minor correction to unit tests

Former-commit-id: 44829f536b0940ed95750890262a1ab668c57745

.gitignore

@@ -15,4 +15,6 @@ dependency-reduced-pom.xml
 #ruby Gemfile, etc. This is a java project, Gemfile is here to check site problem with Jekyll
 Gemfile
 Gemfile.lock
-_site/**
+_site/**
+#unknown as to why these are showing up... but need to be ignored.
+.LCKpom.xml~

dependency-check-ant/pom.xml

@@ -21,7 +21,7 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.1.2</version>
+        <version>1.1.4</version>
     </parent>
 
     <artifactId>dependency-check-ant</artifactId>

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

@@ -457,6 +457,81 @@ public class DependencyCheckTask extends Task {
         this.showSummary = showSummary;
     }
 
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param jarAnalyzerEnabled the value of the new setting
+     */
+    public void setJarAnalyzerEnabled(boolean jarAnalyzerEnabled) {
+        this.jarAnalyzerEnabled = jarAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the Archive Analyzer is enabled.
+     */
+    private boolean archiveAnalyzerEnabled = true;
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public boolean isArchiveAnalyzerEnabled() {
+        return archiveAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the .NET Assembly Analyzer is enabled.
+     */
+    private boolean assemblyAnalyzerEnabled = true;
+
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param archiveAnalyzerEnabled the value of the new setting
+     */
+    public void setArchiveAnalyzerEnabled(boolean archiveAnalyzerEnabled) {
+        this.archiveAnalyzerEnabled = archiveAnalyzerEnabled;
+    }
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public boolean isAssemblyAnalyzerEnabled() {
+        return assemblyAnalyzerEnabled;
+    }
+
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param assemblyAnalyzerEnabled the value of the new setting
+     */
+    public void setAssemblyAnalyzerEnabled(boolean assemblyAnalyzerEnabled) {
+        this.assemblyAnalyzerEnabled = assemblyAnalyzerEnabled;
+    }
+    /**
+     * Whether or not the .NET Nuspec Analyzer is enabled.
+     */
+    private boolean nuspecAnalyzerEnabled = true;
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public boolean isNuspecAnalyzerEnabled() {
+        return nuspecAnalyzerEnabled;
+    }
+
+    /**
+     * Sets whether or not the analyzer is enabled.
+     *
+     * @param nuspecAnalyzerEnabled the value of the new setting
+     */
+    public void setNuspecAnalyzerEnabled(boolean nuspecAnalyzerEnabled) {
+        this.nuspecAnalyzerEnabled = nuspecAnalyzerEnabled;
+    }
+
     /**
      * Whether or not the nexus analyzer is enabled.
      */
@@ -753,6 +828,28 @@ public class DependencyCheckTask extends Task {
     public void setCveUrl20Base(String cveUrl20Base) {
         this.cveUrl20Base = cveUrl20Base;
     }
+    /**
+     * The path to Mono for .NET assembly analysis on non-windows systems.
+     */
+    private String pathToMono;
+
+    /**
+     * Get the value of pathToMono.
+     *
+     * @return the value of pathToMono
+     */
+    public String getPathToMono() {
+        return pathToMono;
+    }
+
+    /**
+     * Set the value of pathToMono.
+     *
+     * @param pathToMono new value of pathToMono
+     */
+    public void setPathToMono(String pathToMono) {
+        this.pathToMono = pathToMono;
+    }
 
     @Override
     public void execute() throws BuildException {
@@ -885,11 +982,29 @@ public class DependencyCheckTask extends Task {
         if (suppressionFile != null && !suppressionFile.isEmpty()) {
             Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
         }
+
+        //File Type Analyzer Settings
+        //JAR ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_JAR_ENABLED, jarAnalyzerEnabled);
+        //NUSPEC ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, nuspecAnalyzerEnabled);
+        //NEXUS ANALYZER
         Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
         if (nexusUrl != null && !nexusUrl.isEmpty()) {
             Settings.setString(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
         }
         Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY, nexusUsesProxy);
+        //ARCHIVE ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, archiveAnalyzerEnabled);
+        if (zipExtensions != null && !zipExtensions.isEmpty()) {
+            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
+        }
+        //ASSEMBLY ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, assemblyAnalyzerEnabled);
+        if (pathToMono != null && !pathToMono.isEmpty()) {
+            Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+        }
+
         if (databaseDriverName != null && !databaseDriverName.isEmpty()) {
             Settings.setString(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
         }
@@ -905,9 +1020,6 @@ public class DependencyCheckTask extends Task {
         if (databasePassword != null && !databasePassword.isEmpty()) {
             Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
         }
-        if (zipExtensions != null && !zipExtensions.isEmpty()) {
-            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
-        }
         if (cveUrl12Modified != null && !cveUrl12Modified.isEmpty()) {
             Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
         }
@@ -1011,4 +1123,18 @@ public class DependencyCheckTask extends Task {
             return values;
         }
     }
+
+    /**
+     * Whether or not the Jar Analyzer is enabled.
+     */
+    private boolean jarAnalyzerEnabled = true;
+
+    /**
+     * Returns whether or not the analyzer is enabled.
+     *
+     * @return true if the analyzer is enabled
+     */
+    public boolean isJarAnalyzerEnabled() {
+        return jarAnalyzerEnabled;
+    }
 }

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

@@ -18,33 +18,60 @@ the project's dependencies.
     </dependency-check>
 </target>
 ```
-The following table lists the configurable properties:
 
-Property              | Description | Requirement | Default Value
+Configuration
-----------------------|-------------|-------------|------------
+====================
-applicationName       | The name of the application to use in the generated report. | Required | &nbsp;
+The following properties can be set on the dependency-check-maven plugin.
-reportFormat          | The format of the report to be generated. Allowed values are: HTML, XML, VULN, or ALL. The default value is HTML.| Optional | HTML
+
-reportOutputDirectory | The directory where dependency-check will store data used for analysis. Defaults to the current working directory. | Optional | &nbsp;
+Property             | Description                        | Default Value
-failBuildOn           | If set and a CVE is found that is greater then the specified value the build will fail. The default value is 11 which means that the build will not fail. Valid values are 0-11. | Optional | 11
+---------------------|------------------------------------|------------------
-autoUpdate            | If set to false the NVD CVE data is not automatically updated. Setting this to false could result in false negatives. However, this may be required in some environments. | Optional | true
+autoUpdate           | Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to false. | true
-dataDirectory         | The directory where dependency-check will store data used for analysis. Defaults to a folder called, called 'dependency-check-data', that is in the same directory as the dependency-check-ant jar file was installed in. *It is not recommended to change this.* | Optional | &nbsp;
+externalReport       | When using as a Site plugin this parameter sets whether or not the external report format should be used. | false
-logFile               | The file path to write verbose logging information. | Optional | &nbsp;
+outputDirectory      | The location to write the report(s). Note, this is not used if generating the report as part of a `mvn site` build | 'target'
-suppressionFile       | An XML file conforming to the suppression schema that suppresses findings; this is used to hide [false positives](../suppression.html). | Optional | &nbsp;
+failBuildOnCVSS      | Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11 which means since the CVSS scores are 0-10, by default the build will never fail.         | 11
-proxyUrl              | Defines the proxy used to connect to the Internet. | Optional | &nbsp;
+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
-proxyPort             | Defines the port for the proxy. | Optional | &nbsp;
+logFile              | The file path to write verbose logging information. | &nbsp;
-proxyUsername         | Defines the proxy user name. | Optional | &nbsp;
+suppressionFile      | The file path to the XML suppression file \- used to suppress [false positives](../suppression.html) | &nbsp;
-proxyPassword         | Defines the proxy password. | Optional | &nbsp;
+proxyUrl             | The Proxy URL.                     | &nbsp;
-connectionTimeout     | The connection timeout used when downloading data files from the Internet. | Optional | &nbsp;
+proxyPort            | The Proxy Port.                    | &nbsp;
-nexusAnalyzerEnabled  | The connection timeout used when downloading data files from the Internet. | Optional | &nbsp;
+proxyUsername        | Defines the proxy user name.       | &nbsp;
-nexusUrl              | The connection timeout used when downloading data files from the Internet. | Optional | &nbsp;
+proxyPassword        | Defines the proxy password.        | &nbsp;
-nexusUsesProxy        | Whether or not the defined proxy should be used when connecting to Nexus. | Optional | true
+connectionTimeout    | The URL Connection Timeout.        | &nbsp;
-databaseDriverName    | The name of the database driver. Example: org.h2.Driver. | Optional | &nbsp;
+
-databaseDriverPath    | The path to the database driver JAR file; only used if the driver is not in the class path. | Optional | &nbsp;
+Analyzer Configuration
-connectionString      | The connection string used to connect to the database. | Optional | &nbsp;
+====================
-databaseUser          | The username used when connecting to the database. | Optional | dcuser
+The following properties are used to configure the various file type analyzers.
-databasePassword      | The password used when connecting to the database. | Optional | &nbsp;
+These properties can be used to turn off specific analyzers if it is not needed.
-zipExtensions         | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. | Optional | &nbsp;
+Note, that specific analyzers will automatically disable themselves if no file
-cveUrl12Modified      | URL for the modified CVE 1.2 | Optional | http://nvd.nist.gov/download/nvdcve-modified.xml
+types that they support are detected - so specifically disabling them may not
-cveUrl20Modified      | URL for the modified CVE 2.0 | Optional | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+be needed.
-cveUrl12Base          | Base URL for each year's CVE 1.2, the %d will be replaced with the year | Optional | http://nvd.nist.gov/download/nvdcve-%d.xml
+
-cveUrl20Base          | Base URL for each year's CVE 2.0, the %d will be replaced with the year | Optional | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+Property                | Description                        | Default Value
+------------------------|------------------------------------|------------------
+archiveAnalyzerEnabled  | Sets whether the Archive Analyzer will be used.                    | true
+zipExtensions           | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. | &nbsp;
+jarAnalyzer             | Sets whether Jar Analyzer will be used.                            | true
+nexusAnalyzerEnabled    | Sets whether Nexus Analyzer will be used.                          | true
+nexusUrl                | Defines the Nexus URL. | https://repository.sonatype.org/service/local/
+nexusUsesProxy          | Whether or not the defined proxy should be used when connecting to Nexus. | true
+nuspecAnalyzerEnabled  | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.   | true
+assemblyAnalyzerEnabled | Sets whether or not the .NET Assembly Analyzer should be used.     | true
+pathToMono              | The path to Mono for .NET assembly analysis on non-windows systems | &nbsp;
+
+Advanced Configuration
+====================
+The following properties can be configured in the plugin. However, they are less frequently changed. One exception
+may be the cvedUrl properties, which can be used to host a mirror of the NVD within an enterprise environment.
+
+Property             | Description                                                             | Default Value
+---------------------|-------------------------------------------------------------------------|------------------
+cveUrl12Modified     | URL for the modified CVE 1.2                                            | http://nvd.nist.gov/download/nvdcve-modified.xml
+cveUrl20Modified     | URL for the modified CVE 2.0                                            | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+cveUrl12Base         | Base URL for each year's CVE 1.2, the %d will be replaced with the year | http://nvd.nist.gov/download/nvdcve-%d.xml
+cveUrl20Base         | Base URL for each year's CVE 2.0, the %d will be replaced with the year | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+dataDirectory        | Data directory to hold SQL CVEs contents. This should generally not be changed.             | &nbsp;
+databaseDriverName   | The name of the database driver. Example: org.h2.Driver.                                    | &nbsp;
+databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path. | &nbsp;
+connectionString     | The connection string used to connect to the database.                                      | &nbsp;
+databaseUser         | The username used when connecting to the database.                                          | &nbsp;
+databasePassword     | The password used when connecting to the database.                                          | &nbsp;

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

@@ -64,7 +64,7 @@ public class DependencyCheckTaskTest extends BuildFileTest {
      */
     @Test
     public void testAddFileSet() throws Exception {
-        File report = new File("target/DependencyCheck-Report.html");
+        File report = new File("target/dependency-check-report.html");
         if (report.exists()) {
             if (!report.delete()) {
                 throw new Exception("Unable to delete 'target/DependencyCheck-Report.html' prior to test.");
@@ -83,7 +83,7 @@ public class DependencyCheckTaskTest extends BuildFileTest {
      */
     @Test
     public void testAddFileList() throws Exception {
-        File report = new File("target/DependencyCheck-Report.xml");
+        File report = new File("target/dependency-check-report.xml");
         if (report.exists()) {
             if (!report.delete()) {
                 throw new Exception("Unable to delete 'target/DependencyCheck-Report.xml' prior to test.");
@@ -101,7 +101,7 @@ public class DependencyCheckTaskTest extends BuildFileTest {
      */
     @Test
     public void testAddDirSet() throws Exception {
-        File report = new File("target/DependencyCheck-Vulnerability.html");
+        File report = new File("target/dependency-check-vulnerability.html");
         if (report.exists()) {
             if (!report.delete()) {
                 throw new Exception("Unable to delete 'target/DependencyCheck-Vulnerability.html' prior to test.");

dependency-check-cli/pom.xml

@@ -21,7 +21,7 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.1.2</version>
+        <version>1.1.4</version>
     </parent>
 
     <artifactId>dependency-check-cli</artifactId>

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

@@ -158,15 +158,19 @@ public class App {
         final String dataDirectory = cli.getDataDirectory();
         final File propertiesFile = cli.getPropertiesFile();
         final String suppressionFile = cli.getSuppressionFile();
+        final boolean jarDisabled = cli.isJarDisabled();
+        final boolean archiveDisabled = cli.isArchiveDisabled();
+        final boolean assemblyDisabled = cli.isAssemblyDisabled();
+        final boolean nuspecDisabled = cli.isNuspecDisabled();
         final boolean nexusDisabled = cli.isNexusDisabled();
         final String nexusUrl = cli.getNexusUrl();
-        final boolean nexusUsesProxy = cli.isNexusUsesProxy();
         final String databaseDriverName = cli.getDatabaseDriverName();
         final String databaseDriverPath = cli.getDatabaseDriverPath();
         final String connectionString = cli.getConnectionString();
         final String databaseUser = cli.getDatabaseUser();
         final String databasePassword = cli.getDatabasePassword();
         final String additionalZipExtensions = cli.getAdditionalZipExtensions();
+        final String pathToMono = cli.getPathToMono();
 
         if (propertiesFile != null) {
             try {
@@ -181,6 +185,10 @@ public class App {
                 Logger.getLogger(App.class.getName()).log(Level.FINE, null, ex);
             }
         }
+        // We have to wait until we've merged the properties before attempting to set whether we use
+        // the proxy for Nexus since it could be disabled in the properties, but not explicitly stated
+        // on the command line
+        final boolean nexusUsesProxy = cli.isNexusUsesProxy();
         if (dataDirectory != null) {
             Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
         } else if (System.getProperty("basedir") != null) {
@@ -212,6 +220,13 @@ public class App {
         if (suppressionFile != null && !suppressionFile.isEmpty()) {
             Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
         }
+
+        //File Type Analyzer Settings
+        Settings.setBoolean(Settings.KEYS.ANALYZER_JAR_ENABLED, !jarDisabled);
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, !archiveDisabled);
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, !nuspecDisabled);
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, !assemblyDisabled);
+
         Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, !nexusDisabled);
         if (nexusUrl != null && !nexusUrl.isEmpty()) {
             Settings.setString(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
@@ -235,5 +250,8 @@ public class App {
         if (additionalZipExtensions != null && !additionalZipExtensions.isEmpty()) {
             Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, additionalZipExtensions);
         }
+        if (pathToMono != null && !pathToMono.isEmpty()) {
+            Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+        }
     }
 }

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

@@ -29,6 +29,7 @@ import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.cli.PosixParser;
 import org.owasp.dependencycheck.reporting.ReportGenerator.Format;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.owasp.dependencycheck.utils.Settings;
 
 /**
@@ -84,8 +85,11 @@ public final class CliParser {
      */
     private void validateArgs() throws FileNotFoundException, ParseException {
         if (isRunScan()) {
-            validatePathExists(getScanFiles(), "scan");
+            validatePathExists(getScanFiles(), ArgumentName.SCAN);
-            validatePathExists(getReportDirectory(), "out");
+            validatePathExists(getReportDirectory(), ArgumentName.OUT);
+            if (getPathToMono() != null) {
+                validatePathExists(getPathToMono(), ArgumentName.PATH_TO_MONO);
+            }
             if (!line.hasOption(ArgumentName.APP_NAME)) {
                 throw new ParseException("Missing 'app' argument; the scan cannot be run without the an application name.");
             }
@@ -121,16 +125,18 @@ public final class CliParser {
      * FileNotFoundException is thrown.
