version 1.2.4

Former-commit-id: 4de7e508eb1885bb72e866960fa5402f72bf8e49

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

@@ -21,16 +21,14 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.4</version>
     </parent>
 
     <artifactId>dependency-check-ant</artifactId>
-    <version>1.2.0.1</version>
-
     <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>
@@ -326,6 +324,9 @@ 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>
@@ -441,6 +442,11 @@ 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.        |  

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

@@ -21,14 +21,14 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.2.0</version>
+        <version>1.2.4</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 +174,9 @@ 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>
@@ -341,5 +344,10 @@ 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/java/org/owasp/dependencycheck/App.java

@@ -62,7 +62,7 @@ public class App {
             final App app = new App();
             app.run(args);
         } finally {
-            Settings.cleanup();
+            Settings.cleanup(true);
         }
     }
 
@@ -161,7 +161,7 @@ public class App {
 
         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();
@@ -212,8 +212,8 @@ 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/cli/CliParser.java

@@ -19,6 +19,7 @@ package org.owasp.dependencycheck.cli;
 
 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) {
@@ -150,7 +155,7 @@ public final class CliParser {
         final Options options = new Options();
         addStandardOptions(options);
         addAdvancedOptions(options);
-
+        addDeprecatedOptions(options);
         return options;
     }
 
@@ -162,44 +167,44 @@ 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)
+        final Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ARGUMENT.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);
+                .create(ARGUMENT.SCAN_SHORT);
 
-        final Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP)
+        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)
+        final Option out = OptionBuilder.withArgName("folder").hasArg().withLongOpt(ARGUMENT.OUT)
                 .withDescription("The folder to write reports to. This defaults to the current directory.")
-                .create(ArgumentName.OUT_SHORT);
+                .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();
 
@@ -230,87 +235,87 @@ 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)
+        final Option nexusUrl = OptionBuilder.withArgName("url").hasArg().withLongOpt(ARGUMENT.NEXUS_URL)
                 .withDescription("The url to the Nexus Server.")
                 .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 +336,30 @@ 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 +368,7 @@ 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 +377,7 @@ 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 +386,7 @@ 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 +395,7 @@ 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 +404,7 @@ 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 +413,7 @@ 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 +422,7 @@ 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 +431,10 @@ 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 +447,14 @@ 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 +465,7 @@ 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"
@@ -466,7 +488,7 @@ 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);
     }
 
     /**
@@ -475,7 +497,7 @@ 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 +506,7 @@ 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 +515,7 @@ 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 +524,7 @@ 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 +533,24 @@ 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 +559,7 @@ 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 +568,7 @@ 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 +577,7 @@ 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 +586,7 @@ 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 +595,7 @@ 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 +608,7 @@ 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 +617,7 @@ 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 +640,7 @@ 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 +649,7 @@ 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 +658,7 @@ 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 +667,7 @@ 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 +676,7 @@ 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 +685,7 @@ 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 +694,13 @@ 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 +762,20 @@ 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.

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

@@ -3,7 +3,7 @@ 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
@@ -18,7 +18,7 @@ Short  | Argument Name         | Parameter       | Description | Requirement
 
 Advanced Options
 ================
-Short  | Argument Name         | Parameter       | Description | Default Value
+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;
@@ -30,7 +30,7 @@ Short  | Argument Name         | Parameter       | Description | Default Value
        | \-\-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;
+       | \-\-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;

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

@@ -44,7 +44,7 @@ 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>1.2.4</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>
@@ -399,6 +407,11 @@ 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>
@@ -419,7 +432,7 @@ 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>
@@ -521,6 +534,13 @@ 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>
@@ -662,11 +682,11 @@ 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 +709,34 @@ 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>
             </dependencies>
         </profile>
     </profiles>

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;
@@ -99,6 +102,11 @@ 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) {
@@ -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()) {
                 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>();
@@ -229,6 +237,40 @@ 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 +453,38 @@ 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 +114,30 @@ 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;
             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);
             }
             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 +164,6 @@ 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 +203,10 @@ 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) {
@@ -240,15 +243,16 @@ 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 +264,6 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                 }
             }
         }
-
         builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
     }
 
@@ -272,7 +275,7 @@ 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.
      *
@@ -524,7 +530,8 @@ public class CPEAnalyzer implements Analyzer {
                     }
                     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"));
+
+                        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 +556,7 @@ 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"));
+        final String url = null;
         if (bestGuessConf == null) {
             bestGuessConf = Confidence.LOW;
         }

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

@@ -88,6 +88,7 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
         removeBadMatches(dependency);
         removeWrongVersionMatches(dependency);
         removeSpuriousCPE(dependency);
+        removeDuplicativeEntriesFromJar(dependency, engine);
         addFalseNegativeCPEs(dependency);
     }
 
@@ -160,11 +161,20 @@ 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 +191,11 @@ 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 +242,33 @@ 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 +279,7 @@ 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 +327,7 @@ 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 +343,92 @@ 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/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.");
@@ -321,7 +321,7 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
 
                     newDependency.setFileName(displayName);
                     newDependency.setFilePath(displayPath);
-                    addPomEvidence(newDependency, pom, pomProperties);
+                    setPomEvidence(newDependency, pom, pomProperties, null);
                     engine.getDependencies().add(newDependency);
                     Collections.sort(engine.getDependencies());
                 } else {
@@ -345,16 +345,25 @@ 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;
     }
@@ -558,10 +567,21 @@ 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);
+        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()) {
             if (groupid.startsWith("org.") || groupid.startsWith("com.")) {
                 groupid = groupid.substring(4);
@@ -571,8 +591,26 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             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);
@@ -582,13 +620,40 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
             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 +712,7 @@ 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 +721,7 @@ 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 +755,7 @@ 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 +829,7 @@ 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 +1177,7 @@ 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 +1204,6 @@ 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.dependency.Identifier;
 import org.owasp.dependencycheck.utils.Settings;
 
 /**
@@ -161,7 +162,18 @@ public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
                 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);
+                boolean found = false;
+                for (Identifier i : dependency.getIdentifiers()) {
+                    if ("maven".equals(i.getType()) && i.getValue().equals(ma.toString())) {
+                        found = true;
+                        i.setConfidence(Confidence.HIGHEST);
+                        i.setUrl(ma.getArtifactUrl());
+                        break;
+                    }
+                }
+                if (!found) {
+                    dependency.addIdentifier("maven", ma.toString(), ma.getArtifactUrl(), Confidence.HIGHEST);
+                }
             }
         } catch (IllegalArgumentException iae) {
             //dependency.addAnalysisException(new AnalysisException("Invalid SHA-1"));

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/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>
@@ -733,8 +736,10 @@ public class CveDB {
         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/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

@@ -37,12 +37,12 @@ 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 +54,7 @@ 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;
@@ -188,6 +188,10 @@ 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;
             }
@@ -203,7 +207,7 @@ 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;
     }

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

@@ -177,6 +177,33 @@ 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>
@@ -369,6 +396,15 @@ 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.
      *

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

@@ -220,22 +220,95 @@ 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

@@ -311,6 +311,26 @@ 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/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/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 +99,10 @@ 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;
         }
     }
 
@@ -123,6 +124,9 @@ 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/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 +234,37 @@ 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;
+    }
 
     /**
      * Processes a given dependency to determine if any CPE, CVE, CWE, or CVSS scores should be suppressed. If any
@@ -248,12 +279,27 @@ 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)) {
+                    if (identifierMatches("cpe", c, i)) {
                         dependency.addSuppressedIdentifier(i);
                         itr.remove();
                         break;
@@ -309,7 +355,7 @@ 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 +382,75 @@ 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/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/dependencycheck-base-suppression.xml

@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<suppressions xmlns="https://www.owasp.org/index.php/OWASP_Dependency_Check_Suppression">
+    <suppress>
+        <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>
+        <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>
+</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.

