
      * 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 disableNSP command line argument was specified.
+     *
+     * @return true if the disableNSP command line argument was specified;
+     * otherwise false
+     */
+    public boolean isNspDisabled() {
+        return hasDisableOption(ARGUMENT.DISABLE_NSP, Settings.KEYS.ANALYZER_NSP_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);
     }
 
     /**
@@ -702,7 +790,7 @@ public final class CliParser {
      * otherwise false
      */
     public boolean isCentralDisabled() {
-        return (line != null) && line.hasOption(ARGUMENT.DISABLE_CENTRAL);
+        return hasDisableOption(ARGUMENT.DISABLE_CENTRAL, Settings.KEYS.ANALYZER_CENTRAL_ENABLED);
     }
 
     /**
@@ -731,7 +819,7 @@ public final class CliParser {
         // 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_USES_PROXY);
+                return settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY);
             } catch (InvalidSettingException ise) {
                 return true;
             }
@@ -753,10 +841,10 @@ public final class CliParser {
         final String helpMsg = String.format("%n%s"
                 + " can be used to identify if there are any known CVE vulnerabilities in libraries utilized by an application. "
                 + "%s will automatically update required data from the Internet, such as the CVE and CPE data files from nvd.nist.gov.%n%n",
-                Settings.getString("application.name", "DependencyCheck"),
-                Settings.getString("application.name", "DependencyCheck"));
+                settings.getString("application.name", "DependencyCheck"),
+                settings.getString("application.name", "DependencyCheck"));
 
-        formatter.printHelp(Settings.getString("application.name", "DependencyCheck"),
+        formatter.printHelp(settings.getString("application.name", "DependencyCheck"),
                 helpMsg,
                 options,
                 "",
@@ -832,7 +920,7 @@ public final class CliParser {
         String name = line.getOptionValue(ARGUMENT.PROJECT);
         if (name == null && appName != null) {
             name = appName;
-            LOGGER.warn("The '" + ARGUMENT.APP_NAME + "' argument should no longer be used; use '" + ARGUMENT.PROJECT + "' instead.");
+            LOGGER.warn("The '{}' argument should no longer be used; use '{}' instead.", ARGUMENT.APP_NAME, ARGUMENT.PROJECT);
         }
         return name;
     }
@@ -959,12 +1047,12 @@ public final class CliParser {
     }
 
     /**
-     * Returns the path to the suppression file.
+     * Returns the paths to the suppression files.
      *
-     * @return the path to the suppression file
+     * @return the paths to the suppression files.
      */
-    public String getSuppressionFile() {
-        return line.getOptionValue(ARGUMENT.SUPPRESSION_FILE);
+    public String[] getSuppressionFiles() {
+        return line.getOptionValues(ARGUMENT.SUPPRESSION_FILES);
     }
 
     /**
@@ -984,8 +1072,8 @@ public final class CliParser {
      */
     public void printVersionInfo() {
         final String version = String.format("%s version %s",
-                Settings.getString(Settings.KEYS.APPLICATION_NAME, "dependency-check"),
-                Settings.getString(Settings.KEYS.APPLICATION_VERSION, "Unknown"));
+                settings.getString(Settings.KEYS.APPLICATION_NAME, "dependency-check"),
+                settings.getString(Settings.KEYS.APPLICATION_VERSION, "Unknown"));
         System.out.println(version);
     }
 
@@ -994,10 +1082,10 @@ public final class CliParser {
      * disabled via the command line this will return false.
      *
      * @return <code>true</code> if auto-update is allowed; otherwise
-     * <code>false</code>
+     * <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;
     }
 
     /**
@@ -1099,10 +1187,38 @@ public final class CliParser {
     /**
      * Returns true if the experimental analyzers are enabled.
      *
-     * @return true if the experimental analyzers are enabled; otherwise false
+     * @return true if the experimental analyzers are enabled; otherwise null
      */
-    public boolean isExperimentalEnabled() {
-        return line.hasOption(ARGUMENT.EXPERIMENTAL);
+    public Boolean isExperimentalEnabled() {
+        return (line != null && line.hasOption(ARGUMENT.EXPERIMENTAL)) ? true : null;
+    }
+
+    /**
+     * Returns true if the retired analyzers are enabled.
+     *
+     * @return true if the retired analyzers are enabled; otherwise null
+     */
+    public Boolean isRetiredEnabled() {
+        return (line != null && line.hasOption(ARGUMENT.RETIRED)) ? 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;
+        }
     }
 
     /**
@@ -1283,12 +1399,11 @@ public final class CliParser {
         public static final String SYM_LINK_DEPTH = "symLink";
         /**
          * The CLI argument name for setting the location of the suppression
-         * file.
+         * file(s).
          */
-        public static final String SUPPRESSION_FILE = "suppression";
+        public static final String SUPPRESSION_FILES = "suppression";
         /**
-         * The CLI argument name for setting the location of the hint
-         * file.
+         * The CLI argument name for setting the location of the hint file.
          */
         public static final String HINTS_FILE = "hints";
         /**
@@ -1328,6 +1443,14 @@ 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.
          */
@@ -1356,6 +1479,10 @@ public final class CliParser {
          * Disables the Node.js Package Analyzer.
          */
         public static final String DISABLE_NODE_JS = "disableNodeJS";
+        /**
+         * Disables the NSP Analyzer.
+         */
+        public static final String DISABLE_NSP = "disableNSP";
         /**
          * The URL of the nexus server.
          */
@@ -1408,5 +1535,13 @@ public final class CliParser {
          * The CLI argument to enable the experimental analyzers.
          */
         private static final String EXPERIMENTAL = "enableExperimental";
+        /**
+         * The CLI argument to enable the retired analyzers.
+         */
+        private static final String RETIRED = "enableRetired";
+        /**
+         * The CLI argument to enable the experimental analyzers.
+         */
+        private static final String FAIL_ON_CVSS = "failOnCVSS";
     }
 }

cli/src/site/markdown/arguments.md

@@ -0,0 +1,69 @@
+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, 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        | \<files\>       | The file paths to the suppression XML files; used to suppress [false positives](../general/suppression.html). This can be specified more than once to utilize multiple suppression files. | 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
+       | \-\-enableRetired      |                 | Enable the [retired analyzers](../analyzers/index.html). If not set the analyzers marked as retired 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                                                     | 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 [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 [retired](../analyzers/index.html) Node.js Package Analyzer will be used.                               | false
+       | \-\-disableNSP         |                 | Sets whether the NSP 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 [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 (requires Nexus Pro). Note, this has been superceded by the Central Analyzer. However, you can configure the Nexus URL to utilize an internally hosted Nexus Pro server. | false
+       | \-\-nexus              | \<url\>         | The url to the Nexus Server's web service end point (example: http://domain.enterprise/nexus/service/local/). If not set the Nexus Analyzer will be disabled. | &nbsp;
+       | \-\-nexusUsesProxy     | \<true\|false\> | Whether or not the defined proxy should be used when connecting to Nexus.        | true
+       | \-\-disableNuspec      |                 | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.                 | false
+       | \-\-disableAssembly    |                 | Sets whether or not the .NET Assembly Analyzer should be used.                   | false
+       | \-\-mono               | \<path\>        | The path to Mono for .NET Assembly analysis on non-windows systems.              | &nbsp;
+       | \-\-bundleAudit        |                 | The path to the bundle-audit executable. | &nbsp;
+       | \-\-proxyserver        | \<server\>      | The proxy server to use when downloading resources; 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;
+       | \-\-proxyuser          | \<user\>        | The proxy username to use when downloading resources.                            | &nbsp;
+       | \-\-connectionString   | \<connStr\>     | The connection string to the database.                                           | &nbsp;
+       | \-\-dbDriverName       | \<driver\>      | The database driver name.                                                        | &nbsp;
+       | \-\-dbDriverPath       | \<path\>        | The path to the database driver; note, this does not need to be set unless the JAR is outside of the class path. | &nbsp;
+       | \-\-dbPassword         | \<password\>    | The password for connecting to the database.                                     | &nbsp;
+       | \-\-dbUser             | \<user\>        | The username used to connect to the database.                                    | &nbsp;
+ \-d   | \-\-data               | \<path\>        | The location of the data directory used to store persistent data. This option should generally not be set. | &nbsp;
+       | \-\-purge              |                 | Delete the local copy of the NVD. This is used to force a refresh of the data.   | &nbsp;

cli/src/test/java/org/owasp/dependencycheck/AppTest.java

@@ -0,0 +1,194 @@
+/*
+ * 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 The OWASP Foundation. All Rights Reserved.
+ */
+package org.owasp.dependencycheck;
+
+import static org.hamcrest.core.Is.is;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+
+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.Rule;
+import org.junit.Test;
+import org.junit.rules.ExpectedException;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.utils.Settings.KEYS;
+
+/**
+ * Tests for the {@link AppTest} class.
+ */
+public class AppTest extends BaseTest {
+
+    /**
+     * Test rule for asserting exceptions and their contents.
+     */
+    @Rule
+    public ExpectedException expectedException = ExpectedException.none();
+
+    /**
+     * Test of ensureCanonicalPath method, of class App.
+     */
+    @Test
+    public void testEnsureCanonicalPath() {
+        String file = "../*.jar";
+        App instance = new App(getSettings());
+        String result = instance.ensureCanonicalPath(file);
+        assertFalse(result.contains(".."));
+        assertTrue(result.endsWith("*.jar"));
+
+        file = "../some/skip/../path/file.txt";
+        String expResult = "/some/path/file.txt";
+        result = instance.ensureCanonicalPath(file);
+        assertTrue("result=" + result, result.endsWith(expResult));
+    }
+
+    /**
+     * Assert that boolean properties can be set on the CLI and parsed into the
+     * {@link Settings}.
+     *
+     * @throws Exception the unexpected {@link Exception}.
+     */
+    @Test
+    public void testPopulateSettings() throws Exception {
+        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));
+    }
+
+    /**
+     * Assert that an {@link UnrecognizedOptionException} is thrown when a
+     * property that is not supported is specified on the CLI.
+     *
+     * @throws Exception the unexpected {@link Exception}.
+     */
+    @Test
+    public void testPopulateSettingsException() throws Exception {
+        String[] args = {"-invalidPROPERTY"};
+
+        expectedException.expect(UnrecognizedOptionException.class);
+        expectedException.expectMessage("Unrecognized option: -invalidPROPERTY");
+        testBooleanProperties(args, null);
+    }
+
+    /**
+     * Assert that a single suppression file can be set using the CLI.
+     *
+     * @throws Exception the unexpected {@link Exception}.
+     */
+    @Test
+    public void testPopulatingSuppressionSettingsWithASingleFile() throws Exception {
+        // GIVEN CLI properties with the mandatory arguments
+        File prop = new File(this.getClass().getClassLoader().getResource("sample.properties").toURI().getPath());
+
+        // AND a single suppression file
+        String[] args = {"-P", prop.getAbsolutePath(), "--suppression", "another-file.xml"};
+
+        // WHEN parsing the CLI arguments
+        final CliParser cli = new CliParser(getSettings());
+        cli.parse(args);
+        final App classUnderTest = new App(getSettings());
+        classUnderTest.populateSettings(cli);
+
+        // THEN the suppression file is set in the settings for use in the application core
+        assertThat("Expected the suppression file to be set in the Settings", getSettings().getString(KEYS.SUPPRESSION_FILE), is("another-file.xml"));
+    }
+
+    /**
+     * Assert that multiple suppression files can be set using the CLI.
+     *
+     * @throws Exception the unexpected {@link Exception}.
+     */
+    @Test
+    public void testPopulatingSuppressionSettingsWithMultipleFiles() throws Exception {
+        // GIVEN CLI properties with the mandatory arguments
+        File prop = new File(this.getClass().getClassLoader().getResource("sample.properties").toURI().getPath());
+
+        // AND a single suppression file
+        String[] args = {"-P", prop.getAbsolutePath(), "--suppression", "first-file.xml", "another-file.xml"};
+
+        // WHEN parsing the CLI arguments
+        final CliParser cli = new CliParser(getSettings());
+        cli.parse(args);
+        final App classUnderTest = new App(getSettings());
+        classUnderTest.populateSettings(cli);
+
+        // THEN the suppression file is set in the settings for use in the application core
+        assertThat("Expected the suppression files to be set in the Settings with a separator", getSettings().getString(KEYS.SUPPRESSION_FILE), is("first-file.xml,another-file.xml"));
+    }
+
+    private boolean testBooleanProperties(String[] args, Map<String, Boolean> expected) throws URISyntaxException, FileNotFoundException, ParseException, InvalidSettingException {
+        this.reloadSettings();
+        final CliParser cli = new CliParser(getSettings());
+        cli.parse(args);
+        App instance = new App(getSettings());
+        instance.populateSettings(cli);
+        boolean results = true;
+        for (Map.Entry<String, Boolean> entry : expected.entrySet()) {
+            results &= getSettings().getBoolean(entry.getKey()) == entry.getValue();
+        }
+        return results;
+    }
+}

cli/src/test/java/org/owasp/dependencycheck/BaseTest.java

@@ -0,0 +1,62 @@
+/*
+ * Copyright 2014 OWASP.
+ *
+ * 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.
+ */
+package org.owasp.dependencycheck;
+
+import org.junit.After;
+import org.junit.Before;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ *
+ * @author Jeremy Long
+ */
+public class BaseTest {
+
+    /**
+     * The configured settings.
+     */
+    private Settings settings;
+
+    /**
+     * Initialize the {@link Settings}.
+     */
+    @Before
+    public void setUp() {
+        settings = new Settings();
+    }
+
+    /**
+     * Clean the {@link Settings}.
+     */
+    @After
+    public void tearDown() {
+        settings.cleanup(true);
+    }
+
+    /**
+     * Returns the settings for the test cases.
+     *
+     * @return
+     */
+    protected Settings getSettings() {
+        return settings;
+    }
+
+    protected void reloadSettings() {
+        tearDown();
+        setUp();
+    }
+}

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;
@@ -36,25 +33,7 @@ import org.owasp.dependencycheck.utils.Settings;
  *
  * @author Jeremy Long
  */
-public class CliParserTest {
-
-    @BeforeClass
-    public static void setUpClass() throws Exception {
-        Settings.initialize();
-    }
-
-    @AfterClass
-    public static void tearDownClass() throws Exception {
-        Settings.cleanup(true);
-    }
-
-    @Before
-    public void setUp() throws Exception {
-    }
-
-    @After
-    public void tearDown() throws Exception {
-    }
+public class CliParserTest extends BaseTest {
 
     /**
      * Test of parse method, of class CliParser.
@@ -70,7 +49,7 @@ public class CliParserTest {
         ByteArrayOutputStream baos = new ByteArrayOutputStream();
         System.setOut(new PrintStream(baos));
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
         instance.parse(args);
 
         Assert.assertFalse(instance.isGetVersion());
@@ -89,7 +68,7 @@ public class CliParserTest {
         String[] args = {"-help"};
         PrintStream out = System.out;
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
         instance.parse(args);
 
         Assert.assertFalse(instance.isGetVersion());
@@ -107,7 +86,7 @@ public class CliParserTest {
 
         String[] args = {"-version"};
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
         instance.parse(args);
         Assert.assertTrue(instance.isGetVersion());
         Assert.assertFalse(instance.isGetHelp());
@@ -115,6 +94,63 @@ 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(getSettings());
+        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(getSettings());
+        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(getSettings());
+        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.
      *
@@ -132,7 +168,7 @@ public class CliParserTest {
         System.setOut(new PrintStream(baos_out));
         System.setErr(new PrintStream(baos_err));
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
 
         try {
             instance.parse(args);
@@ -154,7 +190,7 @@ public class CliParserTest {
 
         String[] args = {"-scan"};
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
 
         try {
             instance.parse(args);
@@ -177,7 +213,7 @@ public class CliParserTest {
 
         String[] args = {"-scan", "jar.that.does.not.exist", "-app", "test"};
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
         try {
             instance.parse(args);
         } catch (FileNotFoundException ex) {
@@ -196,10 +232,10 @@ 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();
+        CliParser instance = new CliParser(getSettings());
         instance.parse(args);
 
         Assert.assertEquals(path.getCanonicalPath(), instance.getScanFiles()[0]);
@@ -221,7 +257,7 @@ public class CliParserTest {
         ByteArrayOutputStream baos = new ByteArrayOutputStream();
         System.setOut(new PrintStream(baos));
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
         instance.printVersionInfo();
         try {
             baos.flush();
@@ -250,7 +286,7 @@ public class CliParserTest {
         ByteArrayOutputStream baos = new ByteArrayOutputStream();
         System.setOut(new PrintStream(baos));
 
-        CliParser instance = new CliParser();
+        CliParser instance = new CliParser(getSettings());
         String[] args = {"-h"};
         instance.parse(args);
         instance.printHelp();

cli/src/test/resources/sample.properties

@@ -0,0 +1,33 @@
+autoupdate=false
+somethingmadeup=test
+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

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

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>1.4.4</version>
+        <version>3.1.2-SNAPSHOT</version>
     </parent>
 
     <artifactId>dependency-check-core</artifactId>
@@ -28,15 +28,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
 
     <name>Dependency-Check Core</name>
     <description>dependency-check-core is the engine and reporting tool used to identify and report if there are any known, publicly disclosed vulnerabilities in the scanned project's dependencies. The engine extracts meta-data from the dependencies and uses this to do fuzzy key-word matching against the Common Platfrom Enumeration (CPE), if any CPE identifiers are found the associated Common Vulnerability and Exposure (CVE) entries are added to the generated report.</description>
-    <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
-    <distributionManagement>
-        <site>
-            <id>github-pages-site</id>
-            <name>Deployment through GitHub's site deployment plugin</name>
-            <url>${basedir}/../target/site/${project.version}/dependency-check-core</url>
-        </site>
-    </distributionManagement>
-    <!-- end copy -->
     <build>
         <resources>
             <resource>
@@ -99,6 +90,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                         <configuration>
                             <outputDirectory>${project.build.directory}/test-classes</outputDirectory>
                             <includeScope>test</includeScope>
+                            <excludeArtifactIds>dependency-check-utils</excludeArtifactIds>
                         </configuration>
                     </execution>
                 </executions>
@@ -121,146 +113,18 @@ 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>
-                    <argLine>-Dfile.encoding=UTF-8</argLine>
-                    <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>${project.build.directory}/temp</value>
-                        </property>
-                    </systemProperties>
-                </configuration>
-            </plugin>
         </plugins>
     </build>
-    <reporting>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-surefire-report-plugin</artifactId>
-                <reportSets>
-                    <reportSet>
-                        <id>integration-tests</id>
-                        <reports>
-                            <report>report-only</report>
-                            <report>failsafe-report-only</report>
-                        </reports>
-                    </reportSet>
-                </reportSets>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-checkstyle-plugin</artifactId>
-                <version>${reporting.checkstyle-plugin.version}</version>
-                <configuration>
-                    <enableRulesSummary>false</enableRulesSummary>
-                    <enableFilesSummary>false</enableFilesSummary>
-                    <configLocation>${basedir}/../src/main/config/checkstyle-checks.xml</configLocation>
-                    <headerLocation>${basedir}/../src/main/config/checkstyle-header.txt</headerLocation>
-                    <suppressionsLocation>${basedir}/../src/main/config/checkstyle-suppressions.xml</suppressionsLocation>
-                    <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-pmd-plugin</artifactId>
-                <version>${reporting.pmd-plugin.version}</version>
-                <configuration>
-                    <targetJdk>1.6</targetJdk>
-                    <linkXref>true</linkXref>
-                    <sourceEncoding>utf-8</sourceEncoding>
-                    <excludes>
-                        <exclude>**/generated/*.java</exclude>
-                    </excludes>
-                    <rulesets>
-                        <ruleset>../src/main/config/dcrules.xml</ruleset>
-                        <ruleset>/rulesets/java/basic.xml</ruleset>
-                        <ruleset>/rulesets/java/imports.xml</ruleset>
-                        <ruleset>/rulesets/java/unusedcode.xml</ruleset>
-                    </rulesets>
-                </configuration>
-            </plugin>
-        </plugins>
-    </reporting>
     <dependencies>
+        <dependency>
+            <groupId>com.vdurmont</groupId>
+            <artifactId>semver4j</artifactId>
+        </dependency>
         <!-- 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>
@@ -336,7 +200,12 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <groupId>com.sun.mail</groupId>
             <artifactId>mailapi</artifactId>
         </dependency>
-        <!-- The following dependencies are only used during testing -->
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+        </dependency>
+        <!-- The following dependencies are only used during testing 
+             and must not be converted to a properties based version number -->
         <dependency>
             <groupId>org.apache.maven.scm</groupId>
             <artifactId>maven-scm-provider-cvsexe</artifactId>
@@ -466,6 +335,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <scope>test</scope>
             <optional>true</optional>
         </dependency>
+
     </dependencies>
     <profiles>
         <profile>
@@ -477,13 +347,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             </activation>
             <build>
                 <plugins>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-surefire-plugin</artifactId>
-                        <configuration>
-                            <skip>true</skip>
-                        </configuration>
-                    </plugin>
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-failsafe-plugin</artifactId>
@@ -503,7 +366,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                                 </property>
                             </systemProperties>
                             <includes>
-                                <include>**/*MySQLTest.java</include>
+                                <include>**/*MySqlIT.java</include>
                             </includes>
                         </configuration>
                         <executions>
@@ -534,13 +397,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             </dependencies>
             <build>
                 <plugins>
-                    <plugin>
-                        <groupId>org.apache.maven.plugins</groupId>
-                        <artifactId>maven-surefire-plugin</artifactId>
-                        <configuration>
-                            <skip>true</skip>
-                        </configuration>
-                    </plugin>
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-failsafe-plugin</artifactId>
@@ -560,7 +416,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                                 </property>
                             </systemProperties>
                             <includes>
-                                <include>**/*MySQLTest.java</include>
+                                <include>**/*MySqlIT.java</include>
                             </includes>
                         </configuration>
                         <executions>
@@ -575,15 +431,19 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 </plugins>
             </build>
         </profile>
-        <profile>
-            <!-- The following profile adds additional
-            dependencies that are only used during testing.
-            Additionally, these are only added when using "allTests" to
-            make the build slightly faster in most cases. -->
+        <!-- 
+            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>
@@ -664,20 +524,6 @@ 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>
@@ -728,6 +574,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                     <optional>true</optional>
                 </dependency>
             </dependencies>
-        </profile>
+        </profile-->
     </profiles>
 </project>

core/src/main/java/org/owasp/dependencycheck/AnalysisTask.java

@@ -21,20 +21,21 @@ 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;
+import javax.annotation.concurrent.ThreadSafe;
 