      *
      * @param path the paths to validate if they exists
-     * @param optType the option being validated (e.g. scan, out, etc.)
+     * @param argumentName the argument being validated (e.g. scan, out, etc.)
      * @throws FileNotFoundException is thrown if the path being validated does not exist.
      */
-    private void validatePathExists(String path, String optType) throws FileNotFoundException {
+    private void validatePathExists(String path, String argumentName) throws FileNotFoundException {
-        final File f = new File(path);
+        if (!path.contains("*.")) {
-        if (!f.exists()) {
+            final File f = new File(path);
-            isValid = false;
+            if (!f.exists()) {
-            final String msg = String.format("Invalid '%s' argument: '%s'", optType, path);
+                isValid = false;
-            throw new FileNotFoundException(msg);
+                final String msg = String.format("Invalid '%s' argument: '%s'", argumentName, path);
-        }
+                throw new FileNotFoundException(msg);
+            }
+        } // else { // TODO add a validation for *.zip extensions rather then relying on the engine to validate it.
     }
 
     /**
@@ -173,7 +179,8 @@ public final class CliParser {
                 .create(ArgumentName.APP_NAME_SHORT);
 
         final Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.SCAN)
-                .withDescription("The path to scan - this option can be specified multiple times.")
+                .withDescription("The path to scan - this option can be specified multiple times. To limit the scan"
+                        + " to specific file types *.[ext] can be added to the end of the path.")
                 .create(ArgumentName.SCAN_SHORT);
 
         final Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP)
@@ -196,24 +203,6 @@ public final class CliParser {
                 .withDescription("The file path to the suppression XML file.")
                 .create();
 
-        final Option disableNexusAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_NEXUS)
-                .withDescription("Disable the Nexus Analyzer.")
-                .create();
-
-        final Option nexusUrl = OptionBuilder.withArgName("url").hasArg().withLongOpt(ArgumentName.NEXUS_URL)
-                .withDescription("The url to the Nexus Server.")
-                .create();
-
-        final Option nexusUsesProxy = OptionBuilder.withArgName("true/false").hasArg().withLongOpt(ArgumentName.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)
-                .withDescription("A comma seperated list of additional extensions to be scanned as ZIP files "
-                        + "(ZIP, EAR, WAR are already treated as zip files)")
-                .create();
-
         //This is an option group because it can be specified more then once.
         final OptionGroup og = new OptionGroup();
         og.addOption(path);
@@ -228,11 +217,7 @@ public final class CliParser {
                 .addOption(noUpdate)
                 .addOption(props)
                 .addOption(verboseLog)
-                .addOption(suppressionFile)
+                .addOption(suppressionFile);
-                .addOption(disableNexusAnalyzer)
-                .addOption(nexusUrl)
-                .addOption(nexusUsesProxy)
-                .addOption(additionalZipExtensions);
     }
 
     /**
@@ -272,19 +257,58 @@ public final class CliParser {
         final Option connectionString = OptionBuilder.withArgName("connStr").hasArg().withLongOpt(ArgumentName.CONNECTION_STRING)
                 .withDescription("The connection string to the database.")
                 .create();
+
         final Option dbUser = OptionBuilder.withArgName("user").hasArg().withLongOpt(ArgumentName.DB_NAME)
                 .withDescription("The username used to connect to the database.")
                 .create();
+
         final Option dbPassword = OptionBuilder.withArgName("password").hasArg().withLongOpt(ArgumentName.DB_PASSWORD)
                 .withDescription("The password for connecting to the database.")
                 .create();
+
         final Option dbDriver = OptionBuilder.withArgName("driver").hasArg().withLongOpt(ArgumentName.DB_DRIVER)
                 .withDescription("The database driver name.")
                 .create();
+
         final Option dbDriverPath = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.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)
+                .withDescription("Disable the Jar Analyzer.")
+                .create();
+        final Option disableArchiveAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_ARCHIVE)
+                .withDescription("Disable the Archive Analyzer.")
+                .create();
+        final Option disableNuspecAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_NUSPEC)
+                .withDescription("Disable the Nuspec Analyzer.")
+                .create();
+        final Option disableAssemblyAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_ASSEMBLY)
+                .withDescription("Disable the .NET Assembly Analyzer.")
+                .create();
+
+        final Option disableNexusAnalyzer = OptionBuilder.withLongOpt(ArgumentName.DISABLE_NEXUS)
+                .withDescription("Disable the Nexus Analyzer.")
+                .create();
+
+        final Option nexusUrl = OptionBuilder.withArgName("url").hasArg().withLongOpt(ArgumentName.NEXUS_URL)
+                .withDescription("The url to the Nexus Server.")
+                .create();
+
+        final Option nexusUsesProxy = OptionBuilder.withArgName("true/false").hasArg().withLongOpt(ArgumentName.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)
+                .withDescription("A comma seperated 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)
+                .withDescription("The path to Mono for .NET Assembly analysis on non-windows systems.")
+                .create();
+
         options.addOption(proxyPort)
                 .addOption(proxyUrl)
                 .addOption(proxyUsername)
@@ -295,7 +319,16 @@ public final class CliParser {
                 .addOption(data)
                 .addOption(dbPassword)
                 .addOption(dbDriver)
-                .addOption(dbDriverPath);
+                .addOption(dbDriverPath)
+                .addOption(disableJarAnalyzer)
+                .addOption(disableArchiveAnalyzer)
+                .addOption(disableAssemblyAnalyzer)
+                .addOption(disableNuspecAnalyzer)
+                .addOption(disableNexusAnalyzer)
+                .addOption(nexusUrl)
+                .addOption(nexusUsesProxy)
+                .addOption(additionalZipExtensions)
+                .addOption(pathToMono);
     }
 
     /**
@@ -325,6 +358,42 @@ public final class CliParser {
         return (line != null) && isValid && line.hasOption(ArgumentName.SCAN);
     }
 
+    /**
+     * Returns true if the disableJar command line argument was specified.
+     *
+     * @return true if the disableJar command line argument was specified; otherwise false
+     */
+    public boolean isJarDisabled() {
+        return (line != null) && line.hasOption(ArgumentName.DISABLE_JAR);
+    }
+
+    /**
+     * Returns true if the disableArchive command line argument was specified.
+     *
+     * @return true if the disableArchive command line argument was specified; otherwise false
+     */
+    public boolean isArchiveDisabled() {
+        return (line != null) && line.hasOption(ArgumentName.DISABLE_ARCHIVE);
+    }
+
+    /**
+     * Returns true if the disableNuspec command line argument was specified.
+     *
+     * @return true if the disableNuspec command line argument was specified; otherwise false
+     */
+    public boolean isNuspecDisabled() {
+        return (line != null) && line.hasOption(ArgumentName.DISABLE_NUSPEC);
+    }
+
+    /**
+     * Returns true if the disableAssembly command line argument was specified.
+     *
+     * @return true if the disableAssembly command line argument was specified; otherwise false
+     */
+    public boolean isAssemblyDisabled() {
+        return (line != null) && line.hasOption(ArgumentName.DISABLE_ASSEMBLY);
+    }
+
     /**
      * Returns true if the disableNexus command line argument was specified.
      *
@@ -354,8 +423,14 @@ public final class CliParser {
      * @return true if the Nexus Analyzer should use the configured proxy to connect to Nexus; otherwise false
      */
     public boolean isNexusUsesProxy() {
+        // If they didn't specify whether Nexus needs to use the proxy, we should
+        // still honor the property if it's set.
         if (line == null || !line.hasOption(ArgumentName.NEXUS_USES_PROXY)) {
-            return true;
+            try {
+                return Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY);
+            } catch (InvalidSettingException ise) {
+                return true;
+            }
         } else {
             return Boolean.parseBoolean(line.getOptionValue(ArgumentName.NEXUS_USES_PROXY));
         }
@@ -403,6 +478,15 @@ public final class CliParser {
         return line.getOptionValue(ArgumentName.OUT, ".");
     }
 
+    /**
+     * Returns the path to Mono for .NET Assembly analysis on non-windows systems.
+     *
+     * @return the path to Mono
+     */
+    public String getPathToMono() {
+        return line.getOptionValue(ArgumentName.PATH_TO_MONO);
+    }
+
     /**
      * Returns the output format specified on the command line. Defaults to HTML if no format was specified.
      *
@@ -683,7 +767,7 @@ public final class CliParser {
         /**
          * The short CLI argument name for setting the location of an additional properties file.
          */
-        public static final String PROP_SHORT = "p";
+        public static final String PROP_SHORT = "P";
         /**
          * The CLI argument name for setting the location of an additional properties file.
          */
@@ -708,6 +792,22 @@ public final class CliParser {
          * The CLI argument name for setting the location of the suppression file.
          */
         public static final String SUPPRESION_FILE = "suppression";
+        /**
+         * Disables the Jar Analyzer.
+         */
+        public static final String DISABLE_JAR = "disableJar";
+        /**
+         * Disables the Archive Analyzer.
+         */
+        public static final String DISABLE_ARCHIVE = "disableArchive";
+        /**
+         * Disables the Assembly Analyzer.
+         */
+        public static final String DISABLE_ASSEMBLY = "disableAssembly";
+        /**
+         * Disables the Nuspec Analyzer.
+         */
+        public static final String DISABLE_NUSPEC = "disableNuspec";
         /**
          * Disables the Nexus Analyzer.
          */
@@ -740,6 +840,10 @@ public final class CliParser {
          * The CLI argument name for setting the path to the database driver; in case it is not on the class path.
          */
         public static final String DB_DRIVER_PATH = "dbDriverPath";
+        /**
+         * The CLI argument name for setting the path to mono for .NET Assembly analysis on non-windows systems.
+         */
+        public static final String PATH_TO_MONO = "mono";
         /**
          * The CLI argument name for setting extra extensions.
