version 1.2.6

Former-commit-id: d32ff0d840fc1d1a3153da73158adc125a589efc

.gitignore

@@ -7,6 +7,9 @@
 # Eclipse project files
 .classpath
 .project
+.settings
+maven-eclipse.xml
+.externalToolBuilders
 # Netbeans configuration
 nb-configuration.xml
 /target/

README.md

@@ -40,7 +40,6 @@ The plugin can be configured using the following:
             <plugin>
               <groupId>org.owasp</groupId>
               <artifactId>dependency-check-maven</artifactId>
-              <version>1.0.2</version>
               <executions>
                   <execution>
                       <goals>
@@ -59,7 +58,7 @@ The plugin can be configured using the following:
 
 ### Ant Task
 
-For instructions on the use of the Ant Task, please see the [dependency-check-ant github page](http://jeremylong.github.io/DependencyCheck/dependency-check-maven/installation.html).
+For instructions on the use of the Ant Task, please see the [dependency-check-ant github page](http://jeremylong.github.io/DependencyCheck/dependency-check-ant/installation.html).
 
 Development Usage
 -------------
@@ -106,4 +105,4 @@ Dependency-Check makes use of several other open source libraries. Please see th
   [wiki]: https://github.com/jeremylong/DependencyCheck/wiki
   [subscribe]: mailto:dependency-check+subscribe@googlegroups.com
   [post]: mailto:dependency-check@googlegroups.com
-  [notices]: https://github.com/jeremylong/DependencyCheck/blob/master/NOTICES.txt
+  [notices]: https://github.com/jeremylong/DependencyCheck/blob/master/NOTICES.txt

dependency-check-ant/pom.xml

@@ -15,20 +15,19 @@ limitations under the License.
 
 Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
 -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.6</version>
     </parent>
 
     <artifactId>dependency-check-ant</artifactId>
     <packaging>jar</packaging>
 
     <name>Dependency-Check Ant Task</name>
-    <description>Dependency-check is a utility that attempts to detect publicly disclosed vulnerabilities contained within project dependencies. It does this by determining if there is a Common Platform Enumeration (CPE) identifier for a given dependency. If found, it will generate a report linking to the associated CVE entries.</description>
+    <description>dependency-check-ant is an Ant Task that uses dependency-check-core to detect publicly disclosed vulnerabilities associated with the project's dependencies. The task will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.</description>
     <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
     <distributionManagement>
         <site>
@@ -324,6 +323,9 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
                             <groupId>org.apache.maven.plugins</groupId>
                             <artifactId>maven-javadoc-plugin</artifactId>
                             <version>2.9.1</version>
+                            <configuration>
+                                <bottom>Copyright© 2012-14 Jeremy Long. All Rights Reserved.</bottom>
+                            </configuration>
                             <reportSets>
                                 <reportSet>
                                     <id>default</id>
@@ -439,6 +441,11 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
             <artifactId>dependency-check-core</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.owasp</groupId>
             <artifactId>dependency-check-core</artifactId>

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

@@ -285,26 +285,50 @@ public class DependencyCheckTask extends Task {
         this.reportFormat = reportFormat.getValue();
     }
     /**
-     * The Proxy URL.
+     * The Proxy Server.
      */
-    private String proxyUrl;
+    private String proxyServer;
 
     /**
-     * Get the value of proxyUrl.
+     * Get the value of proxyServer.
      *
-     * @return the value of proxyUrl
+     * @return the value of proxyServer
      */
-    public String getProxyUrl() {
-        return proxyUrl;
+    public String getProxyServer() {
+        return proxyServer;
     }
 
     /**
-     * Set the value of proxyUrl.
+     * Set the value of proxyServer.
      *
-     * @param proxyUrl new value of proxyUrl
+     * @param server new value of proxyServer
      */
+    public void setProxyServer(String server) {
+        this.proxyServer = server;
+    }
+
+    /**
+     * Get the value of proxyServer.
+     *
+     * @return the value of proxyServer
+     * @deprecated use {@link org.owasp.dependencycheck.taskdefs.DependencyCheckTask#getProxyServer()} instead
+     */
+    @Deprecated
+    public String getProxyUrl() {
+        return proxyServer;
+    }
+
+    /**
+     * Set the value of proxyServer.
+     *
+     * @param proxyUrl new value of proxyServer
+     * @deprecated use {@link org.owasp.dependencycheck.taskdefs.DependencyCheckTask#setProxyServer(java.lang.String)}
+     * instead
+     */
+    @Deprecated
     public void setProxyUrl(String proxyUrl) {
-        this.proxyUrl = proxyUrl;
+        LOGGER.warning("A deprecated configuration option 'proxyUrl' was detected; use 'proxyServer' instead.");
+        this.proxyServer = proxyUrl;
     }
     /**
      * The Proxy Port.
@@ -866,7 +890,7 @@ public class DependencyCheckTask extends Task {
 
         Engine engine = null;
         try {
-            engine = new Engine();
+            engine = new Engine(DependencyCheckTask.class.getClassLoader());
 
             for (Resource resource : path) {
                 final FileProvider provider = resource.as(FileProvider.class);
@@ -912,7 +936,7 @@ public class DependencyCheckTask extends Task {
             LOGGER.log(Level.SEVERE, "Unable to connect to the dependency-check database; analysis has stopped");
             LOGGER.log(Level.FINE, "", ex);
         } finally {
-            Settings.cleanup();
+            Settings.cleanup(true);
             if (engine != null) {
                 engine.cleanup();
             }
@@ -935,7 +959,7 @@ public class DependencyCheckTask extends Task {
 
     /**
      * Takes the properties supplied and updates the dependency-check settings. Additionally, this sets the system
-     * properties required to change the proxy url, port, and connection timeout.
+     * properties required to change the proxy server, port, and connection timeout.
      */
     private void populateSettings() {
         Settings.initialize();
@@ -967,8 +991,8 @@ public class DependencyCheckTask extends Task {
 
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
 
-        if (proxyUrl != null && !proxyUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
+        if (proxyServer != null && !proxyServer.isEmpty()) {
+            Settings.setString(Settings.KEYS.PROXY_SERVER, proxyServer);
         }
         if (proxyPort != null && !proxyPort.isEmpty()) {
             Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);

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

@@ -32,7 +32,7 @@ failBuildOnCVSS      | Specifies if the build should be failed if a CVSS score a
 format               | 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
 logFile              | The file path to write verbose logging information. |  
 suppressionFile      | The file path to the XML suppression file \- used to suppress [false positives](../suppression.html) |  
-proxyUrl             | The Proxy URL.                     |  
+proxyServer          | The Proxy Server.                  |  
 proxyPort            | The Proxy Port.                    |  
 proxyUsername        | Defines the proxy user name.       |  
 proxyPassword        | Defines the proxy password.        |  
@@ -46,17 +46,17 @@ Note, that specific analyzers will automatically disable themselves if no file
 types that they support are detected - so specifically disabling them may not
 be needed.
 
-Property                | Description                        | Default Value
-------------------------|------------------------------------|------------------
-archiveAnalyzerEnabled  | Sets whether the Archive Analyzer will be used.                    | true
+Property                | Description                                                               | Default Value
+------------------------|---------------------------------------------------------------------------|------------------
+archiveAnalyzerEnabled  | Sets whether the Archive Analyzer will be used.                           | true
 zipExtensions           | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. |  
-jarAnalyzer             | Sets whether Jar Analyzer will be used.                            | true
-nexusAnalyzerEnabled    | Sets whether Nexus Analyzer will be used.                          | true
-nexusUrl                | Defines the Nexus URL. | https://repository.sonatype.org/service/local/
+jarAnalyzer             | Sets whether Jar Analyzer will be used.                                   | true
+nexusAnalyzerEnabled    | Sets whether Nexus Analyzer will be used.                                 | true
+nexusUrl                | Defines the Nexus Pro URL. If not set the Nexus Analyzer will be disabled. |  
 nexusUsesProxy          | Whether or not the defined proxy should be used when connecting to Nexus. | true
-nuspecAnalyzerEnabled  | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.   | true
-assemblyAnalyzerEnabled | Sets whether or not the .NET Assembly Analyzer should be used.     | true
-pathToMono              | The path to Mono for .NET assembly analysis on non-windows systems |  
+nuspecAnalyzerEnabled   | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.          | true
+assemblyAnalyzerEnabled | Sets whether or not the .NET Assembly Analyzer should be used.            | true
+pathToMono              | The path to Mono for .NET assembly analysis on non-windows systems.       |  
 
 Advanced Configuration
 ====================

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

@@ -3,7 +3,20 @@ Installation
 Download dependency-check-ant from [bintray here](http://dl.bintray.com/jeremy-long/owasp/dependency-check-ant-${project.version}.jar).
 To install dependency-check-ant place the dependency-check-ant-${project.version}.jar into
 the lib directory of your Ant instalation directory. Once installed you can add
-the taskdef to you build.xml and add the task to a new or existing target.
+the taskdef to you build.xml and add the task to a new or existing target:
+
+```xml
+<taskdef name="dependency-check" classname="org.owasp.dependencycheck.taskdefs.DependencyCheckTask"/>
+```
+
+If you do not want to install dependency-check-ant into your ant's lib directory when you define the task def you
+must add the classpath to the taskdef:
+
+```xml
+<taskdef name="dependency-check" classname="org.owasp.dependencycheck.taskdefs.DependencyCheckTask">
+    <classpath path="[path]/[to]/dependency-check-ant-${project.version}.jar"/>
+</taskdef>
+```
 
 It is important to understand that the first time this task is executed it may
 take 20 minutes or more as it downloads and processes the data from the National

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

@@ -1,11 +1,19 @@
 Usage
 ====================
-First, add the dependency-check-ant taskdef to your build.xml:
+First, add the dependency-check-ant taskdef to your build.xml (see the [installation guide](installation.html):
 
 ```xml
 <taskdef name="dependency-check" classname="org.owasp.dependencycheck.taskdefs.DependencyCheckTask"/>
 ```
 