 /**
- * Task to support parallelism of dependency-check analysis.
- * Analyses a single {@link Dependency} by a specific {@link Analyzer}.
+ * Task to support parallelism of dependency-check analysis. Analyses a single
+ * {@link Dependency} by a specific {@link Analyzer}.
  *
  * @author Stefan Neuhaus
  */
-class AnalysisTask implements Callable<Void> {
+@ThreadSafe
+public class AnalysisTask implements Callable<Void> {
 
     /**
      * Instance of the logger.
@@ -78,12 +79,9 @@ class AnalysisTask implements Callable<Void> {
      * Executes the analysis task.
      *
      * @return null
-     * @throws Exception thrown if unable to execute the analysis task
      */
     @Override
     public Void call() {
-        Settings.initialize();
-
         if (shouldAnalyze()) {
             LOGGER.debug("Begin Analysis of '{}' ({})", dependency.getActualFilePath(), analyzer.getName());
             try {
@@ -99,7 +97,6 @@ class AnalysisTask implements Callable<Void> {
                 exceptions.add(ex);
             }
         }
-
         return null;
     }
 
@@ -108,12 +105,11 @@ class AnalysisTask implements Callable<Void> {
      *
      * @return whether or not the analyzer can analyze the dependency
      */
-    boolean shouldAnalyze() {
+    protected boolean shouldAnalyze() {
         if (analyzer instanceof FileTypeAnalyzer) {
             final FileTypeAnalyzer fileTypeAnalyzer = (FileTypeAnalyzer) analyzer;
             return fileTypeAnalyzer.accept(dependency.getActualFile());
         }
-
         return true;
     }
 }

core/src/main/java/org/owasp/dependencycheck/Engine.java

@@ -24,6 +24,7 @@ import org.owasp.dependencycheck.analyzer.FileTypeAnalyzer;
 import org.owasp.dependencycheck.data.nvdcve.ConnectionFactory;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.data.update.CachedWebDataSource;
 import org.owasp.dependencycheck.data.update.UpdateService;
 import org.owasp.dependencycheck.data.update.exception.UpdateException;
@@ -31,6 +32,8 @@ 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.exception.ReportException;
+import org.owasp.dependencycheck.reporting.ReportGenerator;
 import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
@@ -38,6 +41,8 @@ import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.io.FileFilter;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -53,6 +58,13 @@ import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 import java.util.concurrent.TimeUnit;
+import javax.annotation.concurrent.NotThreadSafe;
+import org.owasp.dependencycheck.exception.H2DBLockException;
+import org.owasp.dependencycheck.utils.H2DBLock;
+
+//CSOFF: AvoidStarImport
+import static org.owasp.dependencycheck.analyzer.AnalysisPhase.*;
+//CSON: AvoidStarImport
 
 /**
  * Scans files, directories, etc. for Dependencies. Analyzers are loaded and
@@ -62,51 +74,167 @@ import java.util.concurrent.TimeUnit;
  *
  * @author Jeremy Long
  */
-public class Engine implements FileFilter {
+@NotThreadSafe
+public class Engine implements FileFilter, AutoCloseable {
+
+    /**
+     * {@link Engine} execution modes.
+     */
+    public enum Mode {
+        /**
+         * In evidence collection mode the {@link Engine} only collects evidence
+         * from the scan targets, and doesn't require a database.
+         */
+        EVIDENCE_COLLECTION(
+                false,
+                INITIAL,
+                PRE_INFORMATION_COLLECTION,
+                INFORMATION_COLLECTION,
+                POST_INFORMATION_COLLECTION
+        ),
+        /**
+         * In evidence processing mode the {@link Engine} processes the evidence
+         * collected using the {@link #EVIDENCE_COLLECTION} mode. Dependencies
+         * should be injected into the {@link Engine} using
+         * {@link Engine#setDependencies(List)}.
+         */
+        EVIDENCE_PROCESSING(
+                true,
+                PRE_IDENTIFIER_ANALYSIS,
+                IDENTIFIER_ANALYSIS,
+                POST_IDENTIFIER_ANALYSIS,
+                PRE_FINDING_ANALYSIS,
+                FINDING_ANALYSIS,
+                POST_FINDING_ANALYSIS,
+                FINAL
+        ),
+        /**
+         * In standalone mode the {@link Engine} will collect and process
+         * evidence in a single execution.
+         */
+        STANDALONE(true, AnalysisPhase.values());
+
+        /**
+         * Whether the database is required in this mode.
+         */
+        private final boolean databaseRequired;
+        /**
+         * The analysis phases included in the mode.
+         */
+        private final AnalysisPhase[] phases;
+
+        /**
+         * Returns true if the database is required; otherwise false.
+         *
+         * @return whether or not the database is required
+         */
+        private boolean isDatabaseRequired() {
+            return databaseRequired;
+        }
+
+        /**
+         * Returns the phases for this mode.
+         *
+         * @return the phases for this mode
+         */
+        public AnalysisPhase[] getPhases() {
+            return phases;
+        }
+
+        /**
+         * Constructs a new mode.
+         *
+         * @param databaseRequired if the database is required for the mode
+         * @param phases the analysis phases to include in the mode
+         */
+        Mode(boolean databaseRequired, AnalysisPhase... phases) {
+            this.databaseRequired = databaseRequired;
+            this.phases = phases;
+        }
+    }
 
     /**
      * The list of dependencies.
      */
     private final List<Dependency> dependencies = Collections.synchronizedList(new ArrayList<Dependency>());
+    /**
+     * The external view of the dependency list.
+     */
+    private Dependency[] dependenciesExternalView = null;
     /**
      * A Map of analyzers grouped by Analysis phase.
      */
-    private final 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 final Set<FileTypeAnalyzer> fileTypeAnalyzers = new HashSet<FileTypeAnalyzer>();
+    private final Set<FileTypeAnalyzer> fileTypeAnalyzers = new HashSet<>();
+
+    /**
+     * The engine execution mode indicating it will either collect evidence or
+     * process evidence or both.
+     */
+    private final Mode mode;
 
     /**
      * The ClassLoader to use when dynamically loading Analyzer and Update
      * services.
      */
-    private ClassLoader serviceClassLoader = Thread.currentThread().getContextClassLoader();
+    private final ClassLoader serviceClassLoader;
+    /**
+     * A reference to the database.
+     */
+    private CveDB database = null;
     /**
      * The Logger for use throughout the class.
      */
     private static final Logger LOGGER = LoggerFactory.getLogger(Engine.class);
+    /**
+     * The configured settings.
+     */
+    private final Settings settings;
+
+    /**
+     * Creates a new {@link Mode#STANDALONE} Engine.
+     *
+     * @param settings reference to the configured settings
+     */
+    public Engine(Settings settings) {
+        this(Mode.STANDALONE, settings);
+    }
 
     /**
      * Creates a new Engine.
      *
-     * @throws DatabaseException thrown if there is an error connecting to the
-     * database
+     * @param mode the mode of operation
+     * @param settings reference to the configured settings
      */
-    public Engine() throws DatabaseException {
-        initializeEngine();
+    public Engine(Mode mode, Settings settings) {
+        this(Thread.currentThread().getContextClassLoader(), mode, settings);
+    }
+
+    /**
+     * Creates a new {@link Mode#STANDALONE} Engine.
+     *
+     * @param serviceClassLoader a reference the class loader being used
+     * @param settings reference to the configured settings
+     */
+    public Engine(ClassLoader serviceClassLoader, Settings settings) {
+        this(serviceClassLoader, Mode.STANDALONE, settings);
     }
 
     /**
      * 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
+     * @param mode the mode of the engine
+     * @param settings reference to the configured settings
      */
-    public Engine(ClassLoader serviceClassLoader) throws DatabaseException {
+    public Engine(ClassLoader serviceClassLoader, Mode mode, Settings settings) {
+        this.settings = settings;
         this.serviceClassLoader = serviceClassLoader;
+        this.mode = mode;
         initializeEngine();
     }
 
@@ -117,16 +245,21 @@ public class Engine implements FileFilter {
      * @throws DatabaseException thrown if there is an error connecting to the
      * database
      */
-    protected final void initializeEngine() throws DatabaseException {
-        ConnectionFactory.initialize();
+    protected final void initializeEngine() {
         loadAnalyzers();
     }
 
     /**
      * Properly cleans up resources allocated during analysis.
      */
-    public void cleanup() {
-        ConnectionFactory.cleanup();
+    @Override
+    public void close() {
+        if (mode.isDatabaseRequired()) {
+            if (database != null) {
+                database.close();
+                database = null;
+            }
+        }
     }
 
     /**
@@ -137,13 +270,13 @@ public class Engine implements FileFilter {
         if (!analyzers.isEmpty()) {
             return;
         }
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
+        for (AnalysisPhase phase : mode.getPhases()) {
             analyzers.put(phase, new ArrayList<Analyzer>());
         }
-
-        final AnalyzerService service = new AnalyzerService(serviceClassLoader);
-        final List<Analyzer> iterator = service.getAnalyzers();
+        final AnalyzerService service = new AnalyzerService(serviceClassLoader, settings);
+        final List<Analyzer> iterator = service.getAnalyzers(mode.getPhases());
         for (Analyzer a : iterator) {
+            a.initialize(this.settings);
             analyzers.get(a.getAnalysisPhase()).add(a);
             if (a instanceof FileTypeAnalyzer) {
                 this.fileTypeAnalyzers.add((FileTypeAnalyzer) a);
@@ -162,17 +295,44 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Get the dependencies identified. The returned list is a reference to the
-     * engine's synchronized list. You must synchronize on it, when you modify
-     * and iterate over it from multiple threads. E.g. this holds for analyzers
-     * supporting parallel processing during their analysis phase.
+     * Adds a dependency.
+     *
+     * @param dependency the dependency to add
+     */
+    public synchronized void addDependency(Dependency dependency) {
+        dependencies.add(dependency);
+        dependenciesExternalView = null;
+    }
+
+    /**
+     * Sorts the dependency list.
+     */
+    public synchronized void sortDependencies() {
+        //TODO - is this actually necassary????
+//        Collections.sort(dependencies);
+//        dependenciesExternalView = null;
+    }
+
+    /**
+     * Removes the dependency.
+     *
+     * @param dependency the dependency to remove.
+     */
+    public synchronized void removeDependency(Dependency dependency) {
+        dependencies.remove(dependency);
+        dependenciesExternalView = null;
+    }
+
+    /**
+     * Returns a copy of the dependencies as an array.
      *
      * @return the dependencies identified
-     * @see Collections#synchronizedList(List)
-     * @see Analyzer#supportsParallelProcessing()
      */
-    public List<Dependency> getDependencies() {
-        return dependencies;
+    public synchronized Dependency[] getDependencies() {
+        if (dependenciesExternalView == null) {
+            dependenciesExternalView = dependencies.toArray(new Dependency[dependencies.size()]);
+        }
+        return dependenciesExternalView;
     }
 
     /**
@@ -180,11 +340,10 @@ public class Engine implements FileFilter {
      *
      * @param dependencies the dependencies
      */
-    public void setDependencies(List<Dependency> dependencies) {
-        synchronized (this.dependencies) {
-            this.dependencies.clear();
-            this.dependencies.addAll(dependencies);
-        }
+    public synchronized void setDependencies(List<Dependency> dependencies) {
+        this.dependencies.clear();
+        this.dependencies.addAll(dependencies);
+        dependenciesExternalView = null;
     }
 
     /**
@@ -212,7 +371,7 @@ public class Engine implements FileFilter {
      * @since v1.4.4
      */
     public List<Dependency> scan(String[] paths, String projectReference) {
-        final List<Dependency> deps = new ArrayList<Dependency>();
+        final List<Dependency> deps = new ArrayList<>();
         for (String path : paths) {
             final List<Dependency> d = scan(path, projectReference);
             if (d != null) {
@@ -275,7 +434,7 @@ public class Engine implements FileFilter {
      * @since v1.4.4
      */
     public List<Dependency> scan(File[] files, String projectReference) {
-        final List<Dependency> deps = new ArrayList<Dependency>();
+        final List<Dependency> deps = new ArrayList<>();
         for (File file : files) {
             final List<Dependency> d = scan(file, projectReference);
             if (d != null) {
@@ -310,7 +469,7 @@ public class Engine implements FileFilter {
      * @since v1.4.4
      */
     public List<Dependency> scan(Collection<File> files, String projectReference) {
-        final List<Dependency> deps = new ArrayList<Dependency>();
+        final List<Dependency> deps = new ArrayList<>();
         for (File file : files) {
             final List<Dependency> d = scan(file, projectReference);
             if (d != null) {
@@ -351,7 +510,7 @@ public class Engine implements FileFilter {
             } else {
                 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;
                 }
@@ -383,7 +542,7 @@ public class Engine implements FileFilter {
      */
     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()) {
@@ -393,7 +552,9 @@ public class Engine implements FileFilter {
                     }
                 } else {
                     final Dependency d = scanFile(f, projectReference);
-                    deps.add(d);
+                    if (d != null) {
+                        deps.add(d);
+                    }
                 }
             }
         }
@@ -421,7 +582,7 @@ public class Engine implements FileFilter {
      * @return the scanned dependency
      * @since v1.4.4
      */
-    protected Dependency scanFile(File file, String projectReference) {
+    protected synchronized Dependency scanFile(File file, String projectReference) {
         Dependency dependency = null;
         if (file.isFile()) {
             if (accept(file)) {
@@ -431,31 +592,31 @@ public class Engine implements FileFilter {
                 }
                 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 (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);
+                if (!found) {
+                    dependencies.add(dependency);
+                    dependenciesExternalView = null;
+                }
             }
+        } else {
+            LOGGER.debug("Path passed to scanFile(File) is not a file that can be scanned by dependency-check: {}. Skipping the file.", file);
         }
         return dependency;
     }
@@ -477,31 +638,14 @@ public class Engine implements FileFilter {
      */
     public void analyzeDependencies() throws ExceptionCollection {
         final List<Throwable> exceptions = Collections.synchronizedList(new ArrayList<Throwable>());
-        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 {
-                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);
-            }
-        }
+
+        initializeAndUpdateDatabase(exceptions);
 
         //need to ensure that data exists
         try {
             ensureDataExists();
         } catch (NoDataException ex) {
             throwFatalExceptionCollection("Unable to continue dependency-check analysis.", ex, exceptions);
-        } catch (DatabaseException ex) {
-            throwFatalExceptionCollection("Unable to connect to the dependency-check database.", ex, exceptions);
         }
 
         LOGGER.debug("\n----------------------------------------------------\nBEGIN ANALYSIS\n----------------------------------------------------");
@@ -509,7 +653,7 @@ public class Engine implements FileFilter {
         final long analysisStart = System.currentTimeMillis();
 
         // analysis phases
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
+        for (AnalysisPhase phase : mode.getPhases()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
 
             for (final Analyzer analyzer : analyzerList) {
@@ -518,17 +662,23 @@ public class Engine implements FileFilter {
                     initializeAnalyzer(analyzer);
                 } catch (InitializationException ex) {
                     exceptions.add(ex);
-                    continue;
+                    if (ex.isFatal()) {
+                        continue;
+                    }
                 }
 
-                executeAnalysisTasks(analyzer, exceptions);
+                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);
+                    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());
+                }
             }
         }
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
+        for (AnalysisPhase phase : mode.getPhases()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
 
             for (Analyzer a : analyzerList) {
@@ -544,6 +694,49 @@ public class Engine implements FileFilter {
         }
     }
 