          */

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

@@ -1,32 +1,43 @@
 Command Line Arguments
-====================
+======================
 
 The following table lists the command line arguments:
 
 Short  | Argument Name         | Parameter       | Description | Requirement
 -------|-----------------------|-----------------|-------------|------------
  \-a   | \-\-app               | \<name\>        | The name of the application being scanned. This is a required argument. | Required
- \-c   | \-\-connectiontimeout | \<timeout\>     | The connection timeout (in milliseconds) to use when downloading resources. | Optional
+ \-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
- \-d   | \-\-data              | \<path\>        | The location of the data directory used to store persistent data. This option should generally not be set. | Optional
+ \-o   | \-\-out               | \<folder\>      | The folder to write reports to. This defaults to the current directory. | Optional
  \-f   | \-\-format            | \<format\>      | The output format to write to (XML, HTML, VULN, ALL). The default is HTML. | Required
- \-h   | \-\-help              |                 | Print the help message. | Optional
  \-l   | \-\-log               | \<file\>        | The file path to write verbose logging information. | Optional
  \-n   | \-\-noupdate          |                 | Disables the automatic updating of the CPE data. | Optional
- \-o   | \-\-out               | \<folder\>      | The folder to write reports to. This defaults to the current directory. | Optional
- \-p   | \-\-proxyport         | \<port\>        | The proxy port to use when downloading resources. | Optional
-       | \-\-proxypass         | \<pass\>        | The proxy password to use when downloading resources. | Optional
-       | \-\-proxyuser         | \<user\>        | The proxy username to use when downloading resources. | Optional
- \-s   | \-\-scan              | \<path\>        | The path to scan \- this option can be specified multiple times. | Required
        | \-\-suppression       | \<file\>        | The file path to the suppression XML file; used to suppress [false positives](../suppression.html). | Optional
- \-u   | \-\-proxyurl          | \<url\>         | The proxy url to use when downloading resources. | Optional
+ \-h   | \-\-help              |                 | Print the help message. | Optional
- \-v   | \-\-version           |                 | Print the version information. | Optional
        | \-\-advancedHelp      |                 | Print the advanced help message. | Optional
-       | \-\-connectionString  | \<connStr\>     | The connection string to the database. | Optional
+ \-v   | \-\-version           |                 | Print the version information. | Optional
-       | \-\-dbDriverName      | \<driver\>      | The database driver name. | Optional
+
-       | \-\-dbDriverPath      | \<path\>        | The path to the database driver; note, this does not need to be set unless the JAR is outside of the class path. | Optional
+Advanced Options
-       | \-\-dbPassword        | \<password\>    | The password for connecting to the database. | Optional
+================
-       | \-\-dbUser            | \<user\>        | The username used to connect to the database. | Optional
+Short  | Argument Name         | Parameter       | Description | Default Value
-       | \-\-disableNexus      |                 | Disable the Nexus Analyzer. | Optional
+-------|-----------------------|-----------------|-------------|---------------
-       | \-\-nexus             | \<url\>         | The url to the Nexus Server. | Optional
+       | \-\-disableArchive    |                 | Sets whether the Archive Analyzer will be used.                      | false
-       | \-\-nexusUsesProxy    | \<true\|false\> | Whether or not the defined proxy should be used when connecting to Nexus. | Optional
+       | \-\-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;
-       | \-\-zipExtensions     | \<strings\>     | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. | Optional
+       | \-\-disableJar        |                 | Sets whether Jar Analyzer will be used.                              | false
+       | \-\-disableNexus      |                 | Sets whether Nexus Analyzer will be used.                            | false
+       | \-\-disableNexus      |                 | Disable the Nexus Analyzer.                                          | &nbsp;
+       | \-\-nexus             | \<url\>         | The url to the Nexus Server. | https://repository.sonatype.org/service/local/
+       | \-\-nexusUsesProxy    | \<true\|false\> | Whether or not the defined proxy should be used when connecting to Nexus. | true
+       | \-\-disableNuspec     |                 | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.     | false
+       | \-\-disableAssembly   |                 | Sets whether or not the .NET Assembly Analyzer should be used.       | false
+       | \-\-pathToMono        | \<path\>        | The path to Mono for .NET Assembly analysis on non-windows systems.  | &nbsp;
+       | \-\-proxyurl          | \<url\>         | The proxy url to use when downloading resources. | &nbsp;
+       | \-\-proxyport         | \<port\>        | The proxy port to use when downloading resources. | &nbsp;
+       | \-\-connectiontimeout | \<timeout\>     | The connection timeout (in milliseconds) to use when downloading resources. | &nbsp;
+       | \-\-proxypass         | \<pass\>        | The proxy password to use when downloading resources. | &nbsp;
+       | \-\-proxyuser         | \<user\>        | The proxy username to use when downloading resources. | &nbsp;
+       | \-\-connectionString  | \<connStr\>     | The connection string to the database. | &nbsp;
+       | \-\-dbDriverName      | \<driver\>      | The database driver name. | &nbsp;
+       | \-\-dbDriverPath      | \<path\>        | The path to the database driver; note, this does not need to be set unless the JAR is outside of the class path. | &nbsp;
+       | \-\-dbPassword        | \<password\>    | The password for connecting to the database. | &nbsp;
+       | \-\-dbUser            | \<user\>        | The username used to connect to the database. | &nbsp;
+ \-d   | \-\-data              | \<path\>        | The location of the data directory used to store persistent data. This option should generally not be set. | &nbsp;

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

@@ -8,20 +8,18 @@ script executable:
     $ chmod +777 dependency-check.sh
 
 To scan a folder on the system you can run:
+#set( $H = '#' )
 
-Windows
+$H$H$H Windows
--------
     dependency-check.bat --app "My App Name" --scan "c:\java\application\lib"
 
-\*nix
+$H$H$H *nix
--------
     dependency-check.sh --app "My App Name" --scan "/java/application/lib"
 
 To view the command line arguments, see the <a href="arguments.html">arguments page</a>, or you can run:
-Windows
+
--------
+$H$H$H Windows
     dependency-check.bat --help
 
-\*nix
+$H$H$H *nix
--------
     dependency-check.sh --help

dependency-check-core/pom.xml

@@ -21,7 +21,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.1.2</version>
+        <version>1.1.4</version>
     </parent>
 
     <artifactId>dependency-check-core</artifactId>
@@ -581,6 +581,13 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <scope>provided</scope>
             <optional>true</optional>
         </dependency>
+        <dependency>
+            <groupId>org.apache.openjpa</groupId>
+            <artifactId>openjpa</artifactId>
+            <version>2.0.1</version>
+            <scope>provided</scope>
+            <optional>true</optional>
+        </dependency>
     </dependencies>
     <profiles>
         <profile>

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

@@ -29,6 +29,7 @@ import java.util.logging.Logger;
 import org.owasp.dependencycheck.analyzer.AnalysisPhase;
 import org.owasp.dependencycheck.analyzer.Analyzer;
 import org.owasp.dependencycheck.analyzer.AnalyzerService;
+import org.owasp.dependencycheck.analyzer.FileTypeAnalyzer;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.data.cpe.CpeMemoryIndex;
 import org.owasp.dependencycheck.data.cpe.IndexException;
@@ -56,15 +57,15 @@ public class Engine {
     /**
      * The list of dependencies.
      */
-    private final List<Dependency> dependencies;
+    private List<Dependency> dependencies;
     /**
      * A Map of analyzers grouped by Analysis phase.
      */
     private final EnumMap<AnalysisPhase, List<Analyzer>> analyzers;
     /**
-     * A set of extensions supported by the analyzers.
+     * A Map of analyzers grouped by Analysis phase.
      */
-    private final Set<String> extensions;
+    private final Set<FileTypeAnalyzer> fileTypeAnalyzers;
 
     /**
      * Creates a new Engine.
@@ -72,9 +73,10 @@ public class Engine {
      * @throws DatabaseException thrown if there is an error connecting to the database
      */
     public Engine() throws DatabaseException {
-        this.extensions = new HashSet<String>();
         this.dependencies = new ArrayList<Dependency>();
         this.analyzers = new EnumMap<AnalysisPhase, List<Analyzer>>(AnalysisPhase.class);
+        this.fileTypeAnalyzers = new HashSet<FileTypeAnalyzer>();
+
         ConnectionFactory.initialize();
 
         boolean autoUpdate = true;
@@ -110,8 +112,8 @@ public class Engine {
         while (iterator.hasNext()) {
             final Analyzer a = iterator.next();
             analyzers.get(a.getAnalysisPhase()).add(a);
-            if (a.getSupportedExtensions() != null) {
+            if (a instanceof FileTypeAnalyzer) {
-                extensions.addAll(a.getSupportedExtensions());
+                this.fileTypeAnalyzers.add((FileTypeAnalyzer) a);
             }
         }
     }
@@ -135,6 +137,13 @@ public class Engine {
         return dependencies;
     }
 
+    public void setDependencies(List<Dependency> dependencies) {
+        this.dependencies = dependencies;
+        //for (Dependency dependency: dependencies) {
+        //    dependencies.add(dependency);
+        //}
+    }
+
     /**
      * Scans an array of files or directories. If a directory is specified, it will be scanned recursively. Any
      * dependencies identified are added to the dependency collection.
@@ -157,8 +166,21 @@ public class Engine {
      * @param path the path to a file or directory to be analyzed.
      */
     public void scan(String path) {
-        final File file = new File(path);
+        if (path.matches("^.*[\\/]\\*\\.[^\\/:*|?<>\"]+$")) {
-        scan(file);
+            final String[] parts = path.split("\\*\\.");
+            final String[] ext = new String[]{parts[parts.length - 1]};
+            final File dir = new File(path.substring(0, path.length() - ext[0].length() - 2));
+            if (dir.isDirectory()) {
+                final List<File> files = (List<File>) org.apache.commons.io.FileUtils.listFiles(dir, ext, true);
+                scan(files);
+            } else {
+                final String msg = String.format("Invalid file path provided to scan '%s'", path);
+                Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, msg);
+            }
+        } else {
+            final File file = new File(path);
+            scan(file);
+        }
     }
 
     /**
@@ -253,7 +275,7 @@ public class Engine {
         final String fileName = file.getName();
         final String extension = FileUtils.getFileExtension(fileName);
         if (extension != null) {
-            if (extensions.contains(extension)) {
+            if (supportsExtension(extension)) {
                 final Dependency dependency = new Dependency(file);
                 dependencies.add(dependency);
             }
@@ -291,32 +313,13 @@ public class Engine {
         Logger.getLogger(Engine.class.getName()).log(Level.FINE, logHeader);
         Logger.getLogger(Engine.class.getName()).log(Level.INFO, "Analysis Starting");
 
-        //phase one initialize
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
-            final List<Analyzer> analyzerList = analyzers.get(phase);
-            for (Analyzer a : analyzerList) {
-                try {
-                    final String msg = String.format("Initializing %s", a.getName());
-                    Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
-                    a.initialize();
-                } catch (Throwable ex) {
-                    final String msg = String.format("Exception occurred initializing %s.", a.getName());
-                    Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, msg);
-                    Logger.getLogger(Engine.class.getName()).log(Level.FINE, null, ex);
-                    try {
-                        a.close();
-                    } catch (Throwable ex1) {
-                        Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex1);
-                    }
-                }
-            }
-        }
-
         // analysis phases
         for (AnalysisPhase phase : AnalysisPhase.values()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
 
             for (Analyzer a : analyzerList) {
+                initializeAnalyzer(a);
+
                 /* need to create a copy of the collection because some of the
                  * analyzers may modify it. This prevents ConcurrentModificationExceptions.
                  * This is okay for adds/deletes because it happens per analyzer.
@@ -326,7 +329,12 @@ public class Engine {
                 final Set<Dependency> dependencySet = new HashSet<Dependency>();
                 dependencySet.addAll(dependencies);
                 for (Dependency d : dependencySet) {
-                    if (a.supportsExtension(d.getFileExtension())) {
+                    boolean shouldAnalyze = true;
+                    if (a instanceof FileTypeAnalyzer) {
+                        final FileTypeAnalyzer fAnalyzer = (FileTypeAnalyzer) a;
+                        shouldAnalyze = fAnalyzer.supportsExtension(d.getFileExtension());
+                    }
+                    if (shouldAnalyze) {
                         final String msgFile = String.format("Begin Analysis of '%s'", d.getActualFilePath());
                         Logger.getLogger(Engine.class.getName()).log(Level.FINE, msgFile);
                         try {
@@ -345,18 +353,11 @@ public class Engine {
                 }
             }
         }
-
-        //close/cleanup
         for (AnalysisPhase phase : AnalysisPhase.values()) {
             final List<Analyzer> analyzerList = analyzers.get(phase);
+
             for (Analyzer a : analyzerList) {
-                final String msg = String.format("Closing Analyzer '%s'", a.getName());
+                closeAnalyzer(a);
-                Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
-                try {
-                    a.close();
-                } catch (Throwable ex) {
-                    Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex);
-                }
             }
         }
 
@@ -368,6 +369,43 @@ public class Engine {
         Logger.getLogger(Engine.class.getName()).log(Level.INFO, "Analysis Complete");
     }
 
+    /**
+     * Initializes the given analyzer.
+     *
+     * @param analyzer the analyzer to initialize
+     */
+    private void initializeAnalyzer(Analyzer analyzer) {
+        try {
+            final String msg = String.format("Initializing %s", analyzer.getName());
+            Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
+            analyzer.initialize();
+        } catch (Throwable ex) {
+            final String msg = String.format("Exception occurred initializing %s.", analyzer.getName());
+            Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, msg);
+            Logger.getLogger(Engine.class.getName()).log(Level.FINE, null, ex);
+            try {
+                analyzer.close();
+            } catch (Throwable ex1) {
+                Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex1);
+            }
+        }
+    }
+
+    /**
+     * Closes the given analyzer.
+     *
+     * @param analyzer the analyzer to close
+     */
+    private void closeAnalyzer(Analyzer analyzer) {
+        final String msg = String.format("Closing Analyzer '%s'", analyzer.getName());
+        Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
+        try {
+            analyzer.close();
+        } catch (Throwable ex) {
+            Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex);
+        }
+    }
+
     /**
      * Cycles through the cached web data sources and calls update on all of them.
      */
@@ -411,15 +449,13 @@ public class Engine {
         if (ext == null) {
             return false;
         }
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
+        boolean scan = false;
-            final List<Analyzer> analyzerList = analyzers.get(phase);
+        for (FileTypeAnalyzer a : this.fileTypeAnalyzers) {
-            for (Analyzer a : analyzerList) {
+            /* note, we can't break early on this loop as the analyzers need to know if
-                if (a.getSupportedExtensions() != null && a.supportsExtension(ext)) {
+             they have files to work on prior to initialization */
-                    return true;
+            scan |= a.supportsExtension(ext);
-                }
-            }
         }
-        return false;
+        return scan;
     }
 
     /**
@@ -447,4 +483,5 @@ public class Engine {
             throw new NoDataException("No documents exist");
         }
     }
+
 }

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

@@ -0,0 +1,973 @@
+/*
+ * 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.agent;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Identifier;
+import org.owasp.dependencycheck.dependency.Vulnerability;
+import org.owasp.dependencycheck.exception.ScanAgentException;
+import org.owasp.dependencycheck.reporting.ReportGenerator;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * This class provides a way to easily conduct a scan solely based on existing evidence metadata rather than collecting
+ * evidence from the files themselves. This class is based on the Ant task and Maven plugin with the exception that it
+ * takes a list of dependencies that can be programmatically added from data in a spreadsheet, database or some other
+ * datasource and conduct a scan based on this pre-defined evidence.