+Or
+
+```xml
+<taskdef name="dependency-check" classname="org.owasp.dependencycheck.taskdefs.DependencyCheckTask">
+    <classpath path="[path]/[to]/dependency-check-ant-${project.version}.jar"/>
+</taskdef>
+```
+
 Next, add the task to a target of your choosing:
 
 ```xml

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

@@ -45,7 +45,7 @@ public class DependencyCheckTaskTest extends BuildFileTest {
     public void tearDown() {
         //no cleanup...
         //executeTarget("cleanup");
-        Settings.cleanup();
+        Settings.cleanup(true);
     }
 
     /**

dependency-check-cli/pom.xml

@@ -15,20 +15,19 @@ limitations under the License.
 
 Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
 -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.6</version>
     </parent>
 
     <artifactId>dependency-check-cli</artifactId>
     <packaging>jar</packaging>
 
     <name>Dependency-Check Command Line</name>
-    <description>Dependency-Check-Maven is a Maven Plugin that attempts to detect publicly disclosed vulnerabilities contained within project dependencies. It does this by determining if there is a Common Platform Enumeration (CPE) identifier for a given dependency. If found, it will generate a report linking to the associated CVE entries.</description>
+    <description>dependency-check-cli is an command line tool that uses dependency-check-core to detect publicly disclosed vulnerabilities associated with the scanned project dependencies. The tool will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.</description>
     <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
     <distributionManagement>
         <site>
@@ -174,6 +173,9 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                             <groupId>org.apache.maven.plugins</groupId>
                             <artifactId>maven-javadoc-plugin</artifactId>
                             <version>2.9.1</version>
+                            <configuration>
+                                <bottom>Copyright© 2012-14 Jeremy Long. All Rights Reserved.</bottom>
+                            </configuration>
                             <reportSets>
                                 <reportSet>
                                     <id>default</id>
@@ -284,12 +286,12 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>appassembler-maven-plugin</artifactId>
-                <version>1.7</version>
+                <version>1.8.1</version>
                 <configuration>
                     <programs>
                         <program>
                             <mainClass>org.owasp.dependencycheck.App</mainClass>
-                            <name>dependency-check</name>
+                            <id>dependency-check</id>
                         </program>
                     </programs>
                     <assembleDirectory>${project.build.directory}/release</assembleDirectory>
@@ -341,5 +343,10 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
             <artifactId>dependency-check-core</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
     </dependencies>
 </project>

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

@@ -2,10 +2,8 @@
 <assembly
     xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="
-    http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
-      http://maven.apache.org/xsd/assembly-1.1.2.xsd
-  "
+    xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2
+      http://maven.apache.org/xsd/assembly-1.1.2.xsd"
 >
     <id>release</id>
     <formats>

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

@@ -21,15 +21,19 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.apache.commons.cli.ParseException;
-import org.owasp.dependencycheck.cli.CliParser;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.org.apache.tools.ant.DirectoryScanner;
 import org.owasp.dependencycheck.reporting.ReportGenerator;
 import org.owasp.dependencycheck.utils.LogUtils;
 import org.owasp.dependencycheck.utils.Settings;
@@ -57,8 +61,13 @@ public class App {
      * @param args the command line arguments
      */
     public static void main(String[] args) {
-        final App app = new App();
-        app.run(args);
+        try {
+            Settings.initialize();
+            final App app = new App();
+            app.run(args);
+        } finally {
+            Settings.cleanup(true);
+        }
     }
 
     /**
@@ -67,8 +76,8 @@ public class App {
      * @param args the command line arguments
      */
     public void run(String[] args) {
-
         final CliParser cli = new CliParser();
+
         try {
             cli.parse(args);
         } catch (FileNotFoundException ex) {
@@ -88,7 +97,11 @@ public class App {
             cli.printVersionInfo();
         } else if (cli.isRunScan()) {
             populateSettings(cli);
-            runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getApplicationName(), cli.getScanFiles());
+            try {
+                runScan(cli.getReportDirectory(), cli.getReportFormat(), cli.getApplicationName(), cli.getScanFiles(), cli.getExcludeList());
+            } catch (InvalidScanPathException ex) {
+                Logger.getLogger(App.class.getName()).log(Level.SEVERE, "An invalid scan path was detected; unable to scan '//*' paths");
+            }
         } else {
             cli.printHelp();
         }
@@ -101,18 +114,71 @@ public class App {
      * @param outputFormat the output format of the report
      * @param applicationName the application name for the report
      * @param files the files/directories to scan
+     * @param excludes the patterns for files/directories to exclude
+     *
+     * @throws InvalidScanPathException thrown if the path to scan starts with "//"
      */
-    private void runScan(String reportDirectory, String outputFormat, String applicationName, String[] files) {
-        Engine scanner = null;
+    private void runScan(String reportDirectory, String outputFormat, String applicationName, String[] files,
+            String[] excludes) throws InvalidScanPathException {
+        Engine engine = null;
         try {
-            scanner = new Engine();
-
-            for (String file : files) {
-                scanner.scan(file);
+            engine = new Engine();
+            List<String> antStylePaths = new ArrayList<String>();
+            if (excludes == null || excludes.length == 0) {
+                for (String file : files) {
+                    if (file.contains("*") || file.contains("?")) {
+                        antStylePaths.add(file);
+                    } else {
+                        engine.scan(file);
+                    }
+                }
+            } else {
+                antStylePaths = Arrays.asList(files);
             }
 
-            scanner.analyzeDependencies();
-            final List<Dependency> dependencies = scanner.getDependencies();
+            final Set<File> paths = new HashSet<File>();
+            for (String file : antStylePaths) {
+                final DirectoryScanner scanner = new DirectoryScanner();
+                String include = file.replace('\\', '/');
+                File baseDir;
+
+                if (include.startsWith("//")) {
+                    throw new InvalidScanPathException("Unable to scan paths specified by //");
+                } else if (include.startsWith("./")) {
+                    baseDir = new File(".");
+                    include = include.substring(2);
+                } else if (include.startsWith("/")) {
+                    baseDir = new File("/");
+                    include = include.substring(1);
+                } else if (include.contains("/")) {
+                    final int pos = include.indexOf('/');
+                    final String tmp = include.substring(0, pos);
+                    if (tmp.contains("*") || tmp.contains("?")) {
+                        baseDir = new File(".");
+                    } else {
+                        baseDir = new File(tmp);
+                        include = include.substring(pos + 1);
+                    }
+                } else { //no path info - must just be a file in the working directory
+                    baseDir = new File(".");
+                }
+                scanner.setBasedir(baseDir);
+                scanner.setIncludes(include);
+                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);
+                        paths.add(f);
+                    }
+                }
+            }
+            engine.scan(paths);
+
+            engine.analyzeDependencies();
+            final List<Dependency> dependencies = engine.getDependencies();
             DatabaseProperties prop = null;
             CveDB cve = null;
             try {
@@ -126,7 +192,7 @@ public class App {
                     cve.close();
                 }
             }
-            final ReportGenerator report = new ReportGenerator(applicationName, dependencies, scanner.getAnalyzers(), prop);
+            final ReportGenerator report = new ReportGenerator(applicationName, dependencies, engine.getAnalyzers(), prop);
             try {
                 report.generateReports(reportDirectory, outputFormat);
             } catch (IOException ex) {
@@ -140,9 +206,8 @@ public class App {
             LOGGER.log(Level.SEVERE, "Unable to connect to the dependency-check database; analysis has stopped");
             LOGGER.log(Level.FINE, "", ex);
         } finally {
-            Settings.cleanup();
-            if (scanner != null) {
-                scanner.cleanup();
+            if (engine != null) {
+                engine.cleanup();
             }
         }
     }
@@ -155,11 +220,9 @@ public class App {
      */
     private void populateSettings(CliParser cli) {
 
-        Settings.initialize();
-
         final boolean autoUpdate = cli.isAutoUpdate();
         final String connectionTimeout = cli.getConnectionTimeout();
-        final String proxyUrl = cli.getProxyUrl();
+        final String proxyServer = cli.getProxyServer();
         final String proxyPort = cli.getProxyPort();
         final String proxyUser = cli.getProxyUsername();
         final String proxyPass = cli.getProxyPassword();
@@ -210,8 +273,8 @@ public class App {
             Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
         }
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
-        if (proxyUrl != null && !proxyUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
+        if (proxyServer != null && !proxyServer.isEmpty()) {
+            Settings.setString(Settings.KEYS.PROXY_SERVER, proxyServer);
         }
         if (proxyPort != null && !proxyPort.isEmpty()) {
             Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);

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

@@ -15,10 +15,11 @@
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
-package org.owasp.dependencycheck.cli;
+package org.owasp.dependencycheck;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.logging.Logger;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.HelpFormatter;
@@ -39,6 +40,10 @@ import org.owasp.dependencycheck.utils.Settings;
  */
 public final class CliParser {
 
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(CliParser.class.getName());
     /**
      * The command line.
      */
@@ -85,16 +90,16 @@ public final class CliParser {
      */
     private void validateArgs() throws FileNotFoundException, ParseException {
         if (isRunScan()) {
-            validatePathExists(getScanFiles(), ArgumentName.SCAN);
-            validatePathExists(getReportDirectory(), ArgumentName.OUT);
+            validatePathExists(getScanFiles(), ARGUMENT.SCAN);
+            validatePathExists(getReportDirectory(), ARGUMENT.OUT);
             if (getPathToMono() != null) {
-                validatePathExists(getPathToMono(), ArgumentName.PATH_TO_MONO);
+                validatePathExists(getPathToMono(), ARGUMENT.PATH_TO_MONO);
             }
-            if (!line.hasOption(ArgumentName.APP_NAME)) {
+            if (!line.hasOption(ARGUMENT.APP_NAME)) {
                 throw new ParseException("Missing 'app' argument; the scan cannot be run without the an application name.");
             }
-            if (line.hasOption(ArgumentName.OUTPUT_FORMAT)) {
-                final String format = line.getOptionValue(ArgumentName.OUTPUT_FORMAT);
+            if (line.hasOption(ARGUMENT.OUTPUT_FORMAT)) {
+                final String format = line.getOptionValue(ARGUMENT.OUTPUT_FORMAT);
                 try {
                     Format.valueOf(format);
                 } catch (IllegalArgumentException ex) {
@@ -129,14 +134,33 @@ public final class CliParser {
      * @throws FileNotFoundException is thrown if the path being validated does not exist.
      */
     private void validatePathExists(String path, String argumentName) throws FileNotFoundException {
-        if (!path.contains("*.")) {
+        if (path == null) {
+            isValid = false;
+            final String msg = String.format("Invalid '%s' argument: null", argumentName);
+            throw new FileNotFoundException(msg);
+        } else if (!path.contains("*") && !path.contains("?")) {
             final File f = new File(path);
-            if (!f.exists()) {
-                isValid = false;
-                final String msg = String.format("Invalid '%s' argument: '%s'", argumentName, path);
-                throw new FileNotFoundException(msg);
+            if ("o".equals(argumentName.substring(0, 1).toLowerCase()) && !"ALL".equals(this.getReportFormat().toUpperCase())) {
+                final String checkPath = path.toLowerCase();
+                if (checkPath.endsWith(".html") || checkPath.endsWith(".xml") || checkPath.endsWith(".htm")) {
+                    if (!f.getParentFile().isDirectory()) {
+                        isValid = false;
+                        final String msg = String.format("Invalid '%s' argument: '%s'", argumentName, path);
+                        throw new FileNotFoundException(msg);
+                    }
+                }
+            } else {
+                if (!f.exists()) {
+                    isValid = false;
+                    final String msg = String.format("Invalid '%s' argument: '%s'", argumentName, path);
+                    throw new FileNotFoundException(msg);
+                }
             }
-        } // else { // TODO add a validation for *.zip extensions rather then relying on the engine to validate it.
+        } 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);
+        }
     }
 
     /**
@@ -146,11 +170,10 @@ public final class CliParser {
      */
     @SuppressWarnings("static-access")
     private Options createCommandLineOptions() {
-
         final Options options = new Options();
         addStandardOptions(options);
         addAdvancedOptions(options);
-
+        addDeprecatedOptions(options);
         return options;
     }
 
@@ -162,44 +185,50 @@ public final class CliParser {
      */
     @SuppressWarnings("static-access")
     private void addStandardOptions(final Options options) throws IllegalArgumentException {
-        final Option help = new Option(ArgumentName.HELP_SHORT, ArgumentName.HELP, false,
+        final Option help = new Option(ARGUMENT.HELP_SHORT, ARGUMENT.HELP, false,
                 "Print this message.");
 
-        final Option advancedHelp = OptionBuilder.withLongOpt(ArgumentName.ADVANCED_HELP)
+        final Option advancedHelp = OptionBuilder.withLongOpt(ARGUMENT.ADVANCED_HELP)
                 .withDescription("Print the advanced help message.").create();
 
-        final Option version = new Option(ArgumentName.VERSION_SHORT, ArgumentName.VERSION,
+        final Option version = new Option(ARGUMENT.VERSION_SHORT, ARGUMENT.VERSION,
                 false, "Print the version information.");
 
-        final Option noUpdate = new Option(ArgumentName.DISABLE_AUTO_UPDATE_SHORT, ArgumentName.DISABLE_AUTO_UPDATE,
+        final Option noUpdate = new Option(ARGUMENT.DISABLE_AUTO_UPDATE_SHORT, ARGUMENT.DISABLE_AUTO_UPDATE,
                 false, "Disables the automatic updating of the CPE data.");
 
-        final Option appName = OptionBuilder.withArgName("name").hasArg().withLongOpt(ArgumentName.APP_NAME)
+        final Option appName = OptionBuilder.withArgName("name").hasArg().withLongOpt(ARGUMENT.APP_NAME)
                 .withDescription("The name of the application being scanned. This is a required argument.")
-                .create(ArgumentName.APP_NAME_SHORT);
+                .create(ARGUMENT.APP_NAME_SHORT);
 
-        final Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.SCAN)
-                .withDescription("The path to scan - this option can be specified multiple times. To limit the scan"
-                        + " to specific file types *.[ext] can be added to the end of the path.")
-                .create(ArgumentName.SCAN_SHORT);
+        final Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ARGUMENT.SCAN)
+                .withDescription("The path to scan - this option can be specified multiple times. Ant style"
+                        + " paths are supported (e.g. path/**/*.jar).")
+                .create(ARGUMENT.SCAN_SHORT);
 
-        final Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP)
+        final Option excludes = OptionBuilder.withArgName("pattern").hasArg().withLongOpt(ARGUMENT.EXCLUDE)
+                .withDescription("Specify and exclusion pattern. This option can be specified multiple times"
+                        + " and it accepts Ant style excludsions.")
+                .create();
+
+        final Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ARGUMENT.PROP)
                 .withDescription("A property file to load.")
-                .create(ArgumentName.PROP_SHORT);
+                .create(ARGUMENT.PROP_SHORT);
 
-        final Option out = OptionBuilder.withArgName("folder").hasArg().withLongOpt(ArgumentName.OUT)
-                .withDescription("The folder to write reports to. This defaults to the current directory.")
-                .create(ArgumentName.OUT_SHORT);
+        final Option out = OptionBuilder.withArgName("path").hasArg().withLongOpt(ARGUMENT.OUT)
+                .withDescription("The folder to write reports to. This defaults to the current directory. "
+                        + "It is possible to set this to a specific file name if the format argument is not set to ALL.")
+                .create(ARGUMENT.OUT_SHORT);
 
-        final Option outputFormat = OptionBuilder.withArgName("format").hasArg().withLongOpt(ArgumentName.OUTPUT_FORMAT)
+        final Option outputFormat = OptionBuilder.withArgName("format").hasArg().withLongOpt(ARGUMENT.OUTPUT_FORMAT)
                 .withDescription("The output format to write to (XML, HTML, VULN, ALL). The default is HTML.")
-                .create(ArgumentName.OUTPUT_FORMAT_SHORT);
+                .create(ARGUMENT.OUTPUT_FORMAT_SHORT);
 
-        final Option verboseLog = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.VERBOSE_LOG)
+        final Option verboseLog = OptionBuilder.withArgName("file").hasArg().withLongOpt(ARGUMENT.VERBOSE_LOG)
                 .withDescription("The file path to write verbose logging information.")
-                .create(ArgumentName.VERBOSE_LOG_SHORT);
+                .create(ARGUMENT.VERBOSE_LOG_SHORT);
 
-        final Option suppressionFile = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.SUPPRESSION_FILE)
+        final Option suppressionFile = OptionBuilder.withArgName("file").hasArg().withLongOpt(ARGUMENT.SUPPRESSION_FILE)
                 .withDescription("The file path to the suppression XML file.")
                 .create();
 
@@ -207,7 +236,11 @@ public final class CliParser {
         final OptionGroup og = new OptionGroup();
         og.addOption(path);
 
+        final OptionGroup exog = new OptionGroup();
+        exog.addOption(excludes);
+
         options.addOptionGroup(og)
+                .addOptionGroup(exog)
                 .addOption(out)
                 .addOption(outputFormat)
                 .addOption(appName)
@@ -230,87 +263,87 @@ public final class CliParser {
     @SuppressWarnings("static-access")
     private void addAdvancedOptions(final Options options) throws IllegalArgumentException {
 
-        final Option data = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.DATA_DIRECTORY)
+        final Option data = OptionBuilder.withArgName("path").hasArg().withLongOpt(ARGUMENT.DATA_DIRECTORY)
                 .withDescription("The location of the H2 Database file. This option should generally not be set.")
-                .create(ArgumentName.DATA_DIRECTORY_SHORT);
+                .create(ARGUMENT.DATA_DIRECTORY_SHORT);
 
-        final Option connectionTimeout = OptionBuilder.withArgName("timeout").hasArg().withLongOpt(ArgumentName.CONNECTION_TIMEOUT)
+        final Option connectionTimeout = OptionBuilder.withArgName("timeout").hasArg().withLongOpt(ARGUMENT.CONNECTION_TIMEOUT)
                 .withDescription("The connection timeout (in milliseconds) to use when downloading resources.")
-                .create(ArgumentName.CONNECTION_TIMEOUT_SHORT);
+                .create(ARGUMENT.CONNECTION_TIMEOUT_SHORT);
 
-        final Option proxyUrl = OptionBuilder.withArgName("url").hasArg().withLongOpt(ArgumentName.PROXY_URL)
-                .withDescription("The proxy url to use when downloading resources.")
-                .create(ArgumentName.PROXY_URL_SHORT);
+        final Option proxyServer = OptionBuilder.withArgName("server").hasArg().withLongOpt(ARGUMENT.PROXY_SERVER)
+                .withDescription("The proxy server to use when downloading resources.")
+                .create();
 
-        final Option proxyPort = OptionBuilder.withArgName("port").hasArg().withLongOpt(ArgumentName.PROXY_PORT)
+        final Option proxyPort = OptionBuilder.withArgName("port").hasArg().withLongOpt(ARGUMENT.PROXY_PORT)
                 .withDescription("The proxy port to use when downloading resources.")
-                .create(ArgumentName.PROXY_PORT_SHORT);
+                .create();
 
-        final Option proxyUsername = OptionBuilder.withArgName("user").hasArg().withLongOpt(ArgumentName.PROXY_USERNAME)
+        final Option proxyUsername = OptionBuilder.withArgName("user").hasArg().withLongOpt(ARGUMENT.PROXY_USERNAME)
                 .withDescription("The proxy username to use when downloading resources.")
                 .create();
 
-        final Option proxyPassword = OptionBuilder.withArgName("pass").hasArg().withLongOpt(ArgumentName.PROXY_PASSWORD)
+        final Option proxyPassword = OptionBuilder.withArgName("pass").hasArg().withLongOpt(ARGUMENT.PROXY_PASSWORD)
                 .withDescription("The proxy password to use when downloading resources.")
                 .create();
 
-        final Option connectionString = OptionBuilder.withArgName("connStr").hasArg().withLongOpt(ArgumentName.CONNECTION_STRING)
+        final Option connectionString = OptionBuilder.withArgName("connStr").hasArg().withLongOpt(ARGUMENT.CONNECTION_STRING)
                 .withDescription("The connection string to the database.")
                 .create();
 
-        final Option dbUser = OptionBuilder.withArgName("user").hasArg().withLongOpt(ArgumentName.DB_NAME)
+        final Option dbUser = OptionBuilder.withArgName("user").hasArg().withLongOpt(ARGUMENT.DB_NAME)
                 .withDescription("The username used to connect to the database.")
                 .create();
 
-        final Option dbPassword = OptionBuilder.withArgName("password").hasArg().withLongOpt(ArgumentName.DB_PASSWORD)
+        final Option dbPassword = OptionBuilder.withArgName("password").hasArg().withLongOpt(ARGUMENT.DB_PASSWORD)
                 .withDescription("The password for connecting to the database.")
                 .create();
 
-        final Option dbDriver = OptionBuilder.withArgName("driver").hasArg().withLongOpt(ArgumentName.DB_DRIVER)
+        final Option dbDriver = OptionBuilder.withArgName("driver").hasArg().withLongOpt(ARGUMENT.DB_DRIVER)
                 .withDescription("The database driver name.")
                 .create();
 
-        final Option dbDriverPath = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.DB_DRIVER_PATH)
+        final Option dbDriverPath = OptionBuilder.withArgName("path").hasArg().withLongOpt(ARGUMENT.DB_DRIVER_PATH)
                 .withDescription("The path to the database driver; note, this does not need to be set unless the JAR is outside of the classpath.")
                 .create();
 
-        final Option disableJarAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_JAR)
+        final Option disableJarAnalyzer = OptionBuilder.withLongOpt(ARGUMENT.DISABLE_JAR)
                 .withDescription("Disable the Jar Analyzer.")
                 .create();
-        final Option disableArchiveAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_ARCHIVE)
+        final Option disableArchiveAnalyzer = OptionBuilder.withLongOpt(ARGUMENT.DISABLE_ARCHIVE)
                 .withDescription("Disable the Archive Analyzer.")
                 .create();
-        final Option disableNuspecAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_NUSPEC)
+        final Option disableNuspecAnalyzer = OptionBuilder.withLongOpt(ARGUMENT.DISABLE_NUSPEC)
                 .withDescription("Disable the Nuspec Analyzer.")
                 .create();
-        final Option disableAssemblyAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_ASSEMBLY)
+        final Option disableAssemblyAnalyzer = OptionBuilder.withLongOpt(ARGUMENT.DISABLE_ASSEMBLY)
                 .withDescription("Disable the .NET Assembly Analyzer.")
                 .create();
 
-        final Option disableNexusAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_NEXUS)
+        final Option disableNexusAnalyzer = OptionBuilder.withLongOpt(ARGUMENT.DISABLE_NEXUS)
                 .withDescription("Disable the Nexus Analyzer.")
                 .create();
 
-        final Option nexusUrl = OptionBuilder.withArgName("url").hasArg().withLongOpt(ArgumentName.NEXUS_URL)
-                .withDescription("The url to the Nexus Server.")
+        final Option nexusUrl = OptionBuilder.withArgName("url").hasArg().withLongOpt(ARGUMENT.NEXUS_URL)
+                .withDescription("The url to the Nexus Pro Server. If not set the Nexus Analyzer will be disabled.")
                 .create();
 
-        final Option nexusUsesProxy = OptionBuilder.withArgName("true/false").hasArg().withLongOpt(ArgumentName.NEXUS_USES_PROXY)
+        final Option nexusUsesProxy = OptionBuilder.withArgName("true/false").hasArg().withLongOpt(ARGUMENT.NEXUS_USES_PROXY)
                 .withDescription("Whether or not the configured proxy should be used when connecting to Nexus.")
                 .create();
 
         final Option additionalZipExtensions = OptionBuilder.withArgName("extensions").hasArg()
-                .withLongOpt(ArgumentName.ADDITIONAL_ZIP_EXTENSIONS)
+                .withLongOpt(ARGUMENT.ADDITIONAL_ZIP_EXTENSIONS)
                 .withDescription("A comma separated list of additional extensions to be scanned as ZIP files "
                         + "(ZIP, EAR, WAR are already treated as zip files)")
                 .create();
 
-        final Option pathToMono = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.PATH_TO_MONO)
+        final Option pathToMono = OptionBuilder.withArgName("path").hasArg().withLongOpt(ARGUMENT.PATH_TO_MONO)
                 .withDescription("The path to Mono for .NET Assembly analysis on non-windows systems.")
                 .create();
 
         options.addOption(proxyPort)
-                .addOption(proxyUrl)
+                .addOption(proxyServer)
                 .addOption(proxyUsername)
                 .addOption(proxyPassword)
                 .addOption(connectionTimeout)
@@ -331,13 +364,30 @@ public final class CliParser {
                 .addOption(pathToMono);
     }
 
+    /**
+     * Adds the deprecated command line options to the given options collection. These are split out for purposes of not
+     * including them in the help message. We need to add the deprecated options so as not to break existing scripts.
+     *
+     * @param options a collection of command line arguments
+     * @throws IllegalArgumentException thrown if there is an exception
+     */
+    @SuppressWarnings("static-access")
+    private void addDeprecatedOptions(final Options options) throws IllegalArgumentException {
+
+        final Option proxyServer = OptionBuilder.withArgName("url").hasArg().withLongOpt(ARGUMENT.PROXY_URL)
+                .withDescription("The proxy url argument is deprecated, use proxyserver instead.")
+                .create();
+
+        options.addOption(proxyServer);
+    }
+
     /**
      * Determines if the 'version' command line argument was passed in.
      *
      * @return whether or not the 'version' command line argument was passed in
      */
     public boolean isGetVersion() {
-        return (line != null) && line.hasOption(ArgumentName.VERSION);
+        return (line != null) && line.hasOption(ARGUMENT.VERSION);
     }
 
     /**
@@ -346,7 +396,7 @@ public final class CliParser {
      * @return whether or not the 'help' command line argument was passed in
      */
     public boolean isGetHelp() {
-        return (line != null) && line.hasOption(ArgumentName.HELP);
+        return (line != null) && line.hasOption(ARGUMENT.HELP);
     }
 
     /**
@@ -355,7 +405,7 @@ public final class CliParser {
      * @return whether or not the 'scan' command line argument was passed in
      */
     public boolean isRunScan() {
-        return (line != null) && isValid && line.hasOption(ArgumentName.SCAN);
+        return (line != null) && isValid && line.hasOption(ARGUMENT.SCAN);
     }
 
     /**
@@ -364,7 +414,7 @@ public final class CliParser {
      * @return true if the disableJar command line argument was specified; otherwise false
      */
     public boolean isJarDisabled() {
-        return (line != null) && line.hasOption(ArgumentName.DISABLE_JAR);
+        return (line != null) && line.hasOption(ARGUMENT.DISABLE_JAR);
     }
 
     /**
@@ -373,7 +423,7 @@ public final class CliParser {
      * @return true if the disableArchive command line argument was specified; otherwise false
      */
     public boolean isArchiveDisabled() {
-        return (line != null) && line.hasOption(ArgumentName.DISABLE_ARCHIVE);
+        return (line != null) && line.hasOption(ARGUMENT.DISABLE_ARCHIVE);
     }
 
     /**
@@ -382,7 +432,7 @@ public final class CliParser {
      * @return true if the disableNuspec command line argument was specified; otherwise false
      */
     public boolean isNuspecDisabled() {
-        return (line != null) && line.hasOption(ArgumentName.DISABLE_NUSPEC);
+        return (line != null) && line.hasOption(ARGUMENT.DISABLE_NUSPEC);
     }
 
     /**
@@ -391,7 +441,7 @@ public final class CliParser {
      * @return true if the disableAssembly command line argument was specified; otherwise false
      */
     public boolean isAssemblyDisabled() {
-        return (line != null) && line.hasOption(ArgumentName.DISABLE_ASSEMBLY);
+        return (line != null) && line.hasOption(ARGUMENT.DISABLE_ASSEMBLY);
     }
 
     /**
@@ -400,7 +450,7 @@ public final class CliParser {
      * @return true if the disableNexus command line argument was specified; otherwise false
      */
     public boolean isNexusDisabled() {
-        return (line != null) && line.hasOption(ArgumentName.DISABLE_NEXUS);
+        return (line != null) && line.hasOption(ARGUMENT.DISABLE_NEXUS);
     }
 
     /**
@@ -409,10 +459,10 @@ public final class CliParser {
      * @return the url to the nexus server; if none was specified this will return null;
      */
     public String getNexusUrl() {
-        if (line == null || !line.hasOption(ArgumentName.NEXUS_URL)) {
+        if (line == null || !line.hasOption(ARGUMENT.NEXUS_URL)) {
             return null;
         } else {
-            return line.getOptionValue(ArgumentName.NEXUS_URL);
+            return line.getOptionValue(ARGUMENT.NEXUS_URL);
         }
     }
 
@@ -425,14 +475,14 @@ public final class CliParser {
     public boolean isNexusUsesProxy() {
         // If they didn't specify whether Nexus needs to use the proxy, we should
         // still honor the property if it's set.
-        if (line == null || !line.hasOption(ArgumentName.NEXUS_USES_PROXY)) {
+        if (line == null || !line.hasOption(ARGUMENT.NEXUS_USES_PROXY)) {
             try {
                 return Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY);
             } catch (InvalidSettingException ise) {
                 return true;
             }
         } else {
-            return Boolean.parseBoolean(line.getOptionValue(ArgumentName.NEXUS_USES_PROXY));
+            return Boolean.parseBoolean(line.getOptionValue(ARGUMENT.NEXUS_USES_PROXY));
         }
     }
 
@@ -443,7 +493,7 @@ public final class CliParser {
         final HelpFormatter formatter = new HelpFormatter();
         final Options options = new Options();
         addStandardOptions(options);
-        if (line != null && line.hasOption(ArgumentName.ADVANCED_HELP)) {
+        if (line != null && line.hasOption(ARGUMENT.ADVANCED_HELP)) {
             addAdvancedOptions(options);
         }
         final String helpMsg = String.format("%n%s"
@@ -457,7 +507,6 @@ public final class CliParser {
                 options,
                 "",
                 true);
-
     }
 
     /**
@@ -466,7 +515,16 @@ public final class CliParser {
      * @return the file paths specified on the command line for scan
      */
     public String[] getScanFiles() {
-        return line.getOptionValues(ArgumentName.SCAN);
+        return line.getOptionValues(ARGUMENT.SCAN);
+    }
+
+    /**
+     * Retrieves the list of excluded file patterns specified by the 'exclude' argument.
+     *
+     * @return the excluded file patterns
+     */
+    public String[] getExcludeList() {
+        return line.getOptionValues(ARGUMENT.EXCLUDE);
     }
 
     /**
@@ -475,7 +533,7 @@ public final class CliParser {
      * @return the path to the reports directory.
      */
     public String getReportDirectory() {
-        return line.getOptionValue(ArgumentName.OUT, ".");
+        return line.getOptionValue(ARGUMENT.OUT, ".");
     }
 
     /**
@@ -484,7 +542,7 @@ public final class CliParser {
      * @return the path to Mono
      */
     public String getPathToMono() {
-        return line.getOptionValue(ArgumentName.PATH_TO_MONO);
+        return line.getOptionValue(ARGUMENT.PATH_TO_MONO);
     }
 
     /**
@@ -493,7 +551,7 @@ public final class CliParser {
      * @return the output format name.
      */
     public String getReportFormat() {
-        return line.getOptionValue(ArgumentName.OUTPUT_FORMAT, "HTML");
+        return line.getOptionValue(ARGUMENT.OUTPUT_FORMAT, "HTML");
     }
 
     /**
@@ -502,7 +560,7 @@ public final class CliParser {
      * @return the application name.
      */
     public String getApplicationName() {
-        return line.getOptionValue(ArgumentName.APP_NAME);
+        return line.getOptionValue(ARGUMENT.APP_NAME);
     }
 
     /**
@@ -511,16 +569,24 @@ public final class CliParser {
      * @return the connection timeout
      */
     public String getConnectionTimeout() {
-        return line.getOptionValue(ArgumentName.CONNECTION_TIMEOUT);
+        return line.getOptionValue(ARGUMENT.CONNECTION_TIMEOUT);
     }
 
     /**
-     * Returns the proxy url.
+     * Returns the proxy server.
      *
-     * @return the proxy url
+     * @return the proxy server
      */
-    public String getProxyUrl() {
-        return line.getOptionValue(ArgumentName.PROXY_URL);
+    public String getProxyServer() {
+
+        String server = line.getOptionValue(ARGUMENT.PROXY_SERVER);
+        if (server == null) {
+            server = line.getOptionValue(ARGUMENT.PROXY_URL);
+            if (server != null) {
+                LOGGER.warning("An old command line argument 'proxyurl' was detected; use proxyserver instead");
+            }
+        }
+        return server;
     }
 
     /**
@@ -529,7 +595,7 @@ public final class CliParser {
      * @return the proxy port
      */
     public String getProxyPort() {
-        return line.getOptionValue(ArgumentName.PROXY_PORT);
+        return line.getOptionValue(ARGUMENT.PROXY_PORT);
     }
 
     /**
@@ -538,7 +604,7 @@ public final class CliParser {
      * @return the proxy username
      */
     public String getProxyUsername() {
-        return line.getOptionValue(ArgumentName.PROXY_USERNAME);
+        return line.getOptionValue(ARGUMENT.PROXY_USERNAME);
     }
 
     /**
@@ -547,7 +613,7 @@ public final class CliParser {
      * @return the proxy password
      */
     public String getProxyPassword() {
-        return line.getOptionValue(ArgumentName.PROXY_PASSWORD);
+        return line.getOptionValue(ARGUMENT.PROXY_PASSWORD);
     }
 
     /**
@@ -556,7 +622,7 @@ public final class CliParser {
      * @return the value of dataDirectory
      */
     public String getDataDirectory() {
-        return line.getOptionValue(ArgumentName.DATA_DIRECTORY);
+        return line.getOptionValue(ARGUMENT.DATA_DIRECTORY);
     }
 
     /**
@@ -565,7 +631,7 @@ public final class CliParser {
      * @return the properties file specified on the command line
      */
     public File getPropertiesFile() {
-        final String path = line.getOptionValue(ArgumentName.PROP);
+        final String path = line.getOptionValue(ARGUMENT.PROP);
         if (path != null) {
             return new File(path);
         }
@@ -578,7 +644,7 @@ public final class CliParser {
      * @return the path to the verbose log file
      */
     public String getVerboseLog() {
-        return line.getOptionValue(ArgumentName.VERBOSE_LOG);
+        return line.getOptionValue(ARGUMENT.VERBOSE_LOG);
     }
 
     /**
@@ -587,7 +653,7 @@ public final class CliParser {
      * @return the path to the suppression file
      */
     public String getSuppressionFile() {
-        return line.getOptionValue(ArgumentName.SUPPRESSION_FILE);
+        return line.getOptionValue(ARGUMENT.SUPPRESSION_FILE);
     }
 
     /**
@@ -610,7 +676,7 @@ public final class CliParser {
      * @return if auto-update is allowed.
      */
     public boolean isAutoUpdate() {
-        return (line == null) || !line.hasOption(ArgumentName.DISABLE_AUTO_UPDATE);
+        return (line == null) || !line.hasOption(ARGUMENT.DISABLE_AUTO_UPDATE);
     }
 
     /**
@@ -619,7 +685,7 @@ public final class CliParser {
      * @return the database driver name if specified; otherwise null is returned
      */
     public String getDatabaseDriverName() {
-        return line.getOptionValue(ArgumentName.DB_DRIVER);
+        return line.getOptionValue(ARGUMENT.DB_DRIVER);
     }
 
     /**
@@ -628,7 +694,7 @@ public final class CliParser {
      * @return the database driver name if specified; otherwise null is returned
      */
     public String getDatabaseDriverPath() {
-        return line.getOptionValue(ArgumentName.DB_DRIVER_PATH);
+        return line.getOptionValue(ARGUMENT.DB_DRIVER_PATH);
     }
 
     /**
@@ -637,7 +703,7 @@ public final class CliParser {
      * @return the database connection string if specified; otherwise null is returned
      */
     public String getConnectionString() {
-        return line.getOptionValue(ArgumentName.CONNECTION_STRING);
+        return line.getOptionValue(ARGUMENT.CONNECTION_STRING);
     }
 
     /**
@@ -646,7 +712,7 @@ public final class CliParser {
      * @return the database database user name if specified; otherwise null is returned
      */
     public String getDatabaseUser() {
-        return line.getOptionValue(ArgumentName.DB_NAME);
+        return line.getOptionValue(ARGUMENT.DB_NAME);
     }
 
     /**
@@ -655,7 +721,7 @@ public final class CliParser {
      * @return the database database password if specified; otherwise null is returned
      */
     public String getDatabasePassword() {
-        return line.getOptionValue(ArgumentName.DB_PASSWORD);
+        return line.getOptionValue(ARGUMENT.DB_PASSWORD);
     }
 
     /**
@@ -664,13 +730,13 @@ public final class CliParser {
      * @return the additional Extensions; otherwise null is returned
      */
     public String getAdditionalZipExtensions() {
-        return line.getOptionValue(ArgumentName.ADDITIONAL_ZIP_EXTENSIONS);
+        return line.getOptionValue(ARGUMENT.ADDITIONAL_ZIP_EXTENSIONS);
     }
 
     /**
      * A collection of static final strings that represent the possible command line arguments.
      */
-    public static class ArgumentName {
+    public static class ARGUMENT {
 
         /**
          * The long CLI argument name specifying the directory/file to scan.
@@ -732,21 +798,20 @@ public final class CliParser {
          * The short CLI argument name asking for the version.
          */
         public static final String VERSION = "version";
-        /**
-         * The short CLI argument name indicating the proxy port.
-         */
-        public static final String PROXY_PORT_SHORT = "p";
         /**
          * The CLI argument name indicating the proxy port.
          */
         public static final String PROXY_PORT = "proxyport";
         /**
-         * The short CLI argument name indicating the proxy url.
+         * The CLI argument name indicating the proxy server.
          */
-        public static final String PROXY_URL_SHORT = "u";
+        public static final String PROXY_SERVER = "proxyserver";
         /**
          * The CLI argument name indicating the proxy url.
+         *
+         * @deprecated use {@link org.owasp.dependencycheck.cli.CliParser.ArgumentName#PROXY_SERVER} instead
          */
+        @Deprecated
         public static final String PROXY_URL = "proxyurl";
         /**
          * The CLI argument name indicating the proxy username.
@@ -848,5 +913,9 @@ public final class CliParser {
          * The CLI argument name for setting extra extensions.
          */
         public static final String ADDITIONAL_ZIP_EXTENSIONS = "zipExtensions";
+        /**
+         * Exclude path argument.
+         */
+        public static final String EXCLUDE = "exclude";
     }
 }

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

@@ -0,0 +1,59 @@
+/*
+ * 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;
+
+/**
+ * Thrown if an invalid path is encountered.
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+class InvalidScanPathException extends Exception {
+
+    /**
+     * Creates a new InvalidScanPathException.
+     */
+    public InvalidScanPathException() {
+        super();
+    }
+
+    /**
+     * Creates a new InvalidScanPathException.
+     *
+     * @param msg a message for the exception
+     */
+    public InvalidScanPathException(String msg) {
+        super(msg);
+    }
+
+    /**
+     * Creates a new InvalidScanPathException.
+     *
+     * @param ex the cause of the exception
+     */
+    public InvalidScanPathException(Throwable ex) {
+        super(ex);
+    }
+
+    /**
+     * Creates a new InvalidScanPathException.
+     *
+     * @param msg a message for the exception
+     * @param ex the cause of the exception
+     */
+    public InvalidScanPathException(String msg, Throwable ex) {
+        super(msg, ex);
+    }
+}

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

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

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

@@ -3,11 +3,12 @@ Command Line Arguments
 
 The following table lists the command line arguments:
 
-Short  | Argument Name         | Parameter       | Description | Requirement
+Short  | Argument Name   | Parameter       | Description | Requirement
 -------|-----------------------|-----------------|-------------|------------
  \-a   | \-\-app               | \<name\>        | The name of the application being scanned. This is a required argument. | Required
- \-s   | \-\-scan              | \<path\>        | The path to scan \- this option can be specified multiple times. It is also possible to specify specific file types that should be scanned by supplying a scan path of '[path]/[to]/[scan]/*.zip'. The wild card can only be used to denote any file-name with a specific extension. | Required
- \-o   | \-\-out               | \<folder\>      | The folder to write reports to. This defaults to the current directory. | Optional
+ \-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
+ \-o   | \-\-out               | \<path\>        | The folder to write reports to. This defaults to the current directory. If the format is not set to ALL one could specify a specific file name. | Optional
  \-f   | \-\-format            | \<format\>      | The output format to write to (XML, HTML, VULN, ALL). The default is HTML. | Required
  \-l   | \-\-log               | \<file\>        | The file path to write verbose logging information. | Optional
  \-n   | \-\-noupdate          |                 | Disables the automatic updating of the CPE data. | Optional
@@ -18,26 +19,25 @@ Short  | Argument Name         | Parameter       | Description | Requirement
 
 Advanced Options
 ================
-Short  | Argument Name         | Parameter       | Description | Default Value
--------|-----------------------|-----------------|-------------|---------------
-       | \-\-disableArchive    |                 | Sets whether the Archive Analyzer will be used.                      | false
+Short  | Argument&nbsp;Name&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; | Parameter | Description                                | Default&nbsp;Value
+-------|-----------------------|-----------------|-----------------------------------------------------------------------------|---------------
+       | \-\-disableArchive    |                 | Sets whether the Archive Analyzer will be used.                             | 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 Jar Analyzer will be used.                              | false
-       | \-\-disableNexus      |                 | Sets whether Nexus Analyzer will be used.                            | false
-       | \-\-disableNexus      |                 | Disable the Nexus Analyzer.                                          | &nbsp;
-       | \-\-nexus             | \<url\>         | The url to the Nexus Server. | https://repository.sonatype.org/service/local/
-       | \-\-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
-       | \-\-pathToMono        | \<path\>        | The path to Mono for .NET Assembly analysis on non-windows systems.  | &nbsp;
-       | \-\-proxyurl          | \<url\>         | The proxy url to use when downloading resources. | &nbsp;
-       | \-\-proxyport         | \<port\>        | The proxy port to use when downloading resources. | &nbsp;
+       | \-\-disableJar        |                 | Sets whether Jar Analyzer will be used.                                     | false
+       | \-\-disableNexus      |                 | Sets whether Nexus Analyzer will be used.                                   | false
+       | \-\-nexus             | \<url\>         | The url to the Nexus Pro Server. 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
+       | \-\-pathToMono        | \<path\>        | The path to Mono for .NET Assembly analysis on non-windows systems.         | &nbsp;
+       | \-\-proxyserver       | \<server\>      | The proxy server to use when downloading resources.                         | &nbsp;
+       | \-\-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;
+       | \-\-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;
+       | \-\-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;

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

@@ -15,8 +15,9 @@
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
-package org.owasp.dependencycheck.cli;
+package org.owasp.dependencycheck;
 
+import org.owasp.dependencycheck.CliParser;
 import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -44,7 +45,7 @@ public class CliParserTest {
 
     @AfterClass
     public static void tearDownClass() throws Exception {
-        Settings.cleanup();