+    /**
+     * 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 {
+        if (!mode.isDatabaseRequired()) {
+            return;
+        }
+        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 {
+                doUpdates(true);
+            } 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(settings) && !ConnectionFactory.h2DataFileExists(settings)) {
+                    throw new ExceptionCollection(new NoDataException("Autoupdate is disabled and the database does not exist"), true);
+                } else {
+                    openDatabase(true, true);
+                }
+            } 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.
      *
@@ -552,7 +745,7 @@ public class Engine implements FileFilter {
      * @param analyzer the analyzer to execute
      * @throws ExceptionCollection thrown if exceptions occurred during analysis
      */
-    void executeAnalysisTasks(Analyzer analyzer, List<Throwable> exceptions) throws ExceptionCollection {
+    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);
@@ -567,10 +760,11 @@ public class Engine implements FileFilter {
                 } catch (ExecutionException e) {
                     throwFatalExceptionCollection("Analysis task failed with a fatal exception.", e, exceptions);
                 } catch (CancellationException e) {
-                    throwFatalExceptionCollection("Analysis task timed out.", e, exceptions);
+                    throwFatalExceptionCollection("Analysis task was cancelled.", e, exceptions);
                 }
             }
         } catch (InterruptedException e) {
+            Thread.currentThread().interrupt();
             throwFatalExceptionCollection("Analysis has been interrupted.", e, exceptions);
         } finally {
             executorService.shutdown();
@@ -584,13 +778,11 @@ public class Engine implements FileFilter {
      * @param exceptions the collection of exceptions to collect
      * @return a collection of analysis tasks
      */
-    List<AnalysisTask> getAnalysisTasks(Analyzer analyzer, List<Throwable> exceptions) {
-        final List<AnalysisTask> result = new ArrayList<AnalysisTask>();
-        synchronized (dependencies) {
-            for (final Dependency dependency : dependencies) {
-                final AnalysisTask task = new AnalysisTask(analyzer, dependency, this, exceptions);
-                result.add(task);
-            }
+    protected synchronized List<AnalysisTask> getAnalysisTasks(Analyzer analyzer, List<Throwable> exceptions) {
+        final List<AnalysisTask> result = new ArrayList<>();
+        for (final Dependency dependency : dependencies) {
+            final AnalysisTask task = new AnalysisTask(analyzer, dependency, this, exceptions);
+            result.add(task);
         }
         return result;
     }
@@ -601,11 +793,9 @@ public class Engine implements FileFilter {
      * @param analyzer the analyzer to obtain an executor
      * @return the executor service
      */
-    ExecutorService getExecutorService(Analyzer analyzer) {
+    protected ExecutorService getExecutorService(Analyzer analyzer) {
         if (analyzer.supportsParallelProcessing()) {
-            // just a fair trade-off that should be reasonable for all analyzer types
-            final int maximumNumberOfThreads = 4 * Runtime.getRuntime().availableProcessors();
-
+            final int maximumNumberOfThreads = Runtime.getRuntime().availableProcessors();
             LOGGER.debug("Parallel processing with up to {} threads: {}.", maximumNumberOfThreads, analyzer.getName());
             return Executors.newFixedThreadPool(maximumNumberOfThreads);
         } else {
@@ -617,22 +807,23 @@ public class Engine implements FileFilter {
     /**
      * Initializes the given analyzer.
      *
-     * @param analyzer the analyzer to initialize
-     * @return the initialized analyzer
+     * @param analyzer the analyzer to prepare
      * @throws InitializationException thrown when there is a problem
      * initializing the analyzer
      */
-    protected Analyzer initializeAnalyzer(Analyzer analyzer) throws InitializationException {
+    protected void initializeAnalyzer(Analyzer analyzer) throws InitializationException {
         try {
             LOGGER.debug("Initializing {}", analyzer.getName());
-            analyzer.initialize();
+            analyzer.prepare(this);
         } catch (InitializationException ex) {
             LOGGER.error("Exception occurred initializing {}.", analyzer.getName());
             LOGGER.debug("", ex);
-            try {
-                analyzer.close();
-            } catch (Throwable ex1) {
-                LOGGER.trace("", ex1);
+            if (ex.isFatal()) {
+                try {
+                    analyzer.close();
+                } catch (Throwable ex1) {
+                    LOGGER.trace("", ex1);
+                }
             }
             throw ex;
         } catch (Throwable ex) {
@@ -645,7 +836,6 @@ public class Engine implements FileFilter {
             }
             throw new InitializationException("Unexpected Exception", ex);
         }
-        return analyzer;
     }
 
     /**
@@ -669,15 +859,131 @@ public class Engine implements FileFilter {
      * @throws UpdateException thrown if the operation fails
      */
     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();
-            source.update();
+        doUpdates(false);
+    }
+
+    /**
+     * Cycles through the cached web data sources and calls update on all of
+     * them.
+     *
+     * @param remainOpen whether or not the database connection should remain
+     * open
+     * @throws UpdateException thrown if the operation fails
+     */
+    public void doUpdates(boolean remainOpen) throws UpdateException {
+        if (mode.isDatabaseRequired()) {
+            H2DBLock dblock = null;
+            try {
+                if (ConnectionFactory.isH2Connection(settings)) {
+                    dblock = new H2DBLock(settings);
+                    LOGGER.debug("locking for update");
+                    dblock.lock();
+                }
+                openDatabase(false, false);
+                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();
+                    source.update(this);
+                }
+                database.close();
+                database = null;
+                LOGGER.info("Check for updates complete ({} ms)", System.currentTimeMillis() - updateStart);
+                if (remainOpen) {
+                    openDatabase(true, false);
+                }
+            } catch (DatabaseException ex) {
+                throw new UpdateException(ex.getMessage(), ex.getCause());
+            } catch (H2DBLockException ex) {
+                throw new UpdateException("Unable to obtain an exclusive lock on the H2 database to perform updates", ex);
+            } finally {
+                if (dblock != null) {
+                    dblock.release();
+                }
+            }
+        } else {
+            LOGGER.info("Skipping update check in evidence collection mode.");
         }
-        LOGGER.info("Check for updates complete ({} ms)", System.currentTimeMillis() - updateStart);
+    }
+
+    /**
+     * <p>
+     * This method is only public for unit/integration testing. This method
+     * should not be called by any integration that uses
+     * dependency-check-core.</p>
+     * <p>
+     * Opens the database connection.</p>
+     *
+     * @throws DatabaseException if the database connection could not be created
+     */
+    public void openDatabase() throws DatabaseException {
+        openDatabase(false, true);
+    }
+
+    /**
+     * <p>
+     * This method is only public for unit/integration testing. This method
+     * should not be called by any integration that uses
+     * dependency-check-core.</p>
+     * <p>
+     * Opens the database connection; if readOnly is true a copy of the database
+     * will be made.</p>
+     *
+     * @param readOnly whether or not the database connection should be readonly
+     * @param lockRequired whether or not a lock needs to be acquired when
+     * opening the database
+     * @throws DatabaseException if the database connection could not be created
+     */
+    public void openDatabase(boolean readOnly, boolean lockRequired) throws DatabaseException {
+        if (mode.isDatabaseRequired() && database == null) {
+            //needed to update schema any required schema changes
+            database = new CveDB(settings);
+            if (readOnly
+                    && ConnectionFactory.isH2Connection(settings)
+                    && settings.getString(Settings.KEYS.DB_CONNECTION_STRING).contains("file:%s")) {
+                H2DBLock lock = null;
+                try {
+                    final File db = ConnectionFactory.getH2DataFile(settings);
+                    if (db.isFile()) {
+                        database.close();
+                        if (lockRequired) {
+                            lock = new H2DBLock(settings);
+                            lock.lock();
+                        }
+                        LOGGER.debug("copying database");
+                        final File temp = settings.getTempDirectory();
+                        final File tempDB = new File(temp, db.getName());
+                        Files.copy(db.toPath(), tempDB.toPath());
+                        LOGGER.debug("copying complete '{}'", temp.toPath());
+                        settings.setString(Settings.KEYS.DATA_DIRECTORY, temp.getPath());
+                        final String connStr = settings.getString(Settings.KEYS.DB_CONNECTION_STRING);
+                        if (!connStr.contains("ACCESS_MODE_DATA")) {
+                            settings.setString(Settings.KEYS.DB_CONNECTION_STRING, connStr + "ACCESS_MODE_DATA=r");
+                        }
+                        database = new CveDB(settings);
+                    }
+                } catch (IOException ex) {
+                    throw new DatabaseException("Unable to open db in read only mode", ex);
+                } catch (H2DBLockException ex) {
+                    throw new DatabaseException("Failed to obtain lock - unable to open db in read only mode", ex);
+                } finally {
+                    if (lock != null) {
+                        lock.release();
+                    }
+                }
+            }
+        }
+    }
+
+    /**
+     * Returns a reference to the database.
+     *
+     * @return a reference to the database
+     */
+    public CveDB getDatabase() {
+        return this.database;
     }
 
     /**
@@ -687,8 +993,8 @@ public class Engine implements FileFilter {
      * @return a list of Analyzers
      */
     public List<Analyzer> getAnalyzers() {
-        final List<Analyzer> ret = new ArrayList<Analyzer>();
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
+        final List<Analyzer> ret = new ArrayList<>();
+        for (AnalysisPhase phase : mode.getPhases()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
             ret.addAll(analyzerList);
         }
@@ -725,6 +1031,24 @@ public class Engine implements FileFilter {
         return this.fileTypeAnalyzers;
     }
 
+    /**
+     * Returns the configured settings.
+     *
+     * @return the configured settings
+     */
+    public Settings getSettings() {
+        return settings;
+    }
+
+    /**
+     * Returns the mode of the engine.
+     *
+     * @return the mode of the engine
+     */
+    public Mode getMode() {
+        return mode;
+    }
+
     /**
      * Adds a file type analyzer. This has been added solely to assist in unit
      * testing the Engine.
@@ -740,20 +1064,10 @@ public class Engine implements FileFilter {
      * 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 (mode.isDatabaseRequired() && (database == null || !database.dataExists())) {
+            throw new NoDataException("No documents exist");
         }
     }
 
@@ -772,4 +1086,44 @@ public class Engine implements FileFilter {
         exceptions.add(throwable);
         throw new ExceptionCollection(message, exceptions, true);
     }
+
+    /**
+     * Writes the report to the given output directory.
+     *
+     * @param applicationName the name of the application/project
+     * @param groupId the Maven groupId
+     * @param artifactId the Maven artifactId
+     * @param version the Maven version
+     * @param outputDir the path to the output directory (can include the full
+     * file name if the format is not ALL)
+     * @param format the report format (ALL, HTML, CSV, JSON, etc.)
+     * @throws ReportException thrown if there is an error generating the report
+     */
+    public synchronized void writeReports(String applicationName, String groupId, String artifactId,
+            String version, File outputDir, String format) throws ReportException {
+        if (mode == Mode.EVIDENCE_COLLECTION) {
+            throw new UnsupportedOperationException("Cannot generate report in evidence collection mode.");
+        }
+        final DatabaseProperties prop = database.getDatabaseProperties();
+        final ReportGenerator r = new ReportGenerator(applicationName, groupId, artifactId, version, dependencies, getAnalyzers(), prop, settings);
+        try {
+            r.write(outputDir.getAbsolutePath(), format);
+        } catch (ReportException ex) {
+            final String msg = String.format("Error generating the report for %s", applicationName);
+            throw new ReportException(msg, ex);
+        }
+    }
+
+    /**
+     * Writes the report to the given output directory.
+     *
+     * @param applicationName the name of the application/project
+     * @param outputDir the path to the output directory (can include the full
+     * file name if the format is not ALL)
+     * @param format the report format (ALL, HTML, CSV, JSON, etc.)
+     * @throws ReportException thrown if there is an error generating the report
+     */
+    public void writeReports(String applicationName, File outputDir, String format) throws ReportException {
+        writeReports(applicationName, null, null, null, outputDir, format);
+    }
 }

core/src/main/java/org/owasp/dependencycheck/agent/DependencyCheckScanAgent.java

@@ -20,14 +20,15 @@ package org.owasp.dependencycheck.agent;
 import java.io.File;
 import java.io.IOException;
 import java.util.List;
+import javax.annotation.concurrent.NotThreadSafe;
 import org.owasp.dependencycheck.Engine;
-import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
-import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
+import org.owasp.dependencycheck.data.update.exception.UpdateException;
 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;
@@ -46,9 +47,9 @@ import org.slf4j.LoggerFactory;
  * <pre>
  * 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);
- * dependency.getVendorEvidence().addEvidence("my-datasource", "vendor", "mortbay", Confidence.HIGH);
+ * dependency.addEvidence(EvidenceType.PRODUCT, "my-datasource", "name", "Jetty", Confidence.HIGH);
+ * dependency.addEvidence(EvidenceType.VERSION, "my-datasource", "version", "5.1.10", Confidence.HIGH);
+ * dependency.addEvidence(EvidenceType.VENDOR, "my-datasource", "vendor", "mortbay", Confidence.HIGH);
  * dependencies.add(dependency);
  *
  * DependencyCheckScanAgent scan = new DependencyCheckScanAgent();
@@ -61,8 +62,10 @@ import org.slf4j.LoggerFactory;
  * @author Steve Springett
  */
 @SuppressWarnings("unused")
+@NotThreadSafe
 public class DependencyCheckScanAgent {
 
+    //<editor-fold defaultstate="collapsed" desc="private fields">
     /**
      * System specific new line character.
      */
@@ -75,6 +78,160 @@ 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;
+    /**
+     * Sets whether the data directory should be updated without performing a
+     * scan. Default is false.
+     */
+    private boolean updateOnly = false;
+    /**
+     * 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;
+    /**
+     * The starting string that identifies CPEs that are qualified to be imported.
+     */
+    private String cpeStartsWithFilter;
+    /**
+     * 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;
+    /**
+     * The configured settings.
+     */
+    private Settings settings;
+    /**
+     * The path to optional dependency-check properties file. This will be used
+     * to side-load additional user-defined properties.
+     * {@link Settings#mergeProperties(String)}
+     */
+    private String propertiesFilePath;
+    //</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="getters/setters">
 
     /**
      * Get the value of applicationName.
@@ -94,11 +251,6 @@ public class DependencyCheckScanAgent {
         this.applicationName = applicationName;
     }
 
-    /**
-     * The pre-determined dependencies to scan
-     */
-    private List<Dependency> dependencies;
-
     /**
      * Returns a list of pre-determined dependencies.
      *
@@ -117,11 +269,6 @@ public class DependencyCheckScanAgent {
         this.dependencies = dependencies;
     }
 
-    /**
-     * The location of the data directory that contains
-     */
-    private String dataDirectory = null;
-
     /**
      * Get the value of dataDirectory.
      *
@@ -140,12 +287,6 @@ public class DependencyCheckScanAgent {
         this.dataDirectory = dataDirectory;
     }
 
-    /**
-     * Specifies the destination directory for the generated Dependency-Check
-     * report.
-     */
-    private String reportOutputDirectory;
-
     /**
      * Get the value of reportOutputDirectory.
      *
@@ -164,15 +305,6 @@ 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.
      *
@@ -191,12 +323,6 @@ 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.
      *
@@ -216,9 +342,22 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * flag indicating whether or not to generate a report of findings.
+     * Get the value of updateOnly.
+     *
+     * @return the value of updateOnly
      */
-    private boolean generateReport = true;
+    public boolean isUpdateOnly() {
+        return updateOnly;
+    }
+
+    /**
+     * Set the value of updateOnly.
+     *
+     * @param updateOnly new value of updateOnly
+     */
+    public void setUpdateOnly(boolean updateOnly) {
+        this.updateOnly = updateOnly;
+    }
 
     /**
      * Get the value of generateReport.
@@ -238,13 +377,6 @@ 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.
      *
@@ -263,11 +395,6 @@ public class DependencyCheckScanAgent {
         this.reportFormat = reportFormat;
     }
 
-    /**
-     * The Proxy Server.
-     */
-    private String proxyServer;
-
     /**
      * Get the value of proxyServer.
      *
@@ -311,11 +438,6 @@ public class DependencyCheckScanAgent {
         this.proxyServer = proxyUrl;
     }
 
-    /**
-     * The Proxy Port.
-     */
-    private String proxyPort;
-
     /**
      * Get the value of proxyPort.
      *
@@ -334,11 +456,6 @@ public class DependencyCheckScanAgent {
         this.proxyPort = proxyPort;
     }
 
-    /**
-     * The Proxy username.
-     */
-    private String proxyUsername;
-
     /**
      * Get the value of proxyUsername.
      *
@@ -357,11 +474,6 @@ public class DependencyCheckScanAgent {
         this.proxyUsername = proxyUsername;
     }
 
-    /**
-     * The Proxy password.
-     */
-    private String proxyPassword;
-
     /**
      * Get the value of proxyPassword.
      *
@@ -380,11 +492,6 @@ public class DependencyCheckScanAgent {
         this.proxyPassword = proxyPassword;
     }
 
-    /**
-     * The Connection Timeout.
-     */
-    private String connectionTimeout;
-
     /**
      * Get the value of connectionTimeout.
      *
@@ -403,11 +510,6 @@ public class DependencyCheckScanAgent {
         this.connectionTimeout = connectionTimeout;
     }
 
-    /**
-     * The file path used for verbose logging.
-     */
-    private String logFile = null;
-
     /**
      * Get the value of logFile.
      *
@@ -426,11 +528,6 @@ public class DependencyCheckScanAgent {
         this.logFile = logFile;
     }
 
-    /**
-     * The path to the suppression file.
-     */
-    private String suppressionFile;
-
     /**
      * Get the value of suppressionFile.
      *
@@ -449,11 +546,6 @@ 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.
      *
@@ -473,9 +565,20 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Whether or not the Maven Central analyzer is enabled.
+     * Sets starting string that identifies CPEs that are qualified to be imported.
+     * @param cpeStartsWithFilter filters CPEs based on this starting string (i.e. cpe:/a: )
      */
-    private boolean centralAnalyzerEnabled = true;
+    public void setCpeStartsWithFilter(String cpeStartsWithFilter) {
+        this.cpeStartsWithFilter = cpeStartsWithFilter;
+    }
+
+    /**
+     * Returns the starting string that identifies CPEs that are qualified to be imported.
+     * @return the CPE starting filter (i.e. cpe:/a: )
+     */
+    public String getCpeStartsWithFilter() {
+        return cpeStartsWithFilter;
+    }
 
     /**
      * Get the value of centralAnalyzerEnabled.
@@ -495,11 +598,6 @@ public class DependencyCheckScanAgent {
         this.centralAnalyzerEnabled = centralAnalyzerEnabled;
     }
 
-    /**
-     * The URL of Maven Central.
-     */
-    private String centralUrl;
-
     /**
      * Get the value of centralUrl.
      *
@@ -518,11 +616,6 @@ public class DependencyCheckScanAgent {
         this.centralUrl = centralUrl;
     }
 
-    /**
-     * Whether or not the nexus analyzer is enabled.
-     */
-    private boolean nexusAnalyzerEnabled = true;
-
     /**
      * Get the value of nexusAnalyzerEnabled.
      *
@@ -541,11 +634,6 @@ public class DependencyCheckScanAgent {
         this.nexusAnalyzerEnabled = nexusAnalyzerEnabled;
     }
 
-    /**
-     * The URL of the Nexus server.
-     */
-    private String nexusUrl;
-
     /**
      * Get the value of nexusUrl.
      *
@@ -564,11 +652,6 @@ 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.
      *
@@ -587,11 +670,6 @@ public class DependencyCheckScanAgent {
         this.nexusUsesProxy = nexusUsesProxy;
     }
 
-    /**
-     * The database driver name; such as org.h2.Driver.
-     */
-    private String databaseDriverName;
-
     /**
      * Get the value of databaseDriverName.
      *
@@ -610,11 +688,6 @@ 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.
      *
@@ -633,11 +706,6 @@ public class DependencyCheckScanAgent {
         this.databaseDriverPath = databaseDriverPath;
     }
 
-    /**
-     * The database connection string.
-     */
-    private String connectionString;
-
     /**
      * Get the value of connectionString.
      *
@@ -656,11 +724,6 @@ public class DependencyCheckScanAgent {
         this.connectionString = connectionString;
     }
 
-    /**
-     * The user name for connecting to the database.
-     */
-    private String databaseUser;
-
     /**
      * Get the value of databaseUser.
      *
@@ -679,11 +742,6 @@ public class DependencyCheckScanAgent {
         this.databaseUser = databaseUser;
     }
 
-    /**
-     * The password to use when connecting to the database.
-     */
-    private String databasePassword;
-
     /**
      * Get the value of databasePassword.
      *
@@ -702,12 +760,6 @@ 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.
      *
@@ -726,11 +778,6 @@ public class DependencyCheckScanAgent {
         this.zipExtensions = zipExtensions;
     }
 
-    /**
-     * The url for the modified NVD CVE (1.2 schema).
-     */
-    private String cveUrl12Modified;
-
     /**
      * Get the value of cveUrl12Modified.
      *
@@ -749,11 +796,6 @@ public class DependencyCheckScanAgent {
         this.cveUrl12Modified = cveUrl12Modified;
     }
 
-    /**
-     * The url for the modified NVD CVE (2.0 schema).
-     */
-    private String cveUrl20Modified;
-
     /**
      * Get the value of cveUrl20Modified.
      *
@@ -772,11 +814,6 @@ public class DependencyCheckScanAgent {
         this.cveUrl20Modified = cveUrl20Modified;
     }
 