+ *
+ * <h2>Example:</h2>
+ * <pre>
+ * List<Dependency> dependencies = new ArrayList<Dependency>();
+ * Dependency dependency = new Dependency(new File(FileUtils.getBitBucket()));
+ * dependency.getProductEvidence().addEvidence("my-datasource", "name", "Jetty", Confidence.HIGH);
+ * dependency.getVersionEvidence().addEvidence("my-datasource", "version", "5.1.10", Confidence.HIGH);
+ * dependency.getVendorEvidence().addEvidence("my-datasource", "vendor", "mortbay", Confidence.HIGH);
+ * dependencies.add(dependency);
+ *
+ * DependencyCheckScanAgent scan = new DependencyCheckScanAgent();
+ * scan.setDependencies(dependencies);
+ * scan.setReportFormat(ReportGenerator.Format.ALL);
+ * scan.setReportOutputDirectory(System.getProperty("user.home"));
+ * scan.execute();
+ * </pre>
+ *
+ * @author Steve Springett <steve.springett@owasp.org>
+ */
+@SuppressWarnings("unused")
+public class DependencyCheckScanAgent {
+
+    /**
+     * System specific new line character.
+     */
+    private static final String NEW_LINE = System.getProperty("line.separator", "\n").intern();
+
+    /**
+     * The application name for the report.
+     */
+    private String applicationName = "Dependency-Check";
+
+    /**
+     * Get the value of applicationName.
+     *
+     * @return the value of applicationName
+     */
+    public String getApplicationName() {
+        return applicationName;
+    }
+
+    /**
+     * Set the value of applicationName.
+     *
+     * @param applicationName new value of applicationName
+     */
+    public void setApplicationName(String applicationName) {
+        this.applicationName = applicationName;
+    }
+
+    /**
+     * The pre-determined dependencies to scan
+     */
+    private List<Dependency> dependencies;
+
+    /**
+     * Returns a list of pre-determined dependencies.
+     *
+     * @return returns a list of dependencies
+     */
+    public List<Dependency> getDependencies() {
+        return dependencies;
+    }
+
+    /**
+     * Sets the list of dependencies to scan.
+     *
+     * @param dependencies new value of dependencies
+     */
+    public void setDependencies(List<Dependency> dependencies) {
+        this.dependencies = dependencies;
+    }
+
+    /**
+     * The location of the data directory that contains
+     */
+    private String dataDirectory = null;
+
+    /**
+     * Get the value of dataDirectory.
+     *
+     * @return the value of dataDirectory
+     */
+    public String getDataDirectory() {
+        return dataDirectory;
+    }
+
+    /**
+     * Set the value of dataDirectory.
+     *
+     * @param dataDirectory new value of dataDirectory
+     */
+    public void setDataDirectory(String dataDirectory) {
+        this.dataDirectory = dataDirectory;
+    }
+
+    /**
+     * Specifies the destination directory for the generated Dependency-Check report.
+     */
+    private String reportOutputDirectory;
+
+    /**
+     * Get the value of reportOutputDirectory.
+     *
+     * @return the value of reportOutputDirectory
+     */
+    public String getReportOutputDirectory() {
+        return reportOutputDirectory;
+    }
+
+    /**
+     * Set the value of reportOutputDirectory.
+     *
+     * @param reportOutputDirectory new value of reportOutputDirectory
+     */
+    public void setReportOutputDirectory(String reportOutputDirectory) {
+        this.reportOutputDirectory = reportOutputDirectory;
+    }
+
+    /**
+     * Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11
+     * which means since the CVSS scores are 0-10, by default the build will never fail and the CVSS score is set to 11.
+     * The valid range for the fail build on CVSS is 0 to 11, where anything above 10 will not cause the build to fail.
+     */
+    private float failBuildOnCVSS = 11;
+
+    /**
+     * Get the value of failBuildOnCVSS.
+     *
+     * @return the value of failBuildOnCVSS
+     */
+    public float getFailBuildOnCVSS() {
+        return failBuildOnCVSS;
+    }
+
+    /**
+     * Set the value of failBuildOnCVSS.
+     *
+     * @param failBuildOnCVSS new value of failBuildOnCVSS
+     */
+    public void setFailBuildOnCVSS(float failBuildOnCVSS) {
+        this.failBuildOnCVSS = failBuildOnCVSS;
+    }
+
+    /**
+     * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to
+     * false. Default is true.
+     */
+    private boolean autoUpdate = true;
+
+    /**
+     * Get the value of autoUpdate.
+     *
+     * @return the value of autoUpdate
+     */
+    public boolean isAutoUpdate() {
+        return autoUpdate;
+    }
+
+    /**
+     * Set the value of autoUpdate.
+     *
+     * @param autoUpdate new value of autoUpdate
+     */
+    public void setAutoUpdate(boolean autoUpdate) {
+        this.autoUpdate = autoUpdate;
+    }
+
+    /**
+     * The report format to be generated (HTML, XML, VULN, ALL). This configuration option has no affect if using this
+     * within the Site plugin unless the externalReport is set to true. Default is HTML.
+     */
+    private ReportGenerator.Format reportFormat = ReportGenerator.Format.HTML;
+
+    /**
+     * Get the value of reportFormat.
+     *
+     * @return the value of reportFormat
+     */
+    public ReportGenerator.Format getReportFormat() {
+        return reportFormat;
+    }
+
+    /**
+     * Set the value of reportFormat.
+     *
+     * @param reportFormat new value of reportFormat
+     */
+    public void setReportFormat(ReportGenerator.Format reportFormat) {
+        this.reportFormat = reportFormat;
+    }
+
+    /**
+     * The Proxy URL.
+     */
+    private String proxyUrl;
+
+    /**
+     * Get the value of proxyUrl.
+     *
+     * @return the value of proxyUrl
+     */
+    public String getProxyUrl() {
+        return proxyUrl;
+    }
+
+    /**
+     * Set the value of proxyUrl.
+     *
+     * @param proxyUrl new value of proxyUrl
+     */
+    public void setProxyUrl(String proxyUrl) {
+        this.proxyUrl = proxyUrl;
+    }
+
+    /**
+     * The Proxy Port.
+     */
+    private String proxyPort;
+
+    /**
+     * Get the value of proxyPort.
+     *
+     * @return the value of proxyPort
+     */
+    public String getProxyPort() {
+        return proxyPort;
+    }
+
+    /**
+     * Set the value of proxyPort.
+     *
+     * @param proxyPort new value of proxyPort
+     */
+    public void setProxyPort(String proxyPort) {
+        this.proxyPort = proxyPort;
+    }
+
+    /**
+     * The Proxy username.
+     */
+    private String proxyUsername;
+
+    /**
+     * Get the value of proxyUsername.
+     *
+     * @return the value of proxyUsername
+     */
+    public String getProxyUsername() {
+        return proxyUsername;
+    }
+
+    /**
+     * Set the value of proxyUsername.
+     *
+     * @param proxyUsername new value of proxyUsername
+     */
+    public void setProxyUsername(String proxyUsername) {
+        this.proxyUsername = proxyUsername;
+    }
+
+    /**
+     * The Proxy password.
+     */
+    private String proxyPassword;
+
+    /**
+     * Get the value of proxyPassword.
+     *
+     * @return the value of proxyPassword
+     */
+    public String getProxyPassword() {
+        return proxyPassword;
+    }
+
+    /**
+     * Set the value of proxyPassword.
+     *
+     * @param proxyPassword new value of proxyPassword
+     */
+    public void setProxyPassword(String proxyPassword) {
+        this.proxyPassword = proxyPassword;
+    }
+
+    /**
+     * The Connection Timeout.
+     */
+    private String connectionTimeout;
+
+    /**
+     * Get the value of connectionTimeout.
+     *
+     * @return the value of connectionTimeout
+     */
+    public String getConnectionTimeout() {
+        return connectionTimeout;
+    }
+
+    /**
+     * Set the value of connectionTimeout.
+     *
+     * @param connectionTimeout new value of connectionTimeout
+     */
+    public void setConnectionTimeout(String connectionTimeout) {
+        this.connectionTimeout = connectionTimeout;
+    }
+
+    /**
+     * The file path used for verbose logging.
+     */
+    private String logFile = null;
+
+    /**
+     * Get the value of logFile.
+     *
+     * @return the value of logFile
+     */
+    public String getLogFile() {
+        return logFile;
+    }
+
+    /**
+     * Set the value of logFile.
+     *
+     * @param logFile new value of logFile
+     */
+    public void setLogFile(String logFile) {
+        this.logFile = logFile;
+    }
+
+    /**
+     * The path to the suppression file.
+     */
+    private String suppressionFile;
+
+    /**
+     * Get the value of suppressionFile.
+     *
+     * @return the value of suppressionFile
+     */
+    public String getSuppressionFile() {
+        return suppressionFile;
+    }
+
+    /**
+     * Set the value of suppressionFile.
+     *
+     * @param suppressionFile new value of suppressionFile
+     */
+    public void setSuppressionFile(String suppressionFile) {
+        this.suppressionFile = suppressionFile;
+    }
+
+    /**
+     * flag indicating whether or not to show a summary of findings.
+     */
+    private boolean showSummary = true;
+
+    /**
+     * Get the value of showSummary.
+     *
+     * @return the value of showSummary
+     */
+    public boolean isShowSummary() {
+        return showSummary;
+    }
+
+    /**
+     * Set the value of showSummary.
+     *
+     * @param showSummary new value of showSummary
+     */
+    public void setShowSummary(boolean showSummary) {
+        this.showSummary = showSummary;
+    }
+
+    /**
+     * Whether or not the nexus analyzer is enabled.
+     */
+    private boolean nexusAnalyzerEnabled = true;
+
+    /**
+     * Get the value of nexusAnalyzerEnabled.
+     *
+     * @return the value of nexusAnalyzerEnabled
+     */
+    public boolean isNexusAnalyzerEnabled() {
+        return nexusAnalyzerEnabled;
+    }
+
+    /**
+     * Set the value of nexusAnalyzerEnabled.
+     *
+     * @param nexusAnalyzerEnabled new value of nexusAnalyzerEnabled
+     */
+    public void setNexusAnalyzerEnabled(boolean nexusAnalyzerEnabled) {
+        this.nexusAnalyzerEnabled = nexusAnalyzerEnabled;
+    }
+
+    /**
+     * The URL of the Nexus server.
+     */
+    private String nexusUrl;
+
+    /**
+     * Get the value of nexusUrl.
+     *
+     * @return the value of nexusUrl
+     */
+    public String getNexusUrl() {
+        return nexusUrl;
+    }
+
+    /**
+     * Set the value of nexusUrl.
+     *
+     * @param nexusUrl new value of nexusUrl
+     */
+    public void setNexusUrl(String nexusUrl) {
+        this.nexusUrl = nexusUrl;
+    }
+
+    /**
+     * Whether or not the defined proxy should be used when connecting to Nexus.
+     */
+    private boolean nexusUsesProxy = true;
+
+    /**
+     * Get the value of nexusUsesProxy.
+     *
+     * @return the value of nexusUsesProxy
+     */
+    public boolean isNexusUsesProxy() {
+        return nexusUsesProxy;
+    }
+
+    /**
+     * Set the value of nexusUsesProxy.
+     *
+     * @param nexusUsesProxy new value of nexusUsesProxy
+     */
+    public void setNexusUsesProxy(boolean nexusUsesProxy) {
+        this.nexusUsesProxy = nexusUsesProxy;
+    }
+
+    /**
+     * The database driver name; such as org.h2.Driver.
+     */
+    private String databaseDriverName;
+
+    /**
+     * Get the value of databaseDriverName.
+     *
+     * @return the value of databaseDriverName
+     */
+    public String getDatabaseDriverName() {
+        return databaseDriverName;
+    }
+
+    /**
+     * Set the value of databaseDriverName.
+     *
+     * @param databaseDriverName new value of databaseDriverName
+     */
+    public void setDatabaseDriverName(String databaseDriverName) {
+        this.databaseDriverName = databaseDriverName;
+    }
+
+    /**
+     * The path to the database driver JAR file if it is not on the class path.
+     */
+    private String databaseDriverPath;
+
+    /**
+     * Get the value of databaseDriverPath.
+     *
+     * @return the value of databaseDriverPath
+     */
+    public String getDatabaseDriverPath() {
+        return databaseDriverPath;
+    }
+
+    /**
+     * Set the value of databaseDriverPath.
+     *
+     * @param databaseDriverPath new value of databaseDriverPath
+     */
+    public void setDatabaseDriverPath(String databaseDriverPath) {
+        this.databaseDriverPath = databaseDriverPath;
+    }
+
+    /**
+     * The database connection string.
+     */
+    private String connectionString;
+
+    /**
+     * Get the value of connectionString.
+     *
+     * @return the value of connectionString
+     */
+    public String getConnectionString() {
+        return connectionString;
+    }
+
+    /**
+     * Set the value of connectionString.
+     *
+     * @param connectionString new value of connectionString
+     */
+    public void setConnectionString(String connectionString) {
+        this.connectionString = connectionString;
+    }
+
+    /**
+     * The user name for connecting to the database.
+     */
+    private String databaseUser;
+
+    /**
+     * Get the value of databaseUser.
+     *
+     * @return the value of databaseUser
+     */
+    public String getDatabaseUser() {
+        return databaseUser;
+    }
+
+    /**
+     * Set the value of databaseUser.
+     *
+     * @param databaseUser new value of databaseUser
+     */
+    public void setDatabaseUser(String databaseUser) {
+        this.databaseUser = databaseUser;
+    }
+
+    /**
+     * The password to use when connecting to the database.
+     */
+    private String databasePassword;
+
+    /**
+     * Get the value of databasePassword.
+     *
+     * @return the value of databasePassword
+     */
+    public String getDatabasePassword() {
+        return databasePassword;
+    }
+
+    /**
+     * Set the value of databasePassword.
+     *
+     * @param databasePassword new value of databasePassword
+     */
+    public void setDatabasePassword(String databasePassword) {
+        this.databasePassword = databasePassword;
+    }
+
+    /**
+     * Additional ZIP File extensions to add analyze. This should be a comma-separated list of file extensions to treat
+     * like ZIP files.
+     */
+    private String zipExtensions;
+
+    /**
+     * Get the value of zipExtensions.