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"/>

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

@@ -84,13 +84,14 @@ 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 +428,24 @@ 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 +458,7 @@ 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 +488,7 @@ 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 +520,7 @@ 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>: $scanDate</li>
@@ -526,30 +533,103 @@ arising out of or in connection with the use of this tool, the analysis performe
                         <li class="scaninfo hidden"><i>$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 $dependencies)
+                <table class="lined">
+                    <tr style="text-align:left">
+                        <th title="The name of the dependency">Dependency</th>
+                        <th title="The number of related dependencies">#&nbsp;Related</th>
+                        <th title="The Common Platform Enumeration">CPE</th>
+                        <th title="The Maven GAV Coordinates">GAV</th>
+                        <th title="The highest CVE Impact">CVE&nbsp;Impact</th>
+                        <th title="The number of Common Vulnerability and Exposure (CVE) entries">CVE&nbsp;Count</th>
+                        <th title="The confidence rating dependency-check has for the identified CPE">CPE&nbsp;Confidence</th>
+                        <th title="The count of evidence used to identify the CPE">Evidence&nbsp;Count</th>
+                    </tr>
+                    #foreach($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>
+                        <td>$dependency.getRelatedDependencies().size()</td>
+                        #set($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($dependency.description)<br/></p>
@@ -571,7 +651,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                         <div id="content$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($evidence.getValue())</td></tr>
                                 #end
                             </table>
@@ -582,7 +662,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                             <div id="content$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($related.Sha1sum)</li>
@@ -612,7 +692,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                             #end
                         #end
                         <h4 id="header$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 +710,7 @@ 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 +726,7 @@ 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 +748,20 @@ 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="toggleDisplay(this,'.vs$vsctr'); return false;">show all</a>)<ul>
+                                    <li class="vs$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($vs.hasPreviousVersion()) and all previous versions#end</li>
+                                #end
+                                </ul></p>
                             #end
-                            </ul></p>
                         #end
                     </div>
                     #end
@@ -692,7 +779,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                     #foreach($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 +801,7 @@ 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($evidence.getValue())</td></tr>
                                         #end
                                     </table>
@@ -725,7 +812,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                                     <div id="content$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($related.Sha1sum)</li>
@@ -744,7 +831,7 @@ arising out of or in connection with the use of this tool, the analysis performe
                                     #end
                                 #end
                                 <h4 id="header$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 +883,19 @@ 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="toggleDisplay(this,'.vs$vsctr'); return false;">show all</a>)<ul>
+                                            <li class="vs$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

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>

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/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/CPEAnalyzerIntegrationTest.java

@@ -115,16 +115,13 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
         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 +167,10 @@ 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);

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/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/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/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/suppression/SuppressionRuleTest.java

@@ -339,55 +339,70 @@ 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 +413,7 @@ 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();
@@ -455,9 +470,9 @@ public class SuppressionRuleTest {
         assertTrue(dependency.getIdentifiers().isEmpty());
         assertTrue(dependency.getSuppressedIdentifiers().size() == 1);
 
-        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");
+        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);
@@ -467,6 +482,43 @@ public class SuppressionRuleTest {
         assertTrue(dependency.getSuppressedIdentifiers().size() == 3);
     }
 
+    /**
+     * 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() {
         Vulnerability v = new Vulnerability();
         v.setCwe("CWE-287 Improper Authentication");

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.

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>1.2.4</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>1.2.4</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/DependencyCheckMojo.java

@@ -147,15 +147,6 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
     @Parameter(property = "externalReport", defaultValue = "false", required = true)
     private boolean externalReport = false;
-    /**
-     * The Proxy URL.
-     *
-     * @deprecated Please use mavenSettings instead
-     */
-    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
-    @Parameter(property = "proxyUrl", defaultValue = "", required = false)
-    @Deprecated
-    private String proxyUrl = null;
 
     /**
      * The maven settings.
@@ -171,33 +162,6 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     @Parameter(property = "mavenSettingsProxyId", required = false)
     private String mavenSettingsProxyId;
 
-    /**
-     * The Proxy Port.
-     *
-     * @deprecated Please use mavenSettings instead
-     */
-    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
-    @Parameter(property = "proxyPort", defaultValue = "", required = false)
-    @Deprecated
-    private String proxyPort = null;
-    /**
-     * The Proxy username.
-     *
-     * @deprecated Please use mavenSettings instead
-     */
-    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
-    @Parameter(property = "proxyUsername", defaultValue = "", required = false)
-    @Deprecated
-    private String proxyUsername = null;
-    /**
-     * The Proxy password.
-     *
-     * @deprecated Please use mavenSettings instead
-     */
-    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
-    @Parameter(property = "proxyPassword", defaultValue = "", required = false)
-    @Deprecated
-    private String proxyPassword = null;
     /**
      * The Connection Timeout.
      */
@@ -348,6 +312,16 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     @Parameter(property = "pathToMono", defaultValue = "", required = false)
     private String pathToMono;
 
+    /**
+     * The Proxy URL.
+     *
+     * @deprecated Please use mavenSettings instead
+     */
+    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @Parameter(property = "proxyUrl", defaultValue = "", required = false)
+    @Deprecated
+    private String proxyUrl = null;
+
     // </editor-fold>
     /**
      * Executes the Dependency-Check on the dependent libraries.
@@ -613,7 +587,8 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
      */
     private int writeSiteReportDependencyEvidenceUsed(Dependency d, int collapsibleHeaderCount, Sink sink) {
         int cnt = collapsibleHeaderCount;
-        if (d.getEvidenceUsed() != null && d.getEvidenceUsed().size() > 0) {
+        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>");
@@ -625,7 +600,7 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
             writeTableHeaderCell(sink, "Name");
             writeTableHeaderCell(sink, "Value");
             sink.tableRow_();
-            for (Evidence e : d.getEvidenceUsed()) {
+            for (Evidence e : evidence) {
                 sink.tableRow();
                 writeTableCell(sink, e.getSource());
                 writeTableCell(sink, e.getName());
@@ -776,12 +751,12 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     // </editor-fold>
 
     /**
-     * Returns the maven settings proxy url.
+     * Returns the maven settings proxy server.
      *
      * @param proxy the maven proxy
      * @return the proxy url
      */
-    private String getMavenSettingsProxyUrl(Proxy proxy) {
+    private String getMavenSettingsProxyServer(Proxy proxy) {
         return new StringBuilder(proxy.getProtocol()).append("://").append(proxy.getHost()).toString();
     }
 
@@ -835,9 +810,13 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
 
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
 
+        if (proxyUrl != null && !proxyUrl.isEmpty()) {
+            logger.warning("Deprecated configuration detected, proxyUrl will be ignored; use the maven settings to configure the proxy instead");
+        }
+
         final Proxy proxy = getMavenProxy();
         if (proxy != null) {
-            Settings.setString(Settings.KEYS.PROXY_URL, getMavenSettingsProxyUrl(proxy));
+            Settings.setString(Settings.KEYS.PROXY_SERVER, getMavenSettingsProxyServer(proxy));
             Settings.setString(Settings.KEYS.PROXY_PORT, Integer.toString(proxy.getPort()));
             final String userName = proxy.getUsername();
             final String password = proxy.getPassword();
@@ -847,18 +826,6 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
             }
         }
 