-    /**
-     * Base Data Mirror URL for CVE 1.2.
-     */
-    private String cveUrl12Base;
-
     /**
      * Get the value of cveUrl12Base.
      *
@@ -795,11 +832,6 @@ public class DependencyCheckScanAgent {
         this.cveUrl12Base = cveUrl12Base;
     }
 
-    /**
-     * Data Mirror URL for CVE 2.0.
-     */
-    private String cveUrl20Base;
-
     /**
      * Get the value of cveUrl20Base.
      *
@@ -818,11 +850,6 @@ 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.
      *
@@ -842,7 +869,27 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Executes the Dependency-Check on the dependent libraries.
+     * Get the value of propertiesFilePath.
+     *
+     * @return the value of propertiesFilePath
+     */
+    public String getPropertiesFilePath() {
+        return propertiesFilePath;
+    }
+
+    /**
+     * Set the value of propertiesFilePath.
+     *
+     * @param propertiesFilePath new value of propertiesFilePath
+     */
+    public void setPropertiesFilePath(String propertiesFilePath) {
+        this.propertiesFilePath = propertiesFilePath;
+    }
+    //</editor-fold>
+
+    /**
+     * Executes the Dependency-Check on the dependent libraries. <b>Note</b>, the engine
+     * object returned from this method must be closed by calling `close()`
      *
      * @return the Engine used to scan the dependencies.
      * @throws ExceptionCollection a collection of one or more exceptions that
@@ -852,12 +899,22 @@ public class DependencyCheckScanAgent {
         populateSettings();
         final Engine engine;
         try {
-            engine = new Engine();
+            engine = new Engine(settings);
         } catch (DatabaseException ex) {
             throw new ExceptionCollection(ex, true);
         }
-        engine.setDependencies(this.dependencies);
-        engine.analyzeDependencies();
+        if (this.updateOnly) {
+            try {
+                engine.doUpdates();
+            } catch (UpdateException ex) {
+                throw new ExceptionCollection("Unable to perform update", ex);
+            } finally {
+                engine.close();
+            }
+        } else {
+            engine.setDependencies(this.dependencies);
+            engine.analyzeDependencies();
+        }
         return engine;
     }
 
@@ -866,32 +923,15 @@ public class DependencyCheckScanAgent {
      *
      * @param engine a dependency-check engine
      * @param outDirectory the directory to write the reports to
+     * @throws ScanAgentException thrown if there is an error generating the
+     * report
      */
-    private void generateExternalReports(Engine engine, File outDirectory) {
-        DatabaseProperties prop = null;
-        CveDB cve = null;
+    private void generateExternalReports(Engine engine, File outDirectory) throws ScanAgentException {
         try {
-            cve = new CveDB();
-            cve.open();
-            prop = cve.getDatabaseProperties();
-        } catch (DatabaseException ex) {
-            LOGGER.debug("Unable to retrieve DB Properties", ex);
-        } finally {
-            if (cve != null) {
-                cve.close();
-            }
-        }
-        final ReportGenerator 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.");
-            LOGGER.debug("", ex);
+            engine.writeReports(applicationName, outDirectory, this.reportFormat.name());
+        } catch (ReportException ex) {
+            LOGGER.debug("Unexpected exception occurred during analysis; please see the verbose error log for more details.", ex);
+            throw new ScanAgentException("Error generating the report", ex);
         }
     }
 
@@ -901,40 +941,50 @@ public class DependencyCheckScanAgent {
      * proxy server, port, and connection timeout.
      */
     private void populateSettings() {
-        Settings.initialize();
+        settings = new Settings();
         if (dataDirectory != null) {
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
+            settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
         } else {
             final File jarPath = new File(DependencyCheckScanAgent.class.getProtectionDomain().getCodeSource().getLocation().getPath());
             final File base = jarPath.getParentFile();
-            final String sub = Settings.getString(Settings.KEYS.DATA_DIRECTORY);
+            final String sub = settings.getString(Settings.KEYS.DATA_DIRECTORY);
             final File dataDir = new File(base, sub);
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
+            settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
+        }
+        if (propertiesFilePath != null) {
+            try {
+                settings.mergeProperties(propertiesFilePath);
+                LOGGER.info("Successfully loaded user-defined properties");
+            } catch (IOException e) {
+                LOGGER.error("Unable to merge user-defined properties", e);
+                LOGGER.error("Continuing execution");
+            }
         }
 
-        Settings.setBoolean(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, 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);
-        Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_CENTRAL_URL, centralUrl);
-        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
-        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);
+        settings.setBoolean(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, proxyUsername);
+        settings.setStringIfNotEmpty(Settings.KEYS.PROXY_PASSWORD, proxyPassword);
+        settings.setStringIfNotEmpty(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
+        settings.setStringIfNotEmpty(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
+        settings.setStringIfNotEmpty(Settings.KEYS.CVE_CPE_STARTS_WITH_FILTER, cpeStartsWithFilter);
+        settings.setBoolean(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, centralAnalyzerEnabled);
+        settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_CENTRAL_URL, centralUrl);
+        settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
+        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);
     }
 
     /**
@@ -948,14 +998,16 @@ public class DependencyCheckScanAgent {
         Engine engine = null;
         try {
             engine = executeDependencyCheck();
-            if (this.generateReport) {
-                generateExternalReports(engine, new File(this.reportOutputDirectory));
-            }
-            if (this.showSummary) {
-                showSummary(engine.getDependencies());
-            }
-            if (this.failBuildOnCVSS <= 10) {
-                checkForFailure(engine.getDependencies());
+            if (!this.updateOnly) {
+                if (this.generateReport) {
+                    generateExternalReports(engine, new File(this.reportOutputDirectory));
+                }
+                if (this.showSummary) {
+                    showSummary(engine.getDependencies());
+                }
+                if (this.failBuildOnCVSS <= 10) {
+                    checkForFailure(engine.getDependencies());
+                }
             }
         } catch (ExceptionCollection ex) {
             if (ex.isFatal()) {
@@ -964,9 +1016,9 @@ public class DependencyCheckScanAgent {
             }
             throw new ScanAgentException("One or more exceptions occurred during analysis; please see the debug log for more details.", ex);
         } finally {
-            Settings.cleanup(true);
+            settings.cleanup(true);
             if (engine != null) {
-                engine.cleanup();
+                engine.close();
             }
         }
         return engine;
@@ -980,7 +1032,7 @@ public class DependencyCheckScanAgent {
      * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if
      * there is an exception executing the scan.
      */
-    private void checkForFailure(List<Dependency> dependencies) throws ScanAgentException {
+    private void checkForFailure(Dependency[] dependencies) throws ScanAgentException {
         final StringBuilder ids = new StringBuilder();
         for (Dependency d : dependencies) {
             boolean addName = true;
@@ -997,10 +1049,16 @@ 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"
-                    + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
-
+            final String msg;
+            if (showSummary) {
+                msg = String.format("%n%nDependency-Check Failure:%n"
+                        + "One or more dependencies were identified with vulnerabilities that have a CVSS score greater than or equal to '%.1f': %s%n"
+                        + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
+            } else {
+                msg = String.format("%n%nDependency-Check Failure:%n"
+                        + "One or more dependencies were identified with vulnerabilities.%n%n"
+                        + "See the dependency-check report for more details.%n%n");
+            }
             throw new ScanAgentException(msg);
         }
     }
@@ -1011,12 +1069,12 @@ public class DependencyCheckScanAgent {
      *
      * @param dependencies a list of dependency objects
      */
-    private void showSummary(List<Dependency> dependencies) {
+    private void showSummary(Dependency[] dependencies) {
         final StringBuilder summary = new StringBuilder();
         for (Dependency d : dependencies) {
             boolean firstEntry = true;
             final StringBuilder ids = new StringBuilder();
-            for (Vulnerability v : d.getVulnerabilities()) {
+            for (Vulnerability v : d.getVulnerabilities(true)) {
                 if (firstEntry) {
                     firstEntry = false;
                 } else {
@@ -1044,5 +1102,4 @@ public class DependencyCheckScanAgent {
                     summary.toString());
         }
     }
-
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/AbstractAnalyzer.java

@@ -0,0 +1,191 @@
+/*
+ * 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 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 javax.annotation.concurrent.ThreadSafe;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Base class for analyzers to avoid code duplication of prepare and close as
+ * most analyzers do not need these methods.
+ *
+ * @author Jeremy Long
+ */
+@ThreadSafe
+public abstract class AbstractAnalyzer implements 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;
+    /**
+     * The configured settings.
+     */
+    private Settings settings;
+
+    /**
+     * 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;
+    }
+
+    /**
+     * Returns the configured settings.
+     *
+     * @return the configured settings
+     */
+    protected Settings getSettings() {
+        return settings;
+    }
+
+    /**
+     * Initializes the analyzer with the configured settings.
+     *
+     * @param settings the configured settings to use
+     */
+    @Override
+    public void initialize(Settings settings) {
+        this.settings = settings;
+        final String key = getAnalyzerEnabledSettingKey();
+        try {
+            this.setEnabled(settings.getBoolean(key, true));
+        } catch (InvalidSettingException ex) {
+            final String msg = String.format("Invalid setting for property '%s'", key);
+            LOGGER.warn(msg);
+            LOGGER.debug(msg, ex);
+        }
+    }
+
+    /**
+     * Initialize the abstract analyzer.
+     *
+     * @param engine a reference to the dependency-check engine
+     * @throws InitializationException thrown if there is an exception
+     */
+    @Override
+    public final void prepare(Engine engine) throws InitializationException {
+        if (isEnabled()) {
+            prepareAnalyzer(engine);
+        } else {
+            LOGGER.debug("{} has been disabled", getName());
+        }
+    }
+
+    /**
+     * Prepares a given Analyzer. This will be skipped if the analyzer is
+     * disabled.
+     *
+     * @param engine a reference to the dependency-check engine
+     * @throws InitializationException thrown if there is an exception
+     */
+    protected void prepareAnalyzer(Engine engine) throws InitializationException {
+        // Intentionally empty, analyzer will override this if they must prepare anything.
+    }
+
+    /**
+     * 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 (this.isEnabled()) {
+            analyzeDependency(dependency, engine);
+        }
+    }
+
+    /**
+     * Analyzes a given dependency. If the dependency is an archive, such as a
+     * WAR or EAR, the contents are extracted, scanned, and added to the list of
+     * dependencies within the engine.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine scanning
+     * @throws AnalysisException thrown if there is an analysis exception
+     */
+    protected abstract void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException;
+
+    /**
+     * The close method does nothing for this Analyzer.
+     *
+     * @throws Exception thrown if there is an exception
+     */
+    @Override
+    public final void close() throws Exception {
+        if (isEnabled()) {
+            closeAnalyzer();
+        }
+    }
+
+    /**
+     * 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.
+    }
+
+    /**
+     * The default is to support parallel processing.
+     *
+     * @return true
+     */
+    @Override
+    public boolean supportsParallelProcessing() {
+        return true;
+    }
+
+    /**
+     * <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();
+
+}

core/src/main/java/org/owasp/dependencycheck/analyzer/AbstractDependencyComparingAnalyzer.java

@@ -0,0 +1,125 @@
+/*
+ * 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.HashSet;
+import java.util.Set;
+import javax.annotation.concurrent.ThreadSafe;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * <p>
+ * This analyzer ensures dependencies that should be grouped together, to remove
+ * excess noise from the report, are grouped. An example would be Spring, Spring
+ * Beans, Spring MVC, etc. If they are all for the same version and have the
+ * same relative path then these should be grouped into a single dependency
+ * under the core/main library.</p>
+ * <p>
+ * Note, this grouping only works on dependencies with identified CVE
+ * entries</p>
+ *
+ * @author Jeremy Long
+ */
+@ThreadSafe
+public abstract class AbstractDependencyComparingAnalyzer extends AbstractAnalyzer {
+
+    /**
+     * The Logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AbstractDependencyComparingAnalyzer.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;
+    }
+
+    /**
+     * 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 final boolean supportsParallelProcessing() {
+        return false;
+    }
+
+    /**
+     * 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.
+     */
+    @Override
+    protected synchronized void analyzeDependency(Dependency ignore, Engine engine) throws AnalysisException {
+        if (!analyzed) {
+            analyzed = true;
+            final Set<Dependency> dependenciesToRemove = new HashSet<>();
+
+            final Dependency[] dependencies = engine.getDependencies();
+            if (dependencies.length < 2) {
+                return;
+            }
+            for (int x = 0; x < dependencies.length - 1; x++) {
+                final Dependency dependency = dependencies[x];
+                if (!dependenciesToRemove.contains(dependency)) {
+                    for (int y = x + 1; y < dependencies.length; y++) {
+                        final Dependency nextDependency = dependencies[y];
+                        if (evaluateDependencies(dependency, nextDependency, dependenciesToRemove)) {
+                            break;
+                        }
+                    }
+                }
+            }
+            for (Dependency d : dependenciesToRemove) {
+                engine.removeDependency(d);
+            }
+        }
+    }
+
+    /**
+     * Evaluates the dependencies
+     *
+     * @param dependency a dependency to compare
+     * @param nextDependency a dependency to compare
+     * @param dependenciesToRemove a set of dependencies that will be removed
+     * @return true if a dependency is removed; otherwise false
+     */
+    protected abstract boolean evaluateDependencies(final Dependency dependency,
+            final Dependency nextDependency, final Set<Dependency> dependenciesToRemove);
+}

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;
 
@@ -30,6 +25,8 @@ import java.io.FileFilter;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
+import javax.annotation.concurrent.ThreadSafe;
+import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
@@ -38,19 +35,10 @@ import org.owasp.dependencycheck.exception.InitializationException;
  *
  * @author Jeremy Long
  */
+@ThreadSafe
 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.
      */
@@ -60,16 +48,6 @@ 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.
-     *
-     * @return the value of filesMatched
-     */
-    protected boolean isFilesMatched() {
-        return filesMatched;
-    }
-
     /**
      * Set the value of filesMatched. A flag indicating whether the scan
      * included any file types this analyzer supports.
@@ -80,30 +58,25 @@ 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 volatile boolean enabled = true;
-
-    /**
-     * Get the value of enabled.
+     * Initializes the analyzer.
      *
-     * @return the value of enabled
+     * @param engine a reference to the dependency-check engine
+     * @throws InitializationException thrown if there is an exception during
+     * initialization
      */
-    public boolean isEnabled() {
-        return enabled;
+    @Override
+    protected final void prepareAnalyzer(Engine engine) throws InitializationException {
+        if (filesMatched) {
+            prepareFileTypeAnalyzer(engine);
+        } 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>
@@ -120,87 +93,29 @@ public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implemen
     protected abstract FileFilter getFileFilter();
 
     /**
-     * Initializes the file type analyzer.
+     * Prepares the file type analyzer for dependency analysis.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException thrown if there is an exception during
      * initialization
      */
-    protected abstract void initializeFileTypeAnalyzer() throws InitializationException;
+    protected abstract void prepareFileTypeAnalyzer(Engine engine) 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 InitializationException thrown if there is an exception during
-     * initialization
-     */
-    @Override
-    public final void initialize() throws InitializationException {
-        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;
@@ -209,24 +124,20 @@ 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>
      * This implementation was copied from
-     * http://stackoverflow.com/questions/2041778/initialize-java-hashset-values-by-construction</p>
+     * http://stackoverflow.com/questions/2041778/prepare-java-hashset-values-by-construction</p>
      *
      * @param strings a list of strings to add to the set.
      * @return a Set of strings.
      */
     protected static Set<String> newHashSet(String... strings) {
-        final Set<String> set = new HashSet<String>(strings.length);
+        final Set<String> set = new HashSet<>(strings.length);
         Collections.addAll(set, strings);
         return set;
     }
-
-//</editor-fold>
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/AbstractNpmAnalyzer.java