+     *
+     * @return the value of zipExtensions
+     */
+    public String getZipExtensions() {
+        return zipExtensions;
+    }
+
+    /**
+     * Set the value of zipExtensions.
+     *
+     * @param zipExtensions new value of zipExtensions
+     */
+    public void setZipExtensions(String zipExtensions) {
+        this.zipExtensions = zipExtensions;
+    }
+
+    /**
+     * The url for the modified NVD CVE (1.2 schema).
+     */
+    private String cveUrl12Modified;
+
+    /**
+     * Get the value of cveUrl12Modified.
+     *
+     * @return the value of cveUrl12Modified
+     */
+    public String getCveUrl12Modified() {
+        return cveUrl12Modified;
+    }
+
+    /**
+     * Set the value of cveUrl12Modified.
+     *
+     * @param cveUrl12Modified new value of cveUrl12Modified
+     */
+    public void setCveUrl12Modified(String cveUrl12Modified) {
+        this.cveUrl12Modified = cveUrl12Modified;
+    }
+
+    /**
+     * The url for the modified NVD CVE (2.0 schema).
+     */
+    private String cveUrl20Modified;
+
+    /**
+     * Get the value of cveUrl20Modified.
+     *
+     * @return the value of cveUrl20Modified
+     */
+    public String getCveUrl20Modified() {
+        return cveUrl20Modified;
+    }
+
+    /**
+     * Set the value of cveUrl20Modified.
+     *
+     * @param cveUrl20Modified new value of cveUrl20Modified
+     */
+    public void setCveUrl20Modified(String cveUrl20Modified) {
+        this.cveUrl20Modified = cveUrl20Modified;
+    }
+
+    /**
+     * Base Data Mirror URL for CVE 1.2.
+     */
+    private String cveUrl12Base;
+
+    /**
+     * Get the value of cveUrl12Base.
+     *
+     * @return the value of cveUrl12Base
+     */
+    public String getCveUrl12Base() {
+        return cveUrl12Base;
+    }
+
+    /**
+     * Set the value of cveUrl12Base.
+     *
+     * @param cveUrl12Base new value of cveUrl12Base
+     */
+    public void setCveUrl12Base(String cveUrl12Base) {
+        this.cveUrl12Base = cveUrl12Base;
+    }
+
+    /**
+     * Data Mirror URL for CVE 2.0.
+     */
+    private String cveUrl20Base;
+
+    /**
+     * Get the value of cveUrl20Base.
+     *
+     * @return the value of cveUrl20Base
+     */
+    public String getCveUrl20Base() {
+        return cveUrl20Base;
+    }
+
+    /**
+     * Set the value of cveUrl20Base.
+     *
+     * @param cveUrl20Base new value of cveUrl20Base
+     */
+    public void setCveUrl20Base(String cveUrl20Base) {
+        this.cveUrl20Base = cveUrl20Base;
+    }
+
+    /**
+     * The path to Mono for .NET assembly analysis on non-windows systems.
+     */
+    private String pathToMono;
+
+    /**
+     * Get the value of pathToMono.
+     *
+     * @return the value of pathToMono
+     */
+    public String getPathToMono() {
+        return pathToMono;
+    }
+
+    /**
+     * Set the value of pathToMono.
+     *
+     * @param pathToMono new value of pathToMono
+     */
+    public void setPathToMono(String pathToMono) {
+        this.pathToMono = pathToMono;
+    }
+
+    /**
+     * Executes the Dependency-Check on the dependent libraries.
+     *
+     * @return the Engine used to scan the dependencies.
+     * @throws org.owasp.dependencycheck.data.nvdcve.DatabaseException thrown if there is an exception connecting to the
+     * database
+     */
+    private Engine executeDependencyCheck() throws DatabaseException {
+        populateSettings();
+        Engine engine = null;
+        try {
+            engine = new Engine();
+            engine.setDependencies(this.dependencies);
+            engine.analyzeDependencies();
+
+        } finally {
+            if (engine != null) {
+                engine.cleanup();
+            }
+        }
+        return engine;
+    }
+
+    /**
+     * Generates the reports for a given dependency-check engine.
+     *
+     * @param engine a dependency-check engine
+     * @param outDirectory the directory to write the reports to
+     */
+    private void generateExternalReports(Engine engine, File outDirectory) {
+        DatabaseProperties prop = null;
+        CveDB cve = null;
+        try {
+            cve = new CveDB();
+            cve.open();
+            prop = cve.getDatabaseProperties();
+        } catch (DatabaseException ex) {
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.FINE, "Unable to retrieve DB Properties", ex);
+        } finally {
+            if (cve != null) {
+                cve.close();
+            }
+        }
+        final ReportGenerator r = new ReportGenerator(this.applicationName, engine.getDependencies(), engine.getAnalyzers(), prop);
+        try {
+            r.generateReports(outDirectory.getCanonicalPath(), this.reportFormat.name());
+        } catch (IOException ex) {
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.SEVERE,
+                    "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.FINE, null, ex);
+        } catch (Throwable ex) {
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.SEVERE,
+                    "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.FINE, null, ex);
+        }
+    }
+
+    /**
+     * Takes the properties supplied and updates the dependency-check settings. Additionally, this sets the system
+     * properties required to change the proxy url, port, and connection timeout.
+     */
+    private void populateSettings() {
+        if (dataDirectory != null) {
+            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
+        } else {
+            final File jarPath = new File(DependencyCheckScanAgent.class.getProtectionDomain().getCodeSource().getLocation().getPath());
+            final File base = jarPath.getParentFile();
+            final String sub = Settings.getString(Settings.KEYS.DATA_DIRECTORY);
+            final File dataDir = new File(base, sub);
+            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDir.getAbsolutePath());
+        }
+
+        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
+
+        if (proxyUrl != null && !proxyUrl.isEmpty()) {
+            Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
+        }
+        if (proxyPort != null && !proxyPort.isEmpty()) {
+            Settings.setString(Settings.KEYS.PROXY_PORT, proxyPort);
+        }
+        if (proxyUsername != null && !proxyUsername.isEmpty()) {
+            Settings.setString(Settings.KEYS.PROXY_USERNAME, proxyUsername);
+        }
+        if (proxyPassword != null && !proxyPassword.isEmpty()) {
+            Settings.setString(Settings.KEYS.PROXY_PASSWORD, proxyPassword);
+        }
+        if (connectionTimeout != null && !connectionTimeout.isEmpty()) {
+            Settings.setString(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
+        }
+        if (suppressionFile != null && !suppressionFile.isEmpty()) {
+            Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
+        }
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
+        if (nexusUrl != null && !nexusUrl.isEmpty()) {
+            Settings.setString(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
+        }
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY, nexusUsesProxy);
+        if (databaseDriverName != null && !databaseDriverName.isEmpty()) {
+            Settings.setString(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
+        }
+        if (databaseDriverPath != null && !databaseDriverPath.isEmpty()) {
+            Settings.setString(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
+        }
+        if (connectionString != null && !connectionString.isEmpty()) {
+            Settings.setString(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
+        }
+        if (databaseUser != null && !databaseUser.isEmpty()) {
+            Settings.setString(Settings.KEYS.DB_USER, databaseUser);
+        }
+        if (databasePassword != null && !databasePassword.isEmpty()) {
+            Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
+        }
+        if (zipExtensions != null && !zipExtensions.isEmpty()) {
+            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
+        }
+        if (cveUrl12Modified != null && !cveUrl12Modified.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
+        }
+        if (cveUrl20Modified != null && !cveUrl20Modified.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
+        }
+        if (cveUrl12Base != null && !cveUrl12Base.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
+        }
+        if (cveUrl20Base != null && !cveUrl20Base.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
+        }
+        if (pathToMono != null && !pathToMono.isEmpty()) {
+            Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+        }
+    }
+
+    /**
+     * Executes the dependency-check and generates the report.
+     *
+     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if there is an exception executing the
+     * scan.
+     */
+    public void execute() throws ScanAgentException {
+        Engine engine = null;
+        try {
+            engine = executeDependencyCheck();
+            generateExternalReports(engine, new File(this.reportOutputDirectory));
+            if (this.showSummary) {
+                showSummary(engine.getDependencies());
+            }
+            if (this.failBuildOnCVSS <= 10) {
+                checkForFailure(engine.getDependencies());
+            }
+        } catch (DatabaseException ex) {
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.SEVERE,
+                    "Unable to connect to the dependency-check database; analysis has stopped");
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.FINE, "", ex);
+        } finally {
+            if (engine != null) {
+                engine.cleanup();
+            }
+        }
+    }
+
+    /**
+     * Checks to see if a vulnerability has been identified with a CVSS score that is above the threshold set in the
+     * configuration.
+     *
+     * @param dependencies the list of dependency objects
+     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if there is an exception executing the
+     * scan.
+     */
+    private void checkForFailure(List<Dependency> dependencies) throws ScanAgentException {
+        final StringBuilder ids = new StringBuilder();
+        for (Dependency d : dependencies) {
+            boolean addName = true;
+            for (Vulnerability v : d.getVulnerabilities()) {
+                if (v.getCvssScore() >= failBuildOnCVSS) {
+                    if (addName) {
+                        addName = false;
+                        ids.append(NEW_LINE).append(d.getFileName()).append(": ");
+                        ids.append(v.getName());
+                    } else {
+                        ids.append(", ").append(v.getName());
+                    }
+                }
+            }
+        }
+        if (ids.length() > 0) {
+            final String msg = String.format("%n%nDependency-Check Failure:%n"
+                    + "One or more dependencies were identified with vulnerabilities that have a CVSS score greater then '%.1f': %s%n"
+                    + "See the dependency-check report for more details.%n%n", failBuildOnCVSS, ids.toString());
+
+            throw new ScanAgentException(msg);
+        }
+    }
+
+    /**
+     * Generates a warning message listing a summary of dependencies and their associated CPE and CVE entries.
+     *
+     * @param dependencies a list of dependency objects
+     */
+    private void showSummary(List<Dependency> dependencies) {
+        final StringBuilder summary = new StringBuilder();
+        for (Dependency d : dependencies) {
+            boolean firstEntry = true;
+            final StringBuilder ids = new StringBuilder();
+            for (Vulnerability v : d.getVulnerabilities()) {
+                if (firstEntry) {
+                    firstEntry = false;
+                } else {
+                    ids.append(", ");
+                }
+                ids.append(v.getName());
+            }
+            if (ids.length() > 0) {
+                summary.append(d.getFileName()).append(" (");
+                firstEntry = true;
+                for (Identifier id : d.getIdentifiers()) {
+                    if (firstEntry) {
+                        firstEntry = false;
+                    } else {
+                        summary.append(", ");
+                    }
+                    summary.append(id.getValue());
+                }
+                summary.append(") : ").append(ids).append(NEW_LINE);
+            }
+        }
+        if (summary.length() > 0) {
+            final String msg = String.format("%n%n"
+                    + "One or more dependencies were identified with known vulnerabilities:%n%n%s"
+                    + "%n%nSee the dependency-check report for more details.%n%n", summary.toString());
+            Logger.getLogger(DependencyCheckScanAgent.class.getName()).log(Level.WARNING, msg);
+        }
+    }
+
+}

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

@@ -0,0 +1,13 @@
+/**
+ * <html>
+ * <head>
+ * <title>org.owasp.dependencycheck.agent</title>
+ * </head>
+ * <body>
+ * The agent package holds an agent API that can be used by other applications that have information about dependencies;
+ * but would rather implement something in their code directly rather then spawn a process to run the entire
+ * dependency-check engine. This basically provides programmatic access to running a scan.
+ * </body>
+ * </html>
+ */
+package org.owasp.dependencycheck.agent;

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

@@ -17,33 +17,12 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
-
 /**
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
 public abstract class AbstractAnalyzer implements Analyzer {
 
-    /**
-     * Utility method to help in the creation of the extensions set. This constructs a new Set that can be used in a
-     * final static declaration.<br/><br/>
-     *
-     * This implementation was copied from
-     * http://stackoverflow.com/questions/2041778/initialize-java-hashset-values-by-construction
-     *
-     * @param strings a list of strings to add to the set.
-     * @return a Set of strings.
-     */
-    protected static Set<String> newHashSet(String... strings) {
-        final Set<String> set = new HashSet<String>();
-
-        Collections.addAll(set, strings);
-        return set;
-    }
-
     /**
      * The initialize method does nothing for this Analyzer.
      *

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

@@ -0,0 +1,229 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * The base FileTypeAnalyzer that all analyzers that have specific file types they analyze should extend.
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public abstract class AbstractFileTypeAnalyzer extends AbstractAnalyzer implements FileTypeAnalyzer {
+
+    //<editor-fold defaultstate="collapsed" desc="Constructor">
+    /**
+     * Base constructor that all children must call. This checks the configuration to determine if the analyzer is
+     * enabled.
+     */
+    public AbstractFileTypeAnalyzer() {
+        final String key = getAnalyzerEnabledSettingKey();
+        try {
+            enabled = Settings.getBoolean(key, true);
+        } catch (InvalidSettingException ex) {
+            String msg = String.format("Invalid settting for property '%s'", key);
+            LOGGER.log(Level.WARNING, msg);
+            LOGGER.log(Level.FINE, "", ex);
+            msg = String.format("%s has been disabled", getName());
+            LOGGER.log(Level.WARNING, msg);
+        }
+    }
+//</editor-fold>
+
+    //<editor-fold defaultstate="collapsed" desc="Field defentitions">
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(AbstractFileTypeAnalyzer.class.getName());
+    /**
+     * Whether the file type analyzer detected any files it needs to analyze.
+     */
+    private boolean filesMatched = false;
+
+    /**
+     * Get the value of filesMatched. A flag indicating whether the scan included any file types this analyzer supports.
+     *
+     * @return the value of filesMatched
+     */
+    protected boolean isFilesMatched() {
+        return filesMatched;
+    }
+
+    /**
+     * Set the value of filesMatched. A flag indicating whether the scan included any file types this analyzer supports.
+     *
+     * @param filesMatched new value of filesMatched
+     */
+    protected void setFilesMatched(boolean filesMatched) {
+        this.filesMatched = filesMatched;
+    }
+
+    /**
+     * A flag indicating whether or not the analyzer is enabled.