+        Settings.cleanup(true);
     }
 
     @Before

dependency-check-core/pom.xml

@@ -15,19 +15,19 @@ limitations under the License.
 
 Copyright (c) 2012 Jeremy Long. All Rights Reserved.
 -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.6</version>
     </parent>
 
     <artifactId>dependency-check-core</artifactId>
     <packaging>jar</packaging>
 
     <name>Dependency-Check Core</name>
+    <description>dependency-check-core is the engine and reporting tool used to identify and report if there are any known, publicly disclosed vulnerabilities in the scanned project's dependencies. The engine extracts meta-data from the dependencies and uses this to do fuzzy key-word matching against the Common Platfrom Enumeration (CPE), if any CPE identifiers are found the associated Common Vulnerability and Exposure (CVE) entries are added to the generated report.</description>
     <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
     <distributionManagement>
         <site>
@@ -220,6 +220,11 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                             <name>data.directory</name>
                             <value>${project.build.directory}/data</value>
                         </property>
+                        <property>
+                            <name>temp.directory</name>
+                            <value>${project.build.directory}/temp</value>
+                        </property>
+
                     </systemProperties>
                     <includes>
                         <include>**/*IntegrationTest.java</include>
@@ -267,6 +272,9 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                             <groupId>org.apache.maven.plugins</groupId>
                             <artifactId>maven-javadoc-plugin</artifactId>
                             <version>2.9.1</version>
+                            <configuration>
+                                <bottom>Copyright© 2012-14 Jeremy Long. All Rights Reserved.</bottom>
+                            </configuration>
                             <reportSets>
                                 <reportSet>
                                     <id>default</id>
@@ -392,6 +400,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 <version>3.1</version>
                 <configuration>
                     <showDeprecation>false</showDeprecation>
+                    <compilerArgument>-Xlint:unchecked</compilerArgument>
                     <source>1.6</source>
                     <target>1.6</target>
                 </configuration>
@@ -399,12 +408,23 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
         </plugins>
     </build>
     <dependencies>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-test-framework</artifactId>
             <version>4.3.1</version>
             <scope>test</scope>
         </dependency>
+        <!--dependency>
+            <groupId>org.jmockit</groupId>
+            <artifactId>jmockit</artifactId>
+            <version>1.12</version>
+            <scope>test</scope>
+        </dependency-->
         <dependency>
             <groupId>com.google.code.findbugs</groupId>
             <artifactId>annotations</artifactId>
@@ -419,7 +439,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-compress</artifactId>
-            <version>1.8</version>
+            <version>1.8.1</version>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>
@@ -451,50 +471,6 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <artifactId>velocity</artifactId>
             <version>1.7</version>
         </dependency>
-        <dependency>
-            <groupId>org.apache.velocity</groupId>
-            <artifactId>velocity-tools</artifactId>
-            <version>2.0</version>
-            <!-- very limited use of the velocity-tools, not all of the dependencies are needed-->
-            <exclusions>
-                <exclusion>
-                    <groupId>commons-chain</groupId>
-                    <artifactId>commons-chain</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>javax.servlet</groupId>
-                    <artifactId>servlet-api</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>commons-validator</groupId>
-                    <artifactId>commons-validator</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>dom4j</groupId>
-                    <artifactId>dom4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>sslext</groupId>
-                    <artifactId>sslext</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.struts</groupId>
-                    <artifactId>struts-core</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>antlr</groupId>
-                    <artifactId>antlr</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.struts</groupId>
-                    <artifactId>struts-taglib</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.struts</groupId>
-                    <artifactId>struts-tiles</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
         <dependency>
             <groupId>com.h2database</groupId>
             <artifactId>h2</artifactId>
@@ -521,6 +497,13 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <scope>provided</scope>
             <optional>true</optional>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.security</groupId>
+            <artifactId>spring-security-web</artifactId>
+            <version>3.0.0.RELEASE</version>
+            <scope>provided</scope>
+            <optional>true</optional>
+        </dependency>
         <dependency>
             <groupId>com.hazelcast</groupId>
             <artifactId>hazelcast</artifactId>
@@ -601,6 +584,13 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <scope>provided</scope>
             <optional>true</optional>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.retry</groupId>
+            <artifactId>spring-retry</artifactId>
+            <version>1.1.0.RELEASE</version>
+            <scope>provided</scope>
+            <optional>true</optional>
+        </dependency>
     </dependencies>
     <profiles>
         <profile>
@@ -662,11 +652,11 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             Additionally, these are only added when using "allTests" to
             make the build slightly faster in most cases. -->
             <id>False Positive Tests</id>
-            <!--activation>
+            <activation>
                 <property>
                     <name>allTests</name>
                 </property>
-            </activation-->
+            </activation>
             <dependencies>
                 <dependency>
                     <groupId>org.apache.xmlgraphics</groupId>
@@ -689,6 +679,56 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                     <scope>provided</scope>
                     <optional>true</optional>
                 </dependency>
+                <dependency>
+                    <groupId>com.ganyo</groupId>
+                    <artifactId>gcm-server</artifactId>
+                    <version>1.0.2</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.python</groupId>
+                    <artifactId>jython-standalone</artifactId>
+                    <version>2.7-b1</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.jruby</groupId>
+                    <artifactId>jruby-complete</artifactId>
+                    <version>1.7.4</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.jruby</groupId>
+                    <artifactId>jruby</artifactId>
+                    <version>1.6.3</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.glassfish.jersey.core</groupId>
+                    <artifactId>jersey-client</artifactId>
+                    <version>2.12</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.sun.jersey</groupId>
+                    <artifactId>jersey-client</artifactId>
+                    <version>1.11.1</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.sun.faces</groupId>
+                    <artifactId>jsf-impl</artifactId>
+                    <version>2.2.8-02</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+
             </dependencies>
         </profile>
     </profiles>

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

@@ -18,6 +18,7 @@
 package org.owasp.dependencycheck;
 
 import java.io.File;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.EnumMap;
 import java.util.HashSet;
@@ -52,7 +53,7 @@ import org.owasp.dependencycheck.utils.Settings;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class Engine {
+public class Engine implements Serializable {
 
     /**
      * The list of dependencies.
@@ -61,19 +62,19 @@ public class Engine {
     /**
      * A Map of analyzers grouped by Analysis phase.
      */
-    private final EnumMap<AnalysisPhase, List<Analyzer>> analyzers;
+    private final transient EnumMap<AnalysisPhase, List<Analyzer>> analyzers;
     /**
      * A Map of analyzers grouped by Analysis phase.
      */
-    private final Set<FileTypeAnalyzer> fileTypeAnalyzers;
+    private final transient Set<FileTypeAnalyzer> fileTypeAnalyzers;
     /**
      * The ClassLoader to use when dynamically loading Analyzer and Update services.
      */
-    private ClassLoader serviceClassLoader;
+    private transient ClassLoader serviceClassLoader;
     /**
      * The Logger for use throughout the class.
      */
-    private static final Logger LOGGER = Logger.getLogger(Engine.class.getName());
+    private static final transient Logger LOGGER = Logger.getLogger(Engine.class.getName());
 
     /**
      * Creates a new Engine.
@@ -167,142 +168,171 @@ public class Engine {
      * Scans an array of files or directories. If a directory is specified, it will be scanned recursively. Any
      * dependencies identified are added to the dependency collection.
      *
-     * @since v0.3.2.5
+     * @param paths an array of paths to files or directories to be analyzed
+     * @return the list of dependencies scanned
      *
-     * @param paths an array of paths to files or directories to be analyzed.
+     * @since v0.3.2.5
      */
-    public void scan(String[] paths) {
+    public List<Dependency> scan(String[] paths) {
+        final List<Dependency> deps = new ArrayList<Dependency>();
         for (String path : paths) {
             final File file = new File(path);
-            scan(file);
+            final List<Dependency> d = scan(file);
+            if (d != null) {
+                deps.addAll(d);
+            }
         }
+        return deps;
     }
 
     /**
      * Scans a given file or directory. If a directory is specified, it will be scanned recursively. Any dependencies
      * identified are added to the dependency collection.
      *
-     * @param path the path to a file or directory to be analyzed.
+     * @param path the path to a file or directory to be analyzed
+     * @return the list of dependencies scanned
      */
-    public void scan(String path) {
-        if (path.matches("^.*[\\/]\\*\\.[^\\/:*|?<>\"]+$")) {
-            final String[] parts = path.split("\\*\\.");
-            final String[] ext = new String[]{parts[parts.length - 1]};
-            final File dir = new File(path.substring(0, path.length() - ext[0].length() - 2));
-            if (dir.isDirectory()) {
-                final List<File> files = (List<File>) org.apache.commons.io.FileUtils.listFiles(dir, ext, true);
-                scan(files);
-            } else {
-                final String msg = String.format("Invalid file path provided to scan '%s'", path);
-                LOGGER.log(Level.SEVERE, msg);
-            }
-        } else {
-            final File file = new File(path);
-            scan(file);
-        }
+    public List<Dependency> scan(String path) {
+        final File file = new File(path);
+        return scan(file);
     }
 
     /**
      * Scans an array of files or directories. If a directory is specified, it will be scanned recursively. Any
      * dependencies identified are added to the dependency collection.
      *
-     * @since v0.3.2.5
-     *
      * @param files an array of paths to files or directories to be analyzed.
+     * @return the list of dependencies
+     *
+     * @since v0.3.2.5
      */
-    public void scan(File[] files) {
+    public List<Dependency> scan(File[] files) {
+        final List<Dependency> deps = new ArrayList<Dependency>();
         for (File file : files) {
-            scan(file);
+            final List<Dependency> d = scan(file);
+            if (d != null) {
+                deps.addAll(d);
+            }
         }
+        return deps;
     }
 
     /**
      * Scans a list of files or directories. If a directory is specified, it will be scanned recursively. Any
      * dependencies identified are added to the dependency collection.
      *
-     * @since v0.3.2.5
+     * @param files a set of paths to files or directories to be analyzed
+     * @return the list of dependencies scanned
      *
-     * @param files a set of paths to files or directories to be analyzed.
+     * @since v0.3.2.5
      */
-    public void scan(Set<File> files) {
+    public List<Dependency> scan(Set<File> files) {
+        final List<Dependency> deps = new ArrayList<Dependency>();
         for (File file : files) {
-            scan(file);
+            final List<Dependency> d = scan(file);
+            if (d != null) {
+                deps.addAll(d);
+            }
         }
+        return deps;
     }
 
     /**
      * Scans a list of files or directories. If a directory is specified, it will be scanned recursively. Any
      * dependencies identified are added to the dependency collection.
      *
-     * @since v0.3.2.5
+     * @param files a set of paths to files or directories to be analyzed
+     * @return the list of dependencies scanned
      *
-     * @param files a set of paths to files or directories to be analyzed.
+     * @since v0.3.2.5
      */
-    public void scan(List<File> files) {
+    public List<Dependency> scan(List<File> files) {
+        final List<Dependency> deps = new ArrayList<Dependency>();
         for (File file : files) {
-            scan(file);
+            final List<Dependency> d = scan(file);
+            if (d != null) {
+                deps.addAll(d);
+            }
         }
+        return deps;
     }
 
     /**
      * Scans a given file or directory. If a directory is specified, it will be scanned recursively. Any dependencies
      * identified are added to the dependency collection.
      *
+     * @param file the path to a file or directory to be analyzed
+     * @return the list of dependencies scanned
+     *
      * @since v0.3.2.4
      *
-     * @param file the path to a file or directory to be analyzed.
      */
-    public void scan(File file) {
+    public List<Dependency> scan(File file) {
         if (file.exists()) {
             if (file.isDirectory()) {
-                scanDirectory(file);
+                return scanDirectory(file);
             } else {
-                scanFile(file);
+                final Dependency d = scanFile(file);
+                if (d != null) {
+                    final List<Dependency> deps = new ArrayList<Dependency>();
+                    deps.add(d);
+                    return deps;
+                }
             }
         }
+        return null;
     }
 
     /**
      * Recursively scans files and directories. Any dependencies identified are added to the dependency collection.
      *
-     * @param dir the directory to scan.
+     * @param dir the directory to scan
+     * @return the list of Dependency objects scanned
      */
-    protected void scanDirectory(File dir) {
+    protected List<Dependency> scanDirectory(File dir) {
         final File[] files = dir.listFiles();
+        final List<Dependency> deps = new ArrayList<Dependency>();
         if (files != null) {
             for (File f : files) {
                 if (f.isDirectory()) {
-                    scanDirectory(f);
+                    final List<Dependency> d = scanDirectory(f);
+                    if (d != null) {
+                        deps.addAll(d);
+                    }
                 } else {
-                    scanFile(f);
+                    final Dependency d = scanFile(f);
+                    deps.add(d);
                 }
             }
         }
+        return deps;
     }
 
     /**
      * Scans a specified file. If a dependency is identified it is added to the dependency collection.
      *
-     * @param file The file to scan.
+     * @param file The file to scan
+     * @return the scanned dependency
      */
-    protected void scanFile(File file) {
+    protected Dependency scanFile(File file) {
         if (!file.isFile()) {
             final String msg = String.format("Path passed to scanFile(File) is not a file: %s. Skipping the file.", file.toString());
             LOGGER.log(Level.FINE, msg);
-            return;
+            return null;
         }
         final String fileName = file.getName();
         final String extension = FileUtils.getFileExtension(fileName);
+        Dependency dependency = null;
         if (extension != null) {
             if (supportsExtension(extension)) {
-                final Dependency dependency = new Dependency(file);
+                dependency = new Dependency(file);
                 dependencies.add(dependency);
             }
         } else {
-            final String msg = String.format("No file extension found on file '%s'. The file was not analyzed.",
-                    file.toString());
+            final String msg = String.format("No file extension found on file '%s'. The file was not analyzed.", file.toString());
             LOGGER.log(Level.FINEST, msg);
         }
+        return dependency;
     }
 
     /**
@@ -438,8 +468,7 @@ public class Engine {
             } catch (UpdateException ex) {
                 LOGGER.log(Level.WARNING,
                         "Unable to update Cached Web DataSource, using local data instead. Results may not include recent vulnerabilities.");
-                LOGGER.log(Level.FINE,
-                        String.format("Unable to update details for %s", source.getClass().getName()), ex);
+                LOGGER.log(Level.FINE, String.format("Unable to update details for %s", source.getClass().getName()), ex);
             }
         }
     }

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

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *
- * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ * Copyright (c) 2014 Steve Springett. All Rights Reserved.
  */
 package org.owasp.dependencycheck.agent;
 
@@ -234,26 +234,49 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * The Proxy URL.
+     * The Proxy Server.
      */
-    private String proxyUrl;
+    private String proxyServer;
 
     /**
-     * Get the value of proxyUrl.
+     * Get the value of proxyServer.
      *
-     * @return the value of proxyUrl
+     * @return the value of proxyServer
      */
-    public String getProxyUrl() {
-        return proxyUrl;
+    public String getProxyServer() {
+        return proxyServer;
     }
 
     /**
-     * Set the value of proxyUrl.
+     * Set the value of proxyServer.
      *
-     * @param proxyUrl new value of proxyUrl
+     * @param proxyServer new value of proxyServer
      */
+    public void setProxyServer(String proxyServer) {
+        this.proxyServer = proxyServer;
+    }
+
+    /**
+     * Get the value of proxyServer.
+     *
+     * @return the value of proxyServer
+     * @deprecated use {@link org.owasp.dependencycheck.agent.DependencyCheckScanAgent#getProxyServer()} instead
+     */
+    @Deprecated
+    public String getProxyUrl() {
+        return proxyServer;
+    }
+
+    /**
+     * Set the value of proxyServer.
+     *
+     * @param proxyUrl new value of proxyServer
+     * @deprecated use {@link org.owasp.dependencycheck.agent.DependencyCheckScanAgent#setProxyServer(java.lang.String)
+     * } instead
+     */
+    @Deprecated
     public void setProxyUrl(String proxyUrl) {
-        this.proxyUrl = proxyUrl;
+        this.proxyServer = proxyUrl;
     }
 
     /**
@@ -792,7 +815,7 @@ public class DependencyCheckScanAgent {
 
     /**
      * Takes the properties supplied and updates the dependency-check settings. Additionally, this sets the system
-     * properties required to change the proxy url, port, and connection timeout.
+     * properties required to change the proxy server, port, and connection timeout.
      */
     private void populateSettings() {
         Settings.initialize();
@@ -808,8 +831,8 @@ public class DependencyCheckScanAgent {
 
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
 
-        if (proxyUrl != null && !proxyUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
+        if (proxyServer != null && !proxyServer.isEmpty()) {
+            Settings.setString(Settings.KEYS.PROXY_SERVER, proxyServer);
         }
         if (proxyPort != null && !proxyPort.isEmpty()) {
             Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);
@@ -888,7 +911,7 @@ public class DependencyCheckScanAgent {
                     "Unable to connect to the dependency-check database; analysis has stopped");
             LOGGER.log(Level.FINE, "", ex);
         } finally {
-            Settings.cleanup();
+            Settings.cleanup(true);
             if (engine != null) {
                 engine.cleanup();
             }

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

@@ -98,11 +98,17 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
      * @throws SuppressionParseException thrown if the XML cannot be parsed.
      */
     private void loadSuppressionData() throws SuppressionParseException {
+        final SuppressionParser parser = new SuppressionParser();
+        File file = null;
+        try {
+            rules = parser.parseSuppressionRules(this.getClass().getClassLoader().getResourceAsStream("dependencycheck-base-suppression.xml"));
+        } catch (SuppressionParseException ex) {
+            LOGGER.log(Level.FINE, "Unable to parse the base suppression data file", ex);
+        }
         final String suppressionFilePath = Settings.getString(Settings.KEYS.SUPPRESSION_FILE);
         if (suppressionFilePath == null) {
             return;
         }
-        File file = null;
         boolean deleteTempFile = false;
         try {
             final Pattern uriRx = Pattern.compile("^(https?|file)\\:.*", Pattern.CASE_INSENSITIVE);
@@ -132,9 +138,9 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
             }
 
             if (file != null) {
-                final SuppressionParser parser = new SuppressionParser();
                 try {
-                    rules = parser.parseSuppressionRules(file);
+                    //rules = parser.parseSuppressionRules(file);
+                    rules.addAll(parser.parseSuppressionRules(file));
                     LOGGER.log(Level.FINE, rules.size() + " suppression rules were loaded.");
                 } catch (SuppressionParseException ex) {
                     final String msg = String.format("Unable to parse suppression xml file '%s'", file.getPath());

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

@@ -27,6 +27,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -35,7 +36,9 @@ import java.util.logging.Logger;
 import org.apache.commons.compress.archivers.ArchiveEntry;
 import org.apache.commons.compress.archivers.ArchiveInputStream;
 import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
 import org.apache.commons.compress.archivers.zip.ZipArchiveInputStream;
+import org.apache.commons.compress.archivers.zip.ZipFile;
 import org.apache.commons.compress.compressors.CompressorInputStream;
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.apache.commons.compress.compressors.gzip.GzipUtils;
@@ -99,10 +102,15 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private static final Set<String> EXTENSIONS = newHashSet("tar", "gz", "tgz");
 
+    /**
+     * The set of file extensions to remove from the engine's collection of dependencies.
+     */
+    private static final Set<String> REMOVE_FROM_ANALYSIS = newHashSet("zip", "tar", "gz", "tgz"); //TODO add nupkg, apk, sar?
+
     static {
         final String additionalZipExt = Settings.getString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS);
         if (additionalZipExt != null) {
-            final HashSet ext = new HashSet<String>(Arrays.asList(additionalZipExt));
+            final HashSet<String> ext = new HashSet<String>(Arrays.asList(additionalZipExt));
             ZIPPABLES.addAll(ext);
         }
         EXTENSIONS.addAll(ZIPPABLES);
@@ -178,7 +186,7 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
         if (tempFileLocation != null && tempFileLocation.exists()) {
             LOGGER.log(Level.FINE, "Attempting to delete temporary files");
             final boolean success = FileUtils.delete(tempFileLocation);
-            if (!success) {
+            if (!success && tempFileLocation != null && tempFileLocation.exists() && tempFileLocation.list().length > 0) {
                 LOGGER.log(Level.WARNING, "Failed to delete some temporary files, see the log for more details");
             }
         }
@@ -199,9 +207,9 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
         extractFiles(f, tmpDir, engine);
 
         //make a copy
-        final List<Dependency> dependencies = new ArrayList<Dependency>(engine.getDependencies());
+        List<Dependency> dependencies = new ArrayList<Dependency>(engine.getDependencies());
         engine.scan(tmpDir);
-        final List<Dependency> newDependencies = engine.getDependencies();
+        List<Dependency> newDependencies = engine.getDependencies();
         if (dependencies.size() != newDependencies.size()) {
             //get the new dependencies
             final Set<Dependency> dependencySet = new HashSet<Dependency>();
@@ -213,9 +221,8 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                 final String displayPath = String.format("%s%s",
                         dependency.getFilePath(),
                         d.getActualFilePath().substring(tmpDir.getAbsolutePath().length()));
-                final String displayName = String.format("%s%s%s",
+                final String displayName = String.format("%s: %s",
                         dependency.getFileName(),
-                        File.separator,
                         d.getFileName());
                 d.setFilePath(displayPath);
                 d.setFileName(displayName);
@@ -229,6 +236,40 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
                 }
             }
         }
+        if (this.REMOVE_FROM_ANALYSIS.contains(dependency.getFileExtension())) {
+            if ("zip".equals(dependency.getFileExtension()) && isZipFileActuallyJarFile(dependency)) {
+                final File tdir = getNextTempDirectory();
+                final String fileName = dependency.getFileName();
+
+                LOGGER.info(String.format("The zip file '%s' appears to be a JAR file, making a copy and analyzing it as a JAR.", fileName));
+
+                final File tmpLoc = new File(tdir, fileName.substring(0, fileName.length() - 3) + "jar");
+                try {
+                    org.apache.commons.io.FileUtils.copyFile(tdir, tmpLoc);
+                    dependencies = new ArrayList<Dependency>(engine.getDependencies());
+                    engine.scan(tmpLoc);
+                    newDependencies = engine.getDependencies();
+                    if (dependencies.size() != newDependencies.size()) {
+                        //get the new dependencies
+                        final Set<Dependency> dependencySet = new HashSet<Dependency>();
+                        dependencySet.addAll(newDependencies);
+                        dependencySet.removeAll(dependencies);
+                        if (dependencySet.size() != 1) {
+                            LOGGER.info("Deep copy of ZIP to JAR file resulted in more then one dependency?");
+                        }
+                        for (Dependency d : dependencySet) {
+                            //fix the dependency's display name and path
+                            d.setFilePath(dependency.getFilePath());
+                            d.setDisplayFileName(dependency.getFileName());
+                        }
+                    }
+                } catch (IOException ex) {
+                    final String msg = String.format("Unable to perform deep copy on '%s'", dependency.getActualFile().getPath());
+                    LOGGER.log(Level.FINE, msg, ex);
+                }
+            }
+            engine.getDependencies().remove(dependency);
+        }
         Collections.sort(engine.getDependencies());
     }
 
@@ -411,4 +452,38 @@ public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
             }
         }
     }
+
+    /**
+     * Attempts to determine if a zip file is actually a JAR file.
+     *
+     * @param dependency the dependency to check
+     * @return true if the dependency appears to be a JAR file; otherwise false
+     */
+    private boolean isZipFileActuallyJarFile(Dependency dependency) {
+        boolean isJar = false;
+        ZipFile zip = null;
+        try {
+            zip = new ZipFile(dependency.getActualFilePath());
+            if (zip.getEntry("META-INF/MANIFEST.MF") != null
+                    || zip.getEntry("META-INF/maven") != null) {
+                final Enumeration<ZipArchiveEntry> entries = zip.getEntries();
+                while (entries.hasMoreElements()) {
+                    final ZipArchiveEntry entry = entries.nextElement();
+                    if (!entry.isDirectory()) {
+                        final String name = entry.getName().toLowerCase();
+                        if (name.endsWith(".class")) {
+                            isJar = true;
+                            break;
+                        }
+                    }
+                }
+            }
+        } catch (IOException ex) {
+            LOGGER.log(Level.FINE, String.format("Unable to unzip zip file '%s'", dependency.getFilePath()), ex);
+        } finally {
+            ZipFile.closeQuietly(zip);
+        }
+
+        return isJar;
+    }
 }

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

@@ -73,7 +73,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Logger
      */
-    private static final Logger LOGGER = Logger.getLogger(AssemblyAnalyzer.class.getName());
+    private static final Logger LOGGER = Logger.getLogger(AssemblyAnalyzer.class.getName(), "dependencycheck-resources");
 
     /**
      * Builds the beginnings of a List for ProcessBuilder
@@ -106,7 +106,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
     public void analyzeFileType(Dependency dependency, Engine engine)
             throws AnalysisException {
         if (grokAssemblyExe == null) {
-            LOGGER.warning("GrokAssembly didn't get deployed");
+            LOGGER.warning("analyzer.AssemblyAnalyzer.notdeployed");
             return;
         }
 
@@ -114,16 +114,32 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
         args.add(dependency.getActualFilePath());
         final ProcessBuilder pb = new ProcessBuilder(args);
         BufferedReader rdr = null;
+        Document doc = null;
         try {
             final Process proc = pb.start();
             // Try evacuating the error stream
             rdr = new BufferedReader(new InputStreamReader(proc.getErrorStream(), "UTF-8"));
             String line = null;
+            // CheckStyle:VisibilityModifier OFF
             while (rdr.ready() && (line = rdr.readLine()) != null) {
-                LOGGER.log(Level.WARNING, "Error from GrokAssembly: {0}", line);
+                LOGGER.log(Level.WARNING, "analyzer.AssemblyAnalyzer.grokassembly.stderr", line);
             }
+            // CheckStyle:VisibilityModifier ON
             int rc = 0;
-            final Document doc = builder.parse(proc.getInputStream());
+            doc = builder.parse(proc.getInputStream());
+
+            try {
+                rc = proc.waitFor();
+            } catch (InterruptedException ie) {
+                return;
+            }
+            if (rc == 3) {
+                LOGGER.log(Level.FINE, "analyzer.AssemblyAnalyzer.notassembly", dependency.getActualFilePath());
+                return;
+            } else if (rc != 0) {
+                LOGGER.log(Level.WARNING, "analyzer.AssemblyAnalyzer.grokassembly.rc", rc);
+            }
+
             final XPath xpath = XPathFactory.newInstance().newXPath();
 
             // First, see if there was an error
@@ -150,18 +166,6 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                         product, Confidence.HIGH));
             }
 
-            try {
-                rc = proc.waitFor();
-            } catch (InterruptedException ie) {
-                return;
-            }
-            if (rc == 3) {
-                LOGGER.log(Level.INFO, "{0} is not a valid assembly", dependency.getActualFilePath());
-                return;
-            } else if (rc != 0) {
-                LOGGER.log(Level.WARNING, "Return code {0} from GrokAssembly", rc);
-            }
-
         } catch (IOException ioe) {
             throw new AnalysisException(ioe);
         } catch (SAXException saxe) {
@@ -201,9 +205,10 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
             grokAssemblyExe = tempFile;
             // Set the temp file to get deleted when we're done
             grokAssemblyExe.deleteOnExit();
-            LOGGER.log(Level.FINE, "Extracted GrokAssembly.exe to {0}", grokAssemblyExe.getPath());
+            LOGGER.log(Level.FINE, "analyzer.AssemblyAnalyzer.grokassembly.deployed", grokAssemblyExe.getPath());
         } catch (IOException ioe) {
-            LOGGER.log(Level.WARNING, "Could not extract GrokAssembly.exe: {0}", ioe.getMessage());
+            this.setEnabled(false);
+            LOGGER.log(Level.WARNING, "analyzer.AssemblyAnalyzer.grokassembly.notdeployed", ioe.getMessage());
             throw new AnalysisException("Could not extract GrokAssembly.exe", ioe);
         } finally {
             if (fos != null) {
@@ -230,9 +235,11 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
             final Process p = pb.start();
             // Try evacuating the error stream
             rdr = new BufferedReader(new InputStreamReader(p.getErrorStream(), "UTF-8"));
+            // CheckStyle:VisibilityModifier OFF
             while (rdr.ready() && rdr.readLine() != null) {
                 // We expect this to complain
             }
+            // CheckStyle:VisibilityModifier ON
             final Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(p.getInputStream());
             final XPath xpath = XPathFactory.newInstance().newXPath();
             final String error = xpath.evaluate("/assembly/error", doc);
@@ -240,15 +247,16 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                 LOGGER.warning("An error occurred with the .NET AssemblyAnalyzer, please see the log for more details.");
                 LOGGER.fine("GrokAssembly.exe is not working properly");
                 grokAssemblyExe = null;
+                this.setEnabled(false);
                 throw new AnalysisException("Could not execute .NET AssemblyAnalyzer");
             }
         } catch (Throwable e) {
             if (e instanceof AnalysisException) {
                 throw (AnalysisException) e;
             } else {
-                LOGGER.warning("An error occured with the .NET AssemblyAnalyzer; "
-                        + "this can be ignored unless you are scanning .NET DLLs. Please see the log for more details.");
-                LOGGER.log(Level.FINE, "Could not execute GrokAssembly {0}", e.getMessage());
+                LOGGER.warning("analyzer.AssemblyAnalyzer.grokassembly.initialization.failed");
+                LOGGER.log(Level.FINE, "analyzer.AssemblyAnalyzer.grokassembly.initialization.message", e.getMessage());
+                this.setEnabled(false);
                 throw new AnalysisException("An error occured with the .NET AssemblyAnalyzer", e);
             }
         } finally {
@@ -260,7 +268,6 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                 }
             }
         }
-
         builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
     }
 
@@ -272,7 +279,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                 grokAssemblyExe.deleteOnExit();
             }
         } catch (SecurityException se) {
-            LOGGER.fine("Can't delete temporary GrokAssembly.exe");
+            LOGGER.fine("analyzer.AssemblyAnalyzer.grokassembly.notdeleted");
         }
     }
 

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

@@ -57,6 +57,7 @@ import org.owasp.dependencycheck.utils.DependencyVersionUtil;
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
 public class CPEAnalyzer implements Analyzer {
+
     /**
      * The Logger.
      */
@@ -90,6 +91,11 @@ public class CPEAnalyzer implements Analyzer {
      */
     private CveDB cve;
 
+    /**
+     * The URL to perform a search of the NVD CVE data at NIST.
+     */
+    public static final String NVD_SEARCH_URL = "https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=%s";
+
     /**
      * Returns the name of this analyzer.
      *
@@ -164,29 +170,10 @@ public class CPEAnalyzer implements Analyzer {
      * @throws ParseException is thrown when the Lucene query cannot be parsed.
      */
     protected void determineCPE(Dependency dependency) throws CorruptIndexException, IOException, ParseException {
-        Confidence confidence = Confidence.HIGHEST;
-
-        String vendors = addEvidenceWithoutDuplicateTerms("", dependency.getVendorEvidence(), confidence);
-        String products = addEvidenceWithoutDuplicateTerms("", dependency.getProductEvidence(), confidence);
-        /* bug fix for #40 - version evidence is not showing up as "used" in the reports if there is no
-         * CPE identified. As such, we are "using" the evidence and ignoring the results. */
-        addEvidenceWithoutDuplicateTerms("", dependency.getVersionEvidence(), confidence);
-
-        int ctr = 0;
-        do {
-            if (!vendors.isEmpty() && !products.isEmpty()) {
-                final List<IndexEntry> entries = searchCPE(vendors, products, dependency.getProductEvidence().getWeighting(),
-                        dependency.getVendorEvidence().getWeighting());
-
-                for (IndexEntry e : entries) {
-                    if (verifyEntry(e, dependency)) {
-                        final String vendor = e.getVendor();
-                        final String product = e.getProduct();
-                        determineIdentifiers(dependency, vendor, product);
-                    }
-                }
-            }
-            confidence = reduceConfidence(confidence);
+        //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);
             }
@@ -195,10 +182,28 @@ public class CPEAnalyzer implements Analyzer {
             }
             /* bug fix for #40 - version evidence is not showing up as "used" in the reports if there is no
              * CPE identified. As such, we are "using" the evidence and ignoring the results. */
-            if (dependency.getVersionEvidence().contains(confidence)) {
-                addEvidenceWithoutDuplicateTerms("", dependency.getVersionEvidence(), confidence);
+//            if (dependency.getVersionEvidence().contains(confidence)) {
+//                addEvidenceWithoutDuplicateTerms("", dependency.getVersionEvidence(), confidence);
+//            }
+            if (!vendors.isEmpty() && !products.isEmpty()) {
+                final List<IndexEntry> entries = searchCPE(vendors, products, dependency.getProductEvidence().getWeighting(),
+                        dependency.getVendorEvidence().getWeighting());
+                if (entries == null) {
+                    continue;
+                }
+                boolean identifierAdded = false;
+                for (IndexEntry e : entries) {
+                    if (verifyEntry(e, dependency)) {
+                        final String vendor = e.getVendor();
+                        final String product = e.getProduct();
+                        identifierAdded |= determineIdentifiers(dependency, vendor, product, confidence);
+                    }
+                }
+                if (identifierAdded) {
+                    break;
+                }
             }
-        } while ((++ctr) < 4);
+        }
     }
 
     /**
@@ -233,22 +238,6 @@ public class CPEAnalyzer implements Analyzer {
         return sb.toString().trim();
     }
 
-    /**
-     * Reduces the given confidence by one level. This returns LOW if the confidence passed in is not HIGH.
-     *
-     * @param c the confidence to reduce.
-     * @return One less then the confidence passed in.
-     */
-    private Confidence reduceConfidence(final Confidence c) {
-        if (c == Confidence.HIGHEST) {
-            return Confidence.HIGH;
-        } else if (c == Confidence.HIGH) {
-            return Confidence.MEDIUM;
-        } else {
-            return Confidence.LOW;
-        }
-    }
-
     /**
      * <p>
      * Searches the Lucene CPE index to identify possible CPE entries associated with the supplied vendor, product, and
@@ -263,27 +252,24 @@ public class CPEAnalyzer implements Analyzer {
      * @param vendorWeightings a list of strings to use to add weighting factors to the vendor field
      * @param productWeightings Adds a list of strings that will be used to add weighting factors to the product search
      * @return a list of possible CPE values
-     * @throws CorruptIndexException when the Lucene index is corrupt
-     * @throws IOException when the Lucene index is not found
-     * @throws ParseException when the generated query is not valid
      */
     protected List<IndexEntry> searchCPE(String vendor, String product,
-            Set<String> vendorWeightings, Set<String> productWeightings)
-            throws CorruptIndexException, IOException, ParseException {
+            Set<String> vendorWeightings, Set<String> productWeightings) {
+
         final ArrayList<IndexEntry> ret = new ArrayList<IndexEntry>(MAX_QUERY_RESULTS);
 
         final String searchString = buildSearch(vendor, product, vendorWeightings, productWeightings);
         if (searchString == null) {
             return ret;
         }
-
-        final TopDocs docs = cpe.search(searchString, MAX_QUERY_RESULTS);
-        for (ScoreDoc d : docs.scoreDocs) {
-            if (d.score >= 0.08) {
-                final Document doc = cpe.getDocument(d.doc);
-                final IndexEntry entry = new IndexEntry();
-                entry.setVendor(doc.get(Fields.VENDOR));
-                entry.setProduct(doc.get(Fields.PRODUCT));
+        try {
+            final TopDocs docs = cpe.search(searchString, MAX_QUERY_RESULTS);
+            for (ScoreDoc d : docs.scoreDocs) {
+                if (d.score >= 0.08) {
+                    final Document doc = cpe.getDocument(d.doc);
+                    final IndexEntry entry = new IndexEntry();
+                    entry.setVendor(doc.get(Fields.VENDOR));
+                    entry.setProduct(doc.get(Fields.PRODUCT));
 //                if (d.score < 0.08) {
 //                    System.out.print(entry.getVendor());
 //                    System.out.print(":");
@@ -291,13 +277,23 @@ public class CPEAnalyzer implements Analyzer {
 //                    System.out.print(":");
 //                    System.out.println(d.score);
 //                }
-                entry.setSearchScore(d.score);
-                if (!ret.contains(entry)) {
-                    ret.add(entry);
+                    entry.setSearchScore(d.score);
+                    if (!ret.contains(entry)) {
+                        ret.add(entry);
+                    }
                 }
             }
+            return ret;
+        } catch (ParseException ex) {
+            final String msg = String.format("Unable to parse: %s", searchString);
+            LOGGER.log(Level.WARNING, "An error occured querying the CPE data. See the log for more details.");
+            LOGGER.log(Level.INFO, msg, ex);
+        } catch (IOException ex) {
+            final String msg = String.format("IO Error with search string: %s", searchString);
+            LOGGER.log(Level.WARNING, "An error occured reading CPE data. See the log for more details.");
+            LOGGER.log(Level.INFO, msg, ex);
         }
-        return ret;
+        return null;
     }
 
     /**
@@ -502,14 +498,21 @@ public class CPEAnalyzer implements Analyzer {
      * @param dependency the Dependency being analyzed
      * @param vendor the vendor for the CPE being analyzed
      * @param product the product for the CPE being analyzed
+     * @param currentConfidence the current confidence being used during analysis
+     * @return <code>true</code> if an identifier was added to the dependency; otherwise <code>false</code>
      * @throws UnsupportedEncodingException is thrown if UTF-8 is not supported
      */
-    private void determineIdentifiers(Dependency dependency, String vendor, String product) throws UnsupportedEncodingException {
+    protected boolean determineIdentifiers(Dependency dependency, String vendor, String product,
+            Confidence currentConfidence) throws UnsupportedEncodingException {
         final Set<VulnerableSoftware> cpes = cve.getCPEs(vendor, product);
         DependencyVersion bestGuess = new DependencyVersion("-");
         Confidence bestGuessConf = null;
+        boolean hasBroadMatch = false;
         final List<IdentifierMatch> collected = new ArrayList<IdentifierMatch>();
         for (Confidence conf : Confidence.values()) {
+//            if (conf.compareTo(currentConfidence) > 0) {
+//                break;
+//            }
             for (Evidence evidence : dependency.getVersionEvidence().iterator(conf)) {
                 final DependencyVersion evVer = DependencyVersionUtil.parseVersion(evidence.getValue());
                 if (evVer == null) {
@@ -522,9 +525,13 @@ public class CPEAnalyzer implements Analyzer {
                     } else {
                         dbVer = DependencyVersionUtil.parseVersion(vs.getVersion());
                     }
-                    if (dbVer == null //special case, no version specified - everything is vulnerable
-                            || evVer.equals(dbVer)) { //yeah! exact match
-                        final String url = String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(vs.getName(), "UTF-8"));
+                    if (dbVer == null) { //special case, no version specified - everything is vulnerable
+                        hasBroadMatch = true;
+                        final String url = String.format(NVD_SEARCH_URL, URLEncoder.encode(vs.getName(), "UTF-8"));
+                        final IdentifierMatch match = new IdentifierMatch("cpe", vs.getName(), url, IdentifierConfidence.BROAD_MATCH, conf);
+                        collected.add(match);
+                    } else if (evVer.equals(dbVer)) { //yeah! exact match
+                        final String url = String.format(NVD_SEARCH_URL, URLEncoder.encode(vs.getName(), "UTF-8"));
                         final IdentifierMatch match = new IdentifierMatch("cpe", vs.getName(), url, IdentifierConfidence.EXACT_MATCH, conf);
                         collected.add(match);
                     } else {
@@ -549,7 +556,11 @@ public class CPEAnalyzer implements Analyzer {
             }
         }
         final String cpeName = String.format("cpe:/a:%s:%s:%s", vendor, product, bestGuess.toString());
-        final String url = null; //String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(cpeName, "UTF-8"));
+        String url = null;
+        if (hasBroadMatch) { //if we have a broad match we can add the URL to the best guess.
+            final String cpeUrlName = String.format("cpe:/a:%s:%s", vendor, product);
+            url = String.format(NVD_SEARCH_URL, URLEncoder.encode(cpeUrlName, "UTF-8"));
+        }
         if (bestGuessConf == null) {
             bestGuessConf = Confidence.LOW;
         }