@@ -0,0 +1,291 @@
+/*
+ * 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 Steve Springett. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import java.io.File;
+import java.io.IOException;
+import java.util.Map;
+import javax.annotation.concurrent.ThreadSafe;
+import javax.json.Json;
+import javax.json.JsonArray;
+import javax.json.JsonObject;
+import javax.json.JsonObjectBuilder;
+import javax.json.JsonString;
+import javax.json.JsonValue;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.EvidenceType;
+import org.owasp.dependencycheck.utils.Checksum;
+
+/**
+ * An abstract NPM analyzer that contains common methods for concrete
+ * implementations.
+ *
+ * @author Steve Springett
+ */
+@ThreadSafe
+public abstract class AbstractNpmAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AbstractNpmAnalyzer.class);
+
+    /**
+     * A descriptor for the type of dependencies processed or added by this
+     * analyzer.
+     */
+    public static final String NPM_DEPENDENCY_ECOSYSTEM = "npm";
+    /**
+     * The file name to scan.
+     */
+    private static final String PACKAGE_JSON = "package.json";
+
+    /**
+     * Determines if the file can be analyzed by the analyzer.
+     *
+     * @param pathname the path to the file
+     * @return true if the file can be analyzed by the given analyzer; otherwise
+     * false
+     */
+    @Override
+    public boolean accept(File pathname) {
+        boolean accept = super.accept(pathname);
+        if (accept) {
+            try {
+                accept |= shouldProcess(pathname);
+            } catch (AnalysisException ex) {
+                throw new RuntimeException(ex.getMessage(), ex.getCause());
+            }
+        }
+
+        return accept;
+    }
+
+    /**
+     * Determines if the path contains "/node_modules/" (i.e. it is a child
+     * module. This analyzer does not scan child modules.
+     *
+     * @param pathname the path to test
+     * @return <code>true</code> if the path does not contain "/node_modules/"
+     * @throws AnalysisException thrown if the canonical path cannot be obtained
+     * from the given file
+     */
+    protected boolean shouldProcess(File pathname) throws AnalysisException {
+        try {
+            // Do not scan the node_modules directory
+            if (pathname.getCanonicalPath().contains(File.separator + "node_modules" + File.separator)) {
+                LOGGER.debug("Skipping analysis of node module: " + pathname.getCanonicalPath());
+                return false;
+            }
+        } catch (IOException ex) {
+            throw new AnalysisException("Unable to process dependency", ex);
+        }
+        return true;
+    }
+
+    /**
+     * Construct a dependency object.
+     *
+     * @param dependency the parent dependency
+     * @param name the name of the dependency to create
+     * @param version the version of the dependency to create
+     * @param scope the scope of the dependency being created
+     * @return the generated dependency
+     */
+    protected Dependency createDependency(Dependency dependency, String name, String version, String scope) {
+        final Dependency nodeModule = new Dependency(new File(dependency.getActualFile() + "?" + name), true);
+        nodeModule.setEcosystem(NPM_DEPENDENCY_ECOSYSTEM);
+        //this is virtual - the sha1 is purely for the hyperlink in the final html report
+        nodeModule.setSha1sum(Checksum.getSHA1Checksum(String.format("%s:%s", name, version)));
+        nodeModule.setMd5sum(Checksum.getMD5Checksum(String.format("%s:%s", name, version)));
+        nodeModule.addEvidence(EvidenceType.PRODUCT, "package.json", "name", name, Confidence.HIGHEST);
+        nodeModule.addEvidence(EvidenceType.VENDOR, "package.json", "name", name, Confidence.HIGH);
+        nodeModule.addEvidence(EvidenceType.VERSION, "package.json", "version", version, Confidence.HIGHEST);
+        nodeModule.addProjectReference(dependency.getName() + ": " + scope);
+        nodeModule.setName(name);
+        nodeModule.setVersion(version);
+        nodeModule.addIdentifier("npm", String.format("%s:%s", name, version), null, Confidence.HIGHEST);
+        return nodeModule;
+    }
+
+    /**
+     * Processes a part of package.json (as defined by JsonArray) and update the
+     * specified dependency with relevant info.
+     *
+     * @param engine the dependency-check engine
+     * @param dependency the Dependency to update
+     * @param jsonArray the jsonArray to parse
+     * @param depType the dependency type
+     */
+    protected void processPackage(Engine engine, Dependency dependency, JsonArray jsonArray, String depType) {
+        final JsonObjectBuilder builder = Json.createObjectBuilder();
+        for (JsonString str : jsonArray.getValuesAs(JsonString.class)) {
+            builder.add(str.toString(), "");
+        }
+        final JsonObject jsonObject = builder.build();
+        processPackage(engine, dependency, jsonObject, depType);
+    }
+
+    /**
+     * Processes a part of package.json (as defined by JsonObject) and update
+     * the specified dependency with relevant info.
+     *
+     * @param engine the dependency-check engine
+     * @param dependency the Dependency to update
+     * @param jsonObject the jsonObject to parse
+     * @param depType the dependency type
+     */
+    protected void processPackage(Engine engine, Dependency dependency, JsonObject jsonObject, String depType) {
+        for (int i = 0; i < jsonObject.size(); i++) {
+            for (Map.Entry<String, JsonValue> entry : jsonObject.entrySet()) {
+
+                final String name = entry.getKey();
+                String version = "";
+                if (entry.getValue() != null && entry.getValue().getValueType() == JsonValue.ValueType.STRING) {
+                    version = ((JsonString) entry.getValue()).getString();
+                }
+                final Dependency existing = findDependency(engine, name, version);
+                if (existing == null) {
+                    final Dependency nodeModule = createDependency(dependency, name, version, depType);
+                    engine.addDependency(nodeModule);
+                } else {
+                    existing.addProjectReference(dependency.getName() + ": " + depType);
+                }
+            }
+        }
+    }
+
+    /**
+     * Adds information to an evidence collection from the node json
+     * configuration.
+     *
+     * @param dep the dependency to add the evidence
+     * @param t the type of evidence to add
+     * @param json information from node.js
+     * @return the actual string set into evidence
+     * @param key the key to obtain the data from the json information
+     */
+    private static String addToEvidence(Dependency dep, EvidenceType t, JsonObject json, String key) {
+        String evidenceStr = null;
+        if (json.containsKey(key)) {
+            final JsonValue value = json.get(key);
+            if (value instanceof JsonString) {
+                evidenceStr = ((JsonString) value).getString();
+                dep.addEvidence(t, PACKAGE_JSON, key, evidenceStr, Confidence.HIGHEST);
+            } else if (value instanceof JsonObject) {
+                final JsonObject jsonObject = (JsonObject) value;
+                for (final Map.Entry<String, JsonValue> entry : jsonObject.entrySet()) {
+                    final String property = entry.getKey();
+                    final JsonValue subValue = entry.getValue();
+                    if (subValue instanceof JsonString) {
+                        evidenceStr = ((JsonString) subValue).getString();
+                        dep.addEvidence(t, PACKAGE_JSON,
+                                String.format("%s.%s", key, property),
+                                evidenceStr,
+                                Confidence.HIGHEST);
+                    } else {
+                        LOGGER.warn("JSON sub-value not string as expected: {}", subValue);
+                    }
+                }
+            } else {
+                LOGGER.warn("JSON value not string or JSON object as expected: {}", value);
+            }
+        }
+        return evidenceStr;
+    }
+
+    /**
+     * Locates the dependency from the list of dependencies that have been
+     * scanned by the engine.
+     *
+     * @param engine the dependency-check engine
+     * @param name the name of the dependency to find
+     * @param version the version of the dependency to find
+     * @return the identified dependency; otherwise null
+     */
+    protected Dependency findDependency(Engine engine, String name, String version) {
+        for (Dependency d : engine.getDependencies()) {
+            if (NPM_DEPENDENCY_ECOSYSTEM.equals(d.getEcosystem()) && name.equals(d.getName()) && version != null && d.getVersion() != null) {
+                final String dependencyVersion = d.getVersion();
+                if (DependencyBundlingAnalyzer.npmVersionsMatch(version, dependencyVersion)) {
+                    return d;
+                }
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Collects evidence from the given JSON for the associated dependency.
+     *
+     * @param json the JSON that contains the evidence to collect
+     * @param dependency the dependency to add the evidence too
+     */
+    public void gatherEvidence(final JsonObject json, Dependency dependency) {
+        if (json.containsKey("name")) {
+            final Object value = json.get("name");
+            if (value instanceof JsonString) {
+                final String valueString = ((JsonString) value).getString();
+                dependency.setName(valueString);
+                dependency.setPackagePath(valueString);
+                dependency.addEvidence(EvidenceType.PRODUCT, PACKAGE_JSON, "name", valueString, Confidence.HIGHEST);
+                dependency.addEvidence(EvidenceType.VENDOR, PACKAGE_JSON, "name", valueString, Confidence.HIGH);
+            } else {
+                LOGGER.warn("JSON value not string as expected: {}", value);
+            }
+        }
+        final String desc = addToEvidence(dependency, EvidenceType.PRODUCT, json, "description");
+        dependency.setDescription(desc);
+        addToEvidence(dependency, EvidenceType.VENDOR, json, "author");
+        final String version = addToEvidence(dependency, EvidenceType.VERSION, json, "version");
+        if (version != null) {
+            dependency.setVersion(version);
+            dependency.addIdentifier("npm", String.format("%s:%s", dependency.getName(), version), null, Confidence.HIGHEST);
+        }
+
+        // Adds the license if defined in package.json
+        if (json.containsKey("license")) {
+            final Object value = json.get("license");
+            if (value instanceof JsonString) {
+                dependency.setLicense(json.getString("license"));
+            } else if (value instanceof JsonArray) {
+                final JsonArray array = (JsonArray) value;
+                final StringBuilder sb = new StringBuilder();
+                boolean addComma = false;
+                for (int x = 0; x < array.size(); x++) {
+                    if (!array.isNull(x)) {
+                        if (addComma) {
+                            sb.append(", ");
+                        } else {
+                            addComma = true;
+                        }
+                        sb.append(array.getString(x));
+                    }
+                }
+                dependency.setLicense(sb.toString());
+            } else {
+                dependency.setLicense(json.getJsonObject("license").getString("type"));
+            }
+        }
+    }
+}

core/src/main/java/org/owasp/dependencycheck/analyzer/AbstractSuppressionAnalyzer.java

@@ -0,0 +1,254 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+import java.util.regex.Pattern;
+import javax.annotation.concurrent.ThreadSafe;
+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.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.
+ *
+ * @author Jeremy Long
+ */
+@ThreadSafe
+public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
+
+    /**
+     * The Logger for use throughout the class.
+     */
+    private static final Logger LOGGER = LoggerFactory.getLogger(AbstractSuppressionAnalyzer.class);
+    /**
+     * The list of suppression rules.
+     */
+    private List<SuppressionRule> rules = new ArrayList<>();
+
+    /**
+     * Get the number of suppression rules.
+     *
+     * @return the number of suppression rules
+     */
+    protected int getRuleCount() {
+        return rules.size();
+    }
+
+    /**
+     * Returns a list of file EXTENSIONS supported by this analyzer.
+     *
+     * @return a list of file EXTENSIONS supported by this analyzer.
+     */
+    public Set<String> getSupportedExtensions() {
+        return null;
+    }
+
+    /**
+     * The prepare method loads the suppression XML file.
+     *
+     * @param engine a reference the dependency-check engine
+     * @throws InitializationException thrown if there is an exception
+     */
+    @Override
+    public synchronized void prepareAnalyzer(Engine engine) throws InitializationException {
+        if (rules.isEmpty()) {
+            try {
+                loadSuppressionBaseData();
+            } catch (SuppressionParseException ex) {
+                throw new InitializationException("Error initializing the suppression analyzer: " + ex.getLocalizedMessage(), ex, true);
+            }
+
+            try {
+                loadSuppressionData();
+            } catch (SuppressionParseException ex) {
+                throw new InitializationException("Warn initializing the suppression analyzer: " + ex.getLocalizedMessage(), ex, false);
+            }
+        }
+    }
+
+    @Override
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
+        if (rules.isEmpty()) {
+            return;
+        }
+        for (final SuppressionRule rule : rules) {
+            rule.process(dependency);
+        }
+    }
+
+    /**
+     * Loads all the suppression rules files configured in the {@link Settings}.
+     *
+     * @throws SuppressionParseException thrown if the XML cannot be parsed.
+     */
+    private void loadSuppressionData() throws SuppressionParseException {
+        final List<SuppressionRule> ruleList = new ArrayList<>();
+        final SuppressionParser parser = new SuppressionParser();
+        final String[] suppressionFilePaths = getSettings().getArray(Settings.KEYS.SUPPRESSION_FILE);
+        final List<String> failedLoadingFiles = new ArrayList<>();
+        if (suppressionFilePaths != null && suppressionFilePaths.length > 0) {
+            // Load all the suppression file paths
+            for (final String suppressionFilePath : suppressionFilePaths) {
+                try {
+                    ruleList.addAll(loadSuppressionFile(parser, suppressionFilePath));
+                } catch (SuppressionParseException ex) {
+                    final String msg = String.format("Failed to load %s, caused by %s. ", suppressionFilePath, ex.getMessage());
+                    failedLoadingFiles.add(msg);
+                }
+            }
+        }
+        LOGGER.debug("{} suppression rules were loaded.", ruleList.size());
+        rules.addAll(ruleList);
+        if (!failedLoadingFiles.isEmpty()) {
+            LOGGER.debug("{} suppression files failed to load.", failedLoadingFiles.size());
+            final StringBuilder sb = new StringBuilder();
+            for (String item : failedLoadingFiles) {
+                sb.append(item);
+            }
+            throw new SuppressionParseException(sb.toString());
+        }
+    }
+
+    /**
+     * Loads all the base suppression rules files.
+     *
+     * @throws SuppressionParseException thrown if the XML cannot be parsed.
+     */
+    private void loadSuppressionBaseData() throws SuppressionParseException {
+        final SuppressionParser parser = new SuppressionParser();
+        List<SuppressionRule> ruleList;
+        try {
+            final InputStream in = FileUtils.getResourceAsStream("dependencycheck-base-suppression.xml");
+            ruleList = parser.parseSuppressionRules(in);
+        } catch (SAXException ex) {
+            throw new SuppressionParseException("Unable to parse the base suppression data file", ex);
+        }
+        rules.addAll(ruleList);
+    }
+
+    /**
+     * Load a single suppression rules file from the path provided using the
+     * parser provided.
+     *
+     * @param parser the parser to use for loading the file
+     * @param suppressionFilePath the path to load
+     * @return the list of loaded suppression rules
+     * @throws SuppressionParseException thrown if the suppression file cannot
+     * be loaded and parsed.
+     */
+    private List<SuppressionRule> loadSuppressionFile(final SuppressionParser parser,
+            final String suppressionFilePath) throws SuppressionParseException {
+        LOGGER.debug("Loading suppression rules from '{}'", suppressionFilePath);
+        final List<SuppressionRule> list = new ArrayList<>();
+        File file = null;
+        boolean deleteTempFile = false;
+        try {
+            final Pattern uriRx = Pattern.compile("^(https?|file)\\:.*", Pattern.CASE_INSENSITIVE);
+            if (uriRx.matcher(suppressionFilePath).matches()) {
+                deleteTempFile = true;
+                file = getSettings().getTempFile("suppression", "xml");
+                final URL url = new URL(suppressionFilePath);
+                final Downloader downloader = new Downloader(getSettings());
+                try {
+                    downloader.fetchFile(url, file, false);
+                } catch (DownloadFailedException ex) {
+                    LOGGER.trace("Failed download - first attempt", ex);
+                    downloader.fetchFile(url, file, true);
+                }
+            } else {
+                file = new File(suppressionFilePath);
+
+                if (!file.exists()) {
+                    try (InputStream suppressionsFromClasspath = FileUtils.getResourceAsStream(suppressionFilePath)) {
+                        if (suppressionsFromClasspath != null) {
+                            deleteTempFile = true;
+                            file = getSettings().getTempFile("suppression", "xml");
+                            try {
+                                org.apache.commons.io.FileUtils.copyInputStreamToFile(suppressionsFromClasspath, file);
+                            } catch (IOException ex) {
+                                throwSuppressionParseException("Unable to locate suppressions file in classpath", ex, suppressionFilePath);
+                            }
+                        }
+                    }
+                }
+            }
+            if (file != null) {
+                if (!file.exists()) {
+                    final String msg = String.format("Suppression file '%s' does not exist", file.getPath());
+                    LOGGER.warn(msg);
+                    throw new SuppressionParseException(msg);
+                }
+                try {
+                    list.addAll(parser.parseSuppressionRules(file));
+                } catch (SuppressionParseException ex) {
+                    LOGGER.warn("Unable to parse suppression xml file '{}'", file.getPath());
+                    LOGGER.warn(ex.getMessage());
+                    throw ex;
+                }
+            }
+        } catch (DownloadFailedException ex) {
+            throwSuppressionParseException("Unable to fetch the configured suppression file", ex, suppressionFilePath);
+        } catch (MalformedURLException ex) {
+            throwSuppressionParseException("Configured suppression file has an invalid URL", ex, suppressionFilePath);
+        } catch (SuppressionParseException ex) {
+            throw ex;
+        } catch (IOException ex) {
+            throwSuppressionParseException("Unable to create temp file for suppressions", ex, suppressionFilePath);
+        } finally {
+            if (deleteTempFile && file != null) {
+                FileUtils.delete(file);
+            }
+        }
+        return list;
+    }
+
+    /**
+     * Utility method to throw parse exceptions.
+     *
+     * @param message the exception message
+     * @param exception the cause of the exception
+     * @param suppressionFilePath the path file
+     * @throws SuppressionParseException throws the generated
+     * SuppressionParseException
+     */
+    private void throwSuppressionParseException(String message, Exception exception, String suppressionFilePath) throws SuppressionParseException {
+        LOGGER.warn(String.format(message + "'%s'", suppressionFilePath));
+        LOGGER.debug("", exception);
+        throw new SuppressionParseException(message, exception);
+    }
+}

core/src/main/java/org/owasp/dependencycheck/analyzer/AnalysisPhase.java

@@ -36,6 +36,10 @@ public enum AnalysisPhase {
      * Information collection phase.
      */
     INFORMATION_COLLECTION,
+    /**
+     * Post information collection phase.
+     */
+    POST_INFORMATION_COLLECTION,
     /**
      * Pre identifier analysis phase.
      */

core/src/main/java/org/owasp/dependencycheck/analyzer/Analyzer.java

@@ -21,11 +21,22 @@ 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.Settings;
 
 /**
+ * <p>
  * 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.
+ * Evidence.</p>
+ * <p>
+ * When the {@link org.owasp.dependencycheck.Engine} executes it will load the
+ * analyzers and call the methods in the following order:</p>
+ * <ol>
+ * <li>{@link #initialize(org.owasp.dependencycheck.utils.Settings)}</li>
+ * <li>{@link #prepare(org.owasp.dependencycheck.Engine)}</li>
+ * <li>{@link #analyze(org.owasp.dependencycheck.dependency.Dependency, org.owasp.dependencycheck.Engine)}</li>
+ * <li>{@link #close()}</li>
+ * </ol>
  *
  * @author Jeremy Long
  */
@@ -60,13 +71,21 @@ public interface Analyzer {
     AnalysisPhase getAnalysisPhase();
 
     /**
-     * The initialize method is called (once) prior to the analyze method being
+     * Initializes the analyzer with the configured settings.
+     *
+     * @param settings the configured settings
+     */
+    void initialize(Settings settings);
+
+    /**
+     * The prepare method is called (once) prior to the analyze method being
      * called on all of the dependencies.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException is thrown if an exception occurs
      * initializing the analyzer.
      */
-    void initialize() throws InitializationException;
+    void prepare(Engine engine) throws InitializationException;
 
     /**
      * The close method is called after all of the dependencies have been
@@ -77,10 +96,20 @@ public interface 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.
+     * 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
+     * @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();
+
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/AnalyzerService.java

@@ -18,20 +18,25 @@
 package org.owasp.dependencycheck.analyzer;
 
 import java.util.ArrayList;
+import org.slf4j.LoggerFactory;
+
+import static java.util.Arrays.asList;
 import java.util.Iterator;
 import java.util.List;
 import java.util.ServiceLoader;
+import javax.annotation.concurrent.ThreadSafe;
 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
- * org.owasp.dependencycheck.analyzer.Analyzer.
+ * {@link org.owasp.dependencycheck.analyzer.Analyzer}.
  *
  * @author Jeremy Long
  */
+@ThreadSafe
 public class AnalyzerService {
+
     /**
      * The Logger for use throughout the class.
      */
@@ -41,14 +46,21 @@ public class AnalyzerService {
      * The service loader for analyzers.
      */
     private final ServiceLoader<Analyzer> service;
+    /**
+     * The configured settings.
+     */
+    private final Settings settings;
 
     /**
      * Creates a new instance of AnalyzerService.
      *
-     * @param classLoader the ClassLoader to use when dynamically loading Analyzer and Update services
+     * @param classLoader the ClassLoader to use when dynamically loading
+     * Analyzer and Update services
+     * @param settings the configured settings
      */
-    public AnalyzerService(ClassLoader classLoader) {
+    public AnalyzerService(ClassLoader classLoader, Settings settings) {
         service = ServiceLoader.load(Analyzer.class, classLoader);
+        this.settings = settings;
     }
 
     /**
@@ -57,19 +69,49 @@ public class AnalyzerService {
      * @return a list of Analyzers.
      */
     public List<Analyzer> getAnalyzers() {
-        final List<Analyzer> analyzers = new ArrayList<Analyzer>();
+        return getAnalyzers(AnalysisPhase.values());
+    }
+
+    /**
+     * Returns a list of all instances of the Analyzer interface that are bound
+     * to one of the given phases.
+     *
+     * @param phases the phases to obtain analyzers for
+     * @return a list of Analyzers.
+     */
+    public List<Analyzer> getAnalyzers(AnalysisPhase... phases) {
+        return getAnalyzers(asList(phases));
+    }
+
+    /**
+     * Returns a list of all instances of the Analyzer interface that are bound
+     * to one of the given phases.
+     *
+     * @param phases the phases to obtain analyzers for
+     * @return a list of Analyzers
+     */
+    private List<Analyzer> getAnalyzers(List<AnalysisPhase> phases) {
+        final List<Analyzer> analyzers = new ArrayList<>();
         final Iterator<Analyzer> iterator = service.iterator();
         boolean experimentalEnabled = false;
+        boolean retiredEnabled = false;
         try {
-            experimentalEnabled = Settings.getBoolean(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, false);
+            experimentalEnabled = settings.getBoolean(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, false);
+            retiredEnabled = settings.getBoolean(Settings.KEYS.ANALYZER_RETIRED_ENABLED, false);
         } catch (InvalidSettingException ex) {
-            LOGGER.error("invalide experimental setting", ex);
+            LOGGER.error("invalid experimental or retired setting", ex);
         }
         while (iterator.hasNext()) {
             final Analyzer a = iterator.next();
+            if (!phases.contains(a.getAnalysisPhase())) {
+                continue;
+            }
             if (!experimentalEnabled && a.getClass().isAnnotationPresent(Experimental.class)) {
                 continue;
             }
+            if (!retiredEnabled && a.getClass().isAnnotationPresent(Retired.class)) {
+                continue;
+            }
             LOGGER.debug("Loaded Analyzer {}", a.getName());
             analyzers.add(a);
         }

core/src/main/java/org/owasp/dependencycheck/analyzer/ArchiveAnalyzer.java

@@ -18,7 +18,6 @@
 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;
@@ -29,6 +28,8 @@ import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
+import javax.annotation.concurrent.ThreadSafe;
 
 import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveInputStream;
@@ -62,6 +63,7 @@ import org.slf4j.LoggerFactory;
  *
  * @author Jeremy Long
  */
+@ThreadSafe
 public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -72,7 +74,7 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * The count of directories created during analysis. This is used for
      * creating temporary directories.
      */
-    private static int dirCount = 0;
+    private static final AtomicInteger DIRECTORY_COUNT = new AtomicInteger(0);
     /**
      * The parent directory for the individual directories per archive.
      */
@@ -81,25 +83,15 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * 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);
+    private int maxScanDepth;
     /**
-     * Tracks the current scan/extraction depth for nested archives.
+     * The file filter used to filter supported files.
      */
-    private int scanDepth = 0;
-
-    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
-    /**
-     * The name of the analyzer.
-     */
-    private static final String ANALYZER_NAME = "Archive Analyzer";
-    /**
-     * The phase that this analyzer is intended to run in.
-     */
-    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INITIAL;
+    private FileFilter fileFilter = null;
     /**
      * 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
@@ -111,33 +103,39 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * 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 String[] ext = additionalZipExt.split("\\s*,\\s*");
-            Collections.addAll(ZIPPABLES, ext);
-        }
-        EXTENSIONS.addAll(ZIPPABLES);
-    }
-
-    /**
-     * The file filter used to filter supported files.
-     */
-    private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(EXTENSIONS).build();
-
-    @Override
-    protected FileFilter getFileFilter() {
-        return FILTER;
-    }
-
+    private static final FileFilter REMOVE_FROM_ANALYSIS = FileFilterBuilder.newInstance()
+            .addExtensions("zip", "tar", "gz", "tgz", "bz2", "tbz2").build();
     /**
      * Detects files with .zip extension.
      */
     private static final FileFilter ZIP_FILTER = FileFilterBuilder.newInstance().addExtensions("zip").build();
 