+     */
+    private boolean enabled = true;
+
+    /**
+     * Get the value of enabled.
+     *
+     * @return the value of enabled
+     */
+    public boolean isEnabled() {
+        return enabled;
+    }
+
+    /**
+     * Set the value of enabled.
+     *
+     * @param enabled new value of enabled
+     */
+    public void setEnabled(boolean enabled) {
+        this.enabled = enabled;
+    }
+//</editor-fold>
+
+    //<editor-fold defaultstate="collapsed" desc="Abstract methods children must implement">
+    /**
+     * <p>
+     * Returns a list of supported file extensions. An example would be an analyzer that inspected java jar files. The
+     * getSupportedExtensions function would return a set with a single element "jar".</p>
+     *
+     * <p>
+     * <b>Note:</b> when implementing this the extensions returned MUST be lowercase.</p>
+     *
+     * @return The file extensions supported by this analyzer.
+     *
+     * <p>
+     * If the analyzer returns null it will not cause additional files to be analyzed but will be executed against every
+     * file loaded</p>
+     */
+    protected abstract Set<String> getSupportedExtensions();
+
+    /**
+     * Initializes the file type analyzer.
+     *
+     * @throws Exception thrown if there is an exception during initialization
+     */
+    protected abstract void initializeFileTypeAnalyzer() throws Exception;
+
+    /**
+     * Analyzes a given dependency. If the dependency is an archive, such as a WAR or EAR, the contents are extracted,
+     * scanned, and added to the list of dependencies within the engine.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine scanning
+     * @throws AnalysisException thrown if there is an analysis exception
+     */
+    protected abstract void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException;
+
+    /**
+     * <p>
+     * Returns the setting key to determine if the analyzer is enabled.</p>
+     *
+     * @return the key for the analyzer's enabled property
+     */
+    protected abstract String getAnalyzerEnabledSettingKey();
+
+//</editor-fold>
+    //<editor-fold defaultstate="collapsed" desc="Final implementations for the Analyzer interface">
+    /**
+     * Initializes the analyzer.
+     *
+     * @throws Exception thrown if there is an exception during initialization
+     */
+    @Override
+    public final void initialize() throws Exception {
+        if (filesMatched) {
+            initializeFileTypeAnalyzer();
+        } else {
+            enabled = false;
+        }
+    }
+
+    /**
+     * Analyzes a given dependency. If the dependency is an archive, such as a WAR or EAR, the contents are extracted,
+     * scanned, and added to the list of dependencies within the engine.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine scanning
+     * @throws AnalysisException thrown if there is an analysis exception
+     */
+    @Override
+    public final void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+        if (enabled) {
+            analyzeFileType(dependency, engine);
+        }
+    }
+
+    /**
+     * Returns whether or not this analyzer can process the given extension.
+     *
+     * @param extension the file extension to test for support.
+     * @return whether or not the specified file extension is supported by this analyzer.
+     */
+    @Override
+    public final boolean supportsExtension(String extension) {
+        if (!enabled) {
+            return false;
+        }
+        final Set<String> ext = getSupportedExtensions();
+        if (ext == null) {
+            final String msg = String.format("The '%s' analyzer is misconfigured and does not have any file extensions;"
+                    + " it will be disabled", getName());
+            Logger.getLogger(AbstractFileTypeAnalyzer.class.getName()).log(Level.SEVERE, msg);
+            return false;
+        } else {
+            final boolean match = ext.contains(extension);
+            if (match) {
+                filesMatched = match;
+            }
+            return match;
+        }
+    }
+//</editor-fold>
+
+    //<editor-fold defaultstate="collapsed" desc="Static utility methods">
+    /**
+     * <p>
+     * Utility method to help in the creation of the extensions set. This constructs a new Set that can be used in a
+     * final static declaration.</p>
+     *
+     * <p>
+     * This implementation was copied from
+     * http://stackoverflow.com/questions/2041778/initialize-java-hashset-values-by-construction</p>
+     *
+     * @param strings a list of strings to add to the set.
+     * @return a Set of strings.
+     */
+    protected static Set<String> newHashSet(String... strings) {
+        final Set<String> set = new HashSet<String>();
+
+        Collections.addAll(set, strings);
+        return set;
+    }
+//</editor-fold>
+}

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

@@ -18,13 +18,20 @@
 package org.owasp.dependencycheck.analyzer;
 
 import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.List;
 import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import java.util.regex.Pattern;
 import org.owasp.dependencycheck.suppression.SuppressionParseException;
 import org.owasp.dependencycheck.suppression.SuppressionParser;
 import org.owasp.dependencycheck.suppression.SuppressionRule;
+import org.owasp.dependencycheck.utils.DownloadFailedException;
+import org.owasp.dependencycheck.utils.Downloader;
+import org.owasp.dependencycheck.utils.FileUtils;
 import org.owasp.dependencycheck.utils.Settings;
 
 /**
@@ -44,17 +51,6 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
         return null;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    @Override
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     //</editor-fold>
     /**
      * The initialize method loads the suppression XML file.
@@ -95,17 +91,58 @@ public abstract class AbstractSuppressionAnalyzer extends AbstractAnalyzer {
      * @throws SuppressionParseException thrown if the XML cannot be parsed.
      */
     private void loadSuppressionData() throws SuppressionParseException {
-        final File file = Settings.getFile(Settings.KEYS.SUPPRESSION_FILE);
+        final String suppressionFilePath = Settings.getString(Settings.KEYS.SUPPRESSION_FILE);
-        if (file != null) {
+        if (suppressionFilePath == null) {
-            final SuppressionParser parser = new SuppressionParser();
+            return;
-            try {
+        }
-                rules = parser.parseSuppressionRules(file);
+        File file = null;
-            } catch (SuppressionParseException ex) {
+        boolean deleteTempFile = false;
-                final String msg = String.format("Unable to parse suppression xml file '%s'", file.getPath());
+        try {
-                Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.WARNING, msg);
+            final Pattern uriRx = Pattern.compile("^(https?|file)\\:.*", Pattern.CASE_INSENSITIVE);
-                Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.WARNING, ex.getMessage());
+            if (uriRx.matcher(suppressionFilePath).matches()) {
-                Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.FINE, null, ex);
+                deleteTempFile = true;
-                throw ex;
+                file = FileUtils.getTempFile("suppression", "xml");
+                final URL url = new URL(suppressionFilePath);
+                try {
+                    Downloader.fetchFile(url, file, false);
+                } catch (DownloadFailedException ex) {
+                    Downloader.fetchFile(url, file, true);
+                }
+            } else {
+                file = new File(suppressionFilePath);
+            }
+
+            if (file != null) {
+                final SuppressionParser parser = new SuppressionParser();
+                try {
+                    rules = parser.parseSuppressionRules(file);
+                    Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).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());
+                    Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.WARNING, msg);
+                    Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.WARNING, ex.getMessage());
+                    Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.FINE, "", ex);
+                    throw ex;
+                }
+            }
+        } catch (DownloadFailedException ex) {
+            Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.WARNING,
+                    "Unable to fetch the configured suppression file");
+            Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.FINE, "", ex);
+            throw new SuppressionParseException("Unable to fetch the configured suppression file", ex);
+        } catch (MalformedURLException ex) {
+            Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.WARNING,
+                    "Configured suppression file has an invalid URL");
+            Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.FINE, "", ex);
+            throw new SuppressionParseException("Configured suppression file has an invalid URL", ex);
+        } catch (IOException ex) {
+            Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.WARNING,
+                    "Unable to create temp file for suppressions");
+            Logger.getLogger(AbstractSuppressionAnalyzer.class.getName()).log(Level.FINE, "", ex);
+            throw new SuppressionParseException("Unable to create temp file for suppressions", ex);
+        } finally {
+            if (deleteTempFile && file != null) {
+                FileUtils.delete(file);
             }
         }
     }

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

@@ -17,9 +17,8 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
-import java.util.Set;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
 
 /**
@@ -42,22 +41,6 @@ public interface Analyzer {
      */
     void analyze(Dependency dependency, Engine engine) throws AnalysisException;
 
-    /**
-     * <p>
-     * Returns a list of supported file extensions. An example would be an analyzer that inspected java jar files. The
-     * getSupportedExtensions function would return a set with a single element "jar".</p>
-     *
-     * <p>
-     * <b>Note:</b> when implementing this the extensions returned MUST be lowercase.</p>
-     *
-     * @return The file extensions supported by this analyzer.
-     *
-     * <p>
-     * If the analyzer returns null it will not cause additional files to be analyzed but will be executed against every
-     * file loaded</p>
-     */
-    Set<String> getSupportedExtensions();
-
     /**
      * Returns the name of the analyzer.
      *
@@ -65,14 +48,6 @@ public interface Analyzer {
      */
     String getName();
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    boolean supportsExtension(String extension);
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *

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

@@ -53,8 +53,12 @@ import org.owasp.dependencycheck.utils.Settings;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
+public class ArchiveAnalyzer extends AbstractFileTypeAnalyzer {
 
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(ArchiveAnalyzer.class.getName());
     /**
      * The buffer size to use when extracting files from the archive.
      */
@@ -75,6 +79,7 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      * Tracks the current scan/extraction depth for nested archives.
      */
     private int scanDepth = 0;
+
     //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
     /**
      * The name of the analyzer.
@@ -108,6 +113,7 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      *
      * @return a list of file EXTENSIONS supported by this analyzer.
      */
+    @Override
     public Set<String> getSupportedExtensions() {
         return EXTENSIONS;
     }
@@ -117,37 +123,39 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return EXTENSIONS.contains(extension);
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
      * @return the phase that the analyzer is intended to run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
     //</editor-fold>
 
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_ARCHIVE_ENABLED;
+    }
+
     /**
      * The initialize method does nothing for this Analyzer.
      *
      * @throws Exception is thrown if there is an exception deleting or creating temporary files
      */
     @Override
-    public void initialize() throws Exception {
+    public void initializeFileTypeAnalyzer() throws Exception {
         final File baseDir = Settings.getTempDirectory();
         if (!baseDir.exists()) {
             if (!baseDir.mkdirs()) {
@@ -174,11 +182,10 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
     @Override
     public void close() throws Exception {
         if (tempFileLocation != null && tempFileLocation.exists()) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, "Attempting to delete temporary files");
+            LOGGER.log(Level.FINE, "Attempting to delete temporary files");
             final boolean success = FileUtils.delete(tempFileLocation);
             if (!success) {
-                Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING,
+                LOGGER.log(Level.WARNING, "Failed to delete some temporary files, see the log for more details");
-                        "Failed to delete some temporary files, see the log for more details");
             }
         }
     }
@@ -192,7 +199,7 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      * @throws AnalysisException thrown if there is an analysis exception
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
         final File f = new File(dependency.getActualFilePath());
         final File tmpDir = getNextTempDirectory();
         extractFiles(f, tmpDir, engine);
@@ -268,7 +275,7 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
         try {
             fis = new FileInputStream(archive);
         } catch (FileNotFoundException ex) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, null, ex);
             throw new AnalysisException("Archive file was not found.", ex);
         }
         final String archiveExt = FileUtils.getFileExtension(archive.getName()).toLowerCase();
@@ -286,17 +293,17 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
             }
         } catch (ArchiveExtractionException ex) {
             final String msg = String.format("Exception extracting archive '%s'.", archive.getName());
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING, msg);
+            LOGGER.log(Level.WARNING, msg);
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, null, ex);
         } catch (IOException ex) {
             final String msg = String.format("Exception reading archive '%s'.", archive.getName());
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING, msg);
+            LOGGER.log(Level.WARNING, msg);
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, null, ex);
         } finally {
             try {
                 fis.close();
             } catch (IOException ex) {
-                Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                LOGGER.log(Level.FINEST, null, ex);
             }
         }
     }
@@ -375,7 +382,7 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
                 try {
                     input.close();
                 } catch (IOException ex) {
-                    Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                    LOGGER.log(Level.FINEST, null, ex);
                 }
             }
         }
@@ -398,17 +405,17 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
                 out.write(buffer, 0, n);
             }
         } catch (FileNotFoundException ex) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, null, ex);
             throw new ArchiveExtractionException(ex);
         } catch (IOException ex) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, null, ex);
             throw new ArchiveExtractionException(ex);
         } finally {
             if (out != null) {
                 try {
                     out.close();
                 } catch (IOException ex) {
-                    Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                    LOGGER.log(Level.FINEST, null, ex);
                 }
             }
         }

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

@@ -17,10 +17,12 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
+import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
@@ -46,7 +48,7 @@ import org.xml.sax.SAXException;
  * @author colezlaw
  *
  */
-public class AssemblyAnalyzer extends AbstractAnalyzer {
+public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
      * The analyzer name
@@ -63,7 +65,7 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
     /**
      * The temp value for GrokAssembly.exe
      */
-    private File grokAssemblyExe;
+    private File grokAssemblyExe = null;
     /**
      * The DocumentBuilder for parsing the XML
      */
@@ -71,7 +73,7 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
     /**
      * Logger
      */
-    private static final Logger LOG = Logger.getLogger(AbstractAnalyzer.class.getName());
+    private static final Logger LOG = Logger.getLogger(AssemblyAnalyzer.class.getName());
 
     /**
      * Builds the beginnings of a List for ProcessBuilder
@@ -101,7 +103,7 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
      * @throws AnalysisException if anything goes sideways
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine)
+    public void analyzeFileType(Dependency dependency, Engine engine)
             throws AnalysisException {
         if (grokAssemblyExe == null) {
             LOG.warning("GrokAssembly didn't get deployed");
@@ -111,8 +113,16 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
         final List<String> args = buildArgumentList();
         args.add(dependency.getActualFilePath());
         final ProcessBuilder pb = new ProcessBuilder(args);
+        BufferedReader rdr = null;
         try {
             final Process proc = pb.start();
+            // Try evacuating the error stream
+            rdr = new BufferedReader(new InputStreamReader(proc.getErrorStream()));
+            String line = null;
+            while (rdr.ready() && (line = rdr.readLine()) != null) {
+                LOG.log(Level.WARNING, "Error from GrokAssembly: {0}", line);
+            }
+            int rc = 0;
             final Document doc = builder.parse(proc.getInputStream());
             final XPath xpath = XPathFactory.newInstance().newXPath();
 
@@ -140,6 +150,18 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
                         product, Confidence.HIGH));
             }
 
+            try {
+                rc = proc.waitFor();
+            } catch (InterruptedException ie) {
+                return;
+            }
+            if (rc == 3) {
+                LOG.log(Level.INFO, "{0} is not a valid assembly", dependency.getActualFilePath());
+                return;
+            } else if (rc != 0) {
+                LOG.log(Level.WARNING, "Return code {0} from GrokAssembly", rc);
+            }
+
         } catch (IOException ioe) {
             throw new AnalysisException(ioe);
         } catch (SAXException saxe) {
@@ -147,6 +169,14 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
         } catch (XPathExpressionException xpe) {
             // This shouldn't happen
             throw new AnalysisException(xpe);
+        } finally {
+            if (rdr != null) {
+                try {
+                    rdr.close();
+                } catch (IOException ex) {
+                    Logger.getLogger(AssemblyAnalyzer.class.getName()).log(Level.FINEST, "ignore", ex);
+                }
+            }
         }
     }
 
@@ -156,9 +186,8 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
      * @throws Exception if anything goes wrong
      */
     @Override
-    public void initialize() throws Exception {
+    public void initializeFileTypeAnalyzer() throws Exception {
-        super.initialize();
+        final File tempFile = File.createTempFile("GKA", ".exe", Settings.getTempDirectory());
-        final File tempFile = File.createTempFile("GKA", ".exe");
         FileOutputStream fos = null;
         InputStream is = null;
         try {
@@ -195,8 +224,16 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
 
         // Now, need to see if GrokAssembly actually runs from this location.