-        if (proxyUrl != null && !proxyUrl.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
-        }
-        if (proxyPort != null && !proxyPort.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);
-        }
-        if (proxyUsername != null && !proxyUsername.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_USERNAME, proxyUsername);
-        }
-        if (proxyPassword != null && !proxyPassword.isEmpty()) {
-            Settings.setString(Settings.KEYS.PROXY_PASSWORD, proxyPassword);
-        }
         if (connectionTimeout != null && !connectionTimeout.isEmpty()) {
             Settings.setString(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
         }
@@ -952,7 +919,7 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
                     "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();
             }
@@ -993,7 +960,7 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
                     "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-maven/src/site/markdown/configuration.md

@@ -55,17 +55,6 @@ databaseUser         | The username used when connecting to the database.
 databasePassword     | The password used when connecting to the database.                                          |  
 
 
-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.
-
-Property             | Description                        | Default Value
----------------------|------------------------------------|------------------
-proxyUrl             | The Proxy URL.                     |  
-proxyPort            | The Proxy Port.                    |  
-proxyUsername        | Defines the proxy user name.       |  
-proxyPassword        | Defines the proxy password.        |  
+Use [Maven's settings](https://maven.apache.org/settings.html#Proxies) to configure a proxy server.

dependency-check-utils/pom.xml

@@ -0,0 +1,283 @@
+<!--
+This file is part of dependency-check-utils.
+
+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.
+-->
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <groupId>org.owasp</groupId>
+        <artifactId>dependency-check-parent</artifactId>
+        <version>1.2.4</version>
+    </parent>
+
+    <artifactId>dependency-check-utils</artifactId>
+    <name>Dependency-Check Utils</name>
+    <description>dependency-check-utils is a collection of common utlity classes used within dependency-check that might be useful in other projects.</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-utils</url>
+        </site>
+    </distributionManagement>
+    <!-- end copy -->
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>cobertura-maven-plugin</artifactId>
+                <version>2.6</version>
+                <configuration>
+                    <instrumentation>
+                        <ignoreTrivial>true</ignoreTrivial>
+                    </instrumentation>
+                    <check>
+                        <branchRate>85</branchRate>
+                        <lineRate>85</lineRate>
+                        <haltOnFailure>false</haltOnFailure>
+                        <totalBranchRate>85</totalBranchRate>
+                        <totalLineRate>85</totalLineRate>
+                        <packageLineRate>85</packageLineRate>
+                        <packageBranchRate>85</packageBranchRate>
+                        <regexes>
+                            <regex>
+                                <pattern>.*\$.*</pattern>
+                                <branchRate>0</branchRate>
+                                <lineRate>0</lineRate>
+                            </regex>
+                        </regexes>
+                    </check>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>clean</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.16</version>
+                <configuration>
+                    <systemProperties>
+                        <property>
+                            <name>temp.directory</name>
+                            <value>${project.build.directory}/temp</value>
+                        </property>
+                    </systemProperties>
+                    <excludes>
+                        <exclude>**/*IntegrationTest.java</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <version>2.16</version>
+                <configuration>
+                    <systemProperties>
+                        <property>
+                            <name>temp.directory</name>
+                            <value>${project.build.directory}/temp</value>
+                        </property>
+                    </systemProperties>
+                    <includes>
+                        <include>**/*IntegrationTest.java</include>
+                    </includes>
+                </configuration>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>integration-test</goal>
+                            <goal>verify</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.1</version>
+                <configuration>
+                    <showDeprecation>false</showDeprecation>
+                    <source>1.6</source>
+                    <target>1.6</target>
+                </configuration>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-site-plugin</artifactId>
+                <version>3.3</version>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.apache.maven.doxia</groupId>
+                        <artifactId>doxia-module-markdown</artifactId>
+                        <version>1.5</version>
+                    </dependency>
+                </dependencies>
+                <configuration>
+                    <skipDeploy>true</skipDeploy>
+                    <reportPlugins>
+                        <plugin>
+                            <groupId>org.apache.maven.plugins</groupId>
+                            <artifactId>maven-project-info-reports-plugin</artifactId>
+                            <version>2.7</version>
+                            <reportSets>
+                                <reportSet>
+                                    <reports>
+                                        <report>index</report>
+                                        <report>summary</report>
+                                        <report>license</report>
+                                        <report>help</report>
+                                    </reports>
+                                </reportSet>
+                            </reportSets>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.apache.maven.plugins</groupId>
+                            <artifactId>maven-javadoc-plugin</artifactId>
+                            <version>2.9.1</version>
+                            <configuration>
+                                <bottom>Copyright© 2012-14 Jeremy Long. All Rights Reserved.</bottom>
+                            </configuration>
+                            <reportSets>
+                                <reportSet>
+                                    <id>default</id>
+                                    <reports>
+                                        <report>javadoc</report>
+                                    </reports>
+                                </reportSet>
+                            </reportSets>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.codehaus.mojo</groupId>
+                            <artifactId>versions-maven-plugin</artifactId>
+                            <version>2.1</version>
+                            <reportSets>
+                                <reportSet>
+                                    <reports>
+                                        <report>dependency-updates-report</report>
+                                        <report>plugin-updates-report</report>
+                                    </reports>
+                                </reportSet>
+                            </reportSets>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.apache.maven.plugins</groupId>
+                            <artifactId>maven-jxr-plugin</artifactId>
+                            <version>2.4</version>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.codehaus.mojo</groupId>
+                            <artifactId>cobertura-maven-plugin</artifactId>
+                            <version>2.6</version>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.apache.maven.plugins</groupId>
+                            <artifactId>maven-surefire-report-plugin</artifactId>
+                            <version>2.16</version>
+                            <reportSets>
+                                <reportSet>
+                                    <reports>
+                                        <report>report-only</report>
+                                    </reports>
+                                </reportSet>
+                            </reportSets>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.codehaus.mojo</groupId>
+                            <artifactId>taglist-maven-plugin</artifactId>
+                            <version>2.4</version>
+                            <configuration>
+                                <tagListOptions>
+                                    <tagClasses>
+                                        <tagClass>
+                                            <displayName>Todo Work</displayName>
+                                            <tags>
+                                                <tag>
+                                                    <matchString>todo</matchString>
+                                                    <matchType>ignoreCase</matchType>
+                                                </tag>
+                                                <tag>
+                                                    <matchString>FIXME</matchString>
+                                                    <matchType>exact</matchType>
+                                                </tag>
+                                            </tags>
+                                        </tagClass>
+                                    </tagClasses>
+                                </tagListOptions>
+                            </configuration>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.apache.maven.plugins</groupId>
+                            <artifactId>maven-checkstyle-plugin</artifactId>
+                            <version>2.11</version>
+                            <configuration>
+                                <enableRulesSummary>false</enableRulesSummary>
+                                <configLocation>${basedir}/../src/main/config/checkstyle-checks.xml</configLocation>
+                                <headerLocation>${basedir}/../src/main/config/checkstyle-header.txt</headerLocation>
+                                <suppressionsLocation>${basedir}/../src/main/config/checkstyle-suppressions.xml</suppressionsLocation>
+                                <suppressionsFileExpression>checkstyle.suppressions.file</suppressionsFileExpression>
+                            </configuration>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.apache.maven.plugins</groupId>
+                            <artifactId>maven-pmd-plugin</artifactId>
+                            <version>3.0.1</version>
+                            <configuration>
+                                <targetJdk>1.6</targetJdk>
+                                <linkXref>true</linkXref>
+                                <sourceEncoding>utf-8</sourceEncoding>
+                                <rulesets>
+                                    <ruleset>../src/main/config/dcrules.xml</ruleset>
+                                    <ruleset>/rulesets/java/basic.xml</ruleset>
+                                    <ruleset>/rulesets/java/imports.xml</ruleset>
+                                    <ruleset>/rulesets/java/unusedcode.xml</ruleset>
+                                </rulesets>
+                            </configuration>
+                        </plugin>
+                        <plugin>
+                            <groupId>org.codehaus.mojo</groupId>
+                            <artifactId>findbugs-maven-plugin</artifactId>
+                            <version>2.5.3</version>
+                        </plugin>
+                    </reportPlugins>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+    <dependencies>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.4</version>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.11</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+</project>