+    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Archive Analyzer";
+    /**
+     * The phase that this analyzer is intended to run in.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INITIAL;
+
+    /**
+     * Initializes the analyzer with the configured settings.
+     *
+     * @param settings the configured settings to use
+     */
+    @Override
+    public void initialize(Settings settings) {
+        super.initialize(settings);
+        initializeSettings();
+    }
+
+    @Override
+    protected FileFilter getFileFilter() {
+        return fileFilter;
+    }
+
     /**
      * Returns the name of the analyzer.
      *
@@ -171,15 +169,16 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-     * The initialize method does nothing for this Analyzer.
+     * The prepare method does nothing for this Analyzer.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException is thrown if there is an exception
      * deleting or creating temporary files
      */
     @Override
-    public void initializeFileTypeAnalyzer() throws InitializationException {
+    public void prepareFileTypeAnalyzer(Engine engine) throws InitializationException {
         try {
-            final File baseDir = Settings.getTempDirectory();
+            final File baseDir = getSettings().getTempDirectory();
             tempFileLocation = File.createTempFile("check", "tmp", baseDir);
             if (!tempFileLocation.delete()) {
                 setEnabled(false);
@@ -205,31 +204,20 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * files
      */
     @Override
-    public void close() throws Exception {
+    public void closeAnalyzer() throws Exception {
         if (tempFileLocation != null && tempFileLocation.exists()) {
-            LOGGER.debug("Attempting to delete temporary files");
+            LOGGER.debug("Attempting to delete temporary files from `{}`", tempFileLocation.toString());
             final boolean success = FileUtils.delete(tempFileLocation);
             if (!success && tempFileLocation.exists()) {
                 final String[] l = tempFileLocation.list();
                 if (l != null && l.length > 0) {
-                    LOGGER.warn("Failed to delete some temporary files, see the log for more details");
+                    LOGGER.warn("Failed to delete the Archive Analyzer's temporary files from `{}`, "
+                            + "see the log for more details", tempFileLocation.toString());
                 }
             }
         }
     }
 
-    /**
-     * Does not support parallel processing as it both modifies and iterates
-     * over the engine's list of dependencies.
-     *
-     * @see #analyzeFileType(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
@@ -240,7 +228,23 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * @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 {
+        extractAndAnalyze(dependency, engine, 0);
+        engine.sortDependencies();
+    }
+
+    /**
+     * Extracts the contents of the archive dependency and scans for additional
+     * dependencies.
+     *
+     * @param dependency the dependency being analyzed
+     * @param engine the engine doing the analysis
+     * @param scanDepth the current scan depth; extracctAndAnalyze is recursive
+     * and will, be default, only go 3 levels deep
+     * @throws AnalysisException thrown if there is a problem analyzing the
+     * dependencies
+     */
+    private void extractAndAnalyze(Dependency dependency, Engine engine, int scanDepth) throws AnalysisException {
         final File f = new File(dependency.getActualFilePath());
         final File tmpDir = getNextTempDirectory();
         extractFiles(f, tmpDir, engine);
@@ -248,7 +252,7 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
         //make a copy
         final List<Dependency> dependencySet = findMoreDependencies(engine, tmpDir);
 
-        if (!dependencySet.isEmpty()) {
+        if (dependencySet != null && !dependencySet.isEmpty()) {
             for (Dependency d : dependencySet) {
                 if (d.getFilePath().startsWith(tmpDir.getAbsolutePath())) {
                     //fix the dependency's display name and path
@@ -260,14 +264,12 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                             d.getFileName());
                     d.setFilePath(displayPath);
                     d.setFileName(displayName);
-                    d.setProjectReferences(dependency.getProjectReferences());
+                    d.addAllProjectReferences(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;
+                    if (this.accept(d.getActualFile()) && scanDepth < maxScanDepth) {
+                        extractAndAnalyze(d, engine, scanDepth + 1);
                     }
                 } else {
                     for (Dependency sub : dependencySet) {
@@ -287,9 +289,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
         }
         if (REMOVE_FROM_ANALYSIS.accept(dependency.getActualFile())) {
             addDisguisedJarsToDependencies(dependency, engine);
-            engine.getDependencies().remove(dependency);
+            engine.removeDependency(dependency);
         }
-        Collections.sort(engine.getDependencies());
     }
 
     /**
@@ -302,11 +303,11 @@ 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();
@@ -314,7 +315,7 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                 dependency.setSha1sum("");
                 org.apache.commons.io.FileUtils.copyFile(dependency.getActualFile(), tmpLoc);
                 final List<Dependency> dependencySet = findMoreDependencies(engine, tmpLoc);
-                if (!dependencySet.isEmpty()) {
+                if (dependencySet != null && !dependencySet.isEmpty()) {
                     for (Dependency d : dependencySet) {
                         //fix the dependency's display name and path
                         if (d.getActualFile().equals(tmpLoc)) {
@@ -346,8 +347,7 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * @return any dependencies that weren't known to the engine before
      */
     private static List<Dependency> findMoreDependencies(Engine engine, File file) {
-        final List<Dependency> added = engine.scan(file);
-        return added;
+        return engine.scan(file);
     }
 
     /**
@@ -357,8 +357,7 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws AnalysisException thrown if unable to create temporary directory
      */
     private File getNextTempDirectory() throws AnalysisException {
-        dirCount += 1;
-        final File directory = new File(tempFileLocation, String.valueOf(dirCount));
+        final File directory = new File(tempFileLocation, String.valueOf(DIRECTORY_COUNT.incrementAndGet()));
         //getting an exception for some directories not being able to be created; might be because the directory already exists?
         if (directory.exists()) {
             return getNextTempDirectory();
@@ -390,8 +389,9 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
             try {
                 fis = new FileInputStream(archive);
             } catch (FileNotFoundException ex) {
-                LOGGER.debug("", ex);
-                throw new AnalysisException("Archive file was not found.", ex);
+                final String msg = String.format("Error extracting file `%s`: %s", archive.getAbsolutePath(), ex.getMessage());
+                LOGGER.debug(msg, ex);
+                throw new AnalysisException(msg);
             }
             BufferedInputStream in = null;
             ZipArchiveInputStream zin = null;
@@ -399,7 +399,7 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
             GzipCompressorInputStream gin = null;
             BZip2CompressorInputStream bzin = null;
             try {
-                if (ZIPPABLES.contains(archiveExt)) {
+                if (KNOWN_ZIP_EXT.contains(archiveExt)) {
                     in = new BufferedInputStream(fis);
                     ensureReadableJar(archiveExt, in);
                     zin = new ZipArchiveInputStream(in);
@@ -434,12 +434,12 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
             } finally {
                 //overly verbose and not needed... but keeping it anyway due to
                 //having issue with file handles being left open
-                close(fis);
-                close(in);
-                close(zin);
-                close(tin);
-                close(gin);
-                close(bzin);
+                FileUtils.close(fis);
+                FileUtils.close(in);
+                FileUtils.close(zin);
+                FileUtils.close(tin);
+                FileUtils.close(gin);
+                FileUtils.close(bzin);
             }
         }
     }
@@ -471,7 +471,10 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                     && b[5] == 'n'
                     && b[6] == '/') {
                 boolean stillLooking = true;
-                int chr, nxtChr;
+                int chr;
+                int nxtChr;
+                //CSOFF: InnerAssignment
+                //CSOFF: NestedIfDepth
                 while (stillLooking && (chr = in.read()) != -1) {
                     if (chr == '\n' || chr == '\r') {
                         in.mark(4);
@@ -489,6 +492,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                         }
                     }
                 }
+                //CSON: InnerAssignment
+                //CSON: NestedIfDepth
             } else {
                 in.reset();
             }
@@ -518,10 +523,10 @@ 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);
         }
     }
 
@@ -534,14 +539,12 @@ 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() && !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);
@@ -551,8 +554,6 @@ 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);
         }
     }
 
@@ -566,34 +567,11 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      */
     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);
-            }
         }
     }
 
@@ -627,7 +605,21 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
         } finally {
             ZipFile.closeQuietly(zip);
         }
-
         return isJar;
     }
+
+    /**
+     * Initializes settings used by the scanning functions of the archive
+     * analyzer.
+     */
+    private void initializeSettings() {
+        maxScanDepth = getSettings().getInt("archive.scan.depth", 3);
+        final String additionalZipExt = getSettings().getString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS);
+        if (additionalZipExt != null) {
+            final String[] ext = additionalZipExt.split("\\s*,\\s*");
+            Collections.addAll(KNOWN_ZIP_EXT, ext);
+        }
+        EXTENSIONS.addAll(KNOWN_ZIP_EXT);
+        fileFilter = FileFilterBuilder.newInstance().addExtensions(EXTENSIONS).build();
+    }
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/AssemblyAnalyzer.java

@@ -28,8 +28,8 @@ import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.dependency.Evidence;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
+import org.owasp.dependencycheck.utils.FileUtils;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -37,15 +37,17 @@ 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.annotation.concurrent.ThreadSafe;
 import javax.xml.parsers.ParserConfigurationException;
 import org.owasp.dependencycheck.exception.InitializationException;
 import org.apache.commons.lang3.SystemUtils;
+import org.owasp.dependencycheck.dependency.EvidenceType;
+import org.owasp.dependencycheck.utils.XmlUtils;
 
 /**
  * Analyzer for getting company, product, and version information from a .NET
@@ -54,6 +56,7 @@ import org.apache.commons.lang3.SystemUtils;
  * @author colezlaw
  *
  */
+@ThreadSafe
 public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -72,6 +75,10 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      * The temp value for GrokAssembly.exe
      */
     private File grokAssemblyExe = null;
+    /**
+     * The temp value for GrokAssembly.exe.config
+     */
+    private File grokAssemblyConfig = null;
     /**
      * Logger
      */
@@ -84,10 +91,10 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      */
     protected List<String> buildArgumentList() {
         // Use file.separator as a wild guess as to whether this is Windows
-        final List<String> args = new ArrayList<String>();
+        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));
+            if (getSettings().getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH) != null) {
+                args.add(getSettings().getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH));
             } else if (isInPath("mono")) {
                 args.add("mono");
             } else {
@@ -106,13 +113,16 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws AnalysisException if anything goes sideways
      */
     @Override
-    public void analyzeFileType(Dependency dependency, Engine engine)
-            throws AnalysisException {
+    public void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
+        final File test = new File(dependency.getActualFilePath());
+        if (!test.isFile()) {
+            throw new AnalysisException(String.format("%s does not exist and cannot be analyzed by dependency-check",
+                    dependency.getActualFilePath()));
+        }
         if (grokAssemblyExe == null) {
             LOGGER.warn("GrokAssembly didn't get deployed");
             return;
         }
-
         final List<String> args = buildArgumentList();
         if (args == null) {
             LOGGER.warn("Assembly Analyzer was unable to execute");
@@ -123,8 +133,8 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
         Document doc = null;
         try {
             final Process proc = pb.start();
+            final DocumentBuilder builder = XmlUtils.buildSecureDocumentBuilder();
 
-            final DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
             doc = builder.parse(proc.getInputStream());
 
             // Try evacuating the error stream
@@ -137,6 +147,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
             try {
                 rc = proc.waitFor();
             } catch (InterruptedException ie) {
+                Thread.currentThread().interrupt();
                 return;
             }
             if (rc == 3) {
@@ -144,7 +155,9 @@ 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();
@@ -157,31 +170,29 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
 
             final String version = xpath.evaluate("/assembly/version", doc);
             if (version != null) {
-                dependency.getVersionEvidence().addEvidence(new Evidence("grokassembly", "version",
-                        version, Confidence.HIGHEST));
+                dependency.addEvidence(EvidenceType.VERSION, "grokassembly", "version", version, Confidence.HIGHEST);
             }
 
             final String vendor = xpath.evaluate("/assembly/company", doc);
             if (vendor != null) {
-                dependency.getVendorEvidence().addEvidence(new Evidence("grokassembly", "vendor",
-                        vendor, Confidence.HIGH));
+                dependency.addEvidence(EvidenceType.VENDOR, "grokassembly", "vendor", vendor, Confidence.HIGH);
             }
 
             final String product = xpath.evaluate("/assembly/product", doc);
             if (product != null) {
-                dependency.getProductEvidence().addEvidence(new Evidence("grokassembly", "product",
-                        product, Confidence.HIGH));
+                dependency.addEvidence(EvidenceType.PRODUCT, "grokassembly", "product", product, Confidence.HIGH);
             }
 
         } catch (ParserConfigurationException pce) {
             throw new AnalysisException("Error initializing the assembly analyzer", pce);
-        } catch (IOException ioe) {
+        } 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);
+            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);
         }
     }
 
@@ -189,45 +200,34 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      * Initialize the analyzer. In this case, extract GrokAssembly.exe to a
      * temporary location.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException thrown if anything goes wrong
      */
     @Override
-    public void initializeFileTypeAnalyzer() throws InitializationException {
+    public void prepareFileTypeAnalyzer(Engine engine) throws InitializationException {
         final File tempFile;
+        final File cfgFile;
         try {
-            tempFile = File.createTempFile("GKA", ".exe", Settings.getTempDirectory());
+            tempFile = File.createTempFile("GKA", ".exe", getSettings().getTempDirectory());
+            cfgFile = new File(tempFile.getPath() + ".config");
         } catch (IOException ex) {
             setEnabled(false);
-            throw new InitializationException("Unable to create temporary file for the assembly analyzerr", ex);
+            throw new InitializationException("Unable to create temporary file for the assembly analyzer", ex);
         }
-        FileOutputStream fos = null;
-        InputStream is = null;
-        try {
-            fos = new FileOutputStream(tempFile);
-            is = AssemblyAnalyzer.class.getClassLoader().getResourceAsStream("GrokAssembly.exe");
+        try (FileOutputStream fos = new FileOutputStream(tempFile);
+                InputStream is = FileUtils.getResourceAsStream("GrokAssembly.exe");
+                FileOutputStream fosCfg = new FileOutputStream(cfgFile);
+                InputStream isCfg = FileUtils.getResourceAsStream("GrokAssembly.exe.config")) {
             IOUtils.copy(is, fos);
-
             grokAssemblyExe = tempFile;
             LOGGER.debug("Extracted GrokAssembly.exe to {}", grokAssemblyExe.getPath());
+            IOUtils.copy(isCfg, fosCfg);
+            grokAssemblyConfig = cfgFile;
+            LOGGER.debug("Extracted GrokAssembly.exe.config to {}", cfgFile);
         } catch (IOException ioe) {
             this.setEnabled(false);
             LOGGER.warn("Could not extract GrokAssembly.exe: {}", ioe.getMessage());
             throw new InitializationException("Could not extract GrokAssembly.exe", ioe);
-        } finally {
-            if (fos != null) {
-                try {
-                    fos.close();
-                } catch (Throwable e) {
-                    LOGGER.debug("Error closing output stream");
-                }
-            }
-            if (is != null) {
-                try {
-                    is.close();
-                } catch (Throwable e) {
-                    LOGGER.debug("Error closing input stream");
-                }
-            }
         }
 
         // Now, need to see if GrokAssembly actually runs from this location.
@@ -238,13 +238,14 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
         //
         // We need to create a non-fatal warning error type that will
         // get added to the report.
-        //TOOD this idea needs to get replicated to the bundle audit analyzer.
+        //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.");
+                    + "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;
         }
@@ -254,9 +255,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
             // Try evacuating the error stream
             IOUtils.copy(p.getErrorStream(), NullOutputStream.NULL_OUTPUT_STREAM);
 
-            final DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
-            factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
-            final DocumentBuilder builder = factory.newDocumentBuilder();
+            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);
@@ -270,7 +269,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
         } catch (InitializationException e) {
             setEnabled(false);
             throw e;
-        } catch (Throwable 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());
@@ -285,8 +284,7 @@ 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");
@@ -296,6 +294,15 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
             LOGGER.debug("Can't delete temporary GrokAssembly.exe");
             grokAssemblyExe.deleteOnExit();
         }
+        try {
+            if (grokAssemblyConfig != null && !grokAssemblyConfig.delete()) {
+                LOGGER.debug("Unable to delete temporary GrokAssembly.exe.config; attempting delete on exit");
+                grokAssemblyConfig.deleteOnExit();
+            }
+        } catch (SecurityException se) {
+            LOGGER.debug("Can't delete temporary GrokAssembly.exe.config");
+            grokAssemblyConfig.deleteOnExit();
+        }
     }
 
     /**
@@ -357,10 +364,8 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
             if (retCode == 0) {
                 return true;
             }
-        } catch (IOException ex) {
-            LOGGER.debug("Path seach failed for " + file);
-        } catch (InterruptedException ex) {
-            LOGGER.debug("Path seach failed for " + file);
+        } catch (IOException | InterruptedException ex) {
+            LOGGER.debug("Path search failed for " + file, ex);
         }
         return false;
     }

core/src/main/java/org/owasp/dependencycheck/analyzer/AutoconfAnalyzer.java

@@ -22,7 +22,6 @@ import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
-import org.owasp.dependencycheck.dependency.EvidenceCollection;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
 import org.owasp.dependencycheck.utils.Settings;
 import org.owasp.dependencycheck.utils.UrlStringUtils;
@@ -33,6 +32,7 @@ import java.io.IOException;
 import java.nio.charset.Charset;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import org.owasp.dependencycheck.dependency.EvidenceType;
 import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
@@ -154,7 +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();
@@ -168,15 +168,14 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
                 final String contents = getFileContents(actualFile);
                 if (!contents.isEmpty()) {
                     if (isOutputScript) {
-                        extractConfigureScriptEvidence(dependency, name,
-                                contents);
+                        extractConfigureScriptEvidence(dependency, name, contents);
                     } else {
                         gatherEvidence(dependency, name, contents);
                     }
                 }
             }
         } else {
-            engine.getDependencies().remove(dependency);
+            engine.removeDependency(dependency);
         }
     }
 