         final List<String> args = buildArgumentList();
+        BufferedReader rdr = null;
         try {
-            final Process p = new ProcessBuilder(args).start();
+            final ProcessBuilder pb = new ProcessBuilder(args);
+            final Process p = pb.start();
+            // Try evacuating the error stream
+            rdr = new BufferedReader(new InputStreamReader(p.getErrorStream()));
+            String line;
+            while (rdr.ready() && (line = rdr.readLine()) != null) {
+                // We expect this to complain
+            }
             final Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(p.getInputStream());
             final XPath xpath = XPathFactory.newInstance().newXPath();
             final String error = xpath.evaluate("/assembly/error", doc);
@@ -211,6 +248,14 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
                     + "this can be ignored unless you are scanning .NET dlls. Please see the log for more details.");
             LOG.log(Level.FINE, "Could not execute GrokAssembly {0}", e.getMessage());
             throw new AnalysisException("An error occured with the .NET AssemblyAnalyzer", e);
+        } finally {
+            if (rdr != null) {
+                try {
+                    rdr.close();
+                } catch (IOException ex) {
+                    Logger.getLogger(AssemblyAnalyzer.class.getName()).log(Level.FINEST, "ignore", ex);
+                }
+            }
         }
 
         builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
@@ -220,7 +265,9 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
     public void close() throws Exception {
         super.close();
         try {
-            grokAssemblyExe.delete();
+            if (grokAssemblyExe != null && !grokAssemblyExe.delete()) {
+                grokAssemblyExe.deleteOnExit();
+            }
         } catch (SecurityException se) {
             LOG.fine("Can't delete temporary GrokAssembly.exe");
         }
@@ -246,17 +293,6 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Gets whether the analyzer supports the provided extension.
-     *
-     * @param extension the extension to check
-     * @return whether the analyzer supports the extension
-     */
-    @Override
-    public boolean supportsExtension(String extension) {
-        return SUPORTED_EXTENSIONS.contains(extension);
-    }
-
     /**
      * Returns the phase this analyzer runs under.
      *
@@ -266,4 +302,14 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED;
+    }
 }

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

@@ -87,6 +87,36 @@ public class CPEAnalyzer implements Analyzer {
      */
     private CveDB cve;
 
+    /**
+     * Returns the name of this analyzer.
+     *
+     * @return the name of this analyzer.
+     */
+    @Override
+    public String getName() {
+        return "CPE Analyzer";
+    }
+
+    /**
+     * Returns the analysis phase that this analyzer should run in.
+     *
+     * @return the analysis phase that this analyzer should run in.
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return AnalysisPhase.IDENTIFIER_ANALYSIS;
+    }
+
+    /**
+     * Creates the CPE Lucene Index.
+     *
+     * @throws Exception is thrown if there is an issue opening the index.
+     */
+    @Override
+    public void initialize() throws Exception {
+        this.open();
+    }
+
     /**
      * Opens the data source.
      *
@@ -461,57 +491,6 @@ public class CPEAnalyzer implements Analyzer {
         }
     }
 
-    /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @return true.
-     */
-    @Override
-    public Set<String> getSupportedExtensions() {
-        return null;
-    }
-
-    /**
-     * Returns the name of this analyzer.
-     *
-     * @return the name of this analyzer.
-     */
-    @Override
-    public String getName() {
-        return "CPE Analyzer";
-    }
-
-    /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @param extension the file extension of the dependency being analyzed.
-     * @return true.
-     */
-    @Override
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
-    /**
-     * Returns the analysis phase that this analyzer should run in.
-     *
-     * @return the analysis phase that this analyzer should run in.
-     */
-    @Override
-    public AnalysisPhase getAnalysisPhase() {
-        return AnalysisPhase.IDENTIFIER_ANALYSIS;
-    }
-
-    /**
-     * Opens the CPE Lucene Index.
-     *
-     * @throws Exception is thrown if there is an issue opening the index.
-     */
-    @Override
-    public void initialize() throws Exception {
-        this.open();
-    }
-
     /**
      * Retrieves a list of CPE values from the CveDB based on the vendor and product passed in. The list is then
      * validated to find only CPEs that are valid for the given dependency. It is possible that the CPE identified is a

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

@@ -17,7 +17,6 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import java.io.File;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -28,6 +27,7 @@ import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Identifier;
 import org.owasp.dependencycheck.utils.DependencyVersion;
@@ -57,10 +57,6 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
     private boolean analyzed = false;
     //</editor-fold>
     //<editor-fold defaultstate="collapsed" desc="All standard implementation details of Analyzer">
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = null;
     /**
      * The name of the analyzer.
      */
@@ -70,15 +66,6 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.PRE_FINDING_ANALYSIS;
 
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
-
     /**
      * Returns the name of the analyzer.
      *
@@ -88,16 +75,6 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *

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

@@ -43,10 +43,6 @@ import org.owasp.dependencycheck.dependency.VulnerableSoftware;
 public class FalsePositiveAnalyzer extends AbstractAnalyzer {
 
     //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = null;
     /**
      * The name of the analyzer.
      */
@@ -56,15 +52,6 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.POST_IDENTIFIER_ANALYSIS;
 
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
-
     /**
      * Returns the name of the analyzer.
      *
@@ -74,16 +61,6 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *

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

@@ -17,10 +17,9 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import java.io.File;
-import java.util.Set;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.utils.DependencyVersion;
@@ -43,19 +42,6 @@ public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
      * The phase that this analyzer is intended to run in.
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = null;
-
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
 
     /**
      * Returns the name of the analyzer.
@@ -66,16 +52,6 @@ public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *

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

@@ -0,0 +1,34 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+/**
+ * An Analyzer that scans specific file types.
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public interface FileTypeAnalyzer extends Analyzer {
+
+    /**
+     * Returns whether or not this analyzer can process the given extension.
+     *
+     * @param extension the file extension to test for support.
+     * @return whether or not the specified file extension is supported by this analyzer.
+     */
+    boolean supportsExtension(String extension);
+}

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

@@ -17,11 +17,11 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.Set;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Evidence;
@@ -41,44 +41,23 @@ public class HintAnalyzer extends AbstractAnalyzer implements Analyzer {
      * The phase that this analyzer is intended to run in.
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.PRE_IDENTIFIER_ANALYSIS;
-    /**
-     * The set of file extensions supported by this analyzer.
-     */
-    private static final Set<String> EXTENSIONS = null;
-
-    /**
-     * Returns a list of file EXTENSIONS supported by this analyzer.
-     *
-     * @return a list of file EXTENSIONS supported by this analyzer.
-     */
-    public Set<String> getSupportedExtensions() {
-        return EXTENSIONS;
-    }
 
     /**
      * Returns the name of the analyzer.
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
      * @return the phase that the analyzer is intended to run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return ANALYSIS_PHASE;
     }

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

@@ -79,9 +79,13 @@ import org.xml.sax.XMLReader;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
+public class JarAnalyzer extends AbstractFileTypeAnalyzer {
 
     //<editor-fold defaultstate="collapsed" desc="Constants and Member Variables">
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(JarAnalyzer.class.getName());
     /**
      * The buffer size to use when extracting files from the archive.
      */
@@ -111,9 +115,15 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             "buildjdk",
             "ant-version",
             "antversion",
+            "dynamicimportpackage",
+            "dynamicimport-package",
+            "dynamic-importpackage",
+            "dynamic-import-package",
             "import-package",
+            "ignore-package",
             "export-package",
             "importpackage",
+            "ignorepackage",
             "exportpackage",
             "sealed",
             "manifest-version",
@@ -125,7 +135,10 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             "tool",
             "bundle-manifestversion",
             "bundlemanifestversion",
-            "include-resource");
+            "include-resource",
+            "embed-dependency",
+            "ipojo-components",
+            "ipojo-extension");
     /**
      * item in some manifest, should be considered medium confidence.
      */
@@ -160,10 +173,11 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             final JAXBContext jaxbContext = JAXBContext.newInstance("org.owasp.dependencycheck.jaxb.pom.generated");
             pomUnmarshaller = jaxbContext.createUnmarshaller();
         } catch (JAXBException ex) { //guess we will just have a null pointer exception later...
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.SEVERE, "Unable to load parser. See the log for more details.");
+            LOGGER.log(Level.SEVERE, "Unable to load parser. See the log for more details.");
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, null, ex);
         }
     }
+
     //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
     /**
      * The name of the analyzer.
@@ -183,6 +197,7 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
      *
      * @return a list of file EXTENSIONS supported by this analyzer.
      */
+    @Override
     public Set<String> getSupportedExtensions() {
         return EXTENSIONS;
     }
@@ -192,20 +207,11 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
      *
      * @return the name of the analyzer.
      */
+    @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    public boolean supportsExtension(String extension) {
-        return EXTENSIONS.contains(extension);
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
@@ -216,6 +222,16 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
     }
     //</editor-fold>
 
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_JAR_ENABLED;
+    }
+
     /**
      * Loads a specified JAR file and collects information from the manifest and checksums to identify the correct CPE
      * information.
@@ -225,7 +241,7 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
      * @throws AnalysisException is thrown if there is an error reading the JAR file.
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
         try {
             final ArrayList<ClassNameInformation> classNames = collectClassNames(dependency);
             final String fileName = dependency.getFileName().toLowerCase();
@@ -263,8 +279,8 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
         } catch (IOException ex) {
             final String msg = String.format("Unable to read JarFile '%s'.", dependency.getActualFilePath());
             //final AnalysisException ax = new AnalysisException(msg, ex);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+            LOGGER.log(Level.WARNING, msg);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, "", ex);
             return false;
         }
         List<String> pomEntries;
@@ -273,8 +289,8 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
         } catch (IOException ex) {
             final String msg = String.format("Unable to read Jar file entries in '%s'.", dependency.getActualFilePath());
             //final AnalysisException ax = new AnalysisException(msg, ex);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+            LOGGER.log(Level.WARNING, msg);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, msg, ex);
+            LOGGER.log(Level.FINE, msg, ex);
             return false;
         }
         if (pomEntries.isEmpty()) {
@@ -285,7 +301,7 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             try {
                 pomProperties = retrievePomProperties(path, jar);
             } catch (IOException ex) {
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, "ignore this, failed reading a non-existent pom.properties", ex);
+                LOGGER.log(Level.FINEST, "ignore this, failed reading a non-existent pom.properties", ex);
             }
             Model pom = null;
             try {
@@ -314,8 +330,8 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
                 }
             } catch (AnalysisException ex) {
                 final String msg = String.format("An error occured while analyzing '%s'.", dependency.getActualFilePath());
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+                LOGGER.log(Level.WARNING, msg);
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, "", ex);
+                LOGGER.log(Level.FINE, "", ex);
             }
         }
         return foundSomething;
@@ -392,7 +408,9 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             bos.flush();
             dependency.setActualFilePath(file.getAbsolutePath());
         } catch (IOException ex) {
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.SEVERE, null, ex);
+            final String msg = String.format("An error occured reading '%s' from '%s'.", path, dependency.getFilePath());
+            LOGGER.warning(msg);
+            LOGGER.log(Level.SEVERE, "", ex);
         } finally {
             closeStream(bos);
             closeStream(fos);
@@ -408,18 +426,18 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             model = readPom(source);
         } catch (FileNotFoundException ex) {
             final String msg = String.format("Unable to parse pom '%s' in jar '%s' (File Not Found)", path, jar.getName());
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+            LOGGER.log(Level.WARNING, msg);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, "", ex);
             throw new AnalysisException(ex);
         } catch (UnsupportedEncodingException ex) {
             final String msg = String.format("Unable to parse pom '%s' in jar '%s' (IO Exception)", path, jar.getName());
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+            LOGGER.log(Level.WARNING, msg);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, "", ex);
             throw new AnalysisException(ex);
         } catch (AnalysisException ex) {
             final String msg = String.format("Unable to parse pom '%s' in jar '%s'", path, jar.getName());
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+            LOGGER.log(Level.WARNING, msg);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.FINE, "", ex);
             throw ex;
         } finally {
             closeStream(fis);
@@ -437,7 +455,7 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             try {
                 stream.close();
             } catch (IOException ex) {
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                LOGGER.log(Level.FINEST, null, ex);
             }
         }
     }
@@ -452,7 +470,7 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             try {
                 stream.close();
             } catch (IOException ex) {
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                LOGGER.log(Level.FINEST, null, ex);
             }
         }
     }
@@ -486,13 +504,13 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
                 throw new AnalysisException(ex);
             } catch (IOException ex) {
                 final String msg = String.format("Unable to parse pom '%s' in jar '%s' (IO Exception)", path, jar.getName());
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+                LOGGER.log(Level.WARNING, msg);
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+                LOGGER.log(Level.FINE, "", ex);
                 throw new AnalysisException(ex);
             } catch (Throwable ex) {
                 final String msg = String.format("Unexpected error during parsing of the pom '%s' in jar '%s'", path, jar.getName());
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
+                LOGGER.log(Level.WARNING, msg);
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+                LOGGER.log(Level.FINE, "", ex);
                 throw new AnalysisException(ex);
             }
         }
@@ -899,12 +917,12 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
     private File tempFileLocation = null;
 
     /**
-     * The initialize method does nothing for this Analyzer.