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

@@ -1,9 +1,27 @@
+/*
+ * 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.utils;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStream;
+import java.nio.MappedByteBuffer;
+import java.nio.channels.FileChannel;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.logging.Level;
@@ -12,19 +30,16 @@ import java.util.logging.Logger;
 /**
  * Includes methods to generate the MD5 and SHA1 checksum.
  *
- * This code was copied from Real's How To. It has been slightly modified.
- *
- * Written and compiled by Réal Gagnon ©1998-2012
- *
- * @author Real's How To: http://www.rgagnon.com/javadetails/java-0416.html
+ * @author Jeremy Long <jeremy.long@owasp.org>
  *
  */
 public final class Checksum {
-    
+
     /**
      * The logger.
      */
     private static final Logger LOGGER = Logger.getLogger(Checksum.class.getName());
+
     /**
      * Private constructor for a utility class.
      */
@@ -32,30 +47,29 @@ public final class Checksum {
     }
 
     /**
-     * <p>Creates the cryptographic checksum of a given file using the specified
-     * algorithm.</p> <p>This algorithm was copied and heavily modified from
-     * Real's How To: http://www.rgagnon.com/javadetails/java-0416.html</p>
+     * <p>
+     * Creates the cryptographic checksum of a given file using the specified algorithm.</p>
      *
      * @param algorithm the algorithm to use to calculate the checksum
      * @param file the file to calculate the checksum for
      * @return the checksum
      * @throws IOException when the file does not exist
-     * @throws NoSuchAlgorithmException when an algorithm is specified that does
-     * not exist
+     * @throws NoSuchAlgorithmException when an algorithm is specified that does not exist
      */
+    @SuppressWarnings("empty-statement")
     public static byte[] getChecksum(String algorithm, File file) throws NoSuchAlgorithmException, IOException {
-        InputStream fis = null;
-        byte[] buffer = new byte[1024];
-        MessageDigest complete = MessageDigest.getInstance(algorithm);
-        int numRead;
+        MessageDigest digest = MessageDigest.getInstance(algorithm);
+        FileInputStream fis = null;
         try {
             fis = new FileInputStream(file);
-            do {
-                numRead = fis.read(buffer);
-                if (numRead > 0) {
-                    complete.update(buffer, 0, numRead);
-                }
-            } while (numRead != -1);
+            FileChannel ch = fis.getChannel();
+            MappedByteBuffer byteBuffer = ch.map(FileChannel.MapMode.READ_ONLY, 0, file.length());
+            digest.update(byteBuffer);
+//            BufferedInputStream bis = new BufferedInputStream(fis);
+//            DigestInputStream dis = new DigestInputStream(bis, digest);
+//            //yes, we are reading in a buffer for performance reasons - 1 byte at a time is SLOW
+//            byte[] buffer = new byte[8192];
+//            while (dis.read(buffer) != -1);
         } finally {
             if (fis != null) {
                 try {
@@ -65,7 +79,7 @@ public final class Checksum {
                 }
             }
         }
-        return complete.digest();
+        return digest.digest();
     }
 
     /**
@@ -93,12 +107,17 @@ public final class Checksum {
         byte[] b = getChecksum("SHA1", file);
         return getHex(b);
     }
+    /**
+     * Hex code characters used in getHex.
+     */
     private static final String HEXES = "0123456789ABCDEF";
 
     /**
-     * <p>Converts a byte array into a hex string.</p>
+     * <p>
+     * Converts a byte array into a hex string.</p>
      *
-     * <p>This method was copied from <a
+     * <p>
+     * This method was copied from <a
      * href="http://www.rgagnon.com/javadetails/java-0596.html">http://www.rgagnon.com/javadetails/java-0596.html</a></p>
      *
      * @param raw a byte array
@@ -110,7 +129,7 @@ public final class Checksum {
         }
         final StringBuilder hex = new StringBuilder(2 * raw.length);
         for (final byte b : raw) {
-            hex.append(HEXES.charAt((b & 0xF0) >> 4)).append(HEXES.charAt((b & 0x0F)));
+            hex.append(HEXES.charAt((b & 0xF0) >> 4)).append(HEXES.charAt(b & 0x0F));
         }
         return hex.toString();
     }

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

@@ -166,7 +166,7 @@ public final class Downloader {
             try {
                 lastModifiedFile = new File(url.toURI());
             } catch (URISyntaxException ex) {
-                final String msg = String.format("Unable to locate '%s'; is the cve.url-2.0.modified property set correctly?", url.toString());
+                final String msg = String.format("Unable to locate '%s'", url.toString());
                 throw new DownloadFailedException(msg);
             }
             timestamp = lastModifiedFile.lastModified();
@@ -176,7 +176,12 @@ public final class Downloader {
                 conn = URLConnectionFactory.createHttpURLConnection(url);
                 conn.setRequestMethod("HEAD");
                 conn.connect();
-                timestamp = conn.getLastModified();
+                final int t = conn.getResponseCode();
+                if (t >= 200 && t < 300) {
+                    timestamp = conn.getLastModified();
+                } else {
+                    throw new DownloadFailedException("HEAD request returned a non-200 status code");
+                }
             } catch (URLConnectionFailureException ex) {
                 throw new DownloadFailedException("Error creating URL Connection for HTTP HEAD request.", ex);
             } catch (IOException ex) {

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

@@ -17,21 +17,13 @@
  */
 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.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
 import java.util.UUID;
 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;
 
 /**
  * A collection of utilities for processing information about files.
@@ -54,11 +46,6 @@ public final class FileUtils {
      */
     private static final String BIT_BUCKET_WIN = "NUL";
 
-    /**
-     * The buffer size to use when extracting files from the archive.
-     */
-    private static final int BUFFER_SIZE = 4096;
-
     /**
      * Private constructor for a utility class.
      */
@@ -155,99 +142,6 @@ public final class FileUtils {
         return jarPath.getParentFile();
     }
 
-    /**
-     * 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);
-            }
-        }
-    }
-
     /**
      * Return the bit bucket for the OS. '/dev/null' for Unix and 'NUL' for Windows
      *