@@ -559,6 +570,7 @@ public class CPEAnalyzer implements Analyzer {
         Collections.sort(collected);
         final IdentifierConfidence bestIdentifierQuality = collected.get(0).getConfidence();
         final Confidence bestEvidenceQuality = collected.get(0).getEvidenceConfidence();
+        boolean identifierAdded = false;
         for (IdentifierMatch m : collected) {
             if (bestIdentifierQuality.equals(m.getConfidence())
                     && bestEvidenceQuality.equals(m.getEvidenceConfidence())) {
@@ -569,8 +581,10 @@ public class CPEAnalyzer implements Analyzer {
                     i.setConfidence(bestEvidenceQuality);
                 }
                 dependency.addIdentifier(i);
+                identifierAdded = true;
             }
         }
+        return identifierAdded;
     }
 
     /**
@@ -585,7 +599,12 @@ public class CPEAnalyzer implements Analyzer {
         /**
          * A best guess for the CPE.
          */
-        BEST_GUESS
+        BEST_GUESS,
+        /**
+         * The entire vendor/product group must be added (without a guess at version) because there is a CVE with a VS
+         * that only specifies vendor/product.
+         */
+        BROAD_MATCH
     }
 
     /**

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

@@ -0,0 +1,201 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URL;
+import java.util.List;
+import java.util.Set;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.data.central.CentralSearch;
+import org.owasp.dependencycheck.data.nexus.MavenArtifact;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * Analyzer which will attempt to locate a dependency, and the GAV information, by querying Central for the dependency's
+ * SHA-1 digest.
+ *
+ * @author colezlaw
+ */
+public class CentralAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(CentralAnalyzer.class.getName());
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Central Analyzer";
+
+    /**
+     * The phase in which this analyzer runs.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The types of files on which this will work.
+     */
+    private static final Set<String> SUPPORTED_EXTENSIONS = newHashSet("jar");
+
+    /**
+     * The analyzer should be disabled if there are errors, so this is a flag to determine if such an error has
+     * occurred.
+     */
+    private boolean errorFlag = false;
+
+    /**
+     * The searcher itself.
+     */
+    private CentralSearch searcher;
+
+    /**
+     * Field indicating if the analyzer is enabled.
+     */
+    private final boolean enabled = checkEnabled();
+
+    /**
+     * Determine whether to enable this analyzer or not.
+     *
+     * @return whether the analyzer should be enabled
+     */
+    @Override
+    public boolean isEnabled() {
+        return enabled;
+    }
+
+    /**
+     * Determines if this analyzer is enabled.
+     *
+     * @return <code>true</code> if the analyzer is enabled; otherwise <code>false</code>
+     */
+    private boolean checkEnabled() {
+        boolean retval = false;
+
+        try {
+            if (Settings.getBoolean(Settings.KEYS.ANALYZER_CENTRAL_ENABLED)) {
+                if (!Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED)
+                        || NexusAnalyzer.DEFAULT_URL.equals(Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL))) {
+                    LOGGER.info("Enabling the Central analyzer");
+                    retval = true;
+                } else {
+                    LOGGER.info("Nexus analyzer is enabled, disabling the Central Analyzer");
+                }
+            } else {
+                LOGGER.info("Central analyzer disabled");
+            }
+        } catch (InvalidSettingException ise) {
+            LOGGER.warning("Invalid setting. Disabling the Central analyzer");
+        }
+        return retval;
+    }
+
+    /**
+     * Initializes the analyzer once before any analysis is performed.
+     *
+     * @throws Exception if there's an error during initialization
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+        LOGGER.fine("Initializing Central analyzer");
+        LOGGER.fine(String.format("Central analyzer enabled: %s", isEnabled()));
+        if (isEnabled()) {
+            final String searchUrl = Settings.getString(Settings.KEYS.ANALYZER_CENTRAL_URL);
+            LOGGER.fine(String.format("Central Analyzer URL: %s", searchUrl));
+            searcher = new CentralSearch(new URL(searchUrl));
+        }
+    }
+
+    /**
+     * Returns the analyzer's name.
+     *
+     * @return the name of the analyzer
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the key used in the properties file to to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key.
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_CENTRAL_ENABLED;
+    }
+
+    /**
+     * Returns the analysis phase under which the analyzer runs.
+     *
+     * @return the phase under which the analyzer runs
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the extensions for which this Analyzer runs.
+     *
+     * @return the extensions for which this Analyzer runs
+     */
+    @Override
+    public Set<String> getSupportedExtensions() {
+        return SUPPORTED_EXTENSIONS;
+    }
+
+    /**
+     * Performs the analysis.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine
+     * @throws AnalysisException when there's an exception during analysis
+     */
+    @Override
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        if (errorFlag || !isEnabled()) {
+            return;
+        }
+
+        try {
+            final List<MavenArtifact> mas = searcher.searchSha1(dependency.getSha1sum());
+            final Confidence confidence = mas.size() > 1 ? Confidence.HIGH : Confidence.HIGHEST;
+            for (MavenArtifact ma : mas) {
+                LOGGER.fine(String.format("Central analyzer found artifact (%s) for dependency (%s)", ma.toString(), dependency.getFileName()));
+                dependency.addAsEvidence("central", ma, confidence);
+            }
+        } catch (IllegalArgumentException iae) {
+            LOGGER.info(String.format("invalid sha1-hash on %s", dependency.getFileName()));
+        } catch (FileNotFoundException fnfe) {
+            LOGGER.fine(String.format("Artifact not found in repository: '%s", dependency.getFileName()));
+        } catch (IOException ioe) {
+            LOGGER.log(Level.FINE, "Could not connect to Central search", ioe);
+            errorFlag = true;
+        }
+    }
+}

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

@@ -112,7 +112,7 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
                     while (subIterator.hasNext()) {
                         final Dependency nextDependency = subIterator.next();
                         if (hashesMatch(dependency, nextDependency)) {
-                            if (isCore(dependency, nextDependency)) {
+                            if (firstPathIsShortest(dependency.getFilePath(), nextDependency.getFilePath())) {
                                 mergeDependencies(dependency, nextDependency, dependenciesToRemove);
                             } else {
                                 mergeDependencies(nextDependency, dependency, dependenciesToRemove);
@@ -390,4 +390,43 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
         }
         return false;
     }
+
+    /**
+     * Determines which path is shortest; if path lengths are equal then we use compareTo of the string method to
+     * determine if the first path is smaller.
+     *
+     * @param left the first path to compare
+     * @param right the second path to compare
+     * @return <code>true</code> if the leftPath is the shortest; otherwise <code>false</code>
+     */
+    protected boolean firstPathIsShortest(String left, String right) {
+        final String leftPath = left.replace('\\', '/');
+        final String rightPath = right.replace('\\', '/');
+
+        final int leftCount = countChar(leftPath, '/');
+        final int rightCount = countChar(rightPath, '/');
+        if (leftCount == rightCount) {
+            return leftPath.compareTo(rightPath) <= 0;
+        } else {
+            return leftCount < rightCount;
+        }
+    }
+
+    /**
+     * Counts the number of times the character is present in the string.
+     *
+     * @param string the string to count the characters in
+     * @param c the character to count
+     * @return the number of times the character is present in the string
+     */
+    private int countChar(String string, char c) {
+        int count = 0;
+        final int max = string.length();
+        for (int i = 0; i < max; i++) {
+            if (c == string.charAt(i)) {
+                count++;
+            }
+        }
+        return count;
+    }
 }

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

@@ -86,11 +86,46 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
     public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
         removeJreEntries(dependency);
         removeBadMatches(dependency);
+        removeBadSpringMatches(dependency);
         removeWrongVersionMatches(dependency);
         removeSpuriousCPE(dependency);
+        removeDuplicativeEntriesFromJar(dependency, engine);
         addFalseNegativeCPEs(dependency);
     }
 
+    /**
+     * Removes inaccurate matches on springframework CPEs.
+     *
+     * @param dependency the dependency to test for and remove known inaccurate CPE matches
+     */
+    private void removeBadSpringMatches(Dependency dependency) {
+        String mustContain = null;
+        for (Identifier i : dependency.getIdentifiers()) {
+            if ("maven".contains(i.getType())) {
+                if (i.getValue() != null && i.getValue().startsWith("org.springframework.")) {
+                    final int endPoint = i.getValue().indexOf(":", 19);
+                    if (endPoint >= 0) {
+                        mustContain = i.getValue().substring(19, endPoint).toLowerCase();
+                        break;
+                    }
+                }
+            }
+        }
+        if (mustContain != null) {
+            final Iterator<Identifier> itr = dependency.getIdentifiers().iterator();
+            while (itr.hasNext()) {
+                final Identifier i = itr.next();
+                if ("cpe".contains(i.getType())
+                        && i.getValue() != null
+                        && i.getValue().startsWith("cpe:/a:springsource:")
+                        && !i.getValue().toLowerCase().contains(mustContain)) {
+                    itr.remove();
+                    //dependency.getIdentifiers().remove(i);
+                }
+            }
+        }
+    }
+
     /**
      * <p>
      * Intended to remove spurious CPE entries. By spurious we mean duplicate, less specific CPE entries.</p>
@@ -160,11 +195,20 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
      */
     public static final Pattern CORE_JAVA = Pattern.compile("^cpe:/a:(sun|oracle|ibm):(j2[ems]e|"
             + "java(_platform_micro_edition|_runtime_environment|_se|virtual_machine|se_development_kit|fx)?|"
-            + "jdk|jre|jsf|jsse)($|:.*)");
+            + "jdk|jre|jsse)($|:.*)");
+
+    /**
+     * Regex to identify core jsf libraries.
+     */
+    public static final Pattern CORE_JAVA_JSF = Pattern.compile("^cpe:/a:(sun|oracle|ibm):jsf($|:.*)");
     /**
      * Regex to identify core java library files. This is currently incomplete.
      */
-    public static final Pattern CORE_FILES = Pattern.compile("^((alt[-])?rt|jsf[-].*|jsse|jfxrt|jfr|jce|javaws|deploy|charsets)\\.jar$");
+    public static final Pattern CORE_FILES = Pattern.compile("(^|/)((alt[-])?rt|jsse|jfxrt|jfr|jce|javaws|deploy|charsets)\\.jar$");
+    /**
+     * Regex to identify core jsf java library files. This is currently incomplete.
+     */
+    public static final Pattern CORE_JSF_FILES = Pattern.compile("(^|/)jsf[-][^/]*\\.jar$");
 
     /**
      * Removes any CPE entries for the JDK/JRE unless the filename ends with rt.jar
@@ -181,27 +225,11 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
             if (coreCPE.matches() && !coreFiles.matches()) {
                 itr.remove();
             }
-
-            //replaced with the regex above.
-            //            if (("cpe:/a:sun:java".equals(i.getValue())
-            //                    || "cpe:/a:oracle:java".equals(i.getValue())
-            //                    || "cpe:/a:ibm:java".equals(i.getValue())
-            //                    || "cpe:/a:sun:j2se".equals(i.getValue())
-            //                    || "cpe:/a:oracle:j2se".equals(i.getValue())
-            //                    || i.getValue().startsWith("cpe:/a:sun:java:")
-            //                    || i.getValue().startsWith("cpe:/a:sun:j2se:")
-            //                    || i.getValue().startsWith("cpe:/a:sun:java:jre")
-            //                    || i.getValue().startsWith("cpe:/a:sun:java:jdk")
-            //                    || i.getValue().startsWith("cpe:/a:sun:java_se")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:java_se")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:java:")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:j2se:")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:jre")
-            //                    || i.getValue().startsWith("cpe:/a:oracle:jdk")
-            //                    || i.getValue().startsWith("cpe:/a:ibm:java:"))
-            //                    && !dependency.getFileName().toLowerCase().endsWith("rt.jar")) {
-            //                itr.remove();
-            //            }
+            final Matcher coreJsfCPE = CORE_JAVA_JSF.matcher(i.getValue());
+            final Matcher coreJsfFiles = CORE_JSF_FILES.matcher(dependency.getFileName());
+            if (coreJsfCPE.matches() && !coreJsfFiles.matches()) {
+                itr.remove();
+            }
         }
     }
 
@@ -248,14 +276,33 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
             //TODO move this startsWith expression to a configuration file?
             if ("cpe".equals(i.getType())) {
                 if ((i.getValue().matches(".*c\\+\\+.*")
-                        || i.getValue().startsWith("cpe:/a:jquery:jquery")
-                        || i.getValue().startsWith("cpe:/a:prototypejs:prototype")
-                        || i.getValue().startsWith("cpe:/a:yahoo:yui")
                         || i.getValue().startsWith("cpe:/a:file:file")
                         || i.getValue().startsWith("cpe:/a:mozilla:mozilla")
                         || i.getValue().startsWith("cpe:/a:cvs:cvs")
                         || i.getValue().startsWith("cpe:/a:ftp:ftp")
-                        || i.getValue().startsWith("cpe:/a:ssh:ssh"))
+                        || i.getValue().startsWith("cpe:/a:tcp:tcp")
+                        || i.getValue().startsWith("cpe:/a:ssh:ssh")
+                        || i.getValue().startsWith("cpe:/a:lookup:lookup"))
+                        && (dependency.getFileName().toLowerCase().endsWith(".jar")
+                        || dependency.getFileName().toLowerCase().endsWith("pom.xml")
+                        || dependency.getFileName().toLowerCase().endsWith(".dll")
+                        || dependency.getFileName().toLowerCase().endsWith(".exe")
+                        || dependency.getFileName().toLowerCase().endsWith(".nuspec")
+                        || dependency.getFileName().toLowerCase().endsWith(".nupkg"))) {
+                    itr.remove();
+                } else if ((i.getValue().startsWith("cpe:/a:jquery:jquery")
+                        || i.getValue().startsWith("cpe:/a:prototypejs:prototype")
+                        || i.getValue().startsWith("cpe:/a:yahoo:yui"))
+                        && (dependency.getFileName().toLowerCase().endsWith(".jar")
+                        || dependency.getFileName().toLowerCase().endsWith("pom.xml")
+                        || dependency.getFileName().toLowerCase().endsWith(".dll")
+                        || dependency.getFileName().toLowerCase().endsWith(".exe"))) {
+                    itr.remove();
+                } else if ((i.getValue().startsWith("cpe:/a:microsoft:excel")
+                        || i.getValue().startsWith("cpe:/a:microsoft:word")
+                        || i.getValue().startsWith("cpe:/a:microsoft:visio")
+                        || i.getValue().startsWith("cpe:/a:microsoft:powerpoint")
+                        || i.getValue().startsWith("cpe:/a:microsoft:office"))
                         && (dependency.getFileName().toLowerCase().endsWith(".jar")
                         || dependency.getFileName().toLowerCase().endsWith("pom.xml"))) {
                     itr.remove();
@@ -266,7 +313,7 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
                         && !dependency.getEvidenceUsed().containsUsedString("m-core")) {
                     itr.remove();
                 } else if (i.getValue().startsWith("cpe:/a:jboss:jboss")
-                        && !dependency.getFileName().toLowerCase().matches("jboss-[\\d\\.]+(GA)?\\.jar")) {
+                        && !dependency.getFileName().toLowerCase().matches("jboss-?[\\d\\.-]+(GA)?\\.jar")) {
                     itr.remove();
                 }
             }
@@ -314,6 +361,7 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
      * @param dependency the dependency being analyzed
      */
     private void addFalseNegativeCPEs(Dependency dependency) {
+        //TODO move this to the hint analyzer
         final Iterator<Identifier> itr = dependency.getIdentifiers().iterator();
         while (itr.hasNext()) {
             final Identifier i = itr.next();
@@ -329,20 +377,92 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
                 try {
                     dependency.addIdentifier("cpe",
                             newCpe,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe, "UTF-8")));
                     dependency.addIdentifier("cpe",
                             newCpe2,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe2, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe2, "UTF-8")));
                     dependency.addIdentifier("cpe",
                             newCpe3,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe3, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe3, "UTF-8")));
                     dependency.addIdentifier("cpe",
                             newCpe4,
-                            String.format("http://web.nvd.nist.gov/view/vuln/search?cpe=%s", URLEncoder.encode(newCpe4, "UTF-8")));
+                            String.format(CPEAnalyzer.NVD_SEARCH_URL, URLEncoder.encode(newCpe4, "UTF-8")));
                 } catch (UnsupportedEncodingException ex) {
                     LOGGER.log(Level.FINE, null, ex);
                 }
             }
         }
     }
+
+    /**
+     * Removes duplicate entries identified that are contained within JAR files. These occasionally crop up due to POM
+     * entries or other types of files (such as DLLs and EXEs) being contained within the JAR.
+     *
+     * @param dependency the dependency that might be a duplicate
+     * @param engine the engine used to scan all dependencies
+     */
+    private void removeDuplicativeEntriesFromJar(Dependency dependency, Engine engine) {
+        if (dependency.getFileName().toLowerCase().endsWith("pom.xml")
+                || "dll".equals(dependency.getFileExtension())
+                || "exe".equals(dependency.getFileExtension())) {
+            String parentPath = dependency.getFilePath().toLowerCase();
+            if (parentPath.contains(".jar")) {
+                parentPath = parentPath.substring(0, parentPath.indexOf(".jar") + 4);
+                final Dependency parent = findDependency(parentPath, engine.getDependencies());
+                if (parent != null) {
+                    boolean remove = false;
+                    for (Identifier i : dependency.getIdentifiers()) {
+                        if ("cpe".equals(i.getType())) {
+                            final String trimmedCPE = trimCpeToVendor(i.getValue());
+                            for (Identifier parentId : parent.getIdentifiers()) {
+                                if ("cpe".equals(parentId.getType()) && parentId.getValue().startsWith(trimmedCPE)) {
+                                    remove |= true;
+                                }
+                            }
+                        }
+                        if (!remove) { //we can escape early
+                            return;
+                        }
+                    }
+                    if (remove) {
+                        engine.getDependencies().remove(dependency);
+                    }
+                }
+            }
+
+        }
+    }
+
+    /**
+     * Retrieves a given dependency, based on a given path, from a list of dependencies.
+     *
+     * @param dependencyPath the path of the dependency to return
+     * @param dependencies the collection of dependencies to search
+     * @return the dependency object for the given path, otherwise null
+     */
+    private Dependency findDependency(String dependencyPath, List<Dependency> dependencies) {
+        for (Dependency d : dependencies) {
+            if (d.getFilePath().equalsIgnoreCase(dependencyPath)) {
+                return d;
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Takes a full CPE and returns the CPE trimmed to include only vendor and product.
+     *
+     * @param value the CPE value to trim
+     * @return a CPE value that only includes the vendor and product
+     */
+    private String trimCpeToVendor(String value) {
+        //cpe:/a:jruby:jruby:1.0.8
+        final int pos1 = value.indexOf(":", 7); //right of vendor
+        final int pos2 = value.indexOf(":", pos1 + 1); //right of product
+        if (pos2 < 0) {
+            return value;
+        } else {
+            return value.substring(0, pos2);
+        }
+    }
 }

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

@@ -73,7 +73,7 @@ public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
     public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
 
         //strip any path information that may get added by ArchiveAnalyzer, etc.
-        final File f = new File(dependency.getFileName());
+        final File f = dependency.getActualFile();
         String fileName = f.getName();
 
         //remove file extension

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

@@ -64,7 +64,6 @@ import org.owasp.dependencycheck.jaxb.pom.MavenNamespaceFilter;
 import org.owasp.dependencycheck.jaxb.pom.generated.License;
 import org.owasp.dependencycheck.jaxb.pom.generated.Model;
 import org.owasp.dependencycheck.jaxb.pom.generated.Organization;
-import org.owasp.dependencycheck.jaxb.pom.generated.Parent;
 import org.owasp.dependencycheck.utils.FileUtils;
 import org.owasp.dependencycheck.utils.NonClosingStream;
 import org.owasp.dependencycheck.utils.Settings;
@@ -74,7 +73,6 @@ import org.xml.sax.XMLFilter;
 import org.xml.sax.XMLReader;
 
 /**
- *
  * Used to load a JAR file and collect information that can be used to determine the associated CPE.
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
@@ -138,7 +136,8 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             "include-resource",
             "embed-dependency",
             "ipojo-components",
-            "ipojo-extension");
+            "ipojo-extension",
+            "eclipse-sourcereferences");
     /**
      * item in some manifest, should be considered medium confidence.
      */
@@ -170,7 +169,8 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      */
     public JarAnalyzer() {
         try {
-            final JAXBContext jaxbContext = JAXBContext.newInstance("org.owasp.dependencycheck.jaxb.pom.generated");
+            //final JAXBContext jaxbContext = JAXBContext.newInstance("org.owasp.dependencycheck.jaxb.pom.generated");
+            final JAXBContext jaxbContext = JAXBContext.newInstance(Model.class);
             pomUnmarshaller = jaxbContext.createUnmarshaller();
         } catch (JAXBException ex) { //guess we will just have a null pointer exception later...
             LOGGER.log(Level.SEVERE, "Unable to load parser. See the log for more details.");
@@ -293,13 +293,27 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             LOGGER.log(Level.FINE, msg, ex);
             return false;
         }
+        File externalPom = null;
         if (pomEntries.isEmpty()) {
-            return false;
+            if (dependency.getActualFilePath().matches(".*\\.m2.repository\\b.*")) {
+                String pomPath = dependency.getActualFilePath();
+                pomPath = pomPath.substring(0, pomPath.lastIndexOf('.')) + ".pom";
+                externalPom = new File(pomPath);
+                if (externalPom.isFile()) {
+                    pomEntries.add(pomPath);
+                } else {
+                    return false;
+                }
+            } else {
+                return false;
+            }
         }
         for (String path : pomEntries) {
             Properties pomProperties = null;
             try {
-                pomProperties = retrievePomProperties(path, jar);
+                if (externalPom == null) {
+                    pomProperties = retrievePomProperties(path, jar);
+                }
             } catch (IOException ex) {
                 LOGGER.log(Level.FINEST, "ignore this, failed reading a non-existent pom.properties", ex);
             }
@@ -313,19 +327,23 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                     final String displayPath = String.format("%s%s%s",
                             dependency.getFilePath(),
                             File.separator,
-                            path); //.replaceAll("[\\/]", File.separator));
+                            path);
                     final String displayName = String.format("%s%s%s",
                             dependency.getFileName(),
                             File.separator,
-                            path); //.replaceAll("[\\/]", File.separator));
+                            path);
 
                     newDependency.setFileName(displayName);
                     newDependency.setFilePath(displayPath);
-                    addPomEvidence(newDependency, pom, pomProperties);
+                    setPomEvidence(newDependency, pom, pomProperties, null);
                     engine.getDependencies().add(newDependency);
                     Collections.sort(engine.getDependencies());
                 } else {
-                    pom = retrievePom(path, jar);
+                    if (externalPom == null) {
+                        pom = retrievePom(path, jar);
+                    } else {
+                        pom = retrievePom(externalPom);
+                    }
                     foundSomething |= setPomEvidence(dependency, pom, pomProperties, classes);
                 }
             } catch (AnalysisException ex) {
@@ -345,16 +363,25 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      * @return a Properties object or null if no pom.properties was found
      * @throws IOException thrown if there is an exception reading the pom.properties
      */
-    @edu.umd.cs.findbugs.annotations.SuppressWarnings(value = "OS_OPEN_STREAM",
-            justification = "The reader is closed by closing the zipEntry")
     private Properties retrievePomProperties(String path, final JarFile jar) throws IOException {
         Properties pomProperties = null;
         final String propPath = path.substring(0, path.length() - 7) + "pom.properies";
         final ZipEntry propEntry = jar.getEntry(propPath);
         if (propEntry != null) {
-            final Reader reader = new InputStreamReader(jar.getInputStream(propEntry), "UTF-8");
-            pomProperties = new Properties();
-            pomProperties.load(reader);
+            Reader reader = null;
+            try {
+                reader = new InputStreamReader(jar.getInputStream(propEntry), "UTF-8");
+                pomProperties = new Properties();
+                pomProperties.load(reader);
+            } finally {
+                if (reader != null) {
+                    try {
+                        reader.close();
+                    } catch (IOException ex) {
+                        LOGGER.log(Level.FINEST, "close error", ex);
+                    }
+                }
+            }
         }
         return pomProperties;
     }
@@ -514,6 +541,41 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
         return model;
     }
 
+    /**
+     * Reads in the specified POM and converts it to a Model.
+     *
+     * @param file the pom.xml file
+     * @return returns a
+     * @throws AnalysisException is thrown if there is an exception extracting or parsing the POM
+     * {@link org.owasp.dependencycheck.jaxb.pom.generated.Model} object
+     */
+    private Model retrievePom(File file) throws AnalysisException {
+        Model model = null;
+        try {
+            final FileInputStream stream = new FileInputStream(file);
+            final InputStreamReader reader = new InputStreamReader(stream, "UTF-8");
+            final InputSource xml = new InputSource(reader);
+            final SAXSource source = new SAXSource(xml);
+            model = readPom(source);
+        } catch (SecurityException ex) {
+            final String msg = String.format("Unable to parse pom '%s'; invalid signature", file.getPath());
+            LOGGER.log(Level.WARNING, msg);
+            LOGGER.log(Level.FINE, null, ex);
+            throw new AnalysisException(ex);
+        } catch (IOException ex) {
+            final String msg = String.format("Unable to parse pom '%s'(IO Exception)", file.getPath());
+            LOGGER.log(Level.WARNING, msg);
+            LOGGER.log(Level.FINE, "", ex);
+            throw new AnalysisException(ex);
+        } catch (Throwable ex) {
+            final String msg = String.format("Unexpected error during parsing of the pom '%s'", file.getPath());
+            LOGGER.log(Level.WARNING, msg);
+            LOGGER.log(Level.FINE, "", ex);
+            throw new AnalysisException(ex);
+        }
+        return model;
+    }
+
     /**
      * Retrieves the specified POM from a jar file and converts it to a Model.
      *
@@ -558,37 +620,90 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private boolean setPomEvidence(Dependency dependency, Model pom, Properties pomProperties, ArrayList<ClassNameInformation> classes) {
         boolean foundSomething = false;
+        boolean addAsIdentifier = true;
         if (pom == null) {
             return foundSomething;
         }
         String groupid = interpolateString(pom.getGroupId(), pomProperties);
-        if (groupid != null && !groupid.isEmpty()) {
-            if (groupid.startsWith("org.") || groupid.startsWith("com.")) {
-                groupid = groupid.substring(4);
+        String parentGroupId = null;
+
+        if (pom.getParent() != null) {
+            parentGroupId = interpolateString(pom.getParent().getGroupId(), pomProperties);
+            if ((groupid == null || groupid.isEmpty()) && parentGroupId != null && !parentGroupId.isEmpty()) {
+                groupid = parentGroupId;
             }
+        }
+        final String originalGroupID = groupid;
+
+        if (groupid != null && !groupid.isEmpty()) {
             foundSomething = true;
-            dependency.getVendorEvidence().addEvidence("pom", "groupid", groupid, Confidence.HIGH);
+            dependency.getVendorEvidence().addEvidence("pom", "groupid", groupid, Confidence.HIGHEST);
             dependency.getProductEvidence().addEvidence("pom", "groupid", groupid, Confidence.LOW);
             addMatchingValues(classes, groupid, dependency.getVendorEvidence());
             addMatchingValues(classes, groupid, dependency.getProductEvidence());
+            if (parentGroupId != null && !parentGroupId.isEmpty() && !parentGroupId.equals(groupid)) {
+                dependency.getVendorEvidence().addEvidence("pom", "parent-groupid", parentGroupId, Confidence.MEDIUM);
+                dependency.getProductEvidence().addEvidence("pom", "parent-groupid", parentGroupId, Confidence.LOW);
+                addMatchingValues(classes, parentGroupId, dependency.getVendorEvidence());
+                addMatchingValues(classes, parentGroupId, dependency.getProductEvidence());
+            }
+        } else {
+            addAsIdentifier = false;
         }
+
         String artifactid = interpolateString(pom.getArtifactId(), pomProperties);
+        String parentArtifactId = null;
+
+        if (pom.getParent() != null) {
+            parentArtifactId = interpolateString(pom.getParent().getArtifactId(), pomProperties);
+            if ((artifactid == null || artifactid.isEmpty()) && parentArtifactId != null && !parentArtifactId.isEmpty()) {
+                artifactid = parentArtifactId;
+            }
+        }
+        final String originalArtifactID = artifactid;
         if (artifactid != null && !artifactid.isEmpty()) {
             if (artifactid.startsWith("org.") || artifactid.startsWith("com.")) {
                 artifactid = artifactid.substring(4);
             }
             foundSomething = true;
-            dependency.getProductEvidence().addEvidence("pom", "artifactid", artifactid, Confidence.HIGH);
+            dependency.getProductEvidence().addEvidence("pom", "artifactid", artifactid, Confidence.HIGHEST);
             dependency.getVendorEvidence().addEvidence("pom", "artifactid", artifactid, Confidence.LOW);
             addMatchingValues(classes, artifactid, dependency.getVendorEvidence());
             addMatchingValues(classes, artifactid, dependency.getProductEvidence());
+            if (parentArtifactId != null && !parentArtifactId.isEmpty() && !parentArtifactId.equals(artifactid)) {
+                dependency.getProductEvidence().addEvidence("pom", "parent-artifactid", parentArtifactId, Confidence.MEDIUM);
+                dependency.getVendorEvidence().addEvidence("pom", "parent-artifactid", parentArtifactId, Confidence.LOW);
+                addMatchingValues(classes, parentArtifactId, dependency.getVendorEvidence());
+                addMatchingValues(classes, parentArtifactId, dependency.getProductEvidence());
+            }
+        } else {
+            addAsIdentifier = false;
         }
         //version
-        final String version = interpolateString(pom.getVersion(), pomProperties);
+        String version = interpolateString(pom.getVersion(), pomProperties);
+        String parentVersion = null;
+
+        if (pom.getParent() != null) {
+            parentVersion = interpolateString(pom.getParent().getVersion(), pomProperties);
+            if ((version == null || version.isEmpty()) && parentVersion != null && !parentVersion.isEmpty()) {
+                version = parentVersion;
+            }
+        }
+
         if (version != null && !version.isEmpty()) {
             foundSomething = true;
             dependency.getVersionEvidence().addEvidence("pom", "version", version, Confidence.HIGHEST);
+            if (parentVersion != null && !parentVersion.isEmpty() && !parentVersion.equals(version)) {
+                dependency.getVersionEvidence().addEvidence("pom", "parent-version", version, Confidence.LOW);
+            }
+        } else {
+            addAsIdentifier = false;
         }
+
+        if (addAsIdentifier) {
+            dependency.addIdentifier("maven", String.format("%s:%s:%s", originalGroupID, originalArtifactID, version), null, Confidence.LOW);
+        }
+
         // org name
         final Organization org = pom.getOrganization();
         if (org != null && org.getName() != null) {
@@ -647,7 +762,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                 //TODO remove weighting
                 vendor.addWeighting(entry.getKey());
                 if (addPackagesAsEvidence && entry.getKey().length() > 1) {
-                    vendor.addEvidence("jar", "package", entry.getKey(), Confidence.LOW);
+                    vendor.addEvidence("jar", "package name", entry.getKey(), Confidence.LOW);
                 }
             }
         }
@@ -656,7 +771,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             if (ratio > 0.5) {
                 product.addWeighting(entry.getKey());
                 if (addPackagesAsEvidence && entry.getKey().length() > 1) {
-                    product.addEvidence("jar", "package", entry.getKey(), Confidence.LOW);
+                    product.addEvidence("jar", "package name", entry.getKey(), Confidence.LOW);
                 }
             }
         }
@@ -690,7 +805,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                         && !dependency.getFileName().toLowerCase().endsWith("-javadoc.jar")
                         && !dependency.getFileName().toLowerCase().endsWith("-src.jar")
                         && !dependency.getFileName().toLowerCase().endsWith("-doc.jar")) {
-                    LOGGER.log(Level.INFO,
+                    LOGGER.log(Level.FINE,
                             String.format("Jar file '%s' does not contain a manifest.",
                                     dependency.getFileName()));
                 }
@@ -764,6 +879,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                             && !key.endsWith("class-path")
                             && !key.endsWith("-scm") //todo change this to a regex?
                             && !key.startsWith("scm-")
+                            && !value.trim().startsWith("scm:")
                             && !isImportPackage(key, value)
                             && !isPackage(key, value)) {
 
@@ -1111,7 +1227,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
      * @param evidence the evidence collection to add new entries too
      */
     private void addMatchingValues(ArrayList<ClassNameInformation> classes, String value, EvidenceCollection evidence) {
-        if (value == null || value.isEmpty()) {
+        if (value == null || value.isEmpty() || classes == null || classes.isEmpty()) {
             return;
         }
         final String text = value.toLowerCase();
@@ -1138,93 +1254,6 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
 
     }
 
-    /**
-     * Adds evidence from the POM to the dependency. This includes the GAV and in some situations the parent GAV if
-     * specified.
-     *
-     * @param dependency the dependency being analyzed
-     * @param pom the POM data
-     * @param pomProperties the properties file associated with the pom
-     */
-    private void addPomEvidence(Dependency dependency, Model pom, Properties pomProperties) {
-        if (pom == null) {
-            return;
-        }
-        String groupid = interpolateString(pom.getGroupId(), pomProperties);
-        if (groupid != null && !groupid.isEmpty()) {
-            if (groupid.startsWith("org.") || groupid.startsWith("com.")) {
-                groupid = groupid.substring(4);
-            }
-            dependency.getVendorEvidence().addEvidence("pom", "groupid", groupid, Confidence.HIGH);
-            dependency.getProductEvidence().addEvidence("pom", "groupid", groupid, Confidence.LOW);
-        }
-        String artifactid = interpolateString(pom.getArtifactId(), pomProperties);
-        if (artifactid != null && !artifactid.isEmpty()) {
-            if (artifactid.startsWith("org.") || artifactid.startsWith("com.")) {
-                artifactid = artifactid.substring(4);
-            }
-            dependency.getProductEvidence().addEvidence("pom", "artifactid", artifactid, Confidence.HIGH);
-            dependency.getVendorEvidence().addEvidence("pom", "artifactid", artifactid, Confidence.LOW);
-        }
-        final String version = interpolateString(pom.getVersion(), pomProperties);
-        if (version != null && !version.isEmpty()) {
-            dependency.getVersionEvidence().addEvidence("pom", "version", version, Confidence.HIGHEST);
-        }
-
-        final Parent parent = pom.getParent(); //grab parent GAV
-        if (parent != null) {
-            final String parentGroupId = interpolateString(parent.getGroupId(), pomProperties);
-            if (parentGroupId != null && !parentGroupId.isEmpty()) {
-                if (groupid == null || groupid.isEmpty()) {
-                    dependency.getVendorEvidence().addEvidence("pom", "parent.groupid", parentGroupId, Confidence.HIGH);
-                } else {
-                    dependency.getVendorEvidence().addEvidence("pom", "parent.groupid", parentGroupId, Confidence.MEDIUM);
-                }
-                dependency.getProductEvidence().addEvidence("pom", "parent.groupid", parentGroupId, Confidence.LOW);
-            }
-            final String parentArtifactId = interpolateString(parent.getArtifactId(), pomProperties);
-            if (parentArtifactId != null && !parentArtifactId.isEmpty()) {
-                if (artifactid == null || artifactid.isEmpty()) {
-                    dependency.getProductEvidence().addEvidence("pom", "parent.artifactid", parentArtifactId, Confidence.HIGH);
-                } else {
-                    dependency.getProductEvidence().addEvidence("pom", "parent.artifactid", parentArtifactId, Confidence.MEDIUM);
-                }
-                dependency.getVendorEvidence().addEvidence("pom", "parent.artifactid", parentArtifactId, Confidence.LOW);
-            }
-            final String parentVersion = interpolateString(parent.getVersion(), pomProperties);
-            if (parentVersion != null && !parentVersion.isEmpty()) {
-                if (version == null || version.isEmpty()) {
-                    dependency.getVersionEvidence().addEvidence("pom", "parent.version", parentVersion, Confidence.HIGH);
-                } else {
-                    dependency.getVersionEvidence().addEvidence("pom", "parent.version", parentVersion, Confidence.LOW);
-                }
-            }
-        }
-        // org name
-        final Organization org = pom.getOrganization();
-        if (org != null && org.getName() != null) {
-            final String orgName = interpolateString(org.getName(), pomProperties);
-            if (orgName != null && !orgName.isEmpty()) {
-                dependency.getVendorEvidence().addEvidence("pom", "organization name", orgName, Confidence.HIGH);
-            }
-        }
-        //pom name
-        final String pomName = interpolateString(pom.getName(), pomProperties);
-        if (pomName != null && !pomName.isEmpty()) {
-            dependency.getProductEvidence().addEvidence("pom", "name", pomName, Confidence.HIGH);
-            dependency.getVendorEvidence().addEvidence("pom", "name", pomName, Confidence.HIGH);
-        }
-
-        //Description
-        if (pom.getDescription() != null) {
-            final String description = interpolateString(pom.getDescription(), pomProperties);
-            if (description != null && !description.isEmpty()) {
-                addDescription(dependency, description, "pom", "description");
-            }
-        }
-        extractLicense(pom, pomProperties, dependency);
-    }
-
     /**
      * Extracts the license information from the pom and adds it to the dependency.
      *

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

@@ -30,6 +30,7 @@ import org.owasp.dependencycheck.data.nexus.MavenArtifact;
 import org.owasp.dependencycheck.data.nexus.NexusSearch;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.owasp.dependencycheck.utils.Settings;
 
 /**
@@ -48,6 +49,11 @@ import org.owasp.dependencycheck.utils.Settings;
  */
 public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
 
+    /**
+     * The default URL - this will be used by the CentralAnalyzer to determine whether to enable this.
+     */
+    public static final String DEFAULT_URL = "https://repository.sonatype.org/service/local/";
+
     /**
      * The logger.
      */
@@ -73,6 +79,47 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
      */
     private NexusSearch searcher;
 
+    /**
+     * Field indicating if the analyzer is enabled.
+     */
+    private final boolean enabled = checkEnabled();
+
+    /**
+     * Determines if this analyzer is enabled
+     *
+     * @return <code>true</code> if the analyzer is enabled; otherwise <code>false</code>
+     */
+    private boolean checkEnabled() {
+        /* Enable this analyzer ONLY if the Nexus URL has been set to something
+         other than the default one (if it's the default one, we'll use the
+         central one) and it's enabled by the user.
+         */
+        boolean retval = false;
+        try {
+            if ((!DEFAULT_URL.equals(Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL)))
+                    && Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED)) {
+                LOGGER.info("Enabling Nexus analyzer");
+                retval = true;
+            } else {
+                LOGGER.info("Nexus analyzer disabled, using Central instead");
+            }
+        } catch (InvalidSettingException ise) {
+            LOGGER.warning("Invalid setting. Disabling Nexus analyzer");
+        }
+
+        return retval;
+    }
+
+    /**
+     * Determine whether to enable this analyzer or not.
+     *
+     * @return whether the analyzer should be enabled
+     */
+    @Override
+    public boolean isEnabled() {
+        return enabled;
+    }
+
     /**
      * Initializes the analyzer once before any analysis is performed.
      *
@@ -149,20 +196,12 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
      */
     @Override
     public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        if (!isEnabled()) {
+            return;
+        }
         try {
             final MavenArtifact ma = searcher.searchSha1(dependency.getSha1sum());
-            if (ma.getGroupId() != null && !"".equals(ma.getGroupId())) {
-                dependency.getVendorEvidence().addEvidence("nexus", "groupid", ma.getGroupId(), Confidence.HIGH);
-            }
-            if (ma.getArtifactId() != null && !"".equals(ma.getArtifactId())) {
-                dependency.getProductEvidence().addEvidence("nexus", "artifactid", ma.getArtifactId(), Confidence.HIGH);
-            }
-            if (ma.getVersion() != null && !"".equals(ma.getVersion())) {
-                dependency.getVersionEvidence().addEvidence("nexus", "version", ma.getVersion(), Confidence.HIGH);
-            }
-            if (ma.getArtifactUrl() != null && !"".equals(ma.getArtifactUrl())) {
-                dependency.addIdentifier("maven", ma.toString(), ma.getArtifactUrl(), Confidence.HIGHEST);
-            }
+            dependency.addAsEvidence("nexus", ma, Confidence.HIGH);
         } catch (IllegalArgumentException iae) {
             //dependency.addAnalysisException(new AnalysisException("Invalid SHA-1"));
             LOGGER.info(String.format("invalid sha-1 hash on %s", dependency.getFileName()));

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

@@ -0,0 +1,151 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.data.central;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathFactory;
+import org.owasp.dependencycheck.data.nexus.MavenArtifact;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.utils.URLConnectionFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+
+/**
+ * Class of methods to search Maven Central via Central.
+ *
+ * @author colezlaw
+ */
+public class CentralSearch {
+
+    /**
+     * The URL for the Central service
+     */
+    private final URL rootURL;
+
+    /**
+     * Whether to use the Proxy when making requests
+     */
+    private boolean useProxy;
+
+    /**
+     * Used for logging.
+     */
+    private static final Logger LOGGER = Logger.getLogger(CentralSearch.class.getName());
+
+    /**
+     * Creates a NexusSearch for the given repository URL.
+     *
+     * @param rootURL the URL of the repository on which searches should execute. Only parameters are added to this (so
+     * it should end in /select)
+     */
+    public CentralSearch(URL rootURL) {
+        this.rootURL = rootURL;
+        if (null != Settings.getString(Settings.KEYS.PROXY_SERVER)) {