@@ -195,17 +194,13 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
             final String value = matcher.group(2);
             if (!value.isEmpty()) {
                 if (variable.endsWith("NAME")) {
-                    dependency.getProductEvidence().addEvidence(name, variable,
-                            value, Confidence.HIGHEST);
+                    dependency.addEvidence(EvidenceType.PRODUCT, name, variable, value, Confidence.HIGHEST);
                 } else if ("VERSION".equals(variable)) {
-                    dependency.getVersionEvidence().addEvidence(name, variable,
-                            value, Confidence.HIGHEST);
+                    dependency.addEvidence(EvidenceType.VERSION, name, variable, value, Confidence.HIGHEST);
                 } else if ("BUGREPORT".equals(variable)) {
-                    dependency.getVendorEvidence().addEvidence(name, variable,
-                            value, Confidence.HIGH);
+                    dependency.addEvidence(EvidenceType.VENDOR, name, variable, value, Confidence.HIGH);
                 } else if ("URL".equals(variable)) {
-                    dependency.getVendorEvidence().addEvidence(name, variable,
-                            value, Confidence.HIGH);
+                    dependency.addEvidence(EvidenceType.VENDOR, name, variable, value, Confidence.HIGH);
                 }
             }
         }
@@ -239,27 +234,19 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
             String contents) {
         final Matcher matcher = AC_INIT_PATTERN.matcher(contents);
         if (matcher.find()) {
-            final EvidenceCollection productEvidence = dependency
-                    .getProductEvidence();
-            productEvidence.addEvidence(name, "Package", matcher.group(1),
-                    Confidence.HIGHEST);
-            dependency.getVersionEvidence().addEvidence(name,
-                    "Package Version", matcher.group(2), Confidence.HIGHEST);
-            final EvidenceCollection vendorEvidence = dependency
-                    .getVendorEvidence();
+            dependency.addEvidence(EvidenceType.PRODUCT, name, "Package", matcher.group(1), Confidence.HIGHEST);
+            dependency.addEvidence(EvidenceType.VERSION, name, "Package Version", matcher.group(2), Confidence.HIGHEST);
+
             if (null != matcher.group(3)) {
-                vendorEvidence.addEvidence(name, "Bug report address",
-                        matcher.group(4), Confidence.HIGH);
+                dependency.addEvidence(EvidenceType.VENDOR, name, "Bug report address", matcher.group(4), Confidence.HIGH);
             }
             if (null != matcher.group(5)) {
-                productEvidence.addEvidence(name, "Tarname", matcher.group(6),
-                        Confidence.HIGH);
+                dependency.addEvidence(EvidenceType.PRODUCT, name, "Tarname", matcher.group(6), Confidence.HIGH);
             }
             if (null != matcher.group(7)) {
                 final String url = matcher.group(8);
                 if (UrlStringUtils.isUrl(url)) {
-                    vendorEvidence.addEvidence(name, "URL", url,
-                            Confidence.HIGH);
+                    dependency.addEvidence(EvidenceType.VENDOR, name, "URL", url, Confidence.HIGH);
                 }
             }
         }
@@ -268,11 +255,12 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the file type analyzer.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException thrown if there is an exception during
      * initialization
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws InitializationException {
+    protected void prepareFileTypeAnalyzer(Engine engine) throws InitializationException {
         // No initialization needed.
     }
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/CMakeAnalyzer.java

@@ -32,12 +32,10 @@ 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.dependency.EvidenceType;
 import org.owasp.dependencycheck.exception.InitializationException;
 
 /**
@@ -57,6 +55,12 @@ import org.owasp.dependencycheck.exception.InitializationException;
 @Experimental
 public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
 
+    /**
+     * A descriptor for the type of dependencies processed or added by this
+     * analyzer.
+     */
+    public static final String DEPENDENCY_ECOSYSTEM = "CMAKE";
+
     /**
      * The logger.
      */
@@ -65,8 +69,7 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Used when compiling file scanning regex patterns.
      */
-    private static final int REGEX_OPTIONS = Pattern.DOTALL
-            | Pattern.CASE_INSENSITIVE | Pattern.MULTILINE;
+    private static final int REGEX_OPTIONS = Pattern.DOTALL | Pattern.CASE_INSENSITIVE | Pattern.MULTILINE;
 
     /**
      * Regex to extract the product information.
@@ -81,10 +84,8 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
      *
      * Group 2: Version
      */
-    private static final Pattern SET_VERSION = Pattern
-            .compile(
-                    "^ *set\\s*\\(\\s*(\\w+)_version\\s+\"?(\\d+(?:\\.\\d+)+)[\\s\"]?\\)",
-                    REGEX_OPTIONS);
+    private static final Pattern SET_VERSION = Pattern.compile(
+            "^ *set\\s*\\(\\s*(\\w+)_version\\s+\"?(\\d+(?:\\.\\d+)+)[\\s\"]?\\)", REGEX_OPTIONS);
 
     /**
      * Detects files that can be analyzed.
@@ -125,17 +126,13 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the analyzer.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException thrown if an exception occurs getting an
      * instance of SHA1
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws InitializationException {
-        try {
-            getSha1MessageDigest();
-        } catch (IllegalStateException ex) {
-            setEnabled(false);
-            throw new InitializationException("Unable to create SHA1 MessageDigest", ex);
-        }
+    protected void prepareFileTypeAnalyzer(Engine engine) throws InitializationException {
+        //do nothing
     }
 
     /**
@@ -147,12 +144,10 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
      * analyzing the dependency
      */
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
-            throws AnalysisException {
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
+        dependency.setEcosystem(DEPENDENCY_ECOSYSTEM);
         final File file = dependency.getActualFile();
-        final String parentName = file.getParentFile().getName();
         final String name = file.getName();
-        dependency.setDisplayFileName(String.format("%s%c%s", parentName, File.separatorChar, name));
         String contents;
         try {
             contents = FileUtils.readFileToString(file, Charset.defaultCharset()).trim();
@@ -160,7 +155,6 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
             throw new AnalysisException(
                     "Problem occurred while reading dependency file.", e);
         }
-
         if (StringUtils.isNotBlank(contents)) {
             final Matcher m = PROJECT.matcher(contents);
             int count = 0;
@@ -170,9 +164,10 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
                         "Found project command match with %d groups: %s",
                         m.groupCount(), m.group(0)));
                 final String group = m.group(1);
-                LOGGER.debug("Group 1: " + group);
-                dependency.getProductEvidence().addEvidence(name, "Project",
-                        group, Confidence.HIGH);
+                LOGGER.debug("Group 1: {}", group);
+                dependency.addEvidence(EvidenceType.PRODUCT, name, "Project", group, Confidence.HIGH);
+                dependency.addEvidence(EvidenceType.VENDOR, name, "Project", group, Confidence.HIGH);
+                dependency.setName(group);
             }
             LOGGER.debug("Found {} matches.", count);
             analyzeSetVersionCommand(dependency, engine, contents);
@@ -188,9 +183,6 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
      * @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) {
         Dependency currentDep = dependency;
 
@@ -202,8 +194,8 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
                     m.groupCount(), m.group(0));
             String product = m.group(1);
             final String version = m.group(2);
-            LOGGER.debug("Group 1: " + product);
-            LOGGER.debug("Group 2: " + version);
+            LOGGER.debug("Group 1: {}", product);
+            LOGGER.debug("Group 2: {}", version);
             final String aliasPrefix = "ALIASOF_";
             if (product.startsWith(aliasPrefix)) {
                 product = product.replaceFirst(aliasPrefix, "");
@@ -211,45 +203,26 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
             if (count > 1) {
                 //TODO - refactor so we do not assign to the parameter (checkstyle)
                 currentDep = new Dependency(dependency.getActualFile());
-                currentDep.setDisplayFileName(String.format("%s:%s", dependency.getDisplayFileName(), product));
+                currentDep.setEcosystem(DEPENDENCY_ECOSYSTEM);
                 final String filePath = String.format("%s:%s", dependency.getFilePath(), product);
                 currentDep.setFilePath(filePath);
 
-                byte[] path;
-                try {
-                    path = filePath.getBytes("UTF-8");
-                } catch (UnsupportedEncodingException ex) {
-                    path = filePath.getBytes();
-                }
-                final MessageDigest sha1 = getSha1MessageDigest();
-                currentDep.setSha1sum(Checksum.getHex(sha1.digest(path)));
-                engine.getDependencies().add(currentDep);
+                currentDep.setSha1sum(Checksum.getSHA1Checksum(filePath));
+                currentDep.setMd5sum(Checksum.getMD5Checksum(filePath));
+                engine.addDependency(currentDep);
             }
-            final String source = currentDep.getDisplayFileName();
-            currentDep.getProductEvidence().addEvidence(source, "Product",
-                    product, Confidence.MEDIUM);
-            currentDep.getVersionEvidence().addEvidence(source, "Version",
-                    version, Confidence.MEDIUM);
+            final String source = currentDep.getFileName();
+            currentDep.addEvidence(EvidenceType.PRODUCT, source, "Product", product, Confidence.MEDIUM);
+            currentDep.addEvidence(EvidenceType.VENDOR, source, "Vendor", product, Confidence.MEDIUM);
+            currentDep.addEvidence(EvidenceType.VERSION, source, "Version", version, Confidence.MEDIUM);
+            currentDep.setName(product);
+            currentDep.setVersion(version);
         }
-        LOGGER.debug(String.format("Found %d matches.", count));
+        LOGGER.debug("Found {} matches.", count);
     }
 
     @Override
     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);
-        }
-    }
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/CPEAnalyzer.java

@@ -21,12 +21,15 @@ import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.concurrent.TimeUnit;
+import javax.annotation.concurrent.ThreadSafe;
 import org.apache.commons.lang3.builder.CompareToBuilder;
+import org.apache.lucene.analysis.util.CharArraySet;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.index.CorruptIndexException;
 import org.apache.lucene.queryparser.classic.ParseException;
@@ -39,17 +42,19 @@ import org.owasp.dependencycheck.data.cpe.Fields;
 import org.owasp.dependencycheck.data.cpe.IndexEntry;
 import org.owasp.dependencycheck.data.cpe.IndexException;
 import org.owasp.dependencycheck.data.lucene.LuceneUtils;
+import org.owasp.dependencycheck.data.lucene.SearchFieldAnalyzer;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Evidence;
-import org.owasp.dependencycheck.dependency.EvidenceCollection;
+import org.owasp.dependencycheck.dependency.EvidenceType;
 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;
 
@@ -60,6 +65,7 @@ import org.slf4j.LoggerFactory;
  *
  * @author Jeremy Long
  */
+@ThreadSafe
 public class CPEAnalyzer extends AbstractAnalyzer {
 
     /**
@@ -69,26 +75,32 @@ public class CPEAnalyzer extends AbstractAnalyzer {
     /**
      * 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.
+     * utilized within the CPE Names. Note, the :/ are included so URLs are
+     * passed into the Lucene query so that the specialized tokenizer can parse
+     * them.
      */
-    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.
      */
-    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.
      */
-    static final int STRING_BUILDER_BUFFER = 20;
+    private static final int STRING_BUILDER_BUFFER = 20;
+    /**
+     * The URL to perform a search of the NVD CVE data at NIST.
+     */
+    public static final String NVD_SEARCH_URL = "https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=%s";
     /**
      * The CPE in memory index.
      */
@@ -97,11 +109,12 @@ public class CPEAnalyzer extends AbstractAnalyzer {
      * The CVE Database.
      */
     private CveDB cve;
-
     /**
-     * The URL to perform a search of the NVD CVE data at NIST.
+     * The list of ecosystems to skip during analysis. These are skipped because
+     * there is generally a more accurate vulnerability analyzer in the
+     * pipeline.
      */
-    public static final String NVD_SEARCH_URL = "https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=%s";
+    private List<String> skipEcosystems;
 
     /**
      * Returns the name of this analyzer.
@@ -126,13 +139,15 @@ public class CPEAnalyzer extends AbstractAnalyzer {
     /**
      * Creates the CPE Lucene Index.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException is thrown if there is an issue opening
      * the index.
      */
     @Override
-    public void initialize() throws InitializationException {
+    public void prepareAnalyzer(Engine engine) throws InitializationException {
+        super.prepareAnalyzer(engine);
         try {
-            this.open();
+            this.open(engine.getDatabase());
         } catch (IOException ex) {
             LOGGER.debug("Exception initializing the Lucene Index", ex);
             throw new InitializationException("An exception occurred initializing the Lucene Index", ex);
@@ -140,30 +155,35 @@ public class CPEAnalyzer extends AbstractAnalyzer {
             LOGGER.debug("Exception accessing the database", ex);
             throw new InitializationException("An exception occurred accessing the database", ex);
         }
+        final String[] tmp = engine.getSettings().getArray(Settings.KEYS.ECOSYSTEM_SKIP_CPEANALYZER);
+        if (tmp == null) {
+            skipEcosystems = new ArrayList<>();
+        } else {
+            LOGGER.info("Skipping CPE Analysis for {}", tmp);
+            skipEcosystems = Arrays.asList(tmp);
+        }
     }
 
     /**
      * Opens the data source.
      *
+     * @param cve a reference to the NVD CVE database
      * @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 {
-        if (!isOpen()) {
-            cve = new CveDB();
-            cve.open();
-            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);
-            }
+    public void open(CveDB cve) throws IOException, DatabaseException {
+        this.cve = cve;
+        this.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);
         }
     }
 
@@ -171,19 +191,11 @@ public class CPEAnalyzer extends AbstractAnalyzer {
      * Closes the data sources.
      */
     @Override
-    public void close() {
+    public void closeAnalyzer() {
         if (cpe != null) {
             cpe.close();
             cpe = null;
         }
-        if (cve != null) {
-            cve.close();
-            cve = null;
-        }
-    }
-
-    public boolean isOpen() {
-        return cpe != null && cpe.isOpen();
     }
 
     /**
@@ -197,21 +209,20 @@ public class CPEAnalyzer extends AbstractAnalyzer {
      * @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
         String vendors = "";
         String products = "";
         for (Confidence confidence : Confidence.values()) {
-            if (dependency.getVendorEvidence().contains(confidence)) {
-                vendors = addEvidenceWithoutDuplicateTerms(vendors, dependency.getVendorEvidence(), confidence);
+            if (dependency.contains(EvidenceType.VENDOR, confidence)) {
+                vendors = addEvidenceWithoutDuplicateTerms(vendors, dependency.getIterator(EvidenceType.VENDOR, confidence));
                 LOGGER.debug("vendor search: {}", vendors);
             }
-            if (dependency.getProductEvidence().contains(confidence)) {
-                products = addEvidenceWithoutDuplicateTerms(products, dependency.getProductEvidence(), confidence);
+            if (dependency.contains(EvidenceType.PRODUCT, confidence)) {
+                products = addEvidenceWithoutDuplicateTerms(products, dependency.getIterator(EvidenceType.PRODUCT, confidence));
                 LOGGER.debug("product search: {}", products);
             }
             if (!vendors.isEmpty() && !products.isEmpty()) {
-                final List<IndexEntry> entries = searchCPE(vendors, products, dependency.getVendorEvidence().getWeighting(),
-                        dependency.getProductEvidence().getWeighting());
+                final List<IndexEntry> entries = searchCPE(vendors, products, dependency.getVendorWeightings(),
+                        dependency.getProductWeightings());
                 if (entries == null) {
                     continue;
                 }
@@ -233,30 +244,31 @@ public class CPEAnalyzer extends AbstractAnalyzer {
     }
 
     /**
+     * <p>
      * 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.
+     * attempts to prevent duplicate terms from being added.</p>
+     * <p>
+     * Note, if the evidence is longer then 200 characters it will be
+     * truncated.</p>
      *
-     * @param text the base text.
-     * @param ec an EvidenceCollection
-     * @param confidenceFilter a Confidence level to filter the evidence by.
+     * @param text the base text
+     * @param evidence an iterable set of evidence to concatenate
      * @return the new evidence text
      */
-    private String addEvidenceWithoutDuplicateTerms(final String text, final EvidenceCollection ec, Confidence confidenceFilter) {
+    @SuppressWarnings("null")
+    protected String addEvidenceWithoutDuplicateTerms(final String text, final Iterable<Evidence> evidence) {
         final String txt = (text == null) ? "" : text;
-        final StringBuilder sb = new StringBuilder(txt.length() + (20 * ec.size()));
+        final StringBuilder sb = new StringBuilder(txt.length() * 2);
         sb.append(' ').append(txt).append(' ');
-        for (Evidence e : ec.iterator(confidenceFilter)) {
+        for (Evidence e : evidence) {
             String value = e.getValue();
-
-            //hack to get around the fact that lucene does a really good job of recognizing domains and not
-            // splitting them. TODO - put together a better lucene analyzer specific to the domain.
-            if (value.startsWith("http://")) {
-                value = value.substring(7).replaceAll("\\.", " ");
-            }
-            if (value.startsWith("https://")) {
-                value = value.substring(8).replaceAll("\\.", " ");
+            if (value.length() > 1000) {
+                value = value.substring(0, 1000);
+                final int pos = value.lastIndexOf(" ");
+                if (pos > 0) {
+                    value = value.substring(0, pos);
+                }
             }
             if (sb.indexOf(" " + value + " ") < 0) {
                 sb.append(value).append(' ');
@@ -285,7 +297,7 @@ public class CPEAnalyzer extends AbstractAnalyzer {
     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) {
@@ -366,7 +378,7 @@ public class CPEAnalyzer extends AbstractAnalyzer {
      * @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(field).append(":(");
 
         final String cleanText = cleanseText(searchText);
 
@@ -377,6 +389,7 @@ public class CPEAnalyzer extends AbstractAnalyzer {
         if (weightedText == null || weightedText.isEmpty()) {
             LuceneUtils.appendEscapedLuceneQuery(sb, cleanText);
         } else {
+            boolean addSpace = false;
             final StringTokenizer tokens = new StringTokenizer(cleanText);
             while (tokens.hasMoreElements()) {
                 final String word = tokens.nextToken();
@@ -388,14 +401,20 @@ public class CPEAnalyzer extends AbstractAnalyzer {
                         LuceneUtils.appendEscapedLuceneQuery(temp, word);
                         temp.append(WEIGHTING_BOOST);
                         if (!word.equalsIgnoreCase(weightedStr)) {
-                            temp.append(' ');
+                            if (temp.length() > 0) {
+                                temp.append(' ');
+                            }
                             LuceneUtils.appendEscapedLuceneQuery(temp, weightedStr);
                             temp.append(WEIGHTING_BOOST);
                         }
                         break;
                     }
                 }
-                sb.append(' ');
+                if (addSpace) {
+                    sb.append(' ');
+                } else {
+                    addSpace = true;
+                }
                 if (temp == null) {
                     LuceneUtils.appendEscapedLuceneQuery(sb, word);
                 } else {
@@ -403,7 +422,7 @@ public class CPEAnalyzer extends AbstractAnalyzer {
                 }
             }
         }
-        sb.append(" ) ");
+        sb.append(")");
         return true;
     }
 
@@ -450,8 +469,8 @@ public class CPEAnalyzer extends AbstractAnalyzer {
 
         //TODO - does this nullify some of the fuzzy matching that happens in the lucene search?
         // for instance CPE some-component and in the evidence we have SomeComponent.
-        if (collectionContainsString(dependency.getProductEvidence(), entry.getProduct())
-                && collectionContainsString(dependency.getVendorEvidence(), entry.getVendor())) {
+        if (collectionContainsString(dependency.getEvidence(EvidenceType.PRODUCT), entry.getProduct())
+                && collectionContainsString(dependency.getEvidence(EvidenceType.VENDOR), entry.getVendor())) {
             //&& collectionContainsVersion(dependency.getVersionEvidence(), entry.getVersion())
             isValid = true;
         }
@@ -461,19 +480,23 @@ public class CPEAnalyzer extends AbstractAnalyzer {
     /**
      * Used to determine if the EvidenceCollection contains a specific string.
      *
-     * @param ec an EvidenceCollection
+     * @param evidence an of evidence object to check
      * @param text the text to search for
      * @return whether or not the EvidenceCollection contains the string
      */
-    private boolean collectionContainsString(EvidenceCollection ec, String text) {
+    private boolean collectionContainsString(Set<Evidence> evidence, String text) {
         //TODO - likely need to change the split... not sure if this will work for CPE with special chars
         if (text == null) {
             return false;
         }
         final String[] words = text.split("[\\s_-]");
-        final List<String> list = new ArrayList<String>();
+        final List<String> list = new ArrayList<>();
         String tempWord = null;
+        final CharArraySet stopWords = SearchFieldAnalyzer.getStopWords();
         for (String word : words) {
+            if (stopWords.contains(word)) {
+                continue;
+            }
             /*
              single letter words should be concatenated with the next word.
              so { "m", "core", "sample" } -> { "mcore", "sample" }
@@ -498,11 +521,24 @@ public class CPEAnalyzer extends AbstractAnalyzer {
         if (list.isEmpty()) {
             return false;
         }
-        boolean contains = true;
+        boolean isValid = true;
         for (String word : list) {
-            contains &= ec.containsUsedString(word);
+            boolean found = false;
+            for (Evidence e : evidence) {
+                if (e.getValue().toLowerCase().contains(word.toLowerCase())) {
+                    if ("http".equals(word) && e.getValue().contains("http:")) {
+                        continue;
+                    }
+                    found = true;
+                    break;
+                }
+            }
+            isValid &= found;
+            if (!isValid) {
+                break;
+            }
         }
-        return contains;
+        return isValid;
     }
 