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

@@ -53,20 +53,24 @@ public final class LogUtils {
         try {
             LogManager.getLogManager().reset();
             LogManager.getLogManager().readConfiguration(in);
+
             if (verboseLogFile != null && !verboseLogFile.isEmpty()) {
                 verboseLoggingEnabled = true;
                 final Logger logger = Logger.getLogger("");
-                final FileHandler handler = new FileHandler(verboseLogFile, true);
-                handler.setFormatter(new SimpleFormatter());
-                handler.setLevel(Level.FINE);
-                handler.setFilter(new LogFilter());
-                logger.addHandler(handler);
+                final FileHandler fileHandler = new FileHandler(verboseLogFile, true);
+                fileHandler.setFormatter(new SimpleFormatter());
+                fileHandler.setLevel(Level.FINE);
+                fileHandler.setFilter(new LogFilter());
+
+                logger.addHandler(fileHandler);
                 logger.setLevel(Level.FINE);
             }
         } catch (IOException ex) {
-            LOGGER.log(Level.FINE, "IO Error preparing the logger", ex);
+            LOGGER.log(Level.WARNING, "IO Error preparing the logger", ex);
         } catch (SecurityException ex) {
-            LOGGER.log(Level.FINE, "Error preparing the logger", ex);
+            LOGGER.log(Level.WARNING, "Error preparing the logger", ex);
+        } catch (Throwable ex) {
+            LOGGER.log(Level.WARNING, "Error preparing the logger", ex);
         } finally {
             if (in != null) {
                 try {

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

@@ -78,6 +78,14 @@ public final class Settings {
          * The base path to use for the data directory (for embedded db).
          */
         public static final String DATA_DIRECTORY = "data.directory";
+        /**
+         * The database file name.
+         */
+        public static final String DB_FILE_NAME = "data.file_name";
+        /**
+         * The database schema version.
+         */
+        public static final String DB_VERSION = "data.version";
         /**
          * The properties key for the URL to retrieve the "meta" data from about the CVE entries.
          */
@@ -97,7 +105,7 @@ public final class Settings {
          */
         public static final String CVE_MODIFIED_VALID_FOR_DAYS = "cve.url.modified.validfordays";
         /**
-         * The properties key for the telling us how many cvr.url.* URLs exists. This is used in combination with
+         * The properties key for the telling us how many cve.url.* URLs exists. This is used in combination with
          * CVE_BASE_URL to be able to retrieve the URLs for all of the files that make up the NVD CVE listing.
          */
         public static final String CVE_START_YEAR = "cve.startyear";
@@ -110,9 +118,16 @@ public final class Settings {
          */
         public static final String CVE_SCHEMA_2_0 = "cve.url-2.0.base";
         /**
-         * The properties key for the proxy url.
+         * The properties key for the proxy server.
+         *
+         * @deprecated use {@link org.owasp.dependencycheck.utils.Settings.KEYS#PROXY_SERVER} instead.
          */
-        public static final String PROXY_URL = "proxy.url";
+        @Deprecated
+        public static final String PROXY_URL = "proxy.server";
+        /**
+         * The properties key for the proxy server.
+         */
+        public static final String PROXY_SERVER = "proxy.server";
         /**
          * The properties key for the proxy port - this must be an integer value.
          */
@@ -193,6 +208,28 @@ public final class Settings {
          * The properties key for whether Provided Scope dependencies should be skipped.
          */
         public static final String SKIP_PROVIDED_SCOPE = "skip.provided.scope";
+
+        /**
+         * The key to obtain the path to the VFEED data file.
+         */
+        public static final String VFEED_DATA_FILE = "vfeed.data_file";
+        /**
+         * The key to obtain the VFEED connection string.
+         */
+        public static final String VFEED_CONNECTION_STRING = "vfeed.connection_string";
+
+        /**
+         * The key to obtain the base download URL for the VFeed data file.
+         */
+        public static final String VFEED_DOWNLOAD_URL = "vfeed.download_url";
+        /**
+         * The key to obtain the download file name for the VFeed data.
+         */
+        public static final String VFEED_DOWNLOAD_FILE = "vfeed.download_file";
+        /**
+         * The key to obtain the VFeed update status.
+         */
+        public static final String VFEED_UPDATE_STATUS = "vfeed.update_status";
     }
     //</editor-fold>
 
@@ -215,12 +252,14 @@ public final class Settings {
 
     /**
      * Private constructor for the Settings class. This class loads the properties files.
+     *
+     * @param propertiesFilePath the path to the base properties file to load
      */
-    private Settings() {
+    private Settings(String propertiesFilePath) {
         InputStream in = null;
         props = new Properties();
         try {
-            in = this.getClass().getClassLoader().getResourceAsStream(PROPERTIES_FILE);
+            in = this.getClass().getClassLoader().getResourceAsStream(propertiesFilePath);
             props.load(in);
         } catch (IOException ex) {
             LOGGER.log(Level.SEVERE, "Unable to load default settings.");
@@ -242,14 +281,34 @@ public final class Settings {
      * However, you must also call Settings.cleanup() to properly release resources.
      */
     public static void initialize() {
-        localSettings.set(new Settings());
+        localSettings.set(new Settings(PROPERTIES_FILE));
+    }
+
+    /**
+     * Initializes the thread local settings object. Note, to use the settings object you must call this method.
+     * However, you must also call Settings.cleanup() to properly release resources.
+     *
+     * @param propertiesFilePath the path to the base properties file to load
+     */
+    public static void initialize(String propertiesFilePath) {
+        localSettings.set(new Settings(propertiesFilePath));
     }
 
     /**
      * Cleans up resources to prevent memory leaks.
+     *
      */
     public static void cleanup() {
-        if (tempDirectory != null && tempDirectory.exists()) {
+        cleanup(true);
+    }
+
+    /**
+     * Cleans up resources to prevent memory leaks.
+     *
+     * @param deleteTemporary flag indicating whether any temporary directories generated should be removed
+     */
+    public static void cleanup(boolean deleteTemporary) {
+        if (deleteTemporary && tempDirectory != null && tempDirectory.exists()) {
             FileUtils.delete(tempDirectory);
         }
         try {
@@ -353,8 +412,19 @@ public final class Settings {
      * @throws IOException is thrown when there is an exception loading/merging the properties
      */
     public static void mergeProperties(File filePath) throws FileNotFoundException, IOException {
-        final FileInputStream fis = new FileInputStream(filePath);
-        mergeProperties(fis);
+        FileInputStream fis = null;
+        try {
+            fis = new FileInputStream(filePath);
+            mergeProperties(fis);
+        } finally {
+            if (fis != null) {
+                try {
+                    fis.close();
+                } catch (IOException ex) {
+                    LOGGER.log(Level.FINEST, "close error", ex);
+                }
+            }
+        }
     }
 
     /**
@@ -367,8 +437,19 @@ public final class Settings {
      * @throws IOException is thrown when there is an exception loading/merging the properties
      */
     public static void mergeProperties(String filePath) throws FileNotFoundException, IOException {
-        final FileInputStream fis = new FileInputStream(filePath);
-        mergeProperties(fis);
+        FileInputStream fis = null;
+        try {
+            fis = new FileInputStream(filePath);
+            mergeProperties(fis);
+        } finally {
+            if (fis != null) {
+                try {
+                    fis.close();
+                } catch (IOException ex) {
+                    LOGGER.log(Level.FINEST, "close error", ex);
+                }
+            }
+        }
     }
 