+            useProxy = true;
+            LOGGER.fine("Using proxy");
+        } else {
+            useProxy = false;
+            LOGGER.fine("Not using proxy");
+        }
+    }
+
+    /**
+     * Searches the configured Central URL for the given sha1 hash. If the artifact is found, a
+     * <code>MavenArtifact</code> is populated with the GAV.
+     *
+     * @param sha1 the SHA-1 hash string for which to search
+     * @return the populated Maven GAV.
+     * @throws IOException if it's unable to connect to the specified repository or if the specified artifact is not
+     * found.
+     */
+    public List<MavenArtifact> searchSha1(String sha1) throws IOException {
+        if (null == sha1 || !sha1.matches("^[0-9A-Fa-f]{40}$")) {
+            throw new IllegalArgumentException("Invalid SHA1 format");
+        }
+
+        final URL url = new URL(rootURL + String.format("?q=1:\"%s\"&wt=xml", sha1));
+
+        LOGGER.fine(String.format("Searching Central url %s", url.toString()));
+
+        // Determine if we need to use a proxy. The rules:
+        // 1) If the proxy is set, AND the setting is set to true, use the proxy
+        // 2) Otherwise, don't use the proxy (either the proxy isn't configured,
+        // or proxy is specifically set to false)
+        final HttpURLConnection conn = URLConnectionFactory.createHttpURLConnection(url, useProxy);
+
+        conn.setDoOutput(true);
+
+        // JSON would be more elegant, but there's not currently a dependency
+        // on JSON, so don't want to add one just for this
+        conn.addRequestProperty("Accept", "application/xml");
+        conn.connect();
+
+        if (conn.getResponseCode() == 200) {
+            boolean missing = false;
+            try {
+                final DocumentBuilder builder = DocumentBuilderFactory
+                        .newInstance().newDocumentBuilder();
+                final Document doc = builder.parse(conn.getInputStream());
+                final XPath xpath = XPathFactory.newInstance().newXPath();
+                final String numFound = xpath.evaluate("/response/result/@numFound", doc);
+                if ("0".equals(numFound)) {
+                    missing = true;
+                } else {
+                    final ArrayList<MavenArtifact> result = new ArrayList<MavenArtifact>();
+                    final NodeList docs = (NodeList) xpath.evaluate("/response/result/doc", doc, XPathConstants.NODESET);
+                    for (int i = 0; i < docs.getLength(); i++) {
+                        final String g = xpath.evaluate("./str[@name='g']", docs.item(i));
+                        LOGGER.finest(String.format("GroupId: %s", g));
+                        final String a = xpath.evaluate("./str[@name='a']", docs.item(i));
+                        LOGGER.finest(String.format("ArtifactId: %s", a));
+                        final String v = xpath.evaluate("./str[@name='v']", docs.item(i));
+                        LOGGER.finest(String.format("Version: %s", v));
+                        result.add(new MavenArtifact(g, a, v, url.toString()));
+                    }
+
+                    return result;
+                }
+            } catch (Throwable e) {
+                // Anything else is jacked up XML stuff that we really can't recover
+                // from well
+                throw new IOException(e.getMessage(), e);
+            }
+
+            if (missing) {
+                throw new FileNotFoundException("Artifact not found in Central");
+            }
+        } else {
+            final String msg = String.format("Could not connect to Central received response code: %d %s",
+                    conn.getResponseCode(), conn.getResponseMessage());
+            LOGGER.fine(msg);
+            throw new IOException(msg);
+        }
+
+        return null;
+    }
+}

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

@@ -0,0 +1,14 @@
+/**
+ * <html>
+ * <head>
+ * <title>org.owasp.dependencycheck.data.central</title>
+ * </head>
+ * <body>
+ * <p>
+ * Contains classes related to searching Maven Central.</p>
+ * <p>
+ * These are used to abstract Maven Central searching away from OWASP Dependency Check so they can be reused elsewhere.</p>
+ * </body>
+ * </html>
+ */
+package org.owasp.dependencycheck.data.central;

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

@@ -54,6 +54,7 @@ import org.owasp.dependencycheck.utils.Pair;
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
 public final class CpeMemoryIndex {
+
     /**
      * The logger.
      */
@@ -160,7 +161,7 @@ public final class CpeMemoryIndex {
      */
     @SuppressWarnings("unchecked")
     private Analyzer createSearchingAnalyzer() {
-        final Map fieldAnalyzers = new HashMap();
+        final Map<String, Analyzer> fieldAnalyzers = new HashMap<String, Analyzer>();
         fieldAnalyzers.put(Fields.DOCUMENT_KEY, new KeywordAnalyzer());
         productSearchFieldAnalyzer = new SearchFieldAnalyzer(LuceneUtils.CURRENT_VERSION);
         vendorSearchFieldAnalyzer = new SearchFieldAnalyzer(LuceneUtils.CURRENT_VERSION);

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

@@ -22,7 +22,7 @@ package org.owasp.dependencycheck.data.cpe;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public abstract class Fields {
+public final class Fields {
 
     /**
      * The key for the name document id.
@@ -36,7 +36,10 @@ public abstract class Fields {
      * The key for the product field.
      */
     public static final String PRODUCT = "product";
+
     /**
-     * The key for the version field.
+     * Private constructor as this is more of an enumeration rather then a full class.
      */
+    private Fields() {
+    }
 }

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

@@ -29,10 +29,12 @@ import java.util.logging.Logger;
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
 public final class CweDB {
+
     /**
      * The Logger.
      */
     private static final Logger LOGGER = Logger.getLogger(CweDB.class.getName());
+
     /**
      * Empty private constructor as this is a utility class.
      */
@@ -55,7 +57,9 @@ public final class CweDB {
             final String filePath = "data/cwe.hashmap.serialized";
             final InputStream input = CweDB.class.getClassLoader().getResourceAsStream(filePath);
             oin = new ObjectInputStream(input);
-            return (HashMap<String, String>) oin.readObject();
+            @SuppressWarnings("unchecked")
+            final HashMap<String, String> ret = (HashMap<String, String>) oin.readObject();
+            return ret;
         } catch (ClassNotFoundException ex) {
             LOGGER.log(Level.WARNING, "Unable to load CWE data. This should not be an issue.");
             LOGGER.log(Level.FINE, null, ex);

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

@@ -64,7 +64,7 @@ public class NexusSearch {
     public NexusSearch(URL rootURL) {
         this.rootURL = rootURL;
         try {
-            if (null != Settings.getString(Settings.KEYS.PROXY_URL)
+            if (null != Settings.getString(Settings.KEYS.PROXY_SERVER)
                     && Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY)) {
                 useProxy = true;
                 LOGGER.fine("Using proxy");

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

@@ -42,6 +42,7 @@ import org.owasp.dependencycheck.utils.Settings;
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
 public final class ConnectionFactory {
+
     /**
      * The Logger.
      */
@@ -49,7 +50,7 @@ public final class ConnectionFactory {
     /**
      * The version of the current DB Schema.
      */
-    public static final String DB_SCHEMA_VERSION = "2.9";
+    public static final String DB_SCHEMA_VERSION = Settings.getString(Settings.KEYS.DB_VERSION);
     /**
      * Resource location for SQL file used to create the database schema.
      */
@@ -111,7 +112,10 @@ public final class ConnectionFactory {
             //yes, yes - hard-coded password - only if there isn't one in the properties file.
             password = Settings.getString(Settings.KEYS.DB_PASSWORD, "DC-Pass1337!");
             try {
-                connectionString = getConnectionString();
+                connectionString = Settings.getConnectionString(
+                        Settings.KEYS.DB_CONNECTION_STRING,
+                        Settings.KEYS.DB_FILE_NAME,
+                        Settings.KEYS.DB_VERSION);
             } catch (IOException ex) {
                 LOGGER.log(Level.FINE,
                         "Unable to retrieve the database connection string", ex);
@@ -120,7 +124,7 @@ public final class ConnectionFactory {
             boolean shouldCreateSchema = false;
             try {
                 if (connectionString.startsWith("jdbc:h2:file:")) { //H2
-                    shouldCreateSchema = !dbSchemaExists();
+                    shouldCreateSchema = !h2DataFileExists();
                     LOGGER.log(Level.FINE, "Need to create DB Structure: {0}", shouldCreateSchema);
                 }
             } catch (IOException ioex) {
@@ -217,51 +221,17 @@ public final class ConnectionFactory {
         return conn;
     }
 
-    /**
-     * Returns the configured connection string. If using the embedded H2 database this function will also ensure the
-     * data directory exists and if not create it.
-     *
-     * @return the connection string
-     * @throws IOException thrown the data directory cannot be created
-     */
-    private static String getConnectionString() throws IOException {
-        final String connStr = Settings.getString(Settings.KEYS.DB_CONNECTION_STRING, "jdbc:h2:file:%s;AUTO_SERVER=TRUE");
-        if (connStr.contains("%s")) {
-            final String directory = getDataDirectory().getCanonicalPath();
-            final File dataFile = new File(directory, "cve." + DB_SCHEMA_VERSION);
-            LOGGER.log(Level.FINE, String.format("File path for H2 file: '%s'", dataFile.toString()));
-            return String.format(connStr, dataFile.getAbsolutePath());
-        }
-        return connStr;
-    }
-
-    /**
-     * Retrieves the directory that the JAR file exists in so that we can ensure we always use a common data directory
-     * for the embedded H2 database. This is public solely for some unit tests; otherwise this should be private.
-     *
-     * @return the data directory to store data files
-     * @throws IOException is thrown if an IOException occurs of course...
-     */
-    public static File getDataDirectory() throws IOException {
-        final File path = Settings.getDataFile(Settings.KEYS.DATA_DIRECTORY);
-        if (!path.exists()) {
-            if (!path.mkdirs()) {
-                throw new IOException("Unable to create NVD CVE Data directory");
-            }
-        }
-        return path;
-    }
-
     /**
      * Determines if the H2 database file exists. If it does not exist then the data structure will need to be created.
      *
      * @return true if the H2 database file does not exist; otherwise false
      * @throws IOException thrown if the data directory does not exist and cannot be created
      */
-    private static boolean dbSchemaExists() throws IOException {
-        final File dir = getDataDirectory();
-        final String name = String.format("cve.%s.h2.db", DB_SCHEMA_VERSION);
-        final File file = new File(dir, name);
+    private static boolean h2DataFileExists() throws IOException {
+        final File dir = Settings.getDataDirectory();
+        final String name = Settings.getString(Settings.KEYS.DB_FILE_NAME);
+        final String fileName = String.format(name, DB_SCHEMA_VERSION);
+        final File file = new File(dir, fileName);
         return file.exists();
     }
 

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

@@ -46,6 +46,7 @@ import org.owasp.dependencycheck.utils.Pair;
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
 public class CveDB {
+
     /**
      * The logger.
      */
@@ -247,6 +248,7 @@ public class CveDB {
     /**
      * SQL Statement to retrieve a property from the database.
      */
+    @SuppressWarnings("unused")
     private static final String SELECT_PROPERTY = "SELECT id, value FROM properties WHERE id = ?";
     /**
      * SQL Statement to insert a new property.
@@ -259,6 +261,7 @@ public class CveDB {
     /**
      * SQL Statement to delete a property.
      */
+    @SuppressWarnings("unused")
     private static final String DELETE_PROPERTY = "DELETE FROM properties WHERE id = ?";
 
     //</editor-fold>
@@ -303,14 +306,14 @@ public class CveDB {
      * @throws DatabaseException thrown when there is an error retrieving the data from the DB
      */
     public Set<Pair<String, String>> getVendorProductList() throws DatabaseException {
-        final HashSet data = new HashSet<Pair<String, String>>();
+        final Set<Pair<String, String>> data = new HashSet<Pair<String, String>>();
         ResultSet rs = null;
         PreparedStatement ps = null;
         try {
             ps = getConnection().prepareStatement(SELECT_VENDOR_PRODUCT_LIST);
             rs = ps.executeQuery();
             while (rs.next()) {
-                data.add(new Pair(rs.getString(1), rs.getString(2)));
+                data.add(new Pair<String, String>(rs.getString(1), rs.getString(2)));
             }
         } catch (SQLException ex) {
             final String msg = "An unexpected SQL Exception occurred; please see the verbose log for more details.";
@@ -728,13 +731,15 @@ public class CveDB {
      * @param previous a flag indicating if previous versions of the product are vulnerable
      * @return true if the identified version is affected, otherwise false
      */
-    private boolean isAffected(String vendor, String product, DependencyVersion identifiedVersion, String cpeId, String previous) {
+    protected boolean isAffected(String vendor, String product, DependencyVersion identifiedVersion, String cpeId, String previous) {
         boolean affected = false;
         final boolean isStruts = "apache".equals(vendor) && "struts".equals(product);
         final DependencyVersion v = parseDependencyVersion(cpeId);
         final boolean prevAffected = previous != null && !previous.isEmpty();
-        if (identifiedVersion == null || "-".equals(identifiedVersion.toString())) {
-            if (v == null || "-".equals(v.toString())) {
+        if (v == null || "-".equals(v.toString())) { //all versions
+            affected = true;
+        } else if (identifiedVersion == null || "-".equals(identifiedVersion.toString())) {
+            if (prevAffected) {
                 affected = true;
             }
         } else if (identifiedVersion.equals(v) || (prevAffected && identifiedVersion.compareTo(v) < 0)) {

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

@@ -142,8 +142,8 @@ public class DatabaseProperties {
      *
      * @return a map of the database meta data
      */
-    public Map getMetaData() {
-        final TreeMap map = new TreeMap();
+    public Map<String, String> getMetaData() {
+        final TreeMap<String, String> map = new TreeMap<String, String>();
         for (Entry<Object, Object> entry : properties.entrySet()) {
             final String key = (String) entry.getKey();
             if (!"version".equals(key)) {
@@ -156,10 +156,10 @@ public class DatabaseProperties {
                         map.put(key, formatted);
                     } catch (Throwable ex) { //deliberately being broad in this catch clause
                         LOGGER.log(Level.FINE, "Unable to parse timestamp from DB", ex);
-                        map.put(key, entry.getValue());
+                        map.put(key, (String) entry.getValue());
                     }
                 } else {
-                    map.put(key, entry.getValue());
+                    map.put(key, (String) entry.getValue());
                 }
             }
         }

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/update/NvdCveUpdater.java

@@ -22,6 +22,7 @@ import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.owasp.dependencycheck.data.update.exception.UpdateException;
 import org.owasp.dependencycheck.utils.DownloadFailedException;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  * Class responsible for updating the NVD CVE and CPE data stores.
@@ -54,7 +55,11 @@ public class NvdCveUpdater implements CachedWebDataSource {
             LOGGER.log(Level.FINE, null, ex);
         } catch (DownloadFailedException ex) {
             LOGGER.log(Level.WARNING,
-                    "Unable to download the NVD CVE data, unable to update the data to use the most current data.");
+                    "Unable to download the NVD CVE data; the results may not include the most recent CPE/CVEs from the NVD.");
+            if (Settings.getString(Settings.KEYS.PROXY_SERVER) == null) {
+                LOGGER.log(Level.INFO,
+                        "If you are behind a proxy you may need to configure dependency-check to use the proxy.");
+            }
             LOGGER.log(Level.FINE, null, ex);
         }
     }

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/update/StandardUpdate.java

@@ -34,7 +34,7 @@ import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import static org.owasp.dependencycheck.data.nvdcve.DatabaseProperties.MODIFIED;
 import org.owasp.dependencycheck.data.update.exception.InvalidDataException;
 import org.owasp.dependencycheck.data.update.exception.UpdateException;
-import org.owasp.dependencycheck.data.update.task.CallableDownloadTask;
+import org.owasp.dependencycheck.data.update.task.DownloadTask;
 import org.owasp.dependencycheck.data.update.task.ProcessTask;
 import org.owasp.dependencycheck.utils.DownloadFailedException;
 import org.owasp.dependencycheck.utils.InvalidSettingException;
@@ -122,7 +122,7 @@ public class StandardUpdate {
             final Set<Future<Future<ProcessTask>>> downloadFutures = new HashSet<Future<Future<ProcessTask>>>(maxUpdates);
             for (NvdCveInfo cve : updateable) {
                 if (cve.getNeedsUpdate()) {
-                    final CallableDownloadTask call = new CallableDownloadTask(cve, processExecutor, cveDB, Settings.getInstance());
+                    final DownloadTask call = new DownloadTask(cve, processExecutor, cveDB, Settings.getInstance());
                     downloadFutures.add(downloadExecutors.submit(call));
                 }
             }
@@ -178,7 +178,9 @@ public class StandardUpdate {
 
             if (maxUpdates >= 1) { //ensure the modified file date gets written (we may not have actually updated it)
                 properties.save(updateable.get(MODIFIED));
+                LOGGER.log(Level.INFO, "Begin database maintenance.");
                 cveDB.cleanupDatabase();
+                LOGGER.log(Level.INFO, "End database maintenance.");
             }
         } finally {
             closeDataStores();

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/update/task/DownloadTask.java

@@ -18,6 +18,9 @@
 package org.owasp.dependencycheck.data.update.task;
 
 import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.net.URL;
 import java.util.concurrent.Callable;
@@ -25,6 +28,8 @@ import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Future;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import java.util.zip.GZIPInputStream;
+import org.apache.commons.io.FileUtils;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.update.NvdCveInfo;
 import org.owasp.dependencycheck.data.update.exception.UpdateException;
@@ -37,12 +42,12 @@ import org.owasp.dependencycheck.utils.Settings;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class CallableDownloadTask implements Callable<Future<ProcessTask>> {
+public class DownloadTask implements Callable<Future<ProcessTask>> {
 
     /**
      * The Logger.
      */
-    private static final Logger LOGGER = Logger.getLogger(CallableDownloadTask.class.getName());
+    private static final Logger LOGGER = Logger.getLogger(DownloadTask.class.getName());
 
     /**
      * Simple constructor for the callable download task.
@@ -54,7 +59,7 @@ public class CallableDownloadTask implements Callable<Future<ProcessTask>> {
      * the dependencies have a correct reference to the global settings.
      * @throws UpdateException thrown if temporary files could not be created
      */
-    public CallableDownloadTask(NvdCveInfo nvdCveInfo, ExecutorService processor, CveDB cveDB, Settings settings) throws UpdateException {
+    public DownloadTask(NvdCveInfo nvdCveInfo, ExecutorService processor, CveDB cveDB, Settings settings) throws UpdateException {
         this.nvdCveInfo = nvdCveInfo;
         this.processorService = processor;
         this.cveDB = cveDB;
@@ -188,13 +193,25 @@ public class CallableDownloadTask implements Callable<Future<ProcessTask>> {
             } catch (DownloadFailedException ex) {
                 msg = String.format("Download Failed for NVD CVE - %s%nSome CVEs may not be reported.", nvdCveInfo.getId());
                 LOGGER.log(Level.WARNING, msg);
+                if (Settings.getString(Settings.KEYS.PROXY_SERVER) == null) {
+                    LOGGER.log(Level.INFO,
+                            "If you are behind a proxy you may need to configure dependency-check to use the proxy.");
+                }
                 LOGGER.log(Level.FINE, null, ex);
                 return null;
             }
+            if (url1.toExternalForm().endsWith(".xml.gz")) {
+                extractGzip(first);
+            }
+            if (url2.toExternalForm().endsWith(".xml.gz")) {
+                extractGzip(second);
+            }
 
             msg = String.format("Download Complete for NVD CVE - %s", nvdCveInfo.getId());
             LOGGER.log(Level.INFO, msg);
-
+            if (this.processorService == null) {
+                return null;
+            }
             final ProcessTask task = new ProcessTask(cveDB, this, settings);
             return this.processorService.submit(task);
 
@@ -203,7 +220,7 @@ public class CallableDownloadTask implements Callable<Future<ProcessTask>> {
             LOGGER.log(Level.WARNING, msg);
             LOGGER.log(Level.FINE, "Download Task Failed", ex);
         } finally {
-            Settings.cleanup();
+            Settings.cleanup(false);
         }
         return null;
     }
@@ -233,4 +250,48 @@ public class CallableDownloadTask implements Callable<Future<ProcessTask>> {
             }
         }
     }
+
+    /**
+     * Extracts the file contained in a gzip archive. The extracted file is placed in the exact same path as the file
+     * specified.
+     *
+     * @param file the archive file
+     * @throws FileNotFoundException thrown if the file does not exist
+     * @throws IOException thrown if there is an error extracting the file.
+     */
+    private void extractGzip(File file) throws FileNotFoundException, IOException {
+        final String originalPath = file.getPath();
+        File gzip = new File(originalPath + ".gz");
+        if (gzip.isFile()) {
+            gzip.delete();
+        }
+        if (!file.renameTo(gzip)) {
+            throw new IOException("Unable to rename '" + file.getPath() + "'");
+        }
+        final File newfile = new File(originalPath);
+
+        final byte[] buffer = new byte[4096];
+
+        GZIPInputStream cin = null;
+        FileOutputStream out = null;
+        try {
+            cin = new GZIPInputStream(new FileInputStream(gzip));
+            out = new FileOutputStream(newfile);
+
+            int len;
+            while ((len = cin.read(buffer)) > 0) {
+                out.write(buffer, 0, len);
+            }
+        } finally {
+            if (cin != null) {
+                cin.close();
+            }
+            if (out != null) {
+                out.close();
+            }
+            if (gzip.isFile()) {
+                FileUtils.deleteQuietly(gzip);
+            }
+        }
+    }
 }

dependency-check-core/src/main/java/org/owasp/dependencycheck/data/update/task/ProcessTask.java

@@ -79,7 +79,7 @@ public class ProcessTask implements Callable<ProcessTask> {
     /**
      * A reference to the callable download task.
      */
-    private final CallableDownloadTask filePair;
+    private final DownloadTask filePair;
     /**
      * A reference to the properties.
      */
@@ -97,7 +97,7 @@ public class ProcessTask implements Callable<ProcessTask> {
      * @param settings a reference to the global settings object; this is necessary so that when the thread is started
      * the dependencies have a correct reference to the global settings.
      */
-    public ProcessTask(final CveDB cveDB, final CallableDownloadTask filePair, Settings settings) {
+    public ProcessTask(final CveDB cveDB, final DownloadTask filePair, Settings settings) {
         this.cveDB = cveDB;
         this.filePair = filePair;
         this.properties = cveDB.getDatabaseProperties();
@@ -119,7 +119,7 @@ public class ProcessTask implements Callable<ProcessTask> {
         } catch (UpdateException ex) {
             this.exception = ex;
         } finally {
-            Settings.cleanup();
+            Settings.cleanup(false);
         }
         return this;
     }

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

@@ -19,12 +19,14 @@ package org.owasp.dependencycheck.dependency;
 
 import java.io.File;
 import java.io.IOException;
+import java.io.Serializable;
 import java.security.NoSuchAlgorithmException;
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import org.owasp.dependencycheck.data.nexus.MavenArtifact;
 import org.owasp.dependencycheck.utils.Checksum;
 import org.owasp.dependencycheck.utils.FileUtils;
 
@@ -35,7 +37,7 @@ import org.owasp.dependencycheck.utils.FileUtils;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class Dependency implements Comparable<Dependency> {
+public class Dependency implements Serializable, Comparable<Dependency> {
 
     /**
      * The logger.
@@ -177,6 +179,33 @@ public class Dependency implements Comparable<Dependency> {
         this.filePath = filePath;
     }
 
+    /**
+     * The file name to display in reports.
+     */
+    private String displayName = null;
+
+    /**
+     * Sets the file name to display in reports.
+     *
+     * @param displayName the name to display
+     */
+    public void setDisplayFileName(String displayName) {
+        this.displayName = displayName;
+    }
+
+    /**
+     * Returns the file name to display in reports; if no display file name has been set it will default to the actual
+     * file name.
+     *
+     * @return the file name to display
+     */
+    public String getDisplayFileName() {
+        if (displayName == null) {
+            return this.fileName;
+        }
+        return this.displayName;
+    }
+
     /**
      * <p>
      * Gets the file path of the dependency.</p>
@@ -288,6 +317,41 @@ public class Dependency implements Comparable<Dependency> {
         this.identifiers.add(i);
     }
 
+    /**
+     * Adds the maven artifact as evidence.
+     *
+     * @param source The source of the evidence
+     * @param mavenArtifact The maven artifact
+     * @param confidence The confidence level of this evidence
+     */
+    public void addAsEvidence(String source, MavenArtifact mavenArtifact, Confidence confidence) {
+        if (mavenArtifact.getGroupId() != null && !mavenArtifact.getGroupId().isEmpty()) {
+            this.getVendorEvidence().addEvidence(source, "groupid", mavenArtifact.getGroupId(), confidence);
+        }
+        if (mavenArtifact.getArtifactId() != null && !mavenArtifact.getArtifactId().isEmpty()) {
+            this.getProductEvidence().addEvidence(source, "artifactid", mavenArtifact.getArtifactId(), confidence);
+        }
+        if (mavenArtifact.getVersion() != null && !mavenArtifact.getVersion().isEmpty()) {
+            this.getVersionEvidence().addEvidence(source, "version", mavenArtifact.getVersion(), confidence);
+        }
+        if (mavenArtifact.getArtifactUrl() != null && !mavenArtifact.getArtifactUrl().isEmpty()) {
+            boolean found = false;
+            for (Identifier i : this.getIdentifiers()) {
+                if ("maven".equals(i.getType()) && i.getValue().equals(mavenArtifact.toString())) {
+                    found = true;
+                    i.setConfidence(Confidence.HIGHEST);
+                    i.setUrl(mavenArtifact.getArtifactUrl());
+                    LOGGER.fine(String.format("Already found identifier %s. Confidence set to highest", i.getValue()));
+                    break;
+                }
+            }
+            if (!found) {
+                LOGGER.fine(String.format("Adding new maven identifier %s", mavenArtifact.toString()));
+                this.addIdentifier("maven", mavenArtifact.toString(), mavenArtifact.getArtifactUrl(), Confidence.HIGHEST);
+            }
+        }
+    }
+
     /**
      * Adds an entry to the list of detected Identifiers for the dependency file.
      *
@@ -296,6 +360,7 @@ public class Dependency implements Comparable<Dependency> {
     public void addIdentifier(Identifier identifier) {
         this.identifiers.add(identifier);
     }
+
     /**
      * A set of identifiers that have been suppressed.
      */
@@ -369,6 +434,15 @@ public class Dependency implements Comparable<Dependency> {
         return EvidenceCollection.merge(this.productEvidence, this.vendorEvidence, this.versionEvidence);
     }
 
+    /**
+     * Returns the evidence used to identify this dependency.
+     *
+     * @return an EvidenceCollection.
+     */
+    public Set<Evidence> getEvidenceForDisplay() {
+        return EvidenceCollection.mergeForDisplay(this.productEvidence, this.vendorEvidence, this.versionEvidence);
+    }
+
     /**
      * Returns the evidence used to identify this dependency.
      *
@@ -404,6 +478,7 @@ public class Dependency implements Comparable<Dependency> {
     public EvidenceCollection getVersionEvidence() {
         return this.versionEvidence;
     }
+
     /**
      * The description of the JAR file.
      */
@@ -426,6 +501,7 @@ public class Dependency implements Comparable<Dependency> {
     public void setDescription(String description) {
         this.description = description;
     }
+
     /**
      * The license that this dependency uses.
      */
@@ -448,6 +524,7 @@ public class Dependency implements Comparable<Dependency> {
     public void setLicense(String license) {
         this.license = license;
     }
+
     /**
      * A list of vulnerabilities for this dependency.
      */
@@ -503,6 +580,7 @@ public class Dependency implements Comparable<Dependency> {
     public void addVulnerability(Vulnerability vulnerability) {
         this.vulnerabilities.add(vulnerability);
     }
+
     /**
      * A collection of related dependencies.
      */
@@ -542,7 +620,7 @@ public class Dependency implements Comparable<Dependency> {
      * @return an integer representing the natural ordering
      */
     public int compareTo(Dependency o) {
-        return this.getFileName().compareToIgnoreCase(o.getFileName());
+        return this.getFilePath().compareToIgnoreCase(o.getFilePath());
     }
 
     /**

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

@@ -17,12 +17,14 @@
  */
 package org.owasp.dependencycheck.dependency;
 
+import java.io.Serializable;
+
 /**
  * Evidence is a piece of information about a Dependency.
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class Evidence implements Comparable<Evidence> {
+public class Evidence implements Serializable, Comparable<Evidence> {
 
     /**
      * Creates a new Evidence object.
@@ -220,22 +222,95 @@ public class Evidence implements Comparable<Evidence> {
      * @return an integer indicating the ordering of the two objects
      */
     public int compareTo(Evidence o) {
-        if (source.equals(o.source)) {
-            if (name.equals(o.name)) {
-                if (value.equals(o.value)) {
-                    if (confidence.equals(o.confidence)) {
+        if (o == null) {
+            return 1;
+        }
+        if (equalsWithNullCheck(source, o.source)) {
+            if (equalsWithNullCheck(name, o.name)) {
+                if (equalsWithNullCheck(value, o.value)) {
+                    if (equalsWithNullCheck(confidence, o.confidence)) {
                         return 0; //they are equal
                     } else {
-                        return confidence.compareTo(o.confidence);
+                        return compareToWithNullCheck(confidence, o.confidence);
                     }
                 } else {
-                    return value.compareToIgnoreCase(o.value);
+                    return compareToIgnoreCaseWithNullCheck(value, o.value);
                 }
             } else {
-                return name.compareToIgnoreCase(o.name);
+                return compareToIgnoreCaseWithNullCheck(name, o.name);
             }
         } else {
-            return source.compareToIgnoreCase(o.source);
+            return compareToIgnoreCaseWithNullCheck(source, o.source);
         }
     }
+
+    /**
+     * Equality check with an exhaustive, possibly duplicative, check against nulls.
+     *
+     * @param me the value to be compared
+     * @param other the other value to be compared
+     * @return true if the values are equal; otherwise false
+     */
+    private boolean equalsWithNullCheck(String me, String other) {
+        if (me == null && other == null) {
+            return true;
+        } else if (me == null || other == null) {
+            return false;
+        }
+        return me.equals(other);
+    }
+
+    /**
+     * Equality check with an exhaustive, possibly duplicative, check against nulls.
+     *
+     * @param me the value to be compared
+     * @param other the other value to be compared
+     * @return true if the values are equal; otherwise false
+     */
+    private boolean equalsWithNullCheck(Confidence me, Confidence other) {
+        if (me == null && other == null) {
+            return true;
+        } else if (me == null || other == null) {
+            return false;
+        }
+        return me.equals(other);
+    }
+
+    /**
+     * Wrapper around {@link java.lang.String#compareToIgnoreCase(java.lang.String) String.compareToIgnoreCase} with an
+     * exhaustive, possibly duplicative, check against nulls.
+     *
+     * @param me the value to be compared
+     * @param other the other value to be compared
+     * @return true if the values are equal; otherwise false
+     */
+    private int compareToIgnoreCaseWithNullCheck(String me, String other) {
+        if (me == null && other == null) {
+            return 0;
+        } else if (me == null) {
+            return -1; //the other string is greater then me
+        } else if (other == null) {
+            return 1; //me is greater then the other string
+        }
+        return me.compareToIgnoreCase(other);
+    }
+
+    /**
+     * Wrapper around {@link java.lang.Enum#compareTo(java.lang.Enum) Enum.compareTo} with an exhaustive, possibly
+     * duplicative, check against nulls.
+     *
+     * @param me the value to be compared
+     * @param other the other value to be compared
+     * @return true if the values are equal; otherwise false
+     */
+    private int compareToWithNullCheck(Confidence me, Confidence other) {
+        if (me == null && other == null) {
+            return 0;
+        } else if (me == null) {
+            return -1; //the other string is greater then me
+        } else if (other == null) {
+            return 1; //me is greater then the other string
+        }
+        return me.compareTo(other);
+    }
 }

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

@@ -17,6 +17,7 @@
  */
 package org.owasp.dependencycheck.dependency;
 
+import java.io.Serializable;
 import java.net.MalformedURLException;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -36,7 +37,7 @@ import org.owasp.dependencycheck.utils.UrlStringUtils;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class EvidenceCollection implements Iterable<Evidence> {
+public class EvidenceCollection implements Serializable, Iterable<Evidence> {
 
     /**
      * The logger.
@@ -311,6 +312,26 @@ public class EvidenceCollection implements Iterable<Evidence> {
         return ret;
     }
 
+    /**
+     * Merges multiple EvidenceCollections together; flattening all of the evidence items by removing the confidence.
+     *
+     * @param ec One or more EvidenceCollections
+     * @return new set of evidence resulting from merging the evidence in the collections
+     */
+    public static Set<Evidence> mergeForDisplay(EvidenceCollection... ec) {
+        final Set<Evidence> ret = new TreeSet<Evidence>();
+        for (EvidenceCollection col : ec) {
+            for (Evidence e : col) {
+                if (e.isUsed()) {
+                    final Evidence newEvidence = new Evidence(e.getSource(), e.getName(), e.getValue(), null);
+                    newEvidence.setUsed(true);
+                    ret.add(newEvidence);
+                }
+            }
+        }
+        return ret;
+    }
+
     /**
      * Returns a string of evidence 'values'.
      *

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

@@ -17,11 +17,13 @@
  */
 package org.owasp.dependencycheck.dependency;
 
+import java.io.Serializable;
+
 /**
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class Identifier implements Comparable<Identifier> {
+public class Identifier implements Serializable, Comparable<Identifier> {
 
     /**
      * Constructs a new Identifier with the specified data.

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

@@ -77,19 +77,19 @@ public class VulnerableSoftware extends IndexEntry implements Serializable, Comp
         if (cpeName != null && cpeName.length() > 7) {
             final String[] data = cpeName.substring(7).split(":");
             if (data.length >= 1) {
-                this.setVendor(URLDecoder.decode(data[0].replace("+", "%2B"), "UTF-8"));
+                this.setVendor(urlDecode(data[0]));
             }
             if (data.length >= 2) {
-                this.setProduct(URLDecoder.decode(data[1].replace("+", "%2B"), "UTF-8"));
+                this.setProduct(urlDecode(data[1]));
             }
             if (data.length >= 3) {
-                version = URLDecoder.decode(data[2].replace("+", "%2B"), "UTF-8");
+                version = urlDecode(data[2]);
             }
             if (data.length >= 4) {
-                revision = URLDecoder.decode(data[3].replace("+", "%2B"), "UTF-8");
+                revision = urlDecode(data[3]);
             }
             if (data.length >= 5) {
-                edition = URLDecoder.decode(data[4].replace("+", "%2B"), "UTF-8");
+                edition = urlDecode(data[4]);
             }
         }
     }
@@ -341,4 +341,25 @@ public class VulnerableSoftware extends IndexEntry implements Serializable, Comp
     public void setEdition(String edition) {
         this.edition = edition;
     }
+
+    /**
+     * Replaces '+' with '%2B' and then URL Decodes the string attempting first UTF-8, then ASCII, then default.
+     *
+     * @param string the string to URL Decode
+     * @return the URL Decoded string
+     */
+    private String urlDecode(String string) {
+        final String text = string.replace("+", "%2B");
+        String result;
+        try {
+            result = URLDecoder.decode(text, "UTF-8");
+        } catch (UnsupportedEncodingException ex) {
+            try {
+                result = URLDecoder.decode(text, "ASCII");
+            } catch (UnsupportedEncodingException ex1) {
+                result = URLDecoder.decode(text);
+            }
+        }
+        return result;
+    }
 }

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

@@ -48,7 +48,7 @@ public class ScanAgentException extends IOException {
     }
 
     /**
-     * Creates a new NoDataException.
+     * Creates a new ScanAgentException.
      *
      * @param ex the cause of the exception.
      */

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

@@ -167,15 +167,28 @@ public class ReportGenerator {
      */
     public void generateReports(String outputDir, String outputFormat) throws IOException, Exception {
         final String format = outputFormat.toUpperCase();
+        final String pathToCheck = outputDir.toLowerCase();
         if (format.matches("^(XML|HTML|VULN|ALL)$")) {
             if ("XML".equalsIgnoreCase(format)) {
-                generateReports(outputDir, Format.XML);
+                if (pathToCheck.endsWith(".xml")) {
+                    generateReport("XmlReport", outputDir);
+                } else {
+                    generateReports(outputDir, Format.XML);
+                }
             }
             if ("HTML".equalsIgnoreCase(format)) {
-                generateReports(outputDir, Format.HTML);
+                if (pathToCheck.endsWith(".html") || pathToCheck.endsWith(".htm")) {
+                    generateReport("HtmlReport", outputDir);
+                } else {
+                    generateReports(outputDir, Format.HTML);
+                }
             }
             if ("VULN".equalsIgnoreCase(format)) {
-                generateReports(outputDir, Format.VULN);
+                if (pathToCheck.endsWith(".html") || pathToCheck.endsWith(".htm")) {
+                    generateReport("VulnReport", outputDir);
+                } else {
+                    generateReports(outputDir, Format.VULN);
+                }
             }
             if ("ALL".equalsIgnoreCase(format)) {
                 generateReports(outputDir, Format.ALL);

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

@@ -54,6 +54,10 @@ public class SuppressionHandler extends DefaultHandler {
      * The CWE element name.
      */
     public static final String CWE = "cwe";
+    /**
+     * The GAV element name.
+     */
+    public static final String GAV = "gav";
     /**
      * The cvssBelow element name.
      */
@@ -95,13 +99,16 @@ public class SuppressionHandler extends DefaultHandler {
      */
     @Override
     public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException {
-        currentAttributes = null;
+        currentAttributes = attributes;
         currentText = new StringBuffer();
-
         if (SUPPRESS.equals(qName)) {
             rule = new SuppressionRule();
-        } else if (FILE_PATH.equals(qName)) {
-            currentAttributes = attributes;
+            final String base = currentAttributes.getValue("base");
+            if (base != null) {
+                rule.setBase(Boolean.parseBoolean(base));
+            } else {
+                rule.setBase(false);
+            }
         }
     }
 
@@ -123,6 +130,9 @@ public class SuppressionHandler extends DefaultHandler {
             rule.setFilePath(pt);
         } else if (SHA1.equals(qName)) {
             rule.setSha1(currentText.toString());
+        } else if (GAV.equals(qName)) {
+            final PropertyType pt = processPropertyType();
+            rule.setGav(pt);
         } else if (CPE.equals(qName)) {
             final PropertyType pt = processPropertyType();
             rule.addCpe(pt);

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

@@ -26,11 +26,6 @@ import java.io.IOException;
  */
 public class SuppressionParseException extends IOException {
 
-    /**
-     * The serial version UID.
-     */
-    private static final long serialVersionUID = 1L;
-
     /**
      * Creates a new SuppressionParseException.
      */
@@ -50,7 +45,7 @@ public class SuppressionParseException extends IOException {
     /**
      * Creates a new SuppressionParseException.
      *
-     * @param ex the cause of the download failure.
+     * @param ex the cause of the parse exception
      */
     public SuppressionParseException(Throwable ex) {
         super(ex);
@@ -60,7 +55,7 @@ public class SuppressionParseException extends IOException {
      * Creates a new SuppressionParseException.
      *
      * @param msg a message for the exception.
-     * @param ex the cause of the download failure.
+     * @param ex the cause of the parse exception
      */
     public SuppressionParseException(String msg, Throwable ex) {
         super(msg, ex);

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

@@ -66,10 +66,35 @@ public class SuppressionParser {
      * @throws SuppressionParseException thrown if the xml file cannot be parsed
      */
     public List<SuppressionRule> parseSuppressionRules(File file) throws SuppressionParseException {
+        FileInputStream fis = null;
+        try {
+            fis = new FileInputStream(file);
+            return parseSuppressionRules(fis);
+        } catch (IOException ex) {
+            LOGGER.log(Level.FINE, null, ex);
+            throw new SuppressionParseException(ex);
+        } finally {
+            if (fis != null) {
+                try {
+                    fis.close();
+                } catch (IOException ex) {
+                    LOGGER.log(Level.FINE, "Unable to close stream", ex);
+                }
+            }
+        }
+    }
+
+    /**
+     * Parses the given xml stream and returns a list of the suppression rules contained.
+     *
+     * @param inputStream an InputStream containing suppression rues
+     * @return a list of suppression rules
+     * @throws SuppressionParseException if the xml cannot be parsed
+     */
+    public List<SuppressionRule> parseSuppressionRules(InputStream inputStream) throws SuppressionParseException {
         try {
             final InputStream schemaStream = this.getClass().getClassLoader().getResourceAsStream("schema/suppression.xsd");
             final SuppressionHandler handler = new SuppressionHandler();
-
             final SAXParserFactory factory = SAXParserFactory.newInstance();
             factory.setNamespaceAware(true);
             factory.setValidating(true);
@@ -80,7 +105,6 @@ public class SuppressionParser {
             xmlReader.setErrorHandler(new SuppressionErrorHandler());
             xmlReader.setContentHandler(handler);
 
-            final InputStream inputStream = new FileInputStream(file);
             final Reader reader = new InputStreamReader(inputStream, "UTF-8");
             final InputSource in = new InputSource(reader);
             //in.setEncoding("UTF-8");

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

@@ -234,6 +234,61 @@ public class SuppressionRule {
     public boolean hasCve() {
         return cve.size() > 0;
     }
+    /**
+     * A Maven GAV to suppression.
+     */
+    private PropertyType gav = null;
+
+    /**
+     * Get the value of Maven GAV.
+     *
+     * @return the value of gav
+     */
+    public PropertyType getGav() {
+        return gav;
+    }
+
+    /**
+     * Set the value of Maven GAV.
+     *
+     * @param gav new value of Maven gav
+     */
+    public void setGav(PropertyType gav) {
+        this.gav = gav;
+    }
+
+    /**
+     * Returns whether or not this suppression rule as GAV entries.
+     *
+     * @return whether or not this suppression rule as GAV entries
+     */
+    public boolean hasGav() {
+        return gav != null;
+    }
+
+    /**
+     * A flag indicating whether or not the suppression rule is a core/base rule that should not be included in the
+     * resulting report in the "suppressed" section.
+     */
+    private boolean base;
+
+    /**
+     * Get the value of base.
+     *
+     * @return the value of base
+     */
+    public boolean isBase() {
+        return base;
+    }
+
+    /**
+     * Set the value of base.
+     *
+     * @param base new value of base
+     */
+    public void setBase(boolean base) {
+        this.base = base;
+    }
 
     /**
      * Processes a given dependency to determine if any CPE, CVE, CWE, or CVSS scores should be suppressed. If any
@@ -248,13 +303,30 @@ public class SuppressionRule {
         if (sha1 != null && !sha1.equalsIgnoreCase(dependency.getSha1sum())) {
             return;
         }
+        if (gav != null) {
+            final Iterator<Identifier> itr = dependency.getIdentifiers().iterator();
+            boolean gavFound = false;
+            while (itr.hasNext()) {
+                final Identifier i = itr.next();
+                if (identifierMatches("maven", this.gav, i)) {
+                    gavFound = true;