     /**
@@ -515,7 +551,10 @@ public class CPEAnalyzer extends AbstractAnalyzer {
      * dependency.
      */
     @Override
-    public synchronized void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    protected void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
+        if (skipEcosystems.contains(dependency.getEcosystem())) {
+            return;
+        }
         try {
             determineCPE(dependency);
         } catch (CorruptIndexException ex) {
@@ -546,16 +585,19 @@ public class CPEAnalyzer extends AbstractAnalyzer {
     protected boolean determineIdentifiers(Dependency dependency, String vendor, String product,
             Confidence currentConfidence) throws UnsupportedEncodingException {
         final Set<VulnerableSoftware> cpes = cve.getCPEs(vendor, product);
+        if (cpes.isEmpty()) {
+            return false;
+        }
         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()) {
-            for (Evidence evidence : dependency.getVersionEvidence().iterator(conf)) {
+            for (Evidence evidence : dependency.getIterator(EvidenceType.VERSION, conf)) {
                 final DependencyVersion evVer = DependencyVersionUtil.parseVersion(evidence.getValue());
                 if (evVer == null) {
                     continue;
@@ -588,11 +630,10 @@ public class CPEAnalyzer extends AbstractAnalyzer {
                         }
                     }
                 }
-                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;
                 }
             }
         }
@@ -602,10 +643,12 @@ public class CPEAnalyzer extends AbstractAnalyzer {
             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);
@@ -628,6 +671,18 @@ public class CPEAnalyzer extends AbstractAnalyzer {
         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.
      */
@@ -655,6 +710,19 @@ public class CPEAnalyzer extends AbstractAnalyzer {
      */
     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.
          *
@@ -671,12 +739,8 @@ public class CPEAnalyzer extends AbstractAnalyzer {
             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
          *
@@ -694,10 +758,6 @@ public class CPEAnalyzer extends AbstractAnalyzer {
         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.
@@ -716,10 +776,6 @@ public class CPEAnalyzer extends AbstractAnalyzer {
         public void setConfidence(IdentifierConfidence confidence) {
             this.confidence = confidence;
         }
-        /**
-         * The CPE identifier.
-         */
-        private Identifier identifier;
 
         /**
          * Get the value of identifier.
@@ -787,10 +843,7 @@ public class CPEAnalyzer extends AbstractAnalyzer {
             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>
 
@@ -808,16 +861,6 @@ public class CPEAnalyzer extends AbstractAnalyzer {
                     .append(evidenceConfidence, o.evidenceConfidence)
                     .append(identifier, o.identifier)
                     .toComparison();
-            /*
-            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;
-             */
         }
     }
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/CentralAnalyzer.java

@@ -36,6 +36,8 @@ import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.List;
+import javax.annotation.concurrent.ThreadSafe;
+import org.owasp.dependencycheck.dependency.EvidenceType;
 import org.owasp.dependencycheck.exception.InitializationException;
 import org.owasp.dependencycheck.utils.DownloadFailedException;
 import org.owasp.dependencycheck.utils.Downloader;
@@ -49,6 +51,7 @@ import org.owasp.dependencycheck.utils.Settings;
  *
  * @author colezlaw
  */
+@ThreadSafe
 public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
@@ -72,28 +75,26 @@ 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.
+     * There may be temporary issues when connecting to MavenCentral. In order
+     * to compensate for 99% of the issues, we perform a retry before finally
+     * failing the analysis.
      */
-    private volatile boolean errorFlag = false;
+    private static final int NUMBER_OF_TRIES = 5;
 
     /**
      * The searcher itself.
      */
     private CentralSearch searcher;
-    /**
-     * Field indicating if the analyzer is enabled.
-     */
-    private final boolean enabled = checkEnabled();
 
     /**
-     * Determine whether to enable this analyzer or not.
+     * Initializes the analyzer with the configured settings.
      *
-     * @return whether the analyzer should be enabled
+     * @param settings the configured settings to use
      */
     @Override
-    public boolean isEnabled() {
-        return enabled;
+    public void initialize(Settings settings) {
+        super.initialize(settings);
+        setEnabled(checkEnabled());
     }
 
     /**
@@ -103,14 +104,14 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
      * <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))) {
+            if (getSettings().getBoolean(Settings.KEYS.ANALYZER_CENTRAL_ENABLED)) {
+                if (!getSettings().getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED)
+                        || NexusAnalyzer.DEFAULT_URL.equals(getSettings().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");
                 }
@@ -120,26 +121,25 @@ 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.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException if there's an error during initialization
      */
     @Override
-    public void initializeFileTypeAnalyzer() throws InitializationException {
+    public void prepareFileTypeAnalyzer(Engine engine) 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);
             try {
-                searcher = new CentralSearch(new URL(searchUrl));
+                searcher = new CentralSearch(getSettings());
             } catch (MalformedURLException ex) {
                 setEnabled(false);
-                throw new InitializationException("The configured URL to Maven Central is malformed: " + searchUrl, ex);
+                throw new InitializationException("The configured URL to Maven Central is malformed", ex);
             }
         }
     }
@@ -193,19 +193,15 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
      * @throws AnalysisException when there's an exception during analysis
      */
     @Override
-    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
-        if (errorFlag || !isEnabled()) {
-            return;
-        }
-
+    public void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         try {
-            final List<MavenArtifact> mas = searcher.searchSha1(dependency.getSha1sum());
+            final List<MavenArtifact> mas = fetchMavenArtifacts(dependency);
             final Confidence confidence = mas.size() > 1 ? Confidence.HIGH : Confidence.HIGHEST;
             for (MavenArtifact ma : mas) {
                 LOGGER.debug("Central analyzer found artifact ({}) for dependency ({})", ma, dependency.getFileName());
                 dependency.addAsEvidence("central", ma, confidence);
                 boolean pomAnalyzed = false;
-                for (Evidence e : dependency.getVendorEvidence()) {
+                for (Evidence e : dependency.getEvidence(EvidenceType.VENDOR)) {
                     if ("pom".equals(e.getSource())) {
                         pomAnalyzed = true;
                         break;
@@ -214,7 +210,7 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
                 if (!pomAnalyzed && ma.getPomUrl() != null) {
                     File pomFile = null;
                     try {
-                        final File baseDir = Settings.getTempDirectory();
+                        final File baseDir = getSettings().getTempDirectory();
                         pomFile = File.createTempFile("pom", ".xml", baseDir);
                         if (!pomFile.delete()) {
                             LOGGER.warn("Unable to fetch pom.xml for {} from Central; "
@@ -222,7 +218,8 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
                             LOGGER.debug("Unable to delete temp file");
                         }
                         LOGGER.debug("Downloading {}", ma.getPomUrl());
-                        Downloader.fetchFile(new URL(ma.getPomUrl()), pomFile);
+                        final Downloader downloader = new Downloader(getSettings());
+                        downloader.fetchFile(new URL(ma.getPomUrl()), pomFile);
                         PomUtils.analyzePOM(dependency, pomFile);
 
                     } catch (DownloadFailedException ex) {
@@ -242,8 +239,61 @@ public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
         } catch (FileNotFoundException fnfe) {
             LOGGER.debug("Artifact not found in repository: '{}", dependency.getFileName());
         } catch (IOException ioe) {
-            LOGGER.debug("Could not connect to Central search", ioe);
-            errorFlag = true;
+            final String message = "Could not connect to Central search. Analysis failed.";
+            LOGGER.error(message, ioe);
+            throw new AnalysisException(message, ioe);
         }
     }
+
+    /**
+     * Downloads the corresponding list of MavenArtifacts of the given
+     * dependency from MavenCentral.
+     * <p>
+     * As the connection to MavenCentral is known to be unreliable, we implement
+     * a simple retry logic in order to compensate for 99% of the issues.
+     *
+     * @param dependency the dependency to analyze
+     * @return the downloaded list of MavenArtifacts
+     * @throws FileNotFoundException if the specified artifact is not found
+     * @throws IOException if connecting to MavenCentral finally failed
+     */
+    protected List<MavenArtifact> fetchMavenArtifacts(Dependency dependency) throws IOException {
+        IOException lastException = null;
+        long sleepingTimeBetweenRetriesInMillis = 1000;
+        int triesLeft = NUMBER_OF_TRIES;
+        while (triesLeft-- > 0) {
+            try {
+                return searcher.searchSha1(dependency.getSha1sum());
+            } catch (FileNotFoundException fnfe) {
+                // retry does not make sense, just throw the exception
+                throw fnfe;
+            } catch (IOException ioe) {
+                LOGGER.debug("Could not connect to Central search (tries left: {}): {}",
+                        triesLeft, ioe.getMessage());
+                lastException = ioe;
+
+                if (triesLeft > 0) {
+                    try {
+                        Thread.sleep(sleepingTimeBetweenRetriesInMillis);
+                        sleepingTimeBetweenRetriesInMillis *= 2;
+                    } catch (InterruptedException e) {
+                        Thread.currentThread().interrupt();
+                    }
+                }
+            }
+        }
+
+        final String message = "Finally failed connecting to Central search."
+                + " Giving up after " + NUMBER_OF_TRIES + " tries.";
+        throw new IOException(message, lastException);
+    }
+
+    /**
+     * Method used by unit tests to setup the analyzer.
+     *
+     * @param searcher the Central Search object to use.
+     */
+    protected void setCentralSearch(CentralSearch searcher) {
+        this.searcher = searcher;
+    }
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/CocoaPodsAnalyzer.java

@@ -23,13 +23,14 @@ import java.io.IOException;
 import java.nio.charset.Charset;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import javax.annotation.concurrent.ThreadSafe;
 
 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.dependency.EvidenceType;
 import org.owasp.dependencycheck.utils.FileFilterBuilder;
 import org.owasp.dependencycheck.utils.Settings;
 
@@ -41,8 +42,15 @@ import org.owasp.dependencycheck.utils.Settings;
  * @author Bianca Jiang (https://twitter.com/biancajiang)
  */
 @Experimental
+@ThreadSafe
 public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
 
+    /**
+     * A descriptor for the type of dependencies processed or added by this
+     * analyzer.
+     */
+    public static final String DEPENDENCY_ECOSYSTEM = "CocoaPod";
+
     /**
      * The logger.
      */
@@ -83,7 +91,7 @@ public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     @Override
-    protected void initializeFileTypeAnalyzer() {
+    protected void prepareFileTypeAnalyzer(Engine engine) {
         // NO-OP
     }
 
@@ -119,9 +127,10 @@ public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     @Override
-    protected void analyzeFileType(Dependency dependency, Engine engine)
+    protected void analyzeDependency(Dependency dependency, Engine engine)
             throws AnalysisException {
 
+        dependency.setEcosystem(DEPENDENCY_ECOSYSTEM);
         String contents;
         try {
             contents = FileUtils.readFileToString(dependency.getActualFile(), Charset.defaultCharset());
@@ -134,21 +143,35 @@ public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
             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);
+            final String name = determineEvidence(contents, blockVariable, "name");
             if (!name.isEmpty()) {
-                vendor.addEvidence(PODSPEC, "name_project", name, Confidence.HIGHEST);
+                dependency.addEvidence(EvidenceType.PRODUCT, PODSPEC, "name_project", name, Confidence.HIGHEST);
+                dependency.addEvidence(EvidenceType.VENDOR, PODSPEC, "name_project", name, Confidence.HIGHEST);
+                dependency.setName(name);
+            }
+            final String summary = determineEvidence(contents, blockVariable, "summary");
+            if (!summary.isEmpty()) {
+                dependency.addEvidence(EvidenceType.PRODUCT, PODSPEC, "summary", summary, 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);
+            final String author = determineEvidence(contents, blockVariable, "authors?");
+            if (!author.isEmpty()) {
+                dependency.addEvidence(EvidenceType.VENDOR, PODSPEC, "author", author, Confidence.HIGHEST);
+            }
+            final String homepage = determineEvidence(contents, blockVariable, "homepage");
+            if (!homepage.isEmpty()) {
+                dependency.addEvidence(EvidenceType.VENDOR, PODSPEC, "homepage", homepage, Confidence.HIGHEST);
+            }
+            final String license = determineEvidence(contents, blockVariable, "licen[cs]es?");
+            if (!license.isEmpty()) {
+                dependency.setLicense(license);
+            }
 
-            addStringEvidence(version, contents, blockVariable, "version", "version", Confidence.HIGHEST);
+            final String version = determineEvidence(contents, blockVariable, "version");
+            if (!version.isEmpty()) {
+                dependency.addEvidence(EvidenceType.VERSION, PODSPEC, "version", version, Confidence.HIGHEST);
+                dependency.setVersion(version);
+            }
         }
 
         setPackagePath(dependency);
@@ -158,16 +181,12 @@ public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
      * 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
+     * @return the evidence
      */
-    private String addStringEvidence(EvidenceCollection evidences, String contents,
-            String blockVariable, String field, String fieldPattern, Confidence confidence) {
+    private String determineEvidence(String contents, String blockVariable, String fieldPattern) {
         String value = "";
 
         //capture array value between [ ]
@@ -184,9 +203,6 @@ public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
                 value = matcher.group(2);
             }
         }
-        if (value.length() > 0) {
-            evidences.addEvidence(PODSPEC, field, value, confidence);
-        }
         return value;
     }
 

core/src/main/java/org/owasp/dependencycheck/analyzer/ComposerLockAnalyzer.java

@@ -33,10 +33,8 @@ import org.slf4j.LoggerFactory;
 
 import java.io.FileFilter;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.nio.charset.Charset;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
+import java.io.IOException;
+import org.owasp.dependencycheck.dependency.EvidenceType;
 
 /**
  * Used to analyze a composer.lock file for a composer PHP app.
@@ -46,6 +44,12 @@ import java.security.NoSuchAlgorithmException;
 @Experimental
 public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
 
+    /**
+     * A descriptor for the type of dependencies processed or added by this
+     * analyzer.
+     */
+    public static final String DEPENDENCY_ECOSYSTEM = "Composer";
+
     /**
      * The logger.
      */
@@ -79,17 +83,13 @@ public class ComposerLockAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the analyzer.
      *
+     * @param engine a reference to the dependency-check engine
      * @throws InitializationException thrown if an exception occurs getting an
      * instance of SHA1
      */
     @Override
-    protected void initializeFileTypeAnalyzer() throws InitializationException {
-        try {
-            getSha1MessageDigest();
-        } catch (IllegalStateException ex) {
-            setEnabled(false);
-            throw new InitializationException("Unable to create SHA1 MessageDigest", ex);
-        }
+    protected void prepareFileTypeAnalyzer(Engine engine) throws InitializationException {
+        // do nothing
     }
 
     /**
@@ -100,38 +100,41 @@ 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());
+            LOGGER.debug("Checking composer.lock file {}", dependency.getActualFilePath());
             clp.process();
+            //if dependencies are found in the lock, then there is always an empty shell dependency left behind for the
+            //composer.lock. The first pass through, reuse the top level dependency, and add new ones for the rest.
+            boolean processedAtLeastOneDep = false;
             for (ComposerDependency dep : clp.getDependencies()) {
                 final Dependency d = new Dependency(dependency.getActualFile());
-                d.setDisplayFileName(String.format("%s:%s/%s", dependency.getDisplayFileName(), dep.getGroup(), dep.getProject()));
-                final String filePath = String.format("%s:%s/%s", dependency.getFilePath(), dep.getGroup(), dep.getProject());
-                final MessageDigest sha1 = getSha1MessageDigest();
+                final String filePath = String.format("%s:%s/%s/%s", dependency.getFilePath(), dep.getGroup(), dep.getProject(), dep.getVersion());
+                d.setName(dep.getProject());
+                d.setVersion(dep.getVersion());
+                d.setEcosystem(DEPENDENCY_ECOSYSTEM);
                 d.setFilePath(filePath);
-                d.setSha1sum(Checksum.getHex(sha1.digest(filePath.getBytes(Charset.defaultCharset()))));
-                d.getVendorEvidence().addEvidence(COMPOSER_LOCK, "vendor", dep.getGroup(), Confidence.HIGHEST);
-                d.getProductEvidence().addEvidence(COMPOSER_LOCK, "product", dep.getProject(), Confidence.HIGHEST);
-                d.getVersionEvidence().addEvidence(COMPOSER_LOCK, "version", dep.getVersion(), Confidence.HIGHEST);
-                LOGGER.info("Adding dependency {}", d);
-                engine.getDependencies().add(d);
+                d.setSha1sum(Checksum.getSHA1Checksum(filePath));
+                d.setMd5sum(Checksum.getMD5Checksum(filePath));
+                d.addEvidence(EvidenceType.VENDOR, COMPOSER_LOCK, "vendor", dep.getGroup(), Confidence.HIGHEST);
+                d.addEvidence(EvidenceType.PRODUCT, COMPOSER_LOCK, "product", dep.getProject(), Confidence.HIGHEST);
+                d.addEvidence(EvidenceType.VERSION, COMPOSER_LOCK, "version", dep.getVersion(), Confidence.HIGHEST);
+                LOGGER.debug("Adding dependency {}", d.getDisplayFileName());
+                engine.addDependency(d);
+                //make sure we only remove the main dependency if we went through this loop at least once.
+                processedAtLeastOneDep = true;
             }
-        } catch (FileNotFoundException fnfe) {
+            // remove the dependency at the end because it's referenced in the loop itself.
+            // double check the name to be sure we only remove the generic entry.
+            if (processedAtLeastOneDep && dependency.getDisplayFileName().equalsIgnoreCase("composer.lock")) {
+                LOGGER.debug("Removing main redundant dependency {}", dependency.getDisplayFileName());
+                engine.removeDependency(dependency);
+            }
+        } 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);
-                }
-            }
         }
     }
 
@@ -164,18 +167,4 @@ 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);
-        }
-    }
 }

core/src/main/java/org/owasp/dependencycheck/analyzer/CpeSuppressionAnalyzer.java

@@ -17,20 +17,19 @@
  */
 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.xml.suppression.SuppressionRule;
+import javax.annotation.concurrent.ThreadSafe;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
- * The suppression analyzer processes an externally defined XML document that complies with the suppressions.xsd schema.
- * Any identified CPE entries within the dependencies that match will be removed.
+ * The suppression analyzer processes an externally defined XML document that
+ * complies with the suppressions.xsd schema. Any identified CPE entries within
+ * the dependencies that match will be removed.
  *
  * @author Jeremy Long
  */
+@ThreadSafe
 public class CpeSuppressionAnalyzer extends AbstractSuppressionAnalyzer {
 
-    //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
      * The name of the analyzer.
      */
@@ -59,17 +58,15 @@ public class CpeSuppressionAnalyzer extends AbstractSuppressionAnalyzer {
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
-    //</editor-fold>
 
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
     @Override
-    public void analyze(final Dependency dependency, final Engine engine) throws AnalysisException {
-
-        if (getRules() == null || getRules().size() <= 0) {
-            return;
-        }
-
-        for (final SuppressionRule rule : getRules()) {
-            rule.process(dependency);
-        }
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_CPE_SUPPRESSION_ENABLED;
     }
 }