     /**
@@ -412,7 +493,7 @@ public final class Settings {
      * @param key the key to lookup within the properties file
      * @return the property from the properties file converted to a File object
      */
-    public static File getDataFile(String key) {
+    protected static File getDataFile(String key) {
         final String file = getString(key);
         LOGGER.log(Level.FINE, String.format("Settings.getDataFile() - file: '%s'", file));
         if (file == null) {
@@ -612,4 +693,74 @@ public final class Settings {
         }
         return value;
     }
+
+    /**
+     * Returns a connection string from the configured properties. If the connection string contains a %s, this method
+     * will determine the 'data' directory and replace the %s with the path to the data directory. If the data directory
+     * does not exists it will be created.
+     *
+     * @param connectionStringKey the property file key for the connection string
+     * @param dbFileNameKey the settings key for the db filename
+     * @param dbVersionKey the settings key for the dbVersion
+     * @return the connection string
+     * @throws IOException thrown the data directory cannot be created
+     * @throws InvalidSettingException thrown if there is an invalid setting
+     */
+    public static String getConnectionString(String connectionStringKey, String dbFileNameKey, String dbVersionKey)
+            throws IOException, InvalidSettingException {
+        final String connStr = Settings.getString(connectionStringKey);
+        if (connStr == null) {
+            final String msg = String.format("Invalid properties file to get the connection string; '%s' must be defined.",
+                    connectionStringKey);
+            throw new InvalidSettingException(msg);
+        }
+        if (connStr.contains("%s")) {
+            final File directory = getDataDirectory();
+            String fileName = null;
+            if (dbFileNameKey != null) {
+                fileName = Settings.getString(dbFileNameKey);
+            }
+            if (fileName == null) {
+                final String msg = String.format("Invalid properties file to get a file based connection string; '%s' must be defined.",
+                        dbFileNameKey);
+                throw new InvalidSettingException(msg);
+            }
+            if (fileName.contains("%s")) {
+                String version = null;
+                if (dbVersionKey != null) {
+                    version = Settings.getString(dbVersionKey);
+                }
+                if (version == null) {
+                    final String msg = String.format("Invalid properties file to get a file based connection string; '%s' must be defined.",
+                            dbFileNameKey);
+                    throw new InvalidSettingException(msg);
+                }
+                fileName = String.format(fileName, version);
+            }
+            if (connStr.startsWith("jdbc:h2:file:") && fileName.endsWith(".h2.db")) {
+                fileName = fileName.substring(0, fileName.length() - 6);
+            }
+            // yes, for H2 this path won't actually exists - but this is sufficient to get the value needed
+            final File dbFile = new File(directory, fileName);
+            final String cString = String.format(connStr, dbFile.getCanonicalPath());
+            LOGGER.log(Level.FINE, String.format("Connection String: '%s'", cString));
+            return cString;
+        }
+        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() || path.mkdirs()) {
+            return path;
+        }
+        throw new IOException(String.format("Unable to create the data directory '%s'", path.getAbsolutePath()));
+    }
 }

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

@@ -50,8 +50,8 @@ public final class URLConnectionFactory {
      */
     public static HttpURLConnection createHttpURLConnection(URL url) throws URLConnectionFailureException {
         HttpURLConnection conn = null;
-        Proxy proxy = null;
-        final String proxyUrl = Settings.getString(Settings.KEYS.PROXY_URL);
+        Proxy proxy;
+        final String proxyUrl = Settings.getString(Settings.KEYS.PROXY_SERVER);
         try {
             if (proxyUrl != null) {
                 final int proxyPort = Settings.getInt(Settings.KEYS.PROXY_PORT);
@@ -96,7 +96,7 @@ public final class URLConnectionFactory {
      * Utility method to create an HttpURLConnection. The use of a proxy here is optional as there may be cases where a
      * proxy is configured but we don't want to use it (for example, if there's an internal repository configured)
      *
-     * @param url the url to connect to
+     * @param url the URL to connect to
      * @param proxy whether to use the proxy (if configured)
      * @return a newly constructed HttpURLConnection
      * @throws URLConnectionFailureException thrown if there is an exception

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

@@ -0,0 +1,11 @@
+/**
+ * <html>
+ * <head>
+ * <title>org.owasp.dependencycheck.utils</title>
+ * </head>
+ * <body>
+ * Includes various utility classes such as a Settings wrapper, utilities to make URL Connections, etc.
+ * </body>
+ * </html>
+ */
+package org.owasp.dependencycheck.utils;

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

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!--
+This file is part of dependency-check-ant.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+-->
+<project name="dependency-check-ant">
+    <bannerLeft>
+        <name>dependency-check-utils</name>
+    </bannerLeft>
+    <body>
+        <breadcrumbs>
+            <item name="dependency-check" href="../index.html"/>
+        </breadcrumbs>
+        <menu ref="Project Documentation" />
+        <menu ref="reports" />
+    </body>
+</project>

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

@@ -0,0 +1,36 @@
+/*
+ * 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.utils;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+
+/**
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public class BaseTest {
+
+    @BeforeClass
+    public static void setUpClass() throws Exception {
+        Settings.initialize();
+    }
+
+    @AfterClass
+    public static void tearDownClass() throws Exception {
+        Settings.cleanup(true);
+    }
+}

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

@@ -26,6 +26,8 @@ import org.junit.Assert;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.owasp.dependencycheck.utils.Checksum;
+import org.owasp.dependencycheck.utils.Checksum;
 
 /**
  *

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

@@ -21,7 +21,6 @@ import java.io.File;
 import java.net.URL;
 import static org.junit.Assert.assertTrue;
 import org.junit.Test;
-import org.owasp.dependencycheck.BaseTest;
 
 /**
  *
@@ -39,7 +38,7 @@ public class DownloaderIntegrationTest extends BaseTest {
 
 //        Settings.setString(Settings.KEYS.CONNECTION_TIMEOUT, "1000");
 //        Settings.setString(Settings.KEYS.PROXY_PORT, "8080");
-//        Settings.setString(Settings.KEYS.PROXY_URL, "127.0.0.1");
+//        Settings.setString(Settings.KEYS.PROXY_SERVER, "127.0.0.1");
         URL url = new URL(Settings.getString(Settings.KEYS.CVE_MODIFIED_20_URL));
         File outputPath = new File("target/downloaded_cve.xml");
         Downloader.fetchFile(url, outputPath);

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

@@ -19,12 +19,9 @@ package org.owasp.dependencycheck.utils;
 
 import java.io.File;
 import java.net.URL;
-import org.junit.After;
-import org.junit.AfterClass;
 import static org.junit.Assert.assertTrue;
-import org.junit.Before;
-import org.junit.BeforeClass;
 import org.junit.Test;
+import org.owasp.dependencycheck.utils.Downloader;
 
 /**
  *
@@ -32,25 +29,9 @@ import org.junit.Test;
  */
 public class DownloaderTest {
 
-    @BeforeClass
-    public static void setUpClass() throws Exception {
-    }
-
-    @AfterClass
-    public static void tearDownClass() throws Exception {
-    }
-
-    @Before
-    public void setUp() {
-    }
-
-    @After
-    public void tearDown() {
-    }
-
     @Test
     public void testGetLastModified_file() throws Exception {
-        File f = new File("target/test-classes/nvdcve-2.0-2012.xml");
+        File f = new File("target/test-classes/dependencycheck.properties");
         URL url = new URL("file:///" + f.getCanonicalPath());
         long timestamp = Downloader.getLastModified(url);
         assertTrue("timestamp equal to zero?", timestamp > 0);

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

@@ -23,7 +23,6 @@ import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 import org.junit.Test;
-import org.owasp.dependencycheck.BaseTest;
 