+                    break;
+                }
+            }
+            if (!gavFound) {
+                return;
+            }
+        }
+
         if (this.hasCpe()) {
             final Iterator<Identifier> itr = dependency.getIdentifiers().iterator();
             while (itr.hasNext()) {
                 final Identifier i = itr.next();
                 for (PropertyType c : this.cpe) {
-                    if (cpeMatches(c, i)) {
-                        dependency.addSuppressedIdentifier(i);
+                    if (identifierMatches("cpe", c, i)) {
+                        if (!isBase()) {
+                            dependency.addSuppressedIdentifier(i);
+                        }
                         itr.remove();
                         break;
                     }
@@ -293,7 +365,9 @@ public class SuppressionRule {
                     }
                 }
                 if (remove) {
-                    dependency.addSuppressedVulnerability(v);
+                    if (!isBase()) {
+                        dependency.addSuppressedVulnerability(v);
+                    }
                     itr.remove();
                 }
             }
@@ -309,7 +383,7 @@ public class SuppressionRule {
     boolean cpeHasNoVersion(PropertyType c) {
         if (c.isRegex()) {
             return false;
-        } // cpe:/a:jboss:jboss:1.0.0:
+        }
         if (countCharacter(c.getValue(), ':') == 3) {
             return true;
         }
@@ -336,26 +410,75 @@ public class SuppressionRule {
     /**
      * Determines if the cpeEntry specified as a PropertyType matches the given Identifier.
      *
-     * @param cpeEntry a suppression rule entry
+     * @param identifierType the type of identifier ("cpe", "maven", etc.)
+     * @param suppressionEntry a suppression rule entry
      * @param identifier a CPE identifier to check
      * @return true if the entry matches; otherwise false
      */
-    boolean cpeMatches(PropertyType cpeEntry, Identifier identifier) {
-        if (cpeEntry.matches(identifier.getValue())) {
-            return true;
-        } else if (cpeHasNoVersion(cpeEntry)) {
-            if (cpeEntry.isCaseSensitive()) {
-                if (identifier.getValue().startsWith(cpeEntry.getValue())) {
-                    return true;
-                }
-            } else {
-                final String id = identifier.getValue().toLowerCase();
-                final String check = cpeEntry.getValue().toLowerCase();
-                if (id.startsWith(check)) {
-                    return true;
+    boolean identifierMatches(String identifierType, PropertyType suppressionEntry, Identifier identifier) {
+        if (identifierType.equals(identifier.getType())) {
+            if (suppressionEntry.matches(identifier.getValue())) {
+                return true;
+            } else if ("cpe".equals(identifierType) && cpeHasNoVersion(suppressionEntry)) {
+                if (suppressionEntry.isCaseSensitive()) {
+                    return identifier.getValue().startsWith(suppressionEntry.getValue());
+                } else {
+                    final String id = identifier.getValue().toLowerCase();
+                    final String check = suppressionEntry.getValue().toLowerCase();
+                    return id.startsWith(check);
                 }
             }
         }
         return false;
     }
+
+    /**
+     * Standard toString implementation.
+     *
+     * @return a string representation of this object
+     */
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder();
+        sb.append("SuppressionRule{");
+        if (filePath != null) {
+            sb.append("filePath=").append(filePath).append(",");
+        }
+        if (sha1 != null) {
+            sb.append("sha1=").append(sha1).append(",");
+        }
+        if (gav != null) {
+            sb.append("gav=").append(gav).append(",");
+        }
+        if (cpe != null && cpe.size() > 0) {
+            sb.append("cpe={");
+            for (PropertyType pt : cpe) {
+                sb.append(pt).append(",");
+            }
+            sb.append("}");
+        }
+        if (cwe != null && cwe.size() > 0) {
+            sb.append("cwe={");
+            for (String s : cwe) {
+                sb.append(s).append(",");
+            }
+            sb.append("}");
+        }
+        if (cve != null && cve.size() > 0) {
+            sb.append("cve={");
+            for (String s : cve) {
+                sb.append(s).append(",");
+            }
+            sb.append("}");
+        }
+        if (cvssBelow != null && cvssBelow.size() > 0) {
+            sb.append("cvssBelow={");
+            for (Float s : cvssBelow) {
+                sb.append(s).append(",");
+            }
+            sb.append("}");
+        }
+        sb.append("}");
+        return sb.toString();
+    }
 }

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

@@ -54,7 +54,9 @@ public final class DBUtils {
         int id = 0;
         try {
             rs = statement.getGeneratedKeys();
-            rs.next();
+            if (!rs.next()) {
+                throw new DatabaseException("Unable to get primary key for inserted row");
+            }
             id = rs.getInt(1);
         } catch (SQLException ex) {
             throw new DatabaseException("Unable to get primary key for inserted row");

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

@@ -65,7 +65,7 @@ public class DependencyVersion implements Iterable, Comparable<DependencyVersion
     public final void parseVersion(String version) {
         versionParts = new ArrayList<String>();
         if (version != null) {
-            final Pattern rx = Pattern.compile("(\\d+|[a-z]+\\d+|(release|beta|alpha)$)");
+            final Pattern rx = Pattern.compile("(\\d+[a-z]{1,3}$|[a-z]+\\d+|\\d+|(release|beta|alpha)$)");
             final Matcher matcher = rx.matcher(version.toLowerCase());
             while (matcher.find()) {
                 versionParts.add(matcher.group());
@@ -189,17 +189,23 @@ public class DependencyVersion implements Iterable, Comparable<DependencyVersion
         if (version == null) {
             return false;
         }
-
-        boolean ret = true;
-        int max = (this.versionParts.size() < version.versionParts.size())
-                ? this.versionParts.size() : version.versionParts.size();
-
-        if (max > 3) {
-            max = 3;
+        if (Math.abs(this.versionParts.size() - version.versionParts.size()) >= 3) {
+            return false;
         }
 
+        final int max = (this.versionParts.size() < version.versionParts.size())
+                ? this.versionParts.size() : version.versionParts.size();
+
+        boolean ret = true;
         for (int i = 0; i < max; i++) {
-            if (this.versionParts.get(i) == null || !this.versionParts.get(i).equals(version.versionParts.get(i))) {
+            final String thisVersion = this.versionParts.get(i);
+            final String otherVersion = version.getVersionParts().get(i);
+            if (i >= 3) {
+                if (thisVersion.compareToIgnoreCase(otherVersion) >= 0) {
+                    ret = false;
+                    break;
+                }
+            } else if (!thisVersion.equals(otherVersion)) {
                 ret = false;
                 break;
             }

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

@@ -32,7 +32,7 @@ public final class DependencyVersionUtil {
     /**
      * Regular expression to extract version numbers from file names.
      */
-    private static final Pattern RX_VERSION = Pattern.compile("\\d+(\\.\\d{1,6})+(\\.?([_-](release|beta|alpha)|[a-zA-Z_-]{1,3}\\d{1,8}))?");
+    private static final Pattern RX_VERSION = Pattern.compile("\\d+(\\.\\d{1,6})+(\\.?([_-](release|beta|alpha|\\d+)|[a-zA-Z_-]{1,3}\\d{0,8}))?");
     /**
      * Regular expression to extract a single version number without periods. This is a last ditch effort just to check
      * in case we are missing a version number using the previous regex.

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

@@ -0,0 +1,147 @@
+/*
+ * 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.utils;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+import org.owasp.dependencycheck.Engine;
+import static org.owasp.dependencycheck.utils.FileUtils.getFileExtension;
+
+/**
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public final class ExtractionUtil {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(ExtractionUtil.class.getName());
+    /**
+     * The buffer size to use when extracting files from the archive.
+     */
+    private static final int BUFFER_SIZE = 4096;
+
+    /**
+     * Private constructor for a utility class.
+     */
+    private ExtractionUtil() {
+    }
+
+    /**
+     * Extracts the contents of an archive into the specified directory.
+     *
+     * @param archive an archive file such as a WAR or EAR
+     * @param extractTo a directory to extract the contents to
+     * @throws ExtractionException thrown if an exception occurs while extracting the files
+     */
+    public static void extractFiles(File archive, File extractTo) throws ExtractionException {
+        extractFiles(archive, extractTo, null);
+    }
+
+    /**
+     * Extracts the contents of an archive into the specified directory. The files are only extracted if they are
+     * supported by the analyzers loaded into the specified engine. If the engine is specified as null then all files
+     * are extracted.
+     *
+     * @param archive an archive file such as a WAR or EAR
+     * @param extractTo a directory to extract the contents to
+     * @param engine the scanning engine
+     * @throws ExtractionException thrown if there is an error extracting the files
+     */
+    public static void extractFiles(File archive, File extractTo, Engine engine) throws ExtractionException {
+        if (archive == null || extractTo == null) {
+            return;
+        }
+
+        FileInputStream fis = null;
+        ZipInputStream zis = null;
+
+        try {
+            fis = new FileInputStream(archive);
+        } catch (FileNotFoundException ex) {
+            LOGGER.log(Level.FINE, null, ex);
+            throw new ExtractionException("Archive file was not found.", ex);
+        }
+        zis = new ZipInputStream(new BufferedInputStream(fis));
+        ZipEntry entry;
+        try {
+            while ((entry = zis.getNextEntry()) != null) {
+                if (entry.isDirectory()) {
+                    final File d = new File(extractTo, entry.getName());
+                    if (!d.exists() && !d.mkdirs()) {
+                        final String msg = String.format("Unable to create '%s'.", d.getAbsolutePath());
+                        throw new ExtractionException(msg);
+                    }
+                } else {
+                    final File file = new File(extractTo, entry.getName());
+                    final String ext = getFileExtension(file.getName());
+                    if (engine == null || engine.supportsExtension(ext)) {
+                        BufferedOutputStream bos = null;
+                        FileOutputStream fos;
+                        try {
+                            fos = new FileOutputStream(file);
+                            bos = new BufferedOutputStream(fos, BUFFER_SIZE);
+                            int count;
+                            final byte data[] = new byte[BUFFER_SIZE];
+                            while ((count = zis.read(data, 0, BUFFER_SIZE)) != -1) {
+                                bos.write(data, 0, count);
+                            }
+                            bos.flush();
+                        } catch (FileNotFoundException ex) {
+                            LOGGER.log(Level.FINE, null, ex);
+                            final String msg = String.format("Unable to find file '%s'.", file.getName());
+                            throw new ExtractionException(msg, ex);
+                        } catch (IOException ex) {
+                            LOGGER.log(Level.FINE, null, ex);
+                            final String msg = String.format("IO Exception while parsing file '%s'.", file.getName());
+                            throw new ExtractionException(msg, ex);
+                        } finally {
+                            if (bos != null) {
+                                try {
+                                    bos.close();
+                                } catch (IOException ex) {
+                                    LOGGER.log(Level.FINEST, null, ex);
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        } catch (IOException ex) {
+            final String msg = String.format("Exception reading archive '%s'.", archive.getName());
+            LOGGER.log(Level.FINE, msg, ex);
+            throw new ExtractionException(msg, ex);
+        } finally {
+            try {
+                zis.close();
+            } catch (IOException ex) {
+                LOGGER.log(Level.FINEST, null, ex);
+            }
+        }
+    }
+}

dependency-check-core/src/main/resources/META-INF/services/org.owasp.dependencycheck.analyzer.Analyzer

@@ -8,6 +8,7 @@ org.owasp.dependencycheck.analyzer.CpeSuppressionAnalyzer
 org.owasp.dependencycheck.analyzer.DependencyBundlingAnalyzer
 org.owasp.dependencycheck.analyzer.NvdCveAnalyzer
 org.owasp.dependencycheck.analyzer.VulnerabilitySuppressionAnalyzer
+org.owasp.dependencycheck.analyzer.CentralAnalyzer
 org.owasp.dependencycheck.analyzer.NexusAnalyzer
 org.owasp.dependencycheck.analyzer.NuspecAnalyzer
 org.owasp.dependencycheck.analyzer.AssemblyAnalyzer

dependency-check-core/src/main/resources/dependencycheck-base-suppression.xml

@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<suppressions xmlns="https://www.owasp.org/index.php/OWASP_Dependency_Check_Suppression">
+    <suppress base="true">
+        <notes><![CDATA[
+        This suppresses false positives identified on spring security.
+        ]]></notes>
+        <gav regex="true">org\.springframework\.security:spring.*</gav>
+        <cpe>cpe:/a:mod_security:mod_security</cpe>
+        <cpe>cpe:/a:springsource:spring_framework</cpe>
+        <cpe>cpe:/a:vmware:springsource_spring_framework</cpe>
+    </suppress>
+    <suppress base="true">
+        <notes><![CDATA[
+        This suppresses false positives identified on spring security.
+        ]]></notes>
+        <filePath regex="true">.*spring-security-[^\\/]*\.jar$</filePath>
+        <cpe>cpe:/a:mod_security:mod_security</cpe>
+        <cpe>cpe:/a:springsource:spring_framework</cpe>
+        <cpe>cpe:/a:vmware:springsource_spring_framework</cpe>
+    </suppress>
+    <suppress base="true">
+        <notes><![CDATA[
+        This suppreses additional false positives for the xstream library that occur because spring has a copy of this library.
+            com.springsource.com.thoughtworks.xstream-1.3.1.jar
+        ]]></notes>
+        <gav regex="true">com\.thoughtworks\.xstream:xstream:.*</gav>
+        <cpe>cpe:/a:springsource:spring_framework</cpe>
+    </suppress>
+    <suppress base="true">
+        <notes><![CDATA[
+        Suppresses false positives on velocity tools.
+        ]]></notes>
+        <gav regex="true">org\.apache\.velocity:velocity-tools:.*</gav>
+        <cpe>cpe:/a:apache:struts</cpe>
+    </suppress>
+    <suppress base="true">
+        <notes><![CDATA[
+        Sandbox is a php blog platform and should not be flagged as a CPE for java or .net dependencies.
+        ]]></notes>
+        <filePath regex="true">.*\.(jar|dll|exe|ear|war|pom)</filePath>
+        <cpe>cpe:/a:sandbox:sandbox</cpe>
+    </suppress>
+    <suppress base="true">
+        <notes><![CDATA[
+        Suppresses false positives on Jersey core client.
+        ]]></notes>
+        <gav regex="true">(com\.sun\.jersey|org\.glassfish\.jersey\.core):jersey-(client|common):.*</gav>
+        <cpe>cpe:/a:oracle:glassfish</cpe>
+        <cpe>cpe:/a:oracle:oracle_client</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+        Suppresses false positives on the grizzly-framework
+        ]]></notes>
+        <gav regex="true">org\.glassfish\.grizzly:grizzly-framework:.*</gav>
+        <cpe>cpe:/a:oracle:glassfish</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+        Suppresses false positives on the grizzly-framework
+        ]]></notes>
+        <gav regex="true">org\.forgerock\.opendj:opendj-ldap-sdk:.*</gav>
+        <cpe>cpe:/a:ldap_project:ldap</cpe>
+    </suppress>
+</suppressions>

dependency-check-core/src/main/resources/dependencycheck-resources.properties

@@ -0,0 +1,10 @@
+analyzer.AssemblyAnalyzer.notdeployed=GrokAssembly didn't get deployed
+analyzer.AssemblyAnalyzer.grokassembly.stderr=Error from GrokAssembly: {0}
+analyzer.AssemblyAnalyzer.notassembly={0} is not a .NET assembly or executable and as such cannot be analyzed by dependency-check
+analyzer.AssemblyAnalyzer.grokassembly.rc=Return code {0} from GrokAssembly
+analyzer.AssemblyAnalyzer.grokassembly.deployed=Extracted GrokAssembly.exe to {0}
+analyzer.AssemblyAnalyzer.grokassembly.notdeployed=Could not extract GrokAssembly.exe: {0}
+analyzer.AssemblyAnalyzer.grokassembly.initialization.failed=An error occurred with the .NET AssemblyAnalyzer; \
+    this can be ignored unless you are scanning .NET DLLs. Please see the log for more details.
+analyzer.AssemblyAnalyzer.grokassembly.initialization.message=Could not execute GrokAssembly {0}
+analyzer.AssemblyAnalyzer.grokassembly.notdeleted=Can't delete temporary GrokAssembly.exe

dependency-check-core/src/main/resources/dependencycheck.properties

@@ -13,8 +13,10 @@ max.download.threads=3
 # will not be used. The data.directory will be resolved and if the connection string
 # below contains a %s then the data.directory will replace the %s.
 data.directory=[JAR]/data
+#if the filename has a %s it will be replaced with the current expected version
+data.file_name=cve.%s.h2.db
+data.version=2.9
 data.connection_string=jdbc:h2:file:%s;FILE_LOCK=SERIALIZED;AUTOCOMMIT=ON;
-#data.connection_string=jdbc:h2:file:%s;AUTO_SERVER=TRUE;AUTOCOMMIT=ON;
 #data.connection_string=jdbc:mysql://localhost:3306/dependencycheck
 
 # user name and password for the database connection. The inherent case is to use H2.
@@ -38,11 +40,16 @@ data.driver_path=
 cve.url.modified.validfordays=7
 
 # the path to the modified nvd cve xml file.
-cve.url-1.2.modified=http://nvd.nist.gov/download/nvdcve-modified.xml
-cve.url-2.0.modified=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+cve.url-1.2.modified=https://nvd.nist.gov/download/nvdcve-Modified.xml.gz
+#cve.url-1.2.modified=http://nvd.nist.gov/download/nvdcve-modified.xml
+cve.url-2.0.modified=https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-Modified.xml.gz
+#cve.url-2.0.modified=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
 cve.startyear=2002
-cve.url-2.0.base=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
-cve.url-1.2.base=http://nvd.nist.gov/download/nvdcve-%d.xml
+cve.url-1.2.base=https://nvd.nist.gov/download/nvdcve-%d.xml.gz
+#cve.url-1.2.base=http://nvd.nist.gov/download/nvdcve-%d.xml
+cve.url-2.0.base=https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml.gz
+#cve.url-2.0.base=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+
 
 # file type analyzer settings:
 analyzer.archive.enabled=true
@@ -56,3 +63,7 @@ analyzer.nexus.url=https://repository.sonatype.org/service/local/
 # If set to true, the proxy will still ONLY be used if the proxy properties (proxy.url, proxy.port)
 # are configured
 analyzer.nexus.proxy=true
+
+# the URL for searching search.maven.org for SHA-1 and whether it's enabled
+analyzer.central.enabled=true
+analyzer.central.url=http://search.maven.org/solrsearch/select

dependency-check-core/src/main/resources/schema/suppression.xsd

@@ -41,6 +41,7 @@
                             <xs:choice minOccurs="0" maxOccurs="1">
                                 <xs:element name="filePath" type="dc:regexStringType"/>
                                 <xs:element name="sha1" type="dc:sha1Type"/>
+                                <xs:element name="gav" type="dc:regexStringType"/>
                             </xs:choice>
                             <xs:choice minOccurs="0" maxOccurs="unbounded">
                                 <xs:element name="cpe" type="dc:regexStringType"/>
@@ -49,6 +50,7 @@
                                 <xs:element name="cvssBelow" type="dc:cvssScoreType"/>
                             </xs:choice>
                         </xs:sequence>
+                        <xs:attribute name="base" use="optional" type="xs:boolean" default="false"/>
                     </xs:complexType>
                 </xs:element>
             </xs:sequence>

dependency-check-core/src/main/resources/templates/HtmlReport.vsl

@@ -33,8 +33,8 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
         </script>
         <script type="text/javascript">
             $(document).ready(function() {
-                $(".expandable").click(function (e) {
-                    e = e || window.event;
+                $(".expandable").click(function (event) {
+                    e = event || window.event;
                     var h = e.target || e.srcElement;
                     var content = "#content" + h.id.substr(6);
                     var header = "#" + h.id;
@@ -56,6 +56,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                         $(header).addClass("expandablesubsection");
                         $(header).removeClass("collaspablesubsection");
                     }
+                    return false;
                 });
             });
 
@@ -84,13 +85,14 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 $('#modal-text').focus();
                 $('#modal-text').select();
             }
-            function toggleDisplay(el, clzName) {
+            function toggleDisplay(el, clzName, all, some) {
                 $(clzName).toggle();
-                if (el.innerHTML == 'show all') {
-                    el.innerHTML = 'less';
+                if (el.innerHTML == all) {
+                    el.innerHTML = some;
                 } else {
-                    el.innerHTML = 'show all';
+                    el.innerHTML = all;
                 }
+                return false;
             }
         </script>
         <style type="text/css">
@@ -427,15 +429,24 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             .indent {
                 margin-left:20px;
             }
-            td, th {
+            td{
+                vertical-align:text-top;
                 padding:6px;
                 margin:0px;
             }
+            th {
+                text-align:left
+                vertical-align:text-top;
+                padding:6px;
+                margin:0px;
+                border-bottom:1px;
+                border-color: black;
+            }
             table {
                 border: 0px;
             }
             table.lined tr:nth-child(even) {
-                background-color: #fbfbfb;
+                background-color: #f3f3f3;
             }
             .fullwidth {
                 width:100%;
@@ -448,10 +459,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 margin-bottom:3px;
             }
             .vulnerable {
-            	color: #f00;
-            }
-            .vulnerable li {
-            	color: #000;
+                color: #000;
             }
             .notvulnerable {
                 display:none;
@@ -481,7 +489,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
         <div id="modal-content">
             <div>Press CTR-C to copy XML&nbsp;<a href="http://jeremylong.github.io/DependencyCheck/suppression.html" class="infolink" target="_blank" title="Help with suppressing false positives">[help]</a></div>
                 <textarea id="modal-text" cols="50" rows="10"></textarea><br/>
-                <button id="modal-add-header" class="modal-button">Complete XML Doc</button><button id="modal-close" class="modal-button-right">Close</button>
+                <button id="modal-add-header" title="Add the parent XML nodes to create the complete XML file that can be used to suppress this finding" class="modal-button">Complete XML Doc</button><button id="modal-close" class="modal-button-right">Close</button>
         </div>
         <div class="wrapper">
             <h1>Dependency-Check Report</h1>
@@ -513,7 +521,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                         #set($vulnSuppressedCount=$vulnSuppressedCount+$dependency.getSuppressedVulnerabilities().size())
                     #end
                 #end
-                Scan Information (<a href="#" onclick="toggleDisplay(this, '.scaninfo');  return false;">show all</a>):<br/>
+                Scan Information (<a href="#" title="Click to toggle display" onclick="return toggleDisplay(this, '.scaninfo', 'show all', 'show less');  return false;">show all</a>):<br/>
                     <ul class="indent">
                         <li><i>dependency-check version</i>: $version</li>
                         <li><i>Report Generated On</i>: $scanDate</li>
@@ -526,30 +534,101 @@ arising out of or in connection with the use of this tool, the analysis performe
                         <li class="scaninfo hidden"><i>$enc.html($prop.key)</i>: $enc.html($prop.value)</li>
                         #end
                     </ul><br/>
-                Dependency Display:&nbsp;<a href="#" onclick="toggleDisplay(this,'.notvulnerable'); return false;">show all</a><br/><br/>
-                <ul class="indent">
+                Display:&nbsp;<a href="#" title="Click to toggle display" onclick="return toggleDisplay(this, '.notvulnerable', 'Showing Vulnerable Dependencies', 'Showing All Dependencies'); return false;">Showing Vulnerable Dependencies</a><br/><br/>
                 #set($lnkcnt=0)
-                #foreach($dependency in $dependencies)
+                <table class="lined">
+                    <tr style="text-align:left">
+                        <th title="The name of the dependency">Dependency</th>
+                        <th title="The Common Platform Enumeration">CPE</th>
+                        <th title="The Maven GAV Coordinates">GAV</th>
+                        <th title="The highest CVE Severity">Highest Severity</th>
+                        <th title="The number of Common Vulnerability and Exposure (CVE) entries">CVE Count</th>
+                        <th title="The confidence rating dependency-check has for the identified CPE">CPE Confidence</th>
+                        <th title="The count of evidence used to identify the CPE">Evidence Count</th>
+                    </tr>
+                    #foreach($dependency in $dependencies)
                     #set($lnkcnt=$lnkcnt+1)
-                    <li class="#if($dependency.getVulnerabilities().size()==0)notvulnerable#else vulnerable#end">
-                    <a href="#l${lnkcnt}_$enc.html($enc.url($dependency.Sha1sum))">$enc.html($dependency.FileName)</a>
-                    #if($dependency.getRelatedDependencies().size()>0)
-                        <ul>
-                        #foreach($related in $dependency.getRelatedDependencies())
-                        <li>$enc.html($related.FileName)</li>
+                    <tr class="#if($dependency.getVulnerabilities().size()==0)notvulnerable#else vulnerable#end">
+                        <td><a href="#l${lnkcnt}_$enc.html($enc.url($dependency.Sha1sum))">$enc.html($dependency.DisplayFileName)</a></td>
+                        #set($mavenlink="")
+                        #set($cpeIdCount=0)
+                        #set($cpeIdConf="")
+                        <td>
+                        #foreach($id in $dependency.getIdentifiers())
+                            #if ($id.type=="maven")
+                                #if ($mavenlink=="" || !$mavenlink.url)
+                                    #set($mavenlink=$id)
+                                #end
+                            #else
+                                #if ($cpeIdCount>=1)
+                                    <br/>
+                                #end
+                                #if( $id.url )
+                                    <a href="$enc.html($id.url)" target="_blank">$enc.html($id.value)</a>
+                                #else
+                                    $enc.html($id.value)
+                                #end
+                                #if ($cpeIdConf == "")
+                                    #set($cpeIdConf=$id.confidence)
+                                #elseif ($cpeIdConf.compareTo($id.confidence)>0)
+                                    #set($cpeIdConf=$id.confidence)
+                                #end
+                                #set($cpeIdCount=$cpeIdCount+1)
+                            #end
                         #end
-                        </ul>
+                        </td>
+                        <td>#if( $mavenlink.url )
+                            ##yes, we are HTML Encoding the href. this is okay. We can't URL encode as we have to trust the analyzer here...
+                            <a href="$enc.html($mavenlink.url)" target="_blank">$enc.html($mavenlink.value)</a>
+                        #elseif ($mavenlink.value)
+                            $enc.html($mavenlink.value)
+                        #end</td>
+                        #set($cveImpact=-1)
+                        #foreach($vuln in $dependency.getVulnerabilities())
+                            #if ($cveImpact<$vuln.cvssScore)
+                                #set($cveImpact=$vuln.cvssScore)
+                            #end
+                        #end
+                        <td>
+                        #if ($cveImpact<0)
+                            &nbsp;
+                        #elseif ($cveImpact<4.0)
+                            Low
+                        #elseif ($cveImpact>=7.0)
+                            High
+                        #else
+                            Medium
+                        #end
+                        </td>
+                        <td>$dependency.getVulnerabilities().size()</td>
+                        <td>$cpeIdConf</td>
+                        <td>$dependency.getEvidenceForDisplay().size()</td>
+                    </tr>
                     #end
-                    </li>
-                #end
-                </ul>
+                </table>
+##                <ul class="indent">
+##                #set($lnkcnt=0)
+##                #foreach($dependency in $dependencies)
+##                    #set($lnkcnt=$lnkcnt+1)
+##                    <li class="#if($dependency.getVulnerabilities().size()==0)notvulnerable#else vulnerable#end">
+##                    <a href="#l${lnkcnt}_$enc.html($enc.url($dependency.Sha1sum))">$enc.html($dependency.DisplayFileName)</a>
+##                    #if($dependency.getRelatedDependencies().size()>0)
+##                        <ul>
+##                        #foreach($related in $dependency.getRelatedDependencies())
+##                        <li>$enc.html($related.DisplayFileName)</li>
+##                        #end
+##                        </ul>
+##                    #end
+##                    </li>
+##                #end
+##                </ul>
                 <h2>Dependencies</h2>
                 #set($lnkcnt=0)
                 #set($cnt=0)
                 #set($vsctr=0) ##counter to create unique groups for vulnerable software
                 #foreach($dependency in $dependencies)
                     #set($lnkcnt=$lnkcnt+1)
-                    <h3 class="subsectionheader standardsubsection#if($dependency.getVulnerabilities().size()==0) notvulnerable#end"><a name="l${lnkcnt}_$enc.html($dependency.Sha1sum)"></a>$enc.html($dependency.FileName)</h3>
+                    <h3 class="subsectionheader standardsubsection#if($dependency.getVulnerabilities().size()==0) notvulnerable#end"><a name="l${lnkcnt}_$enc.html($dependency.Sha1sum)"></a>$enc.html($dependency.DisplayFileName)</h3>
                     <div class="subsectioncontent#if($dependency.getVulnerabilities().size()==0) notvulnerable#end">
                         #if ($dependency.description)
                             <p><b>Description:</b>&nbsp;$enc.html($dependency.description)<br/></p>
@@ -571,7 +650,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                         <div id="content$cnt" class="subsectioncontent standardsubsection hidden">
                             <table class="lined fullwidth" border="0">
                                 <tr><th class="left" style="width:10%;">Source</th><th class="left" style="width:20%;">Name</th><th class="left" style="width:70%;">Value</th></tr>
-                                #foreach($evidence in $dependency.getEvidenceUsed())
+                                #foreach($evidence in $dependency.getEvidenceForDisplay())
                                     <tr><td>$enc.html($evidence.getSource())</td><td>$enc.html($evidence.getName())</td><td>$enc.html($evidence.getValue())</td></tr>
                                 #end
                             </table>
@@ -582,7 +661,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                             <div id="content$cnt" class="subsectioncontent standardsubsection hidden">
                             <ul>
                             #foreach($related in $dependency.getRelatedDependencies())
-                                <li>$enc.html($related.FileName)
+                                <li>$enc.html($related.DisplayFileName)
                                     <ul>
                                         <li>File Path:&nbsp;$enc.html($related.FilePath)</li>
                                         <li>SHA1:&nbsp;$enc.html($related.Sha1sum)</li>
@@ -612,7 +691,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                             #end
                         #end
                         <h4 id="header$cnt" class="subsectionheader white">Identifiers</h4>
-                        ##:&nbsp;<a href="http://web.nvd.nist.gov/view/vuln/search-results?cpe=$enc.url($cpevalue)" target="_blank">$enc.html($cpevalue)</a></h4>
+                        ##:&nbsp;<a href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($cpevalue)" target="_blank">$enc.html($cpevalue)</a></h4>
                         <div id="content$cnt" class="subsectioncontent standardsubsection">
                         #if ($dependency.getIdentifiers().size()==0)
                             <ul><li><b>None</b></li></ul>
@@ -630,7 +709,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                                 #end
                                 #if ($id.type=="cpe")
                                     ##yes, we are HTML Encoding into JavaScript... the escape utils don't have a JS Encode and I haven't written one yet
-                                    &nbsp;&nbsp;<button class="copybutton" onclick="copyText('$enc.html($dependency.FileNameForJavaScript)', '$enc.html($dependency.Sha1sum)', 'cpe', '$enc.html($id.value)')">suppress</button>
+                                    &nbsp;&nbsp;<button class="copybutton" title="Generate Suppression XML for this CPE for this file" onclick="copyText('$enc.html($dependency.FileNameForJavaScript)', '$enc.html($dependency.Sha1sum)', 'cpe', '$enc.html($id.value)')">suppress</button>
                                 #end
                                 #if ($id.description)
                                     <br/>$enc.html($id.description)
@@ -646,7 +725,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                     <div id="content$cnt" class="subsectioncontent standardsubsection">
                         #foreach($vuln in $dependency.getVulnerabilities())
                             #set($vsctr=$vsctr+1)
-                            <p><b><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/detail?vulnId=$enc.url($vuln.name)">$enc.html($vuln.name)</a></b>&nbsp;&nbsp;<button class="copybutton" onclick="copyText('$enc.html($dependency.FileNameForJavaScript)', '$enc.html($dependency.Sha1sum)', 'cve', '$enc.html($vuln.name)')">suppress</button></p>
+                            <p><b><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/detail?vulnId=$enc.url($vuln.name)">$enc.html($vuln.name)</a></b>&nbsp;&nbsp;<button class="copybutton" title="Generate Suppression XML for this CCE for this file" onclick="copyText('$enc.html($dependency.FileNameForJavaScript)', '$enc.html($dependency.Sha1sum)', 'cve', '$enc.html($vuln.name)')">suppress</button></p>
                             <p>Severity:
                             #if ($vuln.cvssScore<4.0)
                                 Low
@@ -668,13 +747,20 @@ arising out of or in connection with the use of this tool, the analysis performe
                                     </ul>
                                 #end
                             </p>
-                            <p>Vulnerable Software &amp; Versions:&nbsp;(<a href="#" onclick="toggleDisplay(this,'.vs$vsctr'); return false;">show all</a>)<ul>
-                                <li class="vs$vsctr"><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/search-results?cpe=$enc.url($vuln.matchedCPE)">$enc.html($vuln.matchedCPE)</a> #if($vuln.hasMatchedAllPreviousCPE()) and all previous versions#end</li>
-                                <li class="vs$vsctr">...</li>
-                            #foreach($vs in $vuln.getVulnerableSoftware())
-                                <li class="vs$vsctr hidden"><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/search-results?cpe=$enc.url($vs.name)">$enc.html($vs.name)</a> #if($vs.hasPreviousVersion()) and all previous versions#end</li>
+
+                            #if ($vuln.getVulnerableSoftware().size()<2)
+                                <p>Vulnerable Software &amp; Versions:<ul>
+                                    <li class="vs$vsctr"><a target="_blank" href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($vuln.matchedCPE)">$enc.html($vuln.matchedCPE)</a> #if($vuln.hasMatchedAllPreviousCPE()) and all previous versions#end</li>
+                                </ul></p>
+                            #else
+                                <p>Vulnerable Software &amp; Versions:&nbsp;(<a href="#" onclick="return toggleDisplay(this,'.vs$vsctr', 'show all', 'show less');">show all</a>)<ul>
+                                    <li class="vs$vsctr"><a target="_blank" href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($vuln.matchedCPE)">$enc.html($vuln.matchedCPE)</a> #if($vuln.hasMatchedAllPreviousCPE()) and all previous versions#end</li>
+                                    <li class="vs$vsctr">...</li>
+                                #foreach($vs in $vuln.getVulnerableSoftware())
+                                    <li class="vs$vsctr hidden"><a target="_blank" href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($vs.name)">$enc.html($vs.name)</a> #if($vs.hasPreviousVersion()) and all previous versions#end</li>
+                                #end
+                                </ul></p>
                             #end
-                            </ul></p>
                         #end
                     </div>
                     #end
@@ -692,7 +778,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                     #foreach($dependency in $dependencies)
                         #if ($dependency.getSuppressedIdentifiers().size()>0 || $dependency.getSuppressedVulnerabilities().size()>0)
                             #set($lnkcnt=$lnkcnt+1)
-                            <h3 class="subsectionheader standardsubsection">$enc.html($dependency.FileName)</h3>
+                            <h3 class="subsectionheader standardsubsection">$enc.html($dependency.DisplayFileName)</h3>
                             <div class="subsectioncontent">
                                 #if ($dependency.description)
                                     <p><b>Description:</b>&nbsp;$enc.html($dependency.description)<br/></p>
@@ -714,7 +800,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                                 <div id="content$cnt" class="subsectioncontent standardsubsection hidden">
                                     <table class="lined fullwidth" border="0">
                                         <tr><th class="left" style="width:10%;">Source</th><th class="left" style="width:20%;">Name</th><th class="left" style="width:70%;">Value</th></tr>
-                                        #foreach($evidence in $dependency.getEvidenceUsed())
+                                        #foreach($evidence in $dependency.getEvidenceForDisplay())
                                             <tr><td>$enc.html($evidence.getSource())</td><td>$enc.html($evidence.getName())</td><td>$enc.html($evidence.getValue())</td></tr>
                                         #end
                                     </table>
@@ -725,7 +811,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                                     <div id="content$cnt" class="subsectioncontent standardsubsection hidden">
                                     <ul>
                                     #foreach($related in $dependency.getRelatedDependencies())
-                                        <li>$enc.html($related.FileName)
+                                        <li>$enc.html($related.DisplayFileName)
                                             <ul>
                                                 <li>File Path:&nbsp;$enc.html($related.FilePath)</li>
                                                 <li>SHA1:&nbsp;$enc.html($related.Sha1sum)</li>
@@ -744,7 +830,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                                     #end
                                 #end
                                 <h4 id="header$cnt" class="subsectionheader white">Suppressed Identifiers</h4>
-                                ##:&nbsp;<a href="http://web.nvd.nist.gov/view/vuln/search-results?cpe=$enc.url($cpevalue)" target="_blank">$enc.html($cpevalue)</a></h4>
+                                ##:&nbsp;<a href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($cpevalue)" target="_blank">$enc.html($cpevalue)</a></h4>
                                 <div id="content$cnt" class="subsectioncontent standardsubsection">
                                 #if ($dependency.getSuppressedIdentifiers().size()==0)
                                     <ul><li><b>None</b></li></ul>
@@ -796,13 +882,19 @@ arising out of or in connection with the use of this tool, the analysis performe
                                             </ul>
                                         #end
                                     </p>
-                                    <p>Vulnerable Software &amp; Versions:&nbsp;(<a href="#" onclick="toggleDisplay(this,'.vs$vsctr'); return false;">show all</a>)<ul>
-                                        <li class="vs$vsctr"><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/search-results?cpe=$enc.url($vuln.matchedCPE)">$enc.html($vuln.matchedCPE)</a> #if($vuln.hasMatchedAllPreviousCPE()) and all previous versions#end</li>
-                                        <li class="vs$vsctr">...</li>
-                                    #foreach($vs in $vuln.getVulnerableSoftware())
-                                        <li class="vs$vsctr hidden"><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/search-results?cpe=$enc.url($vs.name)">$enc.html($vs.name)</a> #if($vs.hasPreviousVersion()) and all previous versions#end</li>
+                                    #if ($vuln.getVulnerableSoftware().size()<2)
+                                        <p>Vulnerable Software &amp; Versions:<ul>
+                                            git st<li class="vs$vsctr"><a target="_blank" href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($vuln.matchedCPE)">$enc.html($vuln.matchedCPE)</a> #if($vuln.hasMatchedAllPreviousCPE()) and all previous versions#end</li>
+                                        </ul></p>
+                                    #else
+                                        <p>Vulnerable Software &amp; Versions:&nbsp;(<a href="#" onclick="return toggleDisplay(this,'.vs$vsctr', 'show all', 'show less');">show all</a>)<ul>
+                                            <li class="vs$vsctr"><a target="_blank" href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($vuln.matchedCPE)">$enc.html($vuln.matchedCPE)</a> #if($vuln.hasMatchedAllPreviousCPE()) and all previous versions#end</li>
+                                            <li class="vs$vsctr">...</li>
+                                        #foreach($vs in $vuln.getVulnerableSoftware())
+                                            <li class="vs$vsctr hidden"><a target="_blank" href="https://web.nvd.nist.gov/view/vuln/search-results?adv_search=true&cves=on&cpe_version=$enc.url($vs.name)">$enc.html($vs.name)</a> #if($vs.hasPreviousVersion()) and all previous versions#end</li>
+                                        #end
+                                        </ul></p>
                                     #end
-                                    </ul></p>
                                 #end
                                 </div>
                             #end
@@ -814,6 +906,6 @@ arising out of or in connection with the use of this tool, the analysis performe
 ## END SUPPRESSED VULNERABILITIES
             </div>
         </div>
-        <div><br/><br/>This report contains data retrieved from the <a href="nvd.nist.gov">National Vulnerability Database</a>.</div>
+        <div><br/><br/>This report contains data retrieved from the <a href="http://nvd.nist.gov">National Vulnerability Database</a>.</div>
     </body>
 </html>

dependency-check-core/src/main/resources/templates/VulnerabilityReport.vsl

@@ -222,10 +222,10 @@ arising out of or in connection with the use of this tool, the analysis performe
                                 ($vuln.cvssScore)
                                 <td>#set($cnt=$cnt+1)
                                     #if($dependency.getRelatedDependencies().size()>0)<span id="header$cnt" class="expandable collapsedList">#end
-                                    $enc.html($dependency.FileName)
+                                    $enc.html($dependency.DisplayFileName)
                                     #if($dependency.getRelatedDependencies().size()>0)&nbsp;&nbsp;&nbsp;</span><div id="content$cnt" class="hidden">#end
                                     #foreach($related in $dependency.getRelatedDependencies())
-                                    $enc.html($related.FileName)<br/>
+                                    $enc.html($related.DisplayFileName)<br/>
                                     #end
                                     #if($dependency.getRelatedDependencies().size()>0)</div#end
                                 </td>
@@ -236,6 +236,6 @@ arising out of or in connection with the use of this tool, the analysis performe
                 </tbody>
                 </table>
             </div>
-        <p><br/><br/>This report contains data retrieved from the <a href="nvd.nist.gov">National Vulnerability Database</a>.</p>
+        <p><br/><br/>This report contains data retrieved from the <a href="http://nvd.nist.gov">National Vulnerability Database</a>.</p>
     </body>
 </html>

dependency-check-core/src/main/resources/templates/XmlReport.vsl

@@ -36,7 +36,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
     <dependencies>
 #foreach($dependency in $dependencies)
         <dependency>
-            <fileName>$enc.xml($dependency.FileName)</fileName>
+            <fileName>$enc.xml($dependency.DisplayFileName)</fileName>
             <filePath>$enc.xml($dependency.FilePath)</filePath>
             <md5>$enc.xml($dependency.Md5sum)</md5>
             <sha1>$enc.xml($dependency.Sha1sum)</sha1>
@@ -68,7 +68,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             </relatedDependencies>
 #end
             <evidenceCollected>
-#foreach($evidence in $dependency.getEvidenceUsed())
+#foreach($evidence in $dependency.getEvidenceForDisplay())
                 <evidence>
                     <source>$enc.xml($evidence.getSource())</source>