 /**
  *

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

@@ -22,7 +22,6 @@ import java.io.IOException;
 import java.net.URISyntaxException;
 import org.junit.Assert;
 import org.junit.Test;
-import org.owasp.dependencycheck.BaseTest;
 
 /**
  *
@@ -158,4 +157,35 @@ public class SettingsTest extends BaseTest {
         ret = Settings.getString(key, dfault);
         Assert.assertEquals(dfault, ret);
     }
+
+    /**
+     * Test of getConnectionString.
+     */
+    @Test
+    public void testGetConnectionString() throws Exception {
+        String value = Settings.getConnectionString(Settings.KEYS.DB_CONNECTION_STRING, Settings.KEYS.DB_FILE_NAME, Settings.KEYS.DB_VERSION);
+        Assert.assertNotNull(value);
+        String msg = null;
+        try {
+            value = Settings.getConnectionString(Settings.KEYS.DB_CONNECTION_STRING, Settings.KEYS.DB_FILE_NAME, null);
+        } catch (InvalidSettingException e) {
+            msg = e.getMessage();
+        }
+        Assert.assertNotNull(msg, msg);
+        try {
+            value = Settings.getConnectionString("invalidKey", null, null);
+        } catch (InvalidSettingException e) {
+            msg = e.getMessage();
+        }
+        Assert.assertNotNull(msg, msg);
+    }
+
+    /**
+     * Test of getTempDirectory.
+     */
+    @Test
+    public void testGetTempDirectory() throws Exception {
+        File tmp = Settings.getTempDirectory();
+        Assert.assertTrue(tmp.exists());
+    }
 }

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

@@ -0,0 +1,59 @@
+application.name=${pom.name}
+application.version=${pom.version}
+autoupdate=true
+max.download.threads=3
+
+#temp.directory defaults to System.getProperty("java.io.tmpdir")
+#temp.directory=[path to temp directory]
+
+# the path to the data directory; the [JAR] signifies to use the relative path
+# to the dependency-check-core JAR file. This path is only used to construct
+# the connection string for the H2 driver (or other drivers that require a file path
+# to be supplied. If you are using another database (MySQL, Oracle, etc.) this property
+# 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
+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.
+# As such, this unsecure username/password exist.
+data.user=dcuser
+data.password=DC-Pass1337!
+# The following are only used if the DB Driver is not JDBC4 compliant and/or the driver
+# is not in the current classpath. Setting these properties will add the give path(s) to
+# the class loader and then register the driver with the DriverManager. If the class is
+# not in the path you must specify both the driver name (aka the fully qualified driver name)
+# and the driver path. The driver path can be a semi-colon separated list of files/directories
+# to ensure any and all needed files can be added to the classpath to load the driver.
+# For non-JDBC4 drivers in the classpath only the driver_name needs to be set.
+# For MOST situations these properties likely do not need to be set.
+data.driver_name=org.h2.Driver
+data.driver_path=
+
+# the path to the cpe xml file
+cpe.url=http://static.nvd.nist.gov/feeds/xml/cpe/dictionary/official-cpe-dictionary_v2.2.xml.gz
+# the path to the cpe meta data file.
+cpe.meta.url=http://static.nvd.nist.gov/feeds/xml/cpe/dictionary/official-cpe-dictionary_v2.2.meta
+
+# the number of days that the modified nvd cve data holds data for. We don't need
+# to update the other files if we are within this timespan. Per NIST this file
+# holds 8 days of updates, we are using 7 just to be safe.
+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
+
+# the URL for searching Nexus for SHA-1 hashes and whether it's enabled
+analyzer.nexus.enabled=true
+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

dependency-check-utils/src/test/resources/test.properties

@@ -0,0 +1 @@
+proxy.port=80

pom.xml

@@ -1,3 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <!--
 This file is part of Dependency-Check.
 
@@ -14,13 +15,12 @@ See the License for the specific language governing permissions and
 limitations under the License.
 
 Copyright (c) 2012 - Jeremy Long
--->
-<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">
+--><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>
 
     <groupId>org.owasp</groupId>
     <artifactId>dependency-check-parent</artifactId>
-    <version>1.2.0</version>
+    <version>1.2.4</version>
     <packaging>pom</packaging>
 
     <modules>
@@ -29,10 +29,11 @@ Copyright (c) 2012 - Jeremy Long
         <module>dependency-check-ant</module>
         <module>dependency-check-maven</module>
         <module>dependency-check-jenkins</module>
+        <module>dependency-check-utils</module>
     </modules>
     <name>Dependency-Check</name>
     <url>https://github.com/jeremylong/DependencyCheck.git</url>
-    <description>dependency-check is a utility that identifies project dependencies and checks if there are any known, publicly disclosed, vulnerabilities. This tool can be part of the solution to the OWASP Top 10 2013: A9 - Using Components with Known Vulnerabilities.</description>
+    <description>dependency-check is a utility that identifies project dependencies and checks if there are any known, publicly disclosed vulnerabilities. This tool can be part of the solution to the OWASP Top 10 2013: A9 - Using Components with Known Vulnerabilities.</description>
     <inceptionYear>2012</inceptionYear>
 
     <organization>
@@ -140,14 +141,6 @@ Copyright (c) 2012 - Jeremy Long
                     <target>1.6</target>
                 </configuration>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-javadoc-plugin</artifactId>
-                <version>2.9.1</version>
-                <configuration>
-                    <bottom>Copyright© 2012-13 Jeremy Long. All Rights Reserved.</bottom>
-                </configuration>
-            </plugin>
             <!-- begin copy from http://minds.coremedia.com/2012/09/11/problem-solved-deploy-multi-module-maven-project-site-as-github-pages/ -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -244,4 +237,4 @@ Copyright (c) 2012 - Jeremy Long
             <type>jar</type>
         </dependency>
     </dependencies>
-</project>
+</project>

src/site/markdown/archive-analyzer.md

@@ -0,0 +1,16 @@
+Archive Analyzer
+==============
+
+Dependency-check includes an analyzer an archive analyzer that will attempt
+to extract files from the archive that are supported by the other file type
+analyzers.
+
+Files Types Scanned: ZIP, EAR, WAR, JAR, SAR, APK, NUPKG, TAR, GZ, TGZ
+
+Additional file extensions for ZIP archives can be added, see the configuration
+section in the Maven, Ant, or CLI interfaces for more information on configuration.
+
+Note, since this analyzer does examine the contents of a JAR file there are times
+that you may see additional entries in the report and/or warnings in the log file (if used)
+for DLL or EXE files contained within the JAR file. In almost all cases these can
+be ignored as it is fairly rare to have a .NET dll or exe within a JAR file.

src/site/markdown/assembly-analyzer.md

@@ -0,0 +1,10 @@
+Assembly Analyzer
+==============
+
+Dependency-check includes an analyzer that scans .NET dll and exe files and collect as
+much information it can about the files as it can. The information collected
+is internally referred to as evidence and is grouped into vendor, product, and version
+buckets. Other analyzers later use this evidence to identify any Common Platform
+Enumeration (CPE) identifiers that apply.
+
+Files Types Scanned: EXE, DLL

src/site/markdown/index.md

@@ -12,11 +12,10 @@ The gist of the paper is that we as a development community include third party
 libraries in our applications that contain well known published vulnerabilities
 \(such as those at the [National Vulnerability Database](http://web.nvd.nist.gov/view/vuln/search)\).
 