                     <name>$enc.xml($evidence.getName())</name>

dependency-check-core/src/test/java/org/owasp/dependencycheck/BaseTest.java

@@ -32,6 +32,6 @@ public class BaseTest {
 
     @AfterClass
     public static void tearDownClass() throws Exception {
-        Settings.cleanup();
+        Settings.cleanup(true);
     }
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/EngineIntegrationTest.java

@@ -23,7 +23,6 @@ import org.junit.Before;
 import org.junit.Test;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
-import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.reporting.ReportGenerator;
 import org.owasp.dependencycheck.utils.Settings;
 
@@ -42,26 +41,6 @@ public class EngineIntegrationTest extends BaseTest {
     public void tearDown() {
     }
 
-    /**
-     * Test of scan method, of class Engine.
-     *
-     * @throws Exception is thrown when an exception occurs.
-     */
-    @Test
-    public void testScan() throws Exception {
-        String testClasses = "target/test-classes/*.zip";
-        boolean autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
-        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
-        Engine instance = new Engine();
-        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
-        instance.scan(testClasses);
-        assertTrue(instance.getDependencies().size() > 0);
-        for (Dependency d : instance.getDependencies()) {
-            assertTrue("non-zip file collected " + d.getFileName(), d.getFileName().toLowerCase().endsWith(".zip"));
-        }
-        instance.cleanup();
-    }
-
     /**
      * Test running the entire engine.
      *
@@ -70,10 +49,10 @@ public class EngineIntegrationTest extends BaseTest {
     @Test
     public void testEngine() throws Exception {
         String testClasses = "target/test-classes";
-//        boolean autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
-//        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+        boolean autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
+        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
         Engine instance = new Engine();
-//        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
+        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
         instance.scan(testClasses);
         assertTrue(instance.getDependencies().size() > 0);
         instance.analyzeDependencies();
@@ -81,8 +60,7 @@ public class EngineIntegrationTest extends BaseTest {
         cveDB.open();
         DatabaseProperties dbProp = cveDB.getDatabaseProperties();
         cveDB.close();
-        ReportGenerator rg = new ReportGenerator("DependencyCheck",
-                instance.getDependencies(), instance.getAnalyzers(), dbProp);
+        ReportGenerator rg = new ReportGenerator("DependencyCheck", instance.getDependencies(), instance.getAnalyzers(), dbProp);
         rg.generateReports("./target/", "ALL");
         instance.cleanup();
     }

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/AbstractSuppressionAnalyzerTest.java

@@ -17,31 +17,78 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.net.MalformedURLException;
-import java.net.URISyntaxException;
-import java.util.List;
-import java.util.Set;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
 import org.junit.Before;
 import org.junit.Test;
 import org.owasp.dependencycheck.BaseTest;
 import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.suppression.SuppressionParseException;
 import org.owasp.dependencycheck.suppression.SuppressionRule;
 import org.owasp.dependencycheck.utils.Settings;
 
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.util.List;
+import java.util.Set;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
 /**
- *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
 public class AbstractSuppressionAnalyzerTest extends BaseTest {
 
+    private AbstractSuppressionAnalyzer instance;
+
     @Before
-    public void setUp() throws Exception {
+    public void createObjectUnderTest() throws Exception {
+        instance = new AbstractSuppressionAnalyzerImpl();
+    }
+
+    /**
+     * Test of getSupportedExtensions method, of class AbstractSuppressionAnalyzer.
+     */
+    @Test
+    public void testGetSupportedExtensions() {
+        Set<String> result = instance.getSupportedExtensions();
+        assertNull(result);
+    }
+
+    /**
+     * Test of getRules method, of class AbstractSuppressionAnalyzer for suppression file declared as URL.
+     */
+    @Test
+    public void testGetRulesFromSuppressionFileFromURL() throws Exception {
+        setSupressionFileFromURL();
+        instance.initialize();
+        int expCount = 5;
+        List<SuppressionRule> result = instance.getRules();
+        assertTrue(expCount <= result.size());
+    }
+
+    /**
+     * Test of getRules method, of class AbstractSuppressionAnalyzer for suppression file declared as URL.
+     */
+    @Test
+    public void testGetRulesFromSuppressionFileInClasspath() throws Exception {
+        Settings.setString(Settings.KEYS.SUPPRESSION_FILE, "suppressions.xml");
+        instance.initialize();
+        int expCount = 5;
+        List<SuppressionRule> result = instance.getRules();
+        assertTrue(expCount <= result.size());
+    }
+
+    @Test(expected = SuppressionParseException.class)
+    public void testFailureToLocateSuppressionFileAnywhere() throws Exception {
+        Settings.setString(Settings.KEYS.SUPPRESSION_FILE, "doesnotexist.xml");
+        instance.initialize();
+    }
+
+    private void setSupressionFileFromURL() throws Exception {
         try {
             final String uri = this.getClass().getClassLoader().getResource("suppressions.xml").toURI().toURL().toString();
             Settings.setString(Settings.KEYS.SUPPRESSION_FILE, uri);
@@ -52,37 +99,6 @@ public class AbstractSuppressionAnalyzerTest extends BaseTest {
         }
     }
 
-    /**
-     * Test of getSupportedExtensions method, of class AbstractSuppressionAnalyzer.
-     */
-    @Test
-    public void testGetSupportedExtensions() {
-        AbstractSuppressionAnalyzer instance = new AbstractSuppressionAnalyzerImpl();
-        Set<String> result = instance.getSupportedExtensions();
-        assertNull(result);
-    }
-
-    /**
-     * Test of initialize method, of class AbstractSuppressionAnalyzer.
-     */
-    @Test
-    public void testInitialize() throws Exception {
-        AbstractSuppressionAnalyzer instance = new AbstractSuppressionAnalyzerImpl();
-        instance.initialize();
-    }
-
-    /**
-     * Test of getRules method, of class AbstractSuppressionAnalyzer.
-     */
-    @Test
-    public void testGetRules() throws Exception {
-        AbstractSuppressionAnalyzer instance = new AbstractSuppressionAnalyzerImpl();
-        instance.initialize();
-        int expCount = 5;
-        List<SuppressionRule> result = instance.getRules();
-        assertEquals(expCount, result.size());
-    }
-
     public class AbstractSuppressionAnalyzerImpl extends AbstractSuppressionAnalyzer {
 
         @Override

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/ArchiveAnalyzerIntegrationTest.java

@@ -40,7 +40,7 @@ public class ArchiveAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
     @Test
     public void testGetSupportedExtensions() {
         ArchiveAnalyzer instance = new ArchiveAnalyzer();
-        Set expResult = new HashSet<String>();
+        Set<String> expResult = new HashSet<String>();
         expResult.add("zip");
         expResult.add("war");
         expResult.add("ear");

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/CPEAnalyzerIntegrationTest.java

@@ -25,9 +25,11 @@ import java.util.Set;
 import org.apache.lucene.index.CorruptIndexException;
 import org.apache.lucene.queryparser.classic.ParseException;
 import org.junit.Assert;
+import static org.junit.Assert.assertTrue;
 import org.junit.Test;
 import org.owasp.dependencycheck.data.cpe.AbstractDatabaseTestCase;
 import org.owasp.dependencycheck.data.cpe.IndexEntry;
+import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Identifier;
 
@@ -81,12 +83,24 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
      */
     @Test
     public void testDetermineCPE_full() throws Exception {
-        callDetermineCPE_full("hazelcast-2.5.jar", null);
-        callDetermineCPE_full("spring-context-support-2.5.5.jar", "cpe:/a:vmware:springsource_spring_framework:2.5.5");
-        callDetermineCPE_full("spring-core-3.0.0.RELEASE.jar", "cpe:/a:vmware:springsource_spring_framework:3.0.0");
-        callDetermineCPE_full("org.mortbay.jetty.jar", "cpe:/a:mortbay_jetty:jetty:4.2");
-        callDetermineCPE_full("jaxb-xercesImpl-1.5.jar", null);
-        callDetermineCPE_full("ehcache-core-2.2.0.jar", null);
+        CPEAnalyzer instance = new CPEAnalyzer();
+        instance.open();
+        FileNameAnalyzer fnAnalyzer = new FileNameAnalyzer();
+        JarAnalyzer jarAnalyzer = new JarAnalyzer();
+        HintAnalyzer hAnalyzer = new HintAnalyzer();
+        FalsePositiveAnalyzer fp = new FalsePositiveAnalyzer();
+
+        try {
+            //callDetermineCPE_full("struts2-core-2.3.16.3.jar", "cpe:/a:apache:struts:2.3.16.3", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+            callDetermineCPE_full("hazelcast-2.5.jar", null, instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+            callDetermineCPE_full("spring-context-support-2.5.5.jar", "cpe:/a:vmware:springsource_spring_framework:2.5.5", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+            callDetermineCPE_full("spring-core-3.0.0.RELEASE.jar", "cpe:/a:vmware:springsource_spring_framework:3.0.0", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+            callDetermineCPE_full("org.mortbay.jetty.jar", "cpe:/a:mortbay_jetty:jetty:4.2", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+            callDetermineCPE_full("jaxb-xercesImpl-1.5.jar", null, instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+            callDetermineCPE_full("ehcache-core-2.2.0.jar", null, instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+        } finally {
+            instance.close();
+        }
     }
 
     /**
@@ -94,37 +108,25 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
      *
      * @throws Exception is thrown when an exception occurs
      */
-    public void callDetermineCPE_full(String depName, String expResult) throws Exception {
+    public void callDetermineCPE_full(String depName, String expResult, CPEAnalyzer instance, FileNameAnalyzer fnAnalyzer, JarAnalyzer jarAnalyzer, HintAnalyzer hAnalyzer, FalsePositiveAnalyzer fp) throws Exception {
 
         File file = new File(this.getClass().getClassLoader().getResource(depName).getPath());
 
         Dependency dep = new Dependency(file);
 
-        FileNameAnalyzer fnAnalyzer = new FileNameAnalyzer();
         fnAnalyzer.analyze(dep, null);
-
-        JarAnalyzer jarAnalyzer = new JarAnalyzer();
         jarAnalyzer.analyze(dep, null);
-        HintAnalyzer hAnalyzer = new HintAnalyzer();
         hAnalyzer.analyze(dep, null);
-
-        CPEAnalyzer instance = new CPEAnalyzer();
-        instance.open();
         instance.analyze(dep, null);
-        instance.close();
-        FalsePositiveAnalyzer fp = new FalsePositiveAnalyzer();
         fp.analyze(dep, null);
 
-//        for (Identifier i : dep.getIdentifiers()) {
-//            System.out.println(i.getValue());
-//        }
         if (expResult != null) {
             Identifier expIdentifier = new Identifier("cpe", expResult, expResult);
             Assert.assertTrue("Incorrect match: { dep:'" + dep.getFileName() + "' }", dep.getIdentifiers().contains(expIdentifier));
-        } else if (dep.getIdentifiers().isEmpty()) {
-            Assert.assertTrue("Match found when an Identifier should not have been found: { dep:'" + dep.getFileName() + "' }", dep.getIdentifiers().isEmpty());
         } else {
-            Assert.assertTrue("Match found when an Identifier should not have been found: { dep:'" + dep.getFileName() + "', identifier:'" + dep.getIdentifiers().iterator().next().getValue() + "' }", dep.getIdentifiers().isEmpty());
+            for (Identifier i : dep.getIdentifiers()) {
+                Assert.assertFalse(String.format("%s - found a CPE identifier when should have been none (found '%s')", dep.getFileName(), i.getValue()), "cpe".equals(i.getType()));
+            }
         }
     }
 
@@ -170,7 +172,10 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
         String expResultSpring = "cpe:/a:springsource:spring_framework:2.5.5";
         String expResultSpring3 = "cpe:/a:vmware:springsource_spring_framework:3.0.0";
 
-        Assert.assertTrue("Apache Common Validator - found an identifier?", commonValidator.getIdentifiers().isEmpty());
+        for (Identifier i : commonValidator.getIdentifiers()) {
+            Assert.assertFalse("Apache Common Validator - found a CPE identifier?", "cpe".equals(i.getType()));
+        }
+
         Assert.assertTrue("Incorrect match size - struts", struts.getIdentifiers().size() >= 1);
         Assert.assertTrue("Incorrect match - struts", struts.getIdentifiers().contains(expIdentifier));
         Assert.assertTrue("Incorrect match size - spring3 - " + spring3.getIdentifiers().size(), spring3.getIdentifiers().size() >= 1);
@@ -180,6 +185,30 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
         //Assert.assertTrue("Incorrect match - spring", spring.getIdentifiers().get(0).getValue().equals(expResultSpring));
     }
 
+    /**
+     * Test of determineIdentifiers method, of class CPEAnalyzer.
+     *
+     * @throws Exception is thrown when an exception occurs
+     */
+    @Test
+    public void testDetermineIdentifiers() throws Exception {
+        Dependency openssl = new Dependency();
+        openssl.getVendorEvidence().addEvidence("test", "vendor", "openssl", Confidence.HIGHEST);
+        openssl.getProductEvidence().addEvidence("test", "product", "openssl", Confidence.HIGHEST);
+        openssl.getVersionEvidence().addEvidence("test", "version", "1.0.1c", Confidence.HIGHEST);
+
+        CPEAnalyzer instance = new CPEAnalyzer();
+        instance.open();
+        instance.determineIdentifiers(openssl, "openssl", "openssl", Confidence.HIGHEST);
+        instance.close();
+
+        String expResult = "cpe:/a:openssl:openssl:1.0.1c";
+        Identifier expIdentifier = new Identifier("cpe", expResult, expResult);
+
+        assertTrue(openssl.getIdentifiers().contains(expIdentifier));
+
+    }
+
     /**
      * Test of searchCPE method, of class CPEAnalyzer.
      *
@@ -190,12 +219,12 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
         String vendor = "apache software foundation";
         String product = "struts 2 core";
         String version = "2.1.2";
-        String expResult = "cpe:/a:apache:struts:2.1.2";
+        String expVendor = "apache";
+        String expProduct = "struts";
 
         CPEAnalyzer instance = new CPEAnalyzer();
         instance.open();
 
-        //TODO - yeah, not a very good test as the results are the same with or without weighting...
         Set<String> productWeightings = new HashSet<String>(1);
         productWeightings.add("struts2");
 
@@ -203,9 +232,16 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
         vendorWeightings.add("apache");
 
         List<IndexEntry> result = instance.searchCPE(vendor, product, productWeightings, vendorWeightings);
-        //TODO fix this assert
-        //Assert.assertEquals(expResult, result.get(0).getName());
-
         instance.close();
+
+        boolean found = false;
+        for (IndexEntry entry : result) {
+            if (expVendor.equals(entry.getVendor()) && expProduct.equals(entry.getProduct())) {
+                found = true;
+                break;
+            }
+        }
+        assertTrue("apache:struts was not identified", found);
+
     }
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/DependencyBundlingAnalyzerTest.java

@@ -86,4 +86,40 @@ public class DependencyBundlingAnalyzerTest extends BaseTest {
         assertEquals(expResult, result);
     }
 
+    @Test
+    public void testFirstPathIsShortest() {
+        DependencyBundlingAnalyzer instance = new DependencyBundlingAnalyzer();
+
+        String left = "./a/c.jar";
+        String right = "./d/e/f.jar";
+        boolean expResult = true;
+        boolean result = instance.firstPathIsShortest(left, right);
+        assertEquals(expResult, result);
+
+        left = "./a/b/c.jar";
+        right = "./d/e/f.jar";
+        expResult = true;
+        result = instance.firstPathIsShortest(left, right);
+        assertEquals(expResult, result);
+
+        left = "./d/b/c.jar";
+        right = "./a/e/f.jar";
+        expResult = false;
+        result = instance.firstPathIsShortest(left, right);
+        assertEquals(expResult, result);
+
+        left = "./a/b/c.jar";
+        right = "./d/f.jar";
+        expResult = false;
+        result = instance.firstPathIsShortest(left, right);
+        assertEquals(expResult, result);
+
+        left = "./a/b/c.jar";
+        right = "./a/b/c.jar";
+        expResult = true;
+        result = instance.firstPathIsShortest(left, right);
+        assertEquals(expResult, result);
+
+    }
+
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/FalsePositiveAnalyzerTest.java

@@ -56,6 +56,7 @@ public class FalsePositiveAnalyzerTest {
     public void testAnalyze() throws Exception {
         Dependency dependency = new Dependency();
         dependency.setFileName("pom.xml");
+        dependency.setFilePath("pom.xml");
         dependency.addIdentifier("cpe", "cpe:/a:file:file:1.2.1", "http://some.org/url");
         Engine engine = null;
         FalsePositiveAnalyzer instance = new FalsePositiveAnalyzer();

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/HintAnalyzerTest.java

@@ -85,7 +85,7 @@ public class HintAnalyzerTest extends BaseTest {
         for (Dependency d : engine.getDependencies()) {
             if (d.getActualFile().equals(guice)) {
                 gdep = d;
-            } else {
+            } else if (d.getActualFile().equals(spring)) {
                 sdep = d;
             }
         }

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/JarAnalyzerTest.java

@@ -93,7 +93,7 @@ public class JarAnalyzerTest extends BaseTest {
     @Test
     public void testGetSupportedExtensions() {
         JarAnalyzer instance = new JarAnalyzer();
-        Set expResult = new HashSet();
+        Set<String> expResult = new HashSet<String>();
         expResult.add("jar");
         expResult.add("war");
         Set result = instance.getSupportedExtensions();

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/JavaScriptAnalyzerTest.java

@@ -38,7 +38,7 @@ public class JavaScriptAnalyzerTest extends BaseTest {
     @Test
     public void testGetSupportedExtensions() {
         JavaScriptAnalyzer instance = new JavaScriptAnalyzer();
-        Set expResult = new HashSet<String>();
+        Set<String> expResult = new HashSet<String>();
         expResult.add("js");
         Set result = instance.getSupportedExtensions();
         assertEquals(expResult, result);

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/VulnerabilitySuppressionAnalyzerIntegrationTest.java

@@ -61,19 +61,26 @@ public class VulnerabilitySuppressionAnalyzerIntegrationTest extends AbstractDat
     @Test
     public void testAnalyze() throws Exception {
 
-        File file = new File(this.getClass().getClassLoader().getResource("FileHelpers.2.0.0.0.nupkg").getPath());
-        File suppression = new File(this.getClass().getClassLoader().getResource("FileHelpers.2.0.0.0.suppression.xml").getPath());
+        File file = new File(this.getClass().getClassLoader().getResource("commons-fileupload-1.2.1.jar").getPath());
+        File suppression = new File(this.getClass().getClassLoader().getResource("commons-fileupload-1.2.1.suppression.xml").getPath());
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
         Engine engine = new Engine();
         engine.scan(file);
         engine.analyzeDependencies();
         Dependency dependency = getDependency(engine, file);
-        assertTrue(dependency.getVulnerabilities().size() > 0);
+        int cveSize = dependency.getVulnerabilities().size();
+        int cpeSize = dependency.getIdentifiers().size();
+        assertTrue(cveSize > 0);
+        assertTrue(cpeSize > 0);
         Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppression.getAbsolutePath());
         VulnerabilitySuppressionAnalyzer instance = new VulnerabilitySuppressionAnalyzer();
         instance.initialize();
         instance.analyze(dependency, engine);
-        assertTrue(dependency.getVulnerabilities().size() == 0);
+        cveSize = cveSize > 1 ? cveSize - 2 : 0;
+        cpeSize = cpeSize > 0 ? cpeSize - 1 : 0;
+        assertTrue(dependency.getVulnerabilities().size() == cveSize);
+        assertTrue(dependency.getIdentifiers().size() == cpeSize);
         engine.cleanup();
     }
 

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/central/CentralSearchTest.java

@@ -0,0 +1,63 @@
+package org.owasp.dependencycheck.data.central;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.owasp.dependencycheck.BaseTest;
+import org.owasp.dependencycheck.data.nexus.MavenArtifact;
+import org.owasp.dependencycheck.utils.Settings;
+
+import java.io.FileNotFoundException;
+import java.net.URL;
+import java.util.List;
+import java.util.logging.Logger;
+
+import static org.junit.Assert.*;
+
+/**
+ * Created by colezlaw on 10/13/14.
+ */
+public class CentralSearchTest extends BaseTest {
+    private static final Logger LOGGER = Logger.getLogger(CentralSearchTest.class.getName());
+    private CentralSearch searcher;
+
+    @Before
+    public void setUp() throws Exception {
+        String centralUrl = Settings.getString(Settings.KEYS.ANALYZER_CENTRAL_URL);
+        LOGGER.fine(centralUrl);
+        searcher = new CentralSearch(new URL(centralUrl));
+    }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testNullSha1() throws Exception { searcher.searchSha1(null); }
+
+    @Test(expected = IllegalArgumentException.class)
+    public void testMalformedSha1() throws Exception {
+        searcher.searchSha1("invalid");
+    }
+
+    // This test does generate network traffic and communicates with a host
+    // you may not be able to reach. Remove the @Ignore annotation if you want to
+    // test it anyway
+    @Test
+    public void testValidSha1() throws Exception {
+        List<MavenArtifact> ma = searcher.searchSha1("9977a8d04e75609cf01badc4eb6a9c7198c4c5ea");
+        assertEquals("Incorrect group", "org.apache.maven.plugins", ma.get(0).getGroupId());
+        assertEquals("Incorrect artifact", "maven-compiler-plugin", ma.get(0).getArtifactId());
+        assertEquals("Incorrect version", "3.1", ma.get(0).getVersion());
+    }
+
+    // This test does generate network traffic and communicates with a host
+    // you may not be able to reach. Remove the @Ignore annotation if you want to
+    // test it anyway
+    @Test(expected = FileNotFoundException.class)
+    public void testMissingSha1() throws Exception {
+        searcher.searchSha1("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
+    }
+
+    // This test should give us multiple results back from Central
+    @Test
+    public void testMultipleReturns() throws Exception {
+        List<MavenArtifact> ma = searcher.searchSha1("94A9CE681A42D0352B3AD22659F67835E560D107");
+        assertTrue(ma.size() > 1);
+    }
+}

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/nvdcve/BaseDBTestCase.java

@@ -45,8 +45,10 @@ public abstract class BaseDBTestCase extends BaseTest {
 
     public static void ensureDBExists() throws Exception {
 
-        java.io.File dataPath = Settings.getDataFile(Settings.KEYS.DATA_DIRECTORY);
-        if (!dataPath.exists() || (dataPath.isDirectory() && dataPath.listFiles().length < 3)) {
+        java.io.File dataPath = Settings.getDataDirectory();
+        String fileName = String.format(Settings.getString(Settings.KEYS.DB_FILE_NAME), Settings.getString(Settings.KEYS.DB_VERSION));
+        java.io.File dataFile = new File(dataPath, fileName);
+        if (!dataPath.exists() || !dataFile.exists()) {
             dataPath.mkdirs();
             FileInputStream fis = null;
             ZipInputStream zin = null;

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/nvdcve/CveDBIntegrationTest.java

@@ -19,9 +19,11 @@ package org.owasp.dependencycheck.data.nvdcve;
 
 import java.util.List;
 import java.util.Set;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import org.junit.Test;
 import org.owasp.dependencycheck.dependency.VulnerableSoftware;
+import org.owasp.dependencycheck.utils.DependencyVersion;
 
 /**
  *
@@ -72,4 +74,21 @@ public class CveDBIntegrationTest extends BaseDBTestCase {
             instance.close();
         }
     }
+
+    /**
+     * Test of isAffected method, of class CveDB.
+     */
+    @Test
+    public void testIsAffected() throws Exception {
+        String vendor = "openssl";
+        String product = "openssl";
+        DependencyVersion identifiedVersion = new DependencyVersion("1.0.1o");
+        String cpeId = "cpe:/a:openssl:openssl:1.0.1e";
+        String previous = "y";
+
+        CveDB instance = new CveDB();
+        assertFalse(instance.isAffected(vendor, product, identifiedVersion, cpeId, previous));
+
+    }
+
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/update/NvdCveUpdaterIntegrationTest.java

@@ -17,8 +17,12 @@
  */
 package org.owasp.dependencycheck.data.update;
 
+import java.io.File;
+import java.util.Calendar;
+import org.junit.Before;
 import org.junit.Test;
 import org.owasp.dependencycheck.BaseTest;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  *
@@ -26,6 +30,32 @@ import org.owasp.dependencycheck.BaseTest;
  */
 public class NvdCveUpdaterIntegrationTest extends BaseTest {
 
+    @Before
+    public void setUp() throws Exception {
+        int year = Calendar.getInstance().get(Calendar.YEAR);
+        if (year <= 2014) {
+            File f = new File(NvdCveUpdaterIntegrationTest.class.getClassLoader().getResource("nvdcve-2.0-2014.xml").getPath());
+            String baseURL = f.toURI().toURL().toString();
+            String modified12 = baseURL.replace("nvdcve-2.0-2014.xml", "nvdcve-modified.xml");
+            String modified20 = baseURL.replace("nvdcve-2.0-2014.xml", "nvdcve-2.0-modified.xml");
+            String full12 = baseURL.replace("nvdcve-2.0-2014.xml", "nvdcve-%d.xml");
+            String full20 = baseURL.replace("nvdcve-2.0-2014.xml", "nvdcve-2.0-%d.xml");
+//        cve.url-1.2.modified=http://nvd.nist.gov/download/nvdcve-modified.xml
+//        cve.url-2.0.modified=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+//        cve.startyear=2014
+//        cve.url-2.0.base=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+//        cve.url-1.2.base=http://nvd.nist.gov/download/nvdcve-%d.xml
+
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, modified12);
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, modified20);
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, full12);
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, full20);
+            Settings.setString(Settings.KEYS.CVE_START_YEAR, "2014");
+        } else {
+            System.err.println("Consider updating the local data files to make the NvdCveUpdaterIntegrationTest perform faster");
+        }
+    }
+
     /**
      * Test of update method, of class NvdCveUpdater.
      */

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/update/StandardUpdateIntegrationTest.java

@@ -67,16 +67,16 @@ public class StandardUpdateIntegrationTest extends BaseTest {
         result = instance.withinRange(lastRun, current, range);
         assertEquals(expResult, result);
     }
-
-    /**
-     * Test of update method, of class StandardUpdate.
-     */
-    @Test
-    public void testUpdate() throws Exception {
-        StandardUpdate instance = getStandardUpdateTask();
-        instance.update();
-        //TODO make this an actual test
-    }
+// test removed as it is duplicative of the EngineIntegrationTest and the NvdCveUpdaterIntergraionTest
+//    /**
+//     * Test of update method, of class StandardUpdate.
+//     */
+//    @Test
+//    public void testUpdate() throws Exception {
+//        StandardUpdate instance = getStandardUpdateTask();
+//        instance.update();
+//        //TODO make this an actual test
+//    }
 
     /**
      * Test of updatesNeeded method, of class StandardUpdate.

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/update/task/DownloadTaskTest.java

@@ -0,0 +1,75 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.data.update.task;
+
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Future;
+import org.junit.After;
+import org.junit.AfterClass;
+import static org.junit.Assert.assertNull;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.update.NvdCveInfo;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public class DownloadTaskTest {
+
+    public DownloadTaskTest() {
+    }
+
+    @BeforeClass
+    public static void setUpClass() {
+    }
+
+    @AfterClass
+    public static void tearDownClass() {
+    }
+
+    @Before
+    public void setUp() {
+        Settings.initialize();
+    }
+
+    @After
+    public void tearDown() {
+        Settings.cleanup();
+    }
+
+    /**
+     * Test of call method, of class DownloadTask.
+     */
+    @Test
+    public void testCall() throws Exception {
+        NvdCveInfo cve = new NvdCveInfo();
+        cve.setId("modified");
+        cve.setNeedsUpdate(true);
+        cve.setUrl(Settings.getString(Settings.KEYS.CVE_MODIFIED_20_URL));
+        cve.setOldSchemaVersionUrl(Settings.getString(Settings.KEYS.CVE_MODIFIED_12_URL));
+        ExecutorService processExecutor = null;
+        CveDB cveDB = null;
+        DownloadTask instance = new DownloadTask(cve, processExecutor, cveDB, Settings.getInstance());;
+        Future<ProcessTask> result = instance.call();
+        assertNull(result);
+    }
+}

dependency-check-core/src/test/java/org/owasp/dependencycheck/dependency/DependencyTest.java

@@ -23,10 +23,12 @@ import java.util.Set;
 import org.junit.After;
 import org.junit.AfterClass;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.owasp.dependencycheck.data.nexus.MavenArtifact;
 
 /**
  *
@@ -152,7 +154,7 @@ public class DependencyTest {
     public void testGetMd5sum() {
         File file = new File(this.getClass().getClassLoader().getResource("struts2-core-2.1.2.jar").getPath());
         Dependency instance = new Dependency(file);
-//        assertEquals("89CE9E36AA9A9E03F1450936D2F4F8DD0F961F8B", result.getSha1sum());
+        //assertEquals("89CE9E36AA9A9E03F1450936D2F4F8DD0F961F8B", result.getSha1sum());
         String expResult = "C30B57142E1CCBC1EFD5CD15F307358F";
         String result = instance.getMd5sum();
         assertEquals(expResult, result);
@@ -294,4 +296,34 @@ public class DependencyTest {
         EvidenceCollection result = instance.getVersionEvidence();
         assertTrue(true); //this is just a getter setter pair.
     }
+
+    /**
+     * Test of addAsEvidence method, of class Dependency.
+     */
+    @Test
+    public void testAddAsEvidence() {
+        Dependency instance = new Dependency();
+        MavenArtifact mavenArtifact = new MavenArtifact("group", "artifact", "version", "url");
+        instance.addAsEvidence("pom", mavenArtifact, Confidence.HIGH);
+        assertTrue(instance.getEvidence().contains(Confidence.HIGH));
+        assertFalse(instance.getEvidence().getEvidence("pom", "groupid").isEmpty());
+        assertFalse(instance.getEvidence().getEvidence("pom", "artifactid").isEmpty());
+        assertFalse(instance.getEvidence().getEvidence("pom", "version").isEmpty());
+        assertFalse(instance.getIdentifiers().isEmpty());
+    }
+
+    /**
+     * Test of addAsEvidence method, of class Dependency.
+     */
+    @Test
+    public void testAddAsEvidenceWithEmptyArtefact() {
+        Dependency instance = new Dependency();
+        MavenArtifact mavenArtifact = new MavenArtifact(null, null, null, null);
+        instance.addAsEvidence("pom", mavenArtifact, Confidence.HIGH);
+        assertFalse(instance.getEvidence().contains(Confidence.HIGH));
+        assertTrue(instance.getEvidence().getEvidence("pom", "groupid").isEmpty());
+        assertTrue(instance.getEvidence().getEvidence("pom", "artifactid").isEmpty());
+        assertTrue(instance.getEvidence().getEvidence("pom", "version").isEmpty());
+        assertTrue(instance.getIdentifiers().isEmpty());
+    }
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/suppression/SuppressionHandlerTest.java

@@ -88,7 +88,15 @@ public class SuppressionHandlerTest {
 
         xmlReader.parse(in);
 
-        List result = handler.getSuppressionRules();
+        List<SuppressionRule> result = handler.getSuppressionRules();
         assertTrue(result.size() > 3);
+        int baseCount = 0;
+        for (SuppressionRule r : result) {
+            if (r.isBase()) {
+                baseCount++;
+            }
+        }
+        assertTrue(baseCount > 0);
+
     }
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/suppression/SuppressionRuleTest.java

@@ -146,6 +146,17 @@ public class SuppressionRuleTest {
         List<String> result = instance.getCve();
         assertEquals(cve, result);
     }
+
+    /**
+     * Test of base property, of class SuppressionRule.
+     */
+    @Test
+    public void testBase() {
+        SuppressionRule instance = new SuppressionRule();
+        assertFalse(instance.isBase());
+        instance.setBase(true);
+        assertTrue(instance.isBase());
+    }
     //</editor-fold>
 
     //<editor-fold defaultstate="collapsed" desc="Ignored duplicate tests, left in, as empty tests, so IDE doesn't re-generate them">
@@ -339,55 +350,70 @@ public class SuppressionRuleTest {
     }
 
     /**
-     * Test of cpeMatches method, of class SuppressionRule.
+     * Test of identifierMatches method, of class SuppressionRule.
      */
     @Test
     public void testCpeMatches() {
-        Identifier identifier = new Identifier("cwe", "cpe:/a:microsoft:.net_framework:4.5", "some url not needed for this test");
+        Identifier identifier = new Identifier("cpe", "cpe:/a:microsoft:.net_framework:4.5", "some url not needed for this test");
 
         PropertyType cpe = new PropertyType();
         cpe.setValue("cpe:/a:microsoft:.net_framework:4.5");
 
         SuppressionRule instance = new SuppressionRule();
         boolean expResult = true;
-        boolean result = instance.cpeMatches(cpe, identifier);
+        boolean result = instance.identifierMatches("cpe", cpe, identifier);
         assertEquals(expResult, result);
 
         cpe.setValue("cpe:/a:microsoft:.net_framework:4.0");
         expResult = false;
-        result = instance.cpeMatches(cpe, identifier);
+        result = instance.identifierMatches("cpe", cpe, identifier);
         assertEquals(expResult, result);
 
         cpe.setValue("CPE:/a:microsoft:.net_framework:4.5");
         cpe.setCaseSensitive(true);
         expResult = false;
-        result = instance.cpeMatches(cpe, identifier);
+        result = instance.identifierMatches("cpe", cpe, identifier);
         assertEquals(expResult, result);
 
         cpe.setValue("cpe:/a:microsoft:.net_framework");
         cpe.setCaseSensitive(false);
         expResult = true;
-        result = instance.cpeMatches(cpe, identifier);
+        result = instance.identifierMatches("cpe", cpe, identifier);
         assertEquals(expResult, result);
 
         cpe.setValue("cpe:/a:microsoft:.*");
         cpe.setRegex(true);
         expResult = true;
-        result = instance.cpeMatches(cpe, identifier);
+        result = instance.identifierMatches("cpe", cpe, identifier);
         assertEquals(expResult, result);
 
         cpe.setValue("CPE:/a:microsoft:.*");
         cpe.setRegex(true);
         cpe.setCaseSensitive(true);
         expResult = false;
-        result = instance.cpeMatches(cpe, identifier);
+        result = instance.identifierMatches("cpe", cpe, identifier);
         assertEquals(expResult, result);
 
         cpe.setValue("cpe:/a:apache:.*");
         cpe.setRegex(true);
         cpe.setCaseSensitive(false);
         expResult = false;
-        result = instance.cpeMatches(cpe, identifier);
+        result = instance.identifierMatches("cpe", cpe, identifier);
+        assertEquals(expResult, result);
+
+        identifier = new Identifier("maven", "org.springframework:spring-core:2.5.5", "https://repository.sonatype.org/service/local/artifact/maven/redirect?r=central-proxy&g=org.springframework&a=spring-core&v=2.5.5&e=jar");
+        cpe.setValue("org.springframework:spring-core:2.5.5");
+        cpe.setRegex(false);
+        cpe.setCaseSensitive(false);
+        expResult = true;
+        result = instance.identifierMatches("maven", cpe, identifier);
+        assertEquals(expResult, result);
+
+        cpe.setValue("org\\.springframework\\.security:spring.*");
+        cpe.setRegex(true);
+        cpe.setCaseSensitive(false);
+        expResult = false;
+        result = instance.identifierMatches("maven", cpe, identifier);
         assertEquals(expResult, result);
     }
 
@@ -398,7 +424,7 @@ public class SuppressionRuleTest {
     public void testProcess() {
         File struts = new File(this.getClass().getClassLoader().getResource("struts2-core-2.1.2.jar").getPath());
         Dependency dependency = new Dependency(struts);
-        dependency.addIdentifier("cwe", "cpe:/a:microsoft:.net_framework:4.5", "some url not needed for this test");
+        dependency.addIdentifier("cpe", "cpe:/a:microsoft:.net_framework:4.5", "some url not needed for this test");
         String sha1 = dependency.getSha1sum();
         dependency.setSha1sum("384FAA82E193D4E4B0546059CA09572654BC3970");
         Vulnerability v = createVulnerability();
@@ -409,33 +435,33 @@ public class SuppressionRuleTest {
         instance.setSha1(sha1);
         instance.addCwe("287");
         instance.process(dependency);
-        assertTrue(dependency.getVulnerabilities().size() == 1);
+        assertEquals(1, dependency.getVulnerabilities().size());
         dependency.setSha1sum(sha1);
         instance.process(dependency);
         assertTrue(dependency.getVulnerabilities().isEmpty());
-        assertTrue(dependency.getSuppressedVulnerabilities().size() == 1);
+        assertEquals(1, dependency.getSuppressedVulnerabilities().size());
 
         //cvss
         dependency.addVulnerability(v);
         instance = new SuppressionRule();
         instance.addCvssBelow(5f);
         instance.process(dependency);
-        assertTrue(dependency.getVulnerabilities().size() == 1);
+        assertEquals(1, dependency.getVulnerabilities().size());
         instance.addCvssBelow(8f);
         instance.process(dependency);
         assertTrue(dependency.getVulnerabilities().isEmpty());
-        assertTrue(dependency.getSuppressedVulnerabilities().size() == 1);
+        assertEquals(1, dependency.getSuppressedVulnerabilities().size());
 
         //cve
         dependency.addVulnerability(v);
         instance = new SuppressionRule();
         instance.addCve("CVE-2012-1337");
         instance.process(dependency);
-        assertTrue(dependency.getVulnerabilities().size() == 1);
+        assertEquals(1, dependency.getVulnerabilities().size());
         instance.addCve("CVE-2013-1337");
         instance.process(dependency);
         assertTrue(dependency.getVulnerabilities().isEmpty());
-        assertTrue(dependency.getSuppressedVulnerabilities().size() == 1);
+        assertEquals(1, dependency.getSuppressedVulnerabilities().size());
 
         //cpe
         instance = new SuppressionRule();
@@ -453,18 +479,58 @@ public class SuppressionRuleTest {
         instance.setFilePath(pt);
         instance.process(dependency);
         assertTrue(dependency.getIdentifiers().isEmpty());
-        assertTrue(dependency.getSuppressedIdentifiers().size() == 1);
+        assertEquals(1, dependency.getSuppressedIdentifiers().size());
 
-        dependency.addIdentifier("cwe", "cpe:/a:microsoft:.net_framework:4.0", "some url not needed for this test");
-        dependency.addIdentifier("cwe", "cpe:/a:microsoft:.net_framework:4.5", "some url not needed for this test");
-        dependency.addIdentifier("cwe", "cpe:/a:microsoft:.net_framework:5.0", "some url not needed for this test");
+        instance = new SuppressionRule();
+        dependency.addIdentifier("cpe", "cpe:/a:microsoft:.net_framework:4.0", "some url not needed for this test");
+        dependency.addIdentifier("cpe", "cpe:/a:microsoft:.net_framework:4.5", "some url not needed for this test");
+        dependency.addIdentifier("cpe", "cpe:/a:microsoft:.net_framework:5.0", "some url not needed for this test");
         pt = new PropertyType();
         pt.setValue("cpe:/a:microsoft:.net_framework");
         instance.addCpe(pt);
-        assertTrue(dependency.getIdentifiers().size() == 3);
+        instance.setBase(true);
+        assertEquals(3, dependency.getIdentifiers().size());
+        assertEquals(1, dependency.getSuppressedIdentifiers().size());
         instance.process(dependency);
         assertTrue(dependency.getIdentifiers().isEmpty());
-        assertTrue(dependency.getSuppressedIdentifiers().size() == 3);
+        assertEquals(1, dependency.getSuppressedIdentifiers().size());
+    }
+
+    /**
+     * Test of process method, of class SuppressionRule.
+     */
+    @Test
+    public void testProcessGAV() {
+        File spring = new File(this.getClass().getClassLoader().getResource("spring-security-web-3.0.0.RELEASE.jar").getPath());
+        Dependency dependency = new Dependency(spring);
+        dependency.addIdentifier("cpe", "cpe:/a:vmware:springsource_spring_framework:3.0.0", "some url not needed for this test");
+        dependency.addIdentifier("cpe", "cpe:/a:springsource:spring_framework:3.0.0", "some url not needed for this test");
+        dependency.addIdentifier("cpe", "cpe:/a:mod_security:mod_security:3.0.0", "some url not needed for this test");
+        dependency.addIdentifier("cpe", "cpe:/a:vmware:springsource_spring_security:3.0.0", "some url not needed for this test");
+        dependency.addIdentifier("maven", "org.springframework.security:spring-security-web:3.0.0.RELEASE", "some url not needed for this test");
+
+        //cpe
+        SuppressionRule instance = new SuppressionRule();
+        PropertyType pt = new PropertyType();
+
+        pt.setValue("org\\.springframework\\.security:spring.*");
+        pt.setRegex(true);
+        pt.setCaseSensitive(false);
+        instance.setGav(pt);
+
+        pt = new PropertyType();
+        pt.setValue("cpe:/a:mod_security:mod_security");
+        instance.addCpe(pt);
+        pt = new PropertyType();
+        pt.setValue("cpe:/a:springsource:spring_framework");
+        instance.addCpe(pt);
+        pt = new PropertyType();
+        pt.setValue("cpe:/a:vmware:springsource_spring_framework");
+        instance.addCpe(pt);
+
+        instance.process(dependency);
+        assertEquals(2, dependency.getIdentifiers().size());
+
     }
 
     private Vulnerability createVulnerability() {

dependency-check-core/src/test/java/org/owasp/dependencycheck/utils/DependencyVersionTest.java

@@ -134,14 +134,14 @@ public class DependencyVersionTest {
     @Test
     public void testMatchesAtLeastThreeLevels() {
 
-        DependencyVersion instance = new DependencyVersion("1.2.3.4");
-        DependencyVersion version = new DependencyVersion("1.2.3.5");
+        DependencyVersion instance = new DependencyVersion("2.3.16.3");
+        DependencyVersion version = new DependencyVersion("2.3.16.4");
         //true tests
         assertEquals(true, instance.matchesAtLeastThreeLevels(version));
-        version = new DependencyVersion("1.2");
+        version = new DependencyVersion("2.3");
         assertEquals(true, instance.matchesAtLeastThreeLevels(version));
         //false tests
-        version = new DependencyVersion("1.2.2.5");
+        version = new DependencyVersion("2.3.16.1");
         assertEquals(false, instance.matchesAtLeastThreeLevels(version));
         version = new DependencyVersion("2");
         assertEquals(false, instance.matchesAtLeastThreeLevels(version));
@@ -165,6 +165,14 @@ public class DependencyVersionTest {
         version = new DependencyVersion("1.2.3.1");
         assertEquals(-1, instance.compareTo(version));
 
+        instance = new DependencyVersion("1.0.1n");
+        version = new DependencyVersion("1.0.1m");
+        assertEquals(1, instance.compareTo(version));
+        version = new DependencyVersion("1.0.1n");
+        assertEquals(0, instance.compareTo(version));
+        version = new DependencyVersion("1.0.1o");
+        assertEquals(-1, instance.compareTo(version));
+
         DependencyVersion[] dv = new DependencyVersion[7];
         dv[0] = new DependencyVersion("2.1.3");
         dv[1] = new DependencyVersion("2.1.3.r2");

dependency-check-core/src/test/java/org/owasp/dependencycheck/utils/DependencyVersionUtilTest.java

@@ -54,13 +54,13 @@ public class DependencyVersionUtilTest {
      * Test of parseVersion method, of class DependencyVersionUtil.
      */
     @Test
-    public void testParseVersionFromFileName() {
+    public void testParseVersion() {
         final String[] fileName = {"something-0.9.5.jar", "lib2-1.1.jar", "lib1.5r4-someflag-R26.jar",
             "lib-1.2.5-dev-20050313.jar", "testlib_V4.4.0.jar", "lib-core-2.0.0-RC1-SNAPSHOT.jar",
             "lib-jsp-2.0.1_R114940.jar", "dev-api-2.3.11_R121413.jar", "lib-api-3.7-SNAPSHOT.jar",
-            "-", "", "1.3-beta", "6"};
+            "-", "", "1.3-beta", "6", "openssl1.0.1c", "jsf-impl-2.2.8-02.jar"};
         final String[] expResult = {"0.9.5", "1.1", "1.5.r4", "1.2.5", "4.4.0", "2.0.0.rc1",
-            "2.0.1.r114940", "2.3.11.r121413", "3.7", "-", null, "1.3.beta", "6"};
+            "2.0.1.r114940", "2.3.11.r121413", "3.7", "-", null, "1.3.beta", "6", "1.0.1c", "2.2.8.02"};
 
         for (int i = 0; i < fileName.length; i++) {
             final DependencyVersion version = DependencyVersionUtil.parseVersion(fileName[i]);

dependency-check-core/src/test/resources/FileHelpers.2.0.0.0.suppression.xml

@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<suppressions xmlns="https://www.owasp.org/index.php/OWASP_Dependency_Check_Suppression">
-	<suppress>
-	   <notes><![CDATA[
-	   file name: FileHelpers.2.0.0.0.nupkg
-	   ]]></notes>
-	   <sha1>30FB37D6163CF16E3BA740343BECDD14D5457619</sha1>
-	   <cve>CVE-2007-1536</cve>
-	</suppress>
-</suppressions>

dependency-check-core/src/test/resources/commons-fileupload-1.2.1.suppression.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<suppressions xmlns="https://www.owasp.org/index.php/OWASP_Dependency_Check_Suppression">
+    <suppress>
+        <notes><![CDATA[
+        file name: commons-fileupload-1.2.1.jar
+        ]]></notes>
+        <sha1>384FAA82E193D4E4B0546059CA09572654BC3970</sha1>
+        <cpe>cpe:/a:apache:commons_fileupload:1.2.1</cpe>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+        file name: commons-fileupload-1.2.1.jar
+        ]]></notes>
+        <sha1>384FAA82E193D4E4B0546059CA09572654BC3970</sha1>
+        <cve>CVE-2014-0050</cve>
+    </suppress>
+    <suppress>
+        <notes><![CDATA[
+        file name: commons-fileupload-1.2.1.jar
+        ]]></notes>
+        <sha1>384FAA82E193D4E4B0546059CA09572654BC3970</sha1>
+        <cve>CVE-2013-0248</cve>
+    </suppress>
+</suppressions>

dependency-check-core/src/test/resources/dependencycheck.properties

@@ -13,8 +13,12 @@ max.download.threads=3
 # will not be used. The data.directory will be resolved and if the connection string
 # below contains a %s then the data.directory will replace the %s.
 data.directory=[JAR]/data
+# if the filename has a %s it will be replaced with the current expected version. For file
+# based databases the below filename will be added to the data directory above and then
+# if the connection string has a %s it will be replaced by the directory/filename path.
+data.file_name=cve.%s.h2.db
+data.version=2.9
 data.connection_string=jdbc:h2:file:%s;FILE_LOCK=SERIALIZED;AUTOCOMMIT=ON;
-#data.connection_string=jdbc:h2:file:%s;AUTO_SERVER=TRUE;AUTOCOMMIT=ON;
 #data.connection_string=jdbc:mysql://localhost:3306/dependencycheck
 
 # user name and password for the database connection. The inherent case is to use H2.
@@ -43,11 +47,16 @@ cpe.meta.url=http://static.nvd.nist.gov/feeds/xml/cpe/dictionary/official-cpe-di
 cve.url.modified.validfordays=7
 
 # the path to the modified nvd cve xml file.
-cve.url-1.2.modified=http://nvd.nist.gov/download/nvdcve-modified.xml
-cve.url-2.0.modified=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
 cve.startyear=2014
-cve.url-2.0.base=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
-cve.url-1.2.base=http://nvd.nist.gov/download/nvdcve-%d.xml
+cve.url-1.2.modified=https://nvd.nist.gov/download/nvdcve-Modified.xml.gz
+#cve.url-1.2.modified=http://nvd.nist.gov/download/nvdcve-modified.xml
+cve.url-2.0.modified=https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-Modified.xml.gz
+#cve.url-2.0.modified=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+cve.url-1.2.base=https://nvd.nist.gov/download/nvdcve-%d.xml.gz
+#cve.url-1.2.base=http://nvd.nist.gov/download/nvdcve-%d.xml
+cve.url-2.0.base=https://nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml.gz
+#cve.url-2.0.base=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+
 
 # the URL for searching Nexus for SHA-1 hashes and whether it's enabled
 analyzer.nexus.enabled=true
@@ -55,3 +64,7 @@ analyzer.nexus.url=https://repository.sonatype.org/service/local/
 # If set to true, the proxy will still ONLY be used if the proxy properties (proxy.url, proxy.port)
 # are configured
 analyzer.nexus.proxy=true
+
+# the URL for searching search.maven.org for SHA-1 and whether it's enabled
+analyzer.central.enabled=true
+analyzer.central.url=http://search.maven.org/solrsearch/select

dependency-check-core/src/test/resources/suppressions.xml

@@ -10,7 +10,7 @@
         <filePath>c:\path\to\some.jar</filePath>
         <cpe>cpe:/a:csv:csv:1.0</cpe>
     </suppress>
-    <suppress>
+    <suppress base="true">
         <notes><![CDATA[
         This suppresses any jboss:jboss cpe for any test.jar in any directory.
         ]]></notes>

dependency-check-jenkins/pom.xml

@@ -1,17 +1,25 @@
 <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>
-
-    <description>This plug-in can independently execute a Dependency-Check analysis and visualize the results.</description>
-    <url>http://wiki.jenkins-ci.org/display/JENKINS/OWASP+Dependency-Check+Plugin</url>
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.6</version>
     </parent>
-
     <groupId>org.owasp</groupId>
     <artifactId>dependency-check-jenkins</artifactId>
     <name>Dependency-Check Jenkins Plugin</name>
+    <url>http://wiki.jenkins-ci.org/display/JENKINS/OWASP+Dependency-Check+Plugin</url>
+    <description>dependency-check-jenkins is a Jenkins plugin that runs dependency-check-core on a project to detect publicly disclosed vulnerabilities associated with the project's dependencies. The plugin will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries. This module is simply a placeholder and does not contain the actual plugin source code. The source code and distribution of the plugin is handled via https://github.com/jenkinsci/dependency-check-jenkins and Jenkin's plugin management.</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-jenkins</url>
+        </site>
+    </distributionManagement>
+    <!-- end copy -->
+
     <packaging>pom</packaging>
     <inceptionYear>2012</inceptionYear>
     <organization>
@@ -31,15 +39,6 @@
             </roles>
         </developer>
     </developers>
-    <!-- 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-maven</url>
-        </site>
-    </distributionManagement>
-    <!-- end copy -->
     <scm>
         <connection>scm:git:git@github.com:jenkinsci/dependency-check-jenkins.git</connection>
         <url>https://github.com/jenkinsci/dependency-check-jenkins</url>

dependency-check-maven/pom.xml

@@ -15,7 +15,6 @@ limitations under the License.
 
 Copyright (c) 2013 Jeremy Long. All Rights Reserved.
 -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <url>http://maven.apache.org</url>
@@ -23,14 +22,14 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.6</version>
     </parent>
 
     <artifactId>dependency-check-maven</artifactId>
     <packaging>maven-plugin</packaging>
 
     <name>Dependency-Check Maven Plugin</name>
-    <description>Dependency-Check-Maven is a Maven Plugin that attempts to detect publicly disclosed vulnerabilities contained within project dependencies. It does this by determining if there is a Common Platform Enumeration (CPE) identifier for a given dependency. If found, it will generate a report linking to the associated CVE entries.</description>
+    <description>dependency-check-maven is a Maven Plugin that uses dependency-check-core to detect publicly disclosed vulnerabilities associated with the project's dependencies. The plugin will generate a report listing the dependency, any identified Common Platform Enumeration (CPE) identifiers, and the associated Common Vulnerability and Exposure (CVE) entries.</description>
     <inceptionYear>2013</inceptionYear>
     <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
     <distributionManagement>
@@ -150,6 +149,9 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
                             <groupId>org.apache.maven.plugins</groupId>
                             <artifactId>maven-javadoc-plugin</artifactId>
                             <version>2.9.1</version>
+                            <configuration>
+                                <bottom>Copyright© 2012-14 Jeremy Long. All Rights Reserved.</bottom>
+                            </configuration>
                             <reportSets>
                                 <reportSet>
                                     <id>default</id>
@@ -239,7 +241,7 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
                                 <linkXref>true</linkXref>
                                 <sourceEncoding>utf-8</sourceEncoding>
                                 <excludes>
-                                    <exclude>**/generated/*.java</exclude>
+                                    <exclude>**/generated/**/*.java</exclude>
                                     <exclude>**/HelpMojo.java</exclude>
                                 </excludes>
                                 <rulesets>
@@ -277,6 +279,11 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
             <artifactId>dependency-check-core</artifactId>
             <version>${project.parent.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.owasp</groupId>
+            <artifactId>dependency-check-utils</artifactId>
+            <version>${project.parent.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.maven</groupId>
             <artifactId>maven-plugin-api</artifactId>

dependency-check-maven/src/main/java/org/owasp/dependencycheck/maven/ReportAggregationMojo.java

@@ -0,0 +1,462 @@
+/*
+ * 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) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.maven;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Set;
+import java.util.logging.Logger;
+import org.apache.maven.doxia.sink.Sink;
+import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.apache.maven.plugins.annotations.Component;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.project.MavenProject;
+import org.apache.maven.reporting.MavenReport;
+import org.apache.maven.reporting.MavenReportException;
+
+/**
+ * <p>
+ * This is an abstract reporting mojo that enables report aggregation. Some of the code in the this class was copied
+ * from the CoberturaReportMojo (http://mojo.codehaus.org/cobertura-maven-plugin/, version 2.6). The authors of the
+ * CoberturaReportMojo were <a href="will.gwaltney@sas.com">Will Gwaltney</a> and
+ * <a href="mailto:joakim@erdfelt.com">Joakim Erdfelt</a>. There working example of how to do report aggregation was
+ * invaluable.</p>
+ * <p>
+ * An important point about using this abstract class is that it is intended for one to write some form of serialized
+ * data (via the {@link org.owasp.dependencycheck.maven.ReportAggregationMojo#writeDataFile() }; note that the
+ * <code>writeDataFile()</code> function is called automatically after either {@link org.owasp.dependencycheck.maven.ReportAggregationMojo#executeNonAggregateReport(org.apache.maven.doxia.sink.Sink,
+ * org.apache.maven.doxia.sink.SinkFactory, java.util.Locale)
+ * } or {@link org.owasp.dependencycheck.maven.ReportAggregationMojo#executeAggregateReport(org.apache.maven.doxia.sink.Sink,
+ * org.apache.maven.doxia.sink.SinkFactory, java.util.Locale)
+ * } are called. When  <code>executeAggregateReport()</code> is implemented, one can call {@link org.owasp.dependencycheck.maven.ReportAggregationMojo#getChildDataFiles()
+ * } to obtain a list of the data files to aggregate.</p>
+ *
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public abstract class ReportAggregationMojo extends AbstractMojo implements MavenReport {
+
+    /**
+     * The Maven Project Object.
+     */
+    @Component
+    private MavenProject project;
+
+    /**
+     * Logger field reference.
+     */
+    private static final Logger LOGGER = Logger.getLogger(ReportAggregationMojo.class.getName());
+
+    /**
+     * List of Maven project of the current build
+     */
+    @Parameter(readonly = true, required = true, property = "reactorProjects")
+    private List<MavenProject> reactorProjects;
+
+    /**
+     * Generate aggregate reports in multi-module projects.
+     */
+    @Parameter(property = "aggregate", defaultValue = "false")
+    private boolean aggregate;
+
+    /**
+     * Sets whether or not the external report format should be used.
+     */
+    @Parameter(property = "metaFileName", defaultValue = "dependency-check.ser", required = true)
+    private String dataFileName;
+    /**
+     * Specifies the destination directory for the generated Dependency-Check report. This generally maps to
+     * "target/site".
+     */
+    @Parameter(property = "reportOutputDirectory", defaultValue = "${project.reporting.outputDirectory}", required = true)
+    private File reportOutputDirectory;
+
+    /**
+     * Sets the Reporting output directory.
+     *
+     * @param directory the output directory
+     */
+    @Override
+    public void setReportOutputDirectory(File directory) {
+        reportOutputDirectory = directory;
+    }
+
+    /**
+     * Returns the output directory.
+     *
+     * @return the output directory
+     */
+    @Override
+    public File getReportOutputDirectory() {
+        return reportOutputDirectory;
+    }
+
+    /**
+     * Returns the output directory for the given project.
+     *
+     * @param project the Maven project to get the output directory for
+     * @return the output directory for the given project
+     */
+    public File getReportOutputDirectory(MavenProject project) {
+        final Object o = project.getContextValue(getOutputDirectoryContextKey());
+        if (o != null && o instanceof File) {
+            return (File) o;
+        }
+        return null;
+    }
+
+    /**
+     * Returns whether this is an external report. This method always returns true.
+     *
+     * @return <code>true</code>
+     */
+    @Override
+    public final boolean isExternalReport() {
+        return true;
+    }
+
+    /**
+     * The collection of child projects.
+     */
+    private final Map<MavenProject, Set<MavenProject>> projectChildren = new HashMap<MavenProject, Set<MavenProject>>();
+
+    /**
+     * Called before execute; allows for any setup that is needed. If this is overridden you must call
+     * </code>super.preExecute()</code>.
+     *
+     * @throws MojoExecutionException thrown if there is an issue executing the mojo
+     * @throws MojoFailureException thrown if there is an issue executing the mojo
+     */
+    protected void preExecute() throws MojoExecutionException, MojoFailureException {
+        buildAggregateInfo();
+    }
+
+    /**
+     * Called when the mojo is being executed.
+     *
+     * @throws MojoExecutionException thrown if there is an issue executing the mojo
+     * @throws MojoFailureException thrown if there is an issue executing the mojo
+     */
+    protected abstract void performExecute() throws MojoExecutionException, MojoFailureException;
+
+    /**
+     * Runs after the mojo has executed. This implementation will call <code>writeDataFile()</code>. As such, it is
+     * important that if this method is overriden that <code>super.postExecute()</code> is called.
+     *
+     * @throws MojoExecutionException thrown if there is an issue executing the mojo
+     * @throws MojoFailureException thrown if there is an issue executing the mojo
+     */
+    protected void postExecute() throws MojoExecutionException, MojoFailureException {
+        final File written = writeDataFile();
+        if (written != null) {
+            project.setContextValue(getDataFileContextKey(), written.getAbsolutePath());
+        }
+    }
+
+    /**
+     * Returns the key used to store the path to the data file that is saved by <code>writeDataFile()</code>. This key
+     * is used in the <code>MavenProject.(set|get)ContextValue</code>.
+     *
+     * @return the key used to store the path to the data file
+     */
+    protected String getDataFileContextKey() {
+        return "dependency-check-path-" + this.getDataFileName();
+    }
+
+    /**
+     * Returns the key used to store the path to the output directory. When generating the report in the
+     * <code>executeAggregateReport()</code> the output directory should be obtained by using this key.
+     *
+     * @return the key used to store the path to the output directory
+     */
+    protected String getOutputDirectoryContextKey() {
+        return "dependency-output-dir-" + this.getDataFileName();
+    }
+
+    /**
+     * Is called by Maven to execute the mojo.
+     *
+     * @throws MojoExecutionException thrown if there is an issue executing the mojo
+     * @throws MojoFailureException thrown if there is an issue executing the mojo
+     */
+    public final void execute() throws MojoExecutionException, MojoFailureException {
+        try {
+            preExecute();
+            performExecute();
+        } finally {
+            postExecute();
+        }
+    }
+
+    /**
+     * Runs prior to the site report generation.
+     *
+     * @throws MavenReportException if a maven report exception occurs
+     */
+    protected void preGenerate() throws MavenReportException {
+        buildAggregateInfo();
+
+        project.setContextValue(getOutputDirectoryContextKey(), getReportOutputDirectory());
+    }
+
+    /**
+     * Executes after the site report has been generated.
+     *
+     * @throws MavenReportException if a maven report exception occurs
+     */
+    protected void postGenerate() throws MavenReportException {
+        final File written = writeDataFile();
+        if (written != null) {
+            project.setContextValue(getDataFileContextKey(), written.getAbsolutePath());
+        }
+    }
+
+    /**
+     * Generates the non aggregate report.
+     *
+     * @param locale the locale to use when generating the report
+     * @throws MavenReportException if a maven report exception occurs
+     */
+    protected abstract void executeNonAggregateReport(Locale locale) throws MavenReportException;
+
+    /**
+     * Generates the aggregate Site Report.
+     *
+     * @param project the maven project used to generate the aggregate report
+     * @param locale the locale to use when generating the report
+     * @throws MavenReportException if a maven report exception occurs
+     */
+    protected abstract void executeAggregateReport(MavenProject project, Locale locale) throws MavenReportException;
+
+    /**
+     * Generates the Dependency-Check Site Report.
+     *
+     * @param sink the sink to write the report to
+     * @param locale the locale to use when generating the report
+     * @throws MavenReportException if a maven report exception occurs
+     * @deprecated use {@link #generate(org.apache.maven.doxia.sink.Sink, java.util.Locale) instead.
+     */
+    @Deprecated
+    public final void generate(@SuppressWarnings("deprecation") org.codehaus.doxia.sink.Sink sink, Locale locale) throws MavenReportException {
+        generate((Sink) sink, locale);
+    }
+
+    /**
+     * Generates the Dependency-Check Site Report.
+     *
+     * @param sink the sink to write the report to
+     * @param locale the locale to use when generating the report
+     * @throws MavenReportException if a maven report exception occurs
+     */
+    public final void generate(Sink sink, Locale locale) throws MavenReportException {
+        try {
+            preGenerate();
+            if (canGenerateNonAggregateReport()) {
+                executeNonAggregateReport(locale);
+            }
+
+            if (canGenerateAggregateReport()) {
+                for (MavenProject proj : reactorProjects) {
+                    if (!isMultiModule(proj)) {
+                        continue;
+                    }
+                    executeAggregateReport(proj, locale);
+                }
+            }
+        } finally {
+            postGenerate();
+        }
+    }
+
+    /**
+     * Returns whether or not the mojo can generate a non-aggregate report for this project.
+     *
+     * @return <code>true</code> if a non-aggregate report can be generated, otherwise <code>false</code>
+     */
+    protected abstract boolean canGenerateNonAggregateReport();
+
+    /**
+     * Returns whether or not we can generate any aggregate reports at this time.
+     *
+     * @return <code>true</code> if an aggregate report can be generated, otherwise <code>false</code>
+     */
+    protected abstract boolean canGenerateAggregateReport();
+
+    /**
+     * Returns the name of the data file that contains the serialized data.
+     *
+     * @return the name of the data file that contains the serialized data
+     */
+    protected String getDataFileName() {
+        return dataFileName;
+    }
+
+    /**
+     * Writes the data file to disk in the target directory.
+     *
+     * @return the File object referencing the data file that was written
+     */
+    protected abstract File writeDataFile();
+
+    /**
+     * Collects the information needed for building aggregate reports.
+     */
+    private void buildAggregateInfo() {
+        // build parent-child map
+        for (MavenProject proj : reactorProjects) {
+            Set<MavenProject> depList = projectChildren.get(proj.getParent());
+            if (depList == null) {
+                depList = new HashSet<MavenProject>();
+                projectChildren.put(proj.getParent(), depList);
+            }
+            depList.add(proj);
+        }
+    }
+
+    /**
+     * Returns a list containing all the recursive, non-pom children of the given project, never <code>null</code>.
+     *
+     * @return a list of child projects
+     */
+    protected List<MavenProject> getAllChildren() {
+        return getAllChildren(project);
+    }
+
+    /**
+     * Returns a list containing all the recursive, non-pom children of the given project, never <code>null</code>.
+     *
+     * @param parentProject the parent project to collect the child project references
+     * @return a list of child projects
+     */
+    protected List<MavenProject> getAllChildren(MavenProject parentProject) {
+        final Set<MavenProject> children = projectChildren.get(parentProject);
+        if (children == null) {
+            return Collections.emptyList();
+        }
+
+        final List<MavenProject> result = new ArrayList<MavenProject>();
+        for (MavenProject child : children) {
+            if (isMultiModule(child)) {
+                result.addAll(getAllChildren(child));
+            } else {
+                result.add(child);
+            }
+        }
+        return result;
+    }
+
+    /**
+     * Returns a list of data files that were produced by the direct children of the given MavenProject.
+     *
+     * @param project the Maven project to obtain the child data files from
+     * @return a list of the data files
+     */
+    protected List<File> getAllChildDataFiles(MavenProject project) {
+        final List<MavenProject> children = getAllChildren(project);
+        return getDataFiles(children);
+    }
+
+    /**
+     * Returns any existing output files from the given list of projects.
+     *
+     * @param projects the list of projects to obtain the output files from
+     * @return a list of output files
+     */
+    protected List<File> getDataFiles(List<MavenProject> projects) {
+        final List<File> files = new ArrayList<File>();
+        for (MavenProject proj : projects) {
+            final Object path = project.getContextValue(getDataFileContextKey());
+            if (path == null) {
+                final String msg = String.format("Unable to aggregate data for '%s' - aggregate data file was not generated",
+                        proj.getName());
+                LOGGER.warning(msg);
+            } else {
+                final File outputFile = new File((String) path);
+                if (outputFile.exists()) {
+                    files.add(outputFile);
+                } else {
+                    if (!isMultiModule(project)) {
+                        final String msg = String.format("Unable to aggregate data for '%s' - missing data file '%s'",
+                                proj.getName(), outputFile.getPath());
+                        LOGGER.warning(msg);
+                    }
+                }
+            }
+        }
+        return files;
+    }
+
+    /**
+     * Test if the project has pom packaging
+     *
+     * @param mavenProject Project to test
+     * @return <code>true</code> if it has a pom packaging; otherwise <code>false</code>
+     */
+    protected boolean isMultiModule(MavenProject mavenProject) {
+        return "pom".equals(mavenProject.getPackaging());
+    }
+
+    /**
+     * Test if the current project has pom packaging
+     *
+     * @return <code>true</code> if it has a pom packaging; otherwise <code>false</code>
+     */
+    protected boolean isMultiModule() {
+        return isMultiModule(project);
+    }
+
+    /**
+     * Check whether the current project is the last project in a multi-module build. If the maven build is not a
+     * multi-module project then this will always return true.
+     *
+     * @return <code>true</code> if the current project is the last project in a multi-module build; otherwise
+     * <code>false</code>
+     */
+    protected boolean isLastProject() {
+        return project.equals(reactorProjects.get(reactorProjects.size() - 1));
+    }
+
+    /**
+     * Returns whether or not the mojo is configured to perform report aggregation.
+     *
+     * @return <code>true</code> if report aggregation is enabled; otherwise <code>false</code>
+     */
+    public boolean isAggregate() {
+        return aggregate;
+    }
+
+    /**
+     * Returns a reference to the current project. This method is used instead of auto-binding the project via component
+     * annotation in concrete implementations of this. If the child has a <code>@Component MavenProject project;</code>
+     * defined then the abstract class (i.e. this class) will not have access to the current project (just the way Maven
+     * works with the binding).
+     *
+     * @return returns a reference to the current project
+     */
+    protected MavenProject getProject() {
+        return project;
+    }
+}

dependency-check-maven/src/main/java/org/owasp/dependencycheck/maven/ReportingUtil.java

@@ -0,0 +1,456 @@
+/*
+ * 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) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.maven;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
+import java.text.DateFormat;
+import java.util.Date;
+import java.util.List;
+import java.util.Set;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.apache.maven.doxia.sink.Sink;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.dependency.Identifier;
+import org.owasp.dependencycheck.dependency.Reference;
+import org.owasp.dependencycheck.dependency.Vulnerability;
+import org.owasp.dependencycheck.dependency.VulnerableSoftware;
+import org.owasp.dependencycheck.reporting.ReportGenerator;
+
+/**
+ * A utility class that encapsulates the report generation for dependency-check-maven.
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+final class ReportingUtil {
+
+    /**
+     * Logger field reference.
+     */
+    private static final Logger LOGGER = Logger.getLogger(ReportingUtil.class.getName());
+
+    /**
+     * Empty private constructor for this utility class.
+     */
+    private ReportingUtil() {
+    }
+
+    /**
+     * Generates the reports for a given dependency-check engine.
+     *
+     * @param engine a dependency-check engine
+     * @param outDirectory the directory to write the reports to
+     * @param projectName the name of the project that a report is being generated for
+     * @param format the format of the report to generate
+     */
+    static void generateExternalReports(Engine engine, File outDirectory, String projectName, String format) {
+        DatabaseProperties prop = null;
+        CveDB cve = null;
+        try {
+            cve = new CveDB();
+            cve.open();
+            prop = cve.getDatabaseProperties();
+        } catch (DatabaseException ex) {
+            LOGGER.log(Level.FINE, "Unable to retrieve DB Properties", ex);
+        } finally {
+            if (cve != null) {
+                cve.close();
+            }
+        }
+        final ReportGenerator r = new ReportGenerator(projectName, engine.getDependencies(), engine.getAnalyzers(), prop);
+        try {
+            r.generateReports(outDirectory.getCanonicalPath(), format);
+        } catch (IOException ex) {
+            LOGGER.log(Level.SEVERE,
+                    "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
+            LOGGER.log(Level.FINE, null, ex);
+        } catch (Throwable ex) {
+            LOGGER.log(Level.SEVERE,
+                    "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
+            LOGGER.log(Level.FINE, null, ex);
+        }
+    }
+
+    /**
+     * Generates a dependency-check report using the Maven Site format.
+     *
+     * @param engine the engine used to scan the dependencies
+     * @param sink the sink to write the data to
+     * @param projectName the name of the project
+     */
+    static void generateMavenSiteReport(final Engine engine, Sink sink, String projectName) {
+        final List<Dependency> dependencies = engine.getDependencies();
+
+        writeSiteReportHeader(sink, projectName);
+        writeSiteReportTOC(sink, dependencies);
+
+        int cnt = 0;
+        for (Dependency d : dependencies) {
+            writeSiteReportDependencyHeader(sink, d);
+            cnt = writeSiteReportDependencyEvidenceUsed(d, cnt, sink);
+            cnt = writeSiteReportDependencyRelatedDependencies(d, cnt, sink);
+            writeSiteReportDependencyIdentifiers(d, sink);
+            writeSiteReportDependencyVulnerabilities(d, sink, cnt);
+        }
+        sink.body_();
+    }
+
+    // <editor-fold defaultstate="collapsed" desc="various writeXXXXX methods to generate the Site Report">
+    /**
+     * Writes the vulnerabilities to the site report.
+     *
+     * @param d the dependency
+     * @param sink the sink to write the data to
+     * @param collapsibleHeaderCount the collapsible header count
+     */
+    private static void writeSiteReportDependencyVulnerabilities(Dependency d, Sink sink, int collapsibleHeaderCount) {
+        int cnt = collapsibleHeaderCount;
+        if (d.getVulnerabilities() != null && !d.getVulnerabilities().isEmpty()) {
+            for (Vulnerability v : d.getVulnerabilities()) {
+
+                sink.paragraph();
+                sink.bold();
+                try {
+                    sink.link("http://web.nvd.nist.gov/view/vuln/detail?vulnId=" + URLEncoder.encode(v.getName(), "US-ASCII"));
+                    sink.text(v.getName());
+                    sink.link_();
+                    sink.bold_();
+                } catch (UnsupportedEncodingException ex) {
+                    sink.text(v.getName());
+                    sink.bold_();
+                    sink.lineBreak();
+                    sink.text("http://web.nvd.nist.gov/view/vuln/detail?vulnId=" + v.getName());
+                }
+                sink.paragraph_();
+                sink.paragraph();
+                sink.text("Severity: ");
+                if (v.getCvssScore() < 4.0) {
+                    sink.text("Low");
+                } else {
+                    if (v.getCvssScore() >= 7.0) {
+                        sink.text("High");
+                    } else {
+                        sink.text("Medium");
+                    }
+                }
+                sink.lineBreak();
+                sink.text("CVSS Score: " + v.getCvssScore());
+                if (v.getCwe() != null && !v.getCwe().isEmpty()) {
+                    sink.lineBreak();
+                    sink.text("CWE: ");
+                    sink.text(v.getCwe());
+                }
+                sink.paragraph_();
+                sink.paragraph();
+                sink.text(v.getDescription());
+                if (v.getReferences() != null && !v.getReferences().isEmpty()) {
+                    sink.list();
+                    for (Reference ref : v.getReferences()) {
+                        sink.listItem();
+                        sink.text(ref.getSource());
+                        sink.text(" - ");
+                        sink.link(ref.getUrl());
+                        sink.text(ref.getName());
+                        sink.link_();
+                        sink.listItem_();
+                    }
+                    sink.list_();
+                }
+                sink.paragraph_();
+                if (v.getVulnerableSoftware() != null && !v.getVulnerableSoftware().isEmpty()) {
+                    sink.paragraph();
+
+                    cnt += 1;
+                    sink.rawText("Vulnerable Software <a href=\"javascript:toggleElement(this, 'vulnSoft" + cnt + "')\">[-]</a>");
+                    sink.rawText("<div id=\"vulnSoft" + cnt + "\" style=\"display:block\">");
+                    sink.list();
+                    for (VulnerableSoftware vs : v.getVulnerableSoftware()) {
+                        sink.listItem();
+                        try {
+                            sink.link("http://web.nvd.nist.gov/view/vuln/search-results?cpe=" + URLEncoder.encode(vs.getName(), "US-ASCII"));
+                            sink.text(vs.getName());
+                            sink.link_();
+                            if (vs.hasPreviousVersion()) {
+                                sink.text(" and all previous versions.");
+                            }
+                        } catch (UnsupportedEncodingException ex) {
+                            sink.text(vs.getName());
+                            if (vs.hasPreviousVersion()) {
+                                sink.text(" and all previous versions.");
+                            }
+                            sink.text(" (http://web.nvd.nist.gov/view/vuln/search-results?cpe=" + vs.getName() + ")");
+                        }
+
+                        sink.listItem_();
+                    }
+                    sink.list_();
+                    sink.rawText("</div>");
+                    sink.paragraph_();
+                }
+            }
+        }
+    }
+
+    /**
+     * Writes the identifiers to the site report.
+     *
+     * @param d the dependency
+     * @param sink the sink to write the data to
+     */
+    private static void writeSiteReportDependencyIdentifiers(Dependency d, Sink sink) {
+        if (d.getIdentifiers() != null && !d.getIdentifiers().isEmpty()) {
+            sink.sectionTitle4();
+            sink.text("Identifiers");
+            sink.sectionTitle4_();
+            sink.list();
+            for (Identifier i : d.getIdentifiers()) {
+                sink.listItem();
+                sink.text(i.getType());
+                sink.text(": ");
+                if (i.getUrl() != null && i.getUrl().length() > 0) {
+                    sink.link(i.getUrl());
+                    sink.text(i.getValue());
+                    sink.link_();
+                } else {
+                    sink.text(i.getValue());
+                }
+                if (i.getDescription() != null && i.getDescription().length() > 0) {
+                    sink.lineBreak();
+                    sink.text(i.getDescription());
+                }
+                sink.listItem_();
+            }
+            sink.list_();
+        }
+    }
+
+    /**
+     * Writes the related dependencies to the site report.
+     *
+     * @param d the dependency
+     * @param sink the sink to write the data to
+     * @param collapsibleHeaderCount the collapsible header count
+     * @return the collapsible header count
+     */
+    private static int writeSiteReportDependencyRelatedDependencies(Dependency d, int collapsibleHeaderCount, Sink sink) {
+        int cnt = collapsibleHeaderCount;
+        if (d.getRelatedDependencies() != null && !d.getRelatedDependencies().isEmpty()) {
+            cnt += 1;
+            sink.sectionTitle4();
+            sink.rawText("Related Dependencies <a href=\"javascript:toggleElement(this, 'related" + cnt + "')\">[+]</a>");
+            sink.sectionTitle4_();
+            sink.rawText("<div id=\"related" + cnt + "\" style=\"display:none\">");
+            sink.list();
+            for (Dependency r : d.getRelatedDependencies()) {
+                sink.listItem();
+                sink.text(r.getFileName());
+                sink.list();
+                writeListItem(sink, "File Path: " + r.getFilePath());
+                writeListItem(sink, "SHA1: " + r.getSha1sum());
+                writeListItem(sink, "MD5: " + r.getMd5sum());
+                sink.list_();
+                sink.listItem_();
+            }
+            sink.list_();
+            sink.rawText("</div>");
+        }
+        return cnt;
+    }
+
+    /**
+     * Writes the evidence used to the site report.
+     *
+     * @param d the dependency
+     * @param sink the sink to write the data to
+     * @param collapsibleHeaderCount the collapsible header count
+     * @return the collapsible header count
+     */
+    private static int writeSiteReportDependencyEvidenceUsed(Dependency d, int collapsibleHeaderCount, Sink sink) {
+        int cnt = collapsibleHeaderCount;
+        final Set<Evidence> evidence = d.getEvidenceForDisplay();
+        if (evidence != null && evidence.size() > 0) {
+            cnt += 1;
+            sink.sectionTitle4();
+            sink.rawText("Evidence Collected <a href=\"javascript:toggleElement(this, 'evidence" + cnt + "')\">[+]</a>");
+            sink.sectionTitle4_();
+            sink.rawText("<div id=\"evidence" + cnt + "\" style=\"display:none\">");
+            sink.table();
+            sink.tableRow();
+            writeTableHeaderCell(sink, "Source");
+            writeTableHeaderCell(sink, "Name");
+            writeTableHeaderCell(sink, "Value");
+            sink.tableRow_();
+            for (Evidence e : evidence) {
+                sink.tableRow();
+                writeTableCell(sink, e.getSource());
+                writeTableCell(sink, e.getName());
+                writeTableCell(sink, e.getValue());
+                sink.tableRow_();
+            }
+            sink.table_();
+            sink.rawText("</div>");
+        }
+        return cnt;
+    }
+
+    /**
+     * Writes the dependency header to the site report.
+     *
+     * @param d the dependency
+     * @param sink the sink to write the data to
+     */
+    private static void writeSiteReportDependencyHeader(Sink sink, Dependency d) {
+        sink.sectionTitle2();
+        sink.anchor("sha1" + d.getSha1sum());
+        sink.text(d.getFileName());
+        sink.anchor_();
+        sink.sectionTitle2_();
+        if (d.getDescription() != null && d.getDescription().length() > 0) {
+            sink.paragraph();
+            sink.bold();
+            sink.text("Description: ");
+            sink.bold_();
+            sink.text(d.getDescription());
+            sink.paragraph_();
+        }
+        if (d.getLicense() != null && d.getLicense().length() > 0) {
+            sink.paragraph();
+            sink.bold();
+            sink.text("License: ");
+            sink.bold_();
+            if (d.getLicense().startsWith("http://") && !d.getLicense().contains(" ")) {
+                sink.link(d.getLicense());
+                sink.text(d.getLicense());
+                sink.link_();
+            } else {
+                sink.text(d.getLicense());
+            }
+            sink.paragraph_();
+        }
+    }
+
+    /**
+     * Adds a list item to the site report.
+     *
+     * @param sink the sink to write the data to
+     * @param text the text to write
+     */
+    private static void writeListItem(Sink sink, String text) {
+        sink.listItem();
+        sink.text(text);
+        sink.listItem_();
+    }
+
+    /**
+     * Adds a table cell to the site report.
+     *
+     * @param sink the sink to write the data to
+     * @param text the text to write
+     */
+    private static void writeTableCell(Sink sink, String text) {
+        sink.tableCell();
+        sink.text(text);
+        sink.tableCell_();
+    }
+
+    /**
+     * Adds a table header cell to the site report.
+     *
+     * @param sink the sink to write the data to
+     * @param text the text to write
+     */
+    private static void writeTableHeaderCell(Sink sink, String text) {
+        sink.tableHeaderCell();
+        sink.text(text);
+        sink.tableHeaderCell_();
+    }
+
+    /**
+     * Writes the TOC for the site report.
+     *
+     * @param sink the sink to write the data to
+     * @param dependencies the dependencies that are being reported on
+     */
+    private static void writeSiteReportTOC(Sink sink, final List<Dependency> dependencies) {
+        sink.list();
+        for (Dependency d : dependencies) {
+            sink.listItem();
+            sink.link("#sha1" + d.getSha1sum());
+            sink.text(d.getFileName());
+            sink.link_();
+            if (!d.getVulnerabilities().isEmpty()) {
+                sink.rawText(" <font style=\"color:red\">•</font>");
+            }
+            if (!d.getRelatedDependencies().isEmpty()) {
+                sink.list();
+                for (Dependency r : d.getRelatedDependencies()) {
+                    writeListItem(sink, r.getFileName());
+                }
+                sink.list_();
+            }
+            sink.listItem_();
+        }
+        sink.list_();
+    }
+
+    /**
+     * Writes the site report header.
+     *
+     * @param sink the sink to write the data to
+     * @param projectName the name of the project
+     */
+    private static void writeSiteReportHeader(Sink sink, String projectName) {
+        sink.head();
+        sink.title();
+        sink.text("Dependency-Check Report: " + projectName);
+        sink.title_();
+        sink.head_();
+        sink.body();
+        sink.rawText("<script type=\"text/javascript\">");
+        sink.rawText("function toggleElement(el, targetId) {");
+        sink.rawText("if (el.innerText == '[+]') {");
+        sink.rawText("    el.innerText = '[-]';");
+        sink.rawText("    document.getElementById(targetId).style.display='block';");
+        sink.rawText("} else {");
+        sink.rawText("    el.innerText = '[+]';");
+        sink.rawText("    document.getElementById(targetId).style.display='none';");
+        sink.rawText("}");
+
+        sink.rawText("}");
+        sink.rawText("</script>");
+        sink.section1();
+        sink.sectionTitle1();
+        sink.text("Project: " + projectName);
+        sink.sectionTitle1_();
+        sink.date();
+        final Date now = new Date();
+        sink.text(DateFormat.getDateTimeInstance().format(now));
+        sink.date_();
+        sink.section1_();
+    }
+    // </editor-fold>
+
+}

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

@@ -4,8 +4,8 @@ The following properties can be set on the dependency-check-maven plugin.
 
 Property             | Description                        | Default Value
 ---------------------|------------------------------------|------------------
+aggregate            | Sets whether report aggregation will be performed for multi-module site reports. This option only affects the report generation when configured within the reporting section. | false
 autoUpdate           | Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to false. | true
-externalReport       | When using as a Site plugin this parameter sets whether or not the external report format should be used. | false
 outputDirectory      | The location to write the report(s). Note, this is not used if generating the report as part of a `mvn site` build | 'target'
 failBuildOnCVSS      | Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11 which means since the CVSS scores are 0-10, by default the build will never fail.         | 11
 format               | 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
@@ -23,49 +23,44 @@ Note, that specific analyzers will automatically disable themselves if no file
 types that they support are detected - so specifically disabling them may not
 be needed.
 
-Property                | Description                        | Default Value
-------------------------|------------------------------------|------------------
-archiveAnalyzerEnabled  | Sets whether the Archive Analyzer will be used.                    | true
+Property                | Description                                                               | Default Value
+------------------------|---------------------------------------------------------------------------|------------------
+archiveAnalyzerEnabled  | Sets whether the Archive Analyzer will be used.                           | true
 zipExtensions           | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. |  
-jarAnalyzer             | Sets whether Jar Analyzer will be used.                            | true
-nexusAnalyzerEnabled    | Sets whether Nexus Analyzer will be used.                          | true
-nexusUrl                | Defines the Nexus URL. | https://repository.sonatype.org/service/local/
+jarAnalyzer             | Sets whether Jar Analyzer will be used.                                   | true
+nexusAnalyzerEnabled    | Sets whether Nexus Analyzer will be used.                                 | true
+nexusUrl                | Defines the Nexus Pro Server URL. If not set the Nexus Analyzer will be disabled. |  
 nexusUsesProxy          | Whether or not the defined proxy should be used when connecting to Nexus. | true
-nuspecAnalyzerEnabled  | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.   | true
-assemblyAnalyzerEnabled | Sets whether or not the .NET Assembly Analyzer should be used.     | true
-pathToMono              | The path to Mono for .NET assembly analysis on non-windows systems |  
+nuspecAnalyzerEnabled   | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.          | true
+assemblyAnalyzerEnabled | Sets whether or not the .NET Assembly Analyzer should be used.            | true
+pathToMono              | The path to Mono for .NET assembly analysis on non-windows systems.       |  
 
 Advanced Configuration
 ====================
 The following properties can be configured in the plugin. However, they are less frequently changed. One exception
 may be the cvedUrl properties, which can be used to host a mirror of the NVD within an enterprise environment.
 
-Property             | Description                                                             | Default Value
----------------------|-------------------------------------------------------------------------|------------------
-cveUrl12Modified     | URL for the modified CVE 1.2                                            | http://nvd.nist.gov/download/nvdcve-modified.xml
-cveUrl20Modified     | URL for the modified CVE 2.0                                            | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
-cveUrl12Base         | Base URL for each year's CVE 1.2, the %d will be replaced with the year | http://nvd.nist.gov/download/nvdcve-%d.xml
-cveUrl20Base         | Base URL for each year's CVE 2.0, the %d will be replaced with the year | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
-connectionTimeout    | The URL Connection Timeout.                                                                 |  
-dataDirectory        | Data directory to hold SQL CVEs contents. This should generally not be changed.             |  
+Property             | Description                                                              | Default Value
+---------------------|--------------------------------------------------------------------------|------------------
+cveUrl12Modified     | URL for the modified CVE 1.2.                                            | http://nvd.nist.gov/download/nvdcve-modified.xml
+cveUrl20Modified     | URL for the modified CVE 2.0.                                            | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+cveUrl12Base         | Base URL for each year's CVE 1.2, the %d will be replaced with the year. | http://nvd.nist.gov/download/nvdcve-%d.xml
+cveUrl20Base         | Base URL for each year's CVE 2.0, the %d will be replaced with the year. | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+connectionTimeout    | Sets the URL Connection Timeout used when downloading external data.     |  
+dataDirectory        | Sets the data directory to hold SQL CVEs contents. This should generally not be changed.    |  
 databaseDriverName   | The name of the database driver. Example: org.h2.Driver.                                    |  
 databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path. |  
 connectionString     | The connection string used to connect to the database.                                      |  
 databaseUser         | The username used when connecting to the database.                                          |  
 databasePassword     | The password used when connecting to the database.                                          |  
+metaFileName         | Sets the name of the file to use for storing the metadata about the project.                | dependency-check.ser
 
-
-Deprecated Configuration
+Proxy Configuration
 ====================
-The following properties have been deprecated. These can still be set in
-the dependency-check-maven plugin's configuration. However, future versions
-will remove these properties. Instead using these properties you should
-use [Maven's settings](https://maven.apache.org/settings.html#Proxies) to
-configure a proxy.
+Use [Maven's settings](https://maven.apache.org/settings.html#Proxies) to configure a proxy server. If multiple proxies
+are configured in the Maven settings file you must tell dependency-check which proxy to use with the following property:
+
+Property             | Description                                                                          | Default Value
+---------------------|--------------------------------------------------------------------------------------|------------------
+mavenSettingsProxyId | The id for the proxy, configured via settings.xml, that dependency-check should use. |  
 
-Property             | Description                        | Default Value
----------------------|------------------------------------|------------------
-proxyUrl             | The Proxy URL.                     |  
-proxyPort            | The Proxy Port.                    |  
-proxyUsername        | Defines the proxy user name.       |  
-proxyPassword        | Defines the proxy password.        |