-Dependency-check scans directories and files and if it contains an Analyzer that
-can scan a particular file type then information from the file is collected. This
-information is then used to identify the [Common Platform Enumeration](http://nvd.nist.gov/cpe.cfm) \(CPE\). If a
-CPE is identified a listing of associated [Common Vulnerability and Exposure](http://cve.mitre.org/) \(CVE\)
-entries are listed in a report.
+More information about dependency-check can be found here:
+
+* [How does dependency-check work](./internals.html)
+* [How to read the report](./thereport.html)
 
 **IMPORTANT NOTE**: Dependency-check automatically updates itself using the NVD Data Feeds hosted by
 NIST. **The initial download of the data may take fifteen minutes

src/site/markdown/internals.md

@@ -0,0 +1,37 @@
+How does dependency-check work?
+===========
+Dependency-check works by collecting information about the files it scans (using Analyzers). The information collected
+is called Evidence; there are three types of evidence collected: vendor, product, and version. For instance, the
+JarAnalyzer will collect information from the Manifest, pom.xml, and the package names within the JAR files scanned and
+it has heuristics to place the information from the various sources into one or more buckets of evidence.
+
+Within the NVD CVE Data (schema can be found [here](http://nvd.nist.gov/schema/nvd-cve-feed_2.0.xsd)) each CVE Entry has
+a list of vulnerable software:
+
+```xml
+  <entry id="CVE-2012-5055">
+  ...
+    <vuln:vulnerable-software-list>
+      <vuln:product>cpe:/a:vmware:springsource_spring_security:3.1.2</vuln:product>
+      <vuln:product>cpe:/a:vmware:springsource_spring_security:2.0.4</vuln:product>
+      <vuln:product>cpe:/a:vmware:springsource_spring_security:3.0.1</vuln:product>
+```
+
+These CPE entries are read "cpe:/[Entry Type]:[Vendor]:[Product]:[Version]:[Revision]:...". The CPE data is collected
+and stored in a [Lucene Index](http://lucene.apache.org/). Dependency-check then use the Evidence collected and attempt
+to match an entry from the Lucene CPE Index. If found, the CPEAnalyzer will add an Identifier to the Dependency and
+subsequently to the report. Once a CPE has been identified the associated CVE entries are added to the report.
+
+One important point about the evidence is that it is rated using different confidence levels - low, medium, high, and
+highest. These confidence levels are applied to each item of evidence. When the CPE is determined it is given a confidence
+level that is equal to the lowest level confidence level of evidence used during identification. If only highest confidence
+evidence was used in determining the CPE then the CPE would have a highest confidence level.
+
+Because of the way dependency-check works both false positives and false negatives may exist. Please read
+[How to read the report](thereport.html) to get a better understanding of sorting through the false positives and false
+negatives.
+
+Dependency-check does not currently use file hashes for identification. If the dependency was built from source the hash
+likely will not match the "published" hash. While the evidence based mechanism currently used can also be unreliable the
+design decision was to avoid maintaining a hash database of known vulnerable libraries. A future enhancement may add some
+hash matching for very common well known libraries (Spring, Struts, etc.).

src/site/markdown/jar-analyzer.md

@@ -0,0 +1,11 @@
+Jar Analyzer
+==============
+
+Dependency-check includes an analyzer that scans JAR files and collect as
+much information it can about the file as it can. The information collected
+is internally referred to as evidence and is grouped into vendor, product, and version
+buckets. Other analyzers later use this evidence to identify any Common Platform
+Enumeration (CPE) identifiers that apply. Additionally, if a POM is present
+the analyzer will add the Maven group, artifact, and version (GAV).
+
+Files Types Scanned: JAR, WAR

src/site/markdown/nexus-analyzer.md

@@ -1,7 +1,7 @@
 Nexus Analyzer
 ==============
 
-Dependency Check includes an analyzer which will check for the Maven GAV
+Dependency-check includes an analyzer that will check for the Maven GAV
 (Group/Artifact/Version) information for artifacts in the scanned area. By
 default the information comes from [Maven Central][1], but can be configured to
 use a local repository if necessary. If the artifact's hash is found in the

src/site/markdown/nuspec-analyzer.md

@@ -0,0 +1,13 @@
+Nuspec Analyzer
+==============
+
+Dependency-check includes an analyzer that will scan NuGet's Nuspec file to
+collect information about the component being used. The evidence collected
+is used by other analyzers to determine if there are any known vulnerabilities
+associated with the component.
+
+Note, the Nuspec Analyzer does not scan dependencies defined. However, if
+the dependencies have been downloaded and may be included in the scan depending
+on configuration.
+
+Files Types Scanned: NUSPEC

src/site/markdown/suppression.md

@@ -64,6 +64,15 @@ HTML version of the report. The other common scenario would be to ignore all CVE
         ]]></notes>
         <cvssBelow>7</cvssBelow>
     </suppress>
+    <suppress>
+        <notes><![CDATA[
+        This suppresses false positives identified on spring security.
+        ]]></notes>
+        <gav regex="true">org\.springframework\.security:spring.*</gav>
+        <cpe>cpe:/a:vmware:springsource_spring_framework</cpe>
+        <cpe>cpe:/a:springsource:spring_framework</cpe>
+        <cpe>cpe:/a:mod_security:mod_security</cpe>
+    </suppress>
 </suppressions>
 ```
 

src/site/markdown/thereport.md

@@ -0,0 +1,26 @@
+How To Read The Report
+========
+There is a lot of information contained in the HTML version of the report. When analyzing the results, the first thing one should do is determine if the CPE looks
+appropriate. Due to the way dependency-check works (see above) the report may contain false positives; these false positives are primarily on the CPE values. If the CPE value
+is wrong, this is usually obvious and one should use the suppression feature in the report to generate a suppression XML file that can be used on future scans. In addition
+to just looking at the CPE values in comparison to the name of the dependency - one may also consider the confidence of the CPE (as discussed in [How does dependency-check
+work](./internals.html)). See the [Suppressing False Positives](./suppression.html) page for more information on how to generate and use the suppression file.
+
+Once you have weeded out any obvious false positives one can then look at the remaining entries and determine if any of the identified CVE entries are actually
+exploitable in your environment. Determining if a CVE is exploitable in your environment can be tricky - for this I do not currently have any tips other then
+upgrade the library if you can just to be safe. Note, some CVE entries can be fixed by either upgrading the library or changing configuration options.
+
+One item that dependency-check flags that many may think is a false positive are old database drivers. One thing to consider about an old database driver is that the
+CPE/CVEs identified are usually for the server rather then the driver. However, the presence of an old driver may indicate that you have an older version of the server
+running in your environment and that server may need to be patched or upgraded. However, in some cases the old database drivers are actually unused, transitive dependencies
+from other dependencies.
+
+Regarding False Negatives
+=======
+As stated above, due to the nature of dependency-check there may be publicly disclosed vulnerabilities in the project dependencies scanned by dependency-check that
+are not identified. With the current version of dependency-check the HTML report has a table at the top that initially displays just the dependencies with identified
+vulnerabilities. This can be toggled to show all dependencies. If you examine the rows that do not have identified CPE/CVE entries you will see an "evidence count".
+If the evidence count is extremely low (0-5 entries) then there may not have been enough information contained in the dependency to identify a CPE and associated CVEs.
+
+It should be noted that while the false positives described above are bad, more concerning is that there may be vulnerabilities within the project dependencies that
+have yet to be publicly known. If one has the resources consider performing security assessments on the project dependencies.