+     * Initializes the JarAnalyzer.
      *
      * @throws Exception is thrown if there is an exception creating a temporary directory
      */
     @Override
-    public void initialize() throws Exception {
+    public void initializeFileTypeAnalyzer() throws Exception {
         final File baseDir = Settings.getTempDirectory();
         if (!baseDir.exists()) {
             if (!baseDir.mkdirs()) {
@@ -929,10 +947,10 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
     @Override
     public void close() {
         if (tempFileLocation != null && tempFileLocation.exists()) {
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, "Attempting to delete temporary files");
+            LOGGER.log(Level.FINE, "Attempting to delete temporary files");
             final boolean success = FileUtils.delete(tempFileLocation);
             if (!success) {
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING,
+                LOGGER.log(Level.WARNING,
                         "Failed to delete some temporary files, see the log for more details");
             }
         }
@@ -1003,11 +1021,9 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
      * @return true or false depending on if it is believed the entry is an "import" entry
      */
     private boolean isImportPackage(String key, String value) {
-        final Pattern packageRx = Pattern.compile("^((([a-zA-Z_#\\$0-9]\\.)+)\\s*\\;\\s*)+$");
+        final Pattern packageRx = Pattern.compile("^([a-zA-Z0-9_#\\$\\*\\.]+\\s*[,;]\\s*)+([a-zA-Z0-9_#\\$\\*\\.]+\\s*)?$");
-        if (packageRx.matcher(value).matches()) {
+        final boolean matches = packageRx.matcher(value).matches();
-            return (key.contains("import") || key.contains("include"));
+        return matches && (key.contains("import") || key.contains("include") || value.length() > 10);
-        }
-        return false;
     }
 
     /**
@@ -1044,7 +1060,7 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
                 try {
                     jar.close();
                 } catch (IOException ex) {
-                    Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                    LOGGER.log(Level.FINEST, null, ex);
                 }
             }
         }

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

@@ -29,6 +29,7 @@ import java.util.regex.Pattern;
 import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  *
@@ -36,7 +37,12 @@ import org.owasp.dependencycheck.dependency.Dependency;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class JavaScriptAnalyzer extends AbstractAnalyzer implements Analyzer {
+public class JavaScriptAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(JavaScriptAnalyzer.class.getName());
 
     //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
     /**
@@ -72,17 +78,6 @@ public class JavaScriptAnalyzer extends AbstractAnalyzer implements Analyzer {
         return ANALYZER_NAME;
     }
 
-    /**
-     * Returns whether or not this analyzer can process the given extension.
-     *
-     * @param extension the file extension to test for support.
-     * @return whether or not the specified file extension is supported by this analyzer.
-     */
-    @Override
-    public boolean supportsExtension(String extension) {
-        return EXTENSIONS.contains(extension);
-    }
-
     /**
      * Returns the phase that the analyzer is intended to run in.
      *
@@ -93,6 +88,15 @@ public class JavaScriptAnalyzer extends AbstractAnalyzer implements Analyzer {
         return ANALYSIS_PHASE;
     }
     //</editor-fold>
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_JAVASCRIPT_ENABLED;
+    }
 
     /**
      * Loads a specified JavaScript file and collects information from the copyright information contained within.
@@ -102,7 +106,7 @@ public class JavaScriptAnalyzer extends AbstractAnalyzer implements Analyzer {
      * @throws AnalysisException is thrown if there is an error reading the JavaScript file.
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
         BufferedReader fin = null;;
         try {
             //  /\*([^\*][^/]|[\r\n\f])+?\*/
@@ -118,15 +122,20 @@ public class JavaScriptAnalyzer extends AbstractAnalyzer implements Analyzer {
             final String msg = String.format("Dependency file not found: '%s'", dependency.getActualFilePath());
             throw new AnalysisException(msg, ex);
         } catch (IOException ex) {
-            Logger.getLogger(JavaScriptAnalyzer.class.getName()).log(Level.SEVERE, null, ex);
+            LOGGER.log(Level.SEVERE, null, ex);
         } finally {
             if (fin != null) {
                 try {
                     fin.close();
                 } catch (IOException ex) {
-                    Logger.getLogger(JavaScriptAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+                    LOGGER.log(Level.FINEST, null, ex);
                 }
             }
         }
     }
+
+    @Override
+    protected void initializeFileTypeAnalyzer() throws Exception {
+
+    }
 }

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

@@ -46,20 +46,20 @@ import org.owasp.dependencycheck.utils.Settings;
  *
  * @author colezlaw
  */
-public class NexusAnalyzer extends AbstractAnalyzer {
+public class NexusAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
-     * The logger
+     * The logger.
      */
     private static final Logger LOGGER = Logger.getLogger(NexusAnalyzer.class.getName());
 
     /**
-     * The name of the analyzer
+     * The name of the analyzer.
      */
     private static final String ANALYZER_NAME = "Nexus Analyzer";
 
     /**
-     * The phase in which the analyzer runs
+     * The phase in which the analyzer runs.
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
 
@@ -68,11 +68,6 @@ public class NexusAnalyzer extends AbstractAnalyzer {
      */
     private static final Set<String> SUPPORTED_EXTENSIONS = newHashSet("jar");
 
-    /**
-     * Whether this is actually enabled. Will get set during initialization.
-     */
-    private boolean enabled = false;
-
     /**
      * The Nexus Search to be set up for this analyzer.
      */
@@ -84,24 +79,23 @@ public class NexusAnalyzer extends AbstractAnalyzer {
      * @throws Exception if there's an error during initialization
      */
     @Override
-    public void initialize() throws Exception {
+    public void initializeFileTypeAnalyzer() throws Exception {
-        enabled = Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED);
         LOGGER.fine("Initializing Nexus Analyzer");
-        LOGGER.fine(String.format("Nexus Analyzer enabled: %s", enabled));
+        LOGGER.fine(String.format("Nexus Analyzer enabled: %s", isEnabled()));
-        if (enabled) {
+        if (isEnabled()) {
             final String searchUrl = Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL);
             LOGGER.fine(String.format("Nexus Analyzer URL: %s", searchUrl));
             try {
                 searcher = new NexusSearch(new URL(searchUrl));
                 if (!searcher.preflightRequest()) {
                     LOGGER.warning("There was an issue getting Nexus status. Disabling analyzer.");
-                    enabled = false;
+                    setEnabled(false);
                 }
             } catch (MalformedURLException mue) {
                 // I know that initialize can throw an exception, but we'll
                 // just disable the analyzer if the URL isn't valid
                 LOGGER.warning(String.format("Property %s not a valid URL. Nexus Analyzer disabled", searchUrl));
-                enabled = false;
+                setEnabled(false);
             }
         }
     }
@@ -116,6 +110,16 @@ public class NexusAnalyzer extends AbstractAnalyzer {
         return ANALYZER_NAME;
     }
 
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_NEXUS_ENABLED;
+    }
+
     /**
      * Returns the analysis phase under which the analyzer runs.
      *
@@ -136,17 +140,6 @@ public class NexusAnalyzer extends AbstractAnalyzer {
         return SUPPORTED_EXTENSIONS;
     }
 
-    /**
-     * Determines whether the incoming extension is supported.
-     *
-     * @param extension the extension to check for support
-     * @return whether the extension is supported
-     */
-    @Override
-    public boolean supportsExtension(String extension) {
-        return SUPPORTED_EXTENSIONS.contains(extension);
-    }
-
     /**
      * Performs the analysis.
      *
@@ -155,12 +148,7 @@ public class NexusAnalyzer extends AbstractAnalyzer {
      * @throws AnalysisException when there's an exception during analysis
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
-        // Make a quick exit if this analyzer is disabled
-        if (!enabled) {
-            return;
-        }
-
         try {
             final MavenArtifact ma = searcher.searchSha1(dependency.getSha1sum());
             if (ma.getGroupId() != null && !"".equals(ma.getGroupId())) {
@@ -188,5 +176,3 @@ public class NexusAnalyzer extends AbstractAnalyzer {
         }
     }
 }
-
-// vim: cc=120:sw=4:ts=4:sts=4

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

@@ -18,36 +18,40 @@
 package org.owasp.dependencycheck.analyzer;
 
 import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.data.nuget.NugetPackage;
+import org.owasp.dependencycheck.data.nuget.NuspecParseException;
 import org.owasp.dependencycheck.data.nuget.NuspecParser;
 import org.owasp.dependencycheck.data.nuget.XPathNuspecParser;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  * Analyzer which will parse a Nuspec file to gather module information.
  *
  * @author colezlaw
  */
-public class NuspecAnalyzer extends AbstractAnalyzer {
+public class NuspecAnalyzer extends AbstractFileTypeAnalyzer {
 
     /**
-     * The logger
+     * The logger.
      */
     private static final Logger LOGGER = Logger.getLogger(NuspecAnalyzer.class.getName());
 
     /**
-     * The name of the analyzer
+     * The name of the analyzer.
      */
     private static final String ANALYZER_NAME = "Nuspec Analyzer";
 
     /**
-     * The phase in which the analyzer runs
+     * The phase in which the analyzer runs.
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
 
@@ -62,7 +66,7 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
      * @throws Exception if there's an error during initialization
      */
     @Override
-    public void initialize() throws Exception {
+    public void initializeFileTypeAnalyzer() throws Exception {
     }
 
     /**
@@ -75,6 +79,16 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
         return ANALYZER_NAME;
     }
 
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_NUSPEC_ENABLED;
+    }
+
     /**
      * Returns the analysis phase under which the analyzer runs.
      *
@@ -95,17 +109,6 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
         return SUPPORTED_EXTENSIONS;
     }
 
-    /**
-     * Determines whether the incoming extension is supported.
-     *
-     * @param extension the extension to check for support
-     * @return whether the extension is supported
-     */
-    @Override
-    public boolean supportsExtension(String extension) {
-        return SUPPORTED_EXTENSIONS.contains(extension);
-    }
-
     /**
      * Performs the analysis.
      *
@@ -114,8 +117,8 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
      * @throws AnalysisException when there's an exception during analysis
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
-        LOGGER.log(Level.INFO, "Checking Nuspec file {0}", dependency.toString());
+        LOGGER.log(Level.FINE, "Checking Nuspec file {0}", dependency.toString());
         try {
             final NuspecParser parser = new XPathNuspecParser();
             NugetPackage np = null;
@@ -123,11 +126,15 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
             try {
                 fis = new FileInputStream(dependency.getActualFilePath());
                 np = parser.parse(fis);
+            } catch (NuspecParseException ex) {
+                throw new AnalysisException(ex);
+            } catch (FileNotFoundException ex) {
+                throw new AnalysisException(ex);
             } finally {
                 if (fis != null) {
                     try {
                         fis.close();
-                    } catch (Throwable e) {
+                    } catch (IOException e) {
                         LOGGER.fine("Error closing input stream");
                     }
                 }
@@ -147,5 +154,3 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
         }
     }
 }
-
-// vim: cc=120:sw=4:ts=4:sts=4

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

@@ -17,12 +17,11 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.List;
-import java.util.Set;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
 import org.owasp.dependencycheck.dependency.Dependency;
@@ -62,6 +61,7 @@ public class NvdCveAnalyzer implements Analyzer {
     /**
      * Closes the data source.
      */
+    @Override
     public void close() {
         cveDB.close();
         cveDB = null;
@@ -96,6 +96,7 @@ public class NvdCveAnalyzer implements Analyzer {
      * @param engine The analysis engine
      * @throws AnalysisException is thrown if there is an issue analyzing the dependency
      */
+    @Override
     public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
         for (Identifier id : dependency.getIdentifiers()) {
             if ("cpe".equals(id.getType())) {
@@ -110,48 +111,32 @@ public class NvdCveAnalyzer implements Analyzer {
         }
     }
 
-    /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @return true.
-     */
-    public Set<String> getSupportedExtensions() {
-        return null;
-    }
-
     /**
      * Returns the name of this analyzer.
      *
      * @return the name of this analyzer.
      */
+    @Override
     public String getName() {
         return "NVD CVE Analyzer";
     }
 
-    /**
-     * Returns true because this analyzer supports all dependency types.
-     *
-     * @param extension the file extension of the dependency being analyzed.
-     * @return true.
-     */
-    public boolean supportsExtension(String extension) {
-        return true;
-    }
-
     /**
      * Returns the analysis phase that this analyzer should run in.
      *
      * @return the analysis phase that this analyzer should run in.
      */
+    @Override
     public AnalysisPhase getAnalysisPhase() {
         return AnalysisPhase.FINDING_ANALYSIS;
     }
 
     /**
-     * Opens the NVD CVE Lucene Index.
+     * Opens the database used to gather NVD CVE data.
      *
      * @throws Exception is thrown if there is an issue opening the index.
      */
+    @Override
     public void initialize() throws Exception {
         this.open();
     }

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

@@ -29,6 +29,7 @@ import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.update.NvdCveInfo;
 import org.owasp.dependencycheck.utils.DownloadFailedException;
 import org.owasp.dependencycheck.utils.Downloader;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  * A callable object to download two files.
@@ -53,8 +54,8 @@ public class CallableDownloadTask implements Callable<Future<ProcessTask>> {
         final File file2;
 
         try {
-            file1 = File.createTempFile("cve" + nvdCveInfo.getId() + "_", ".xml");
+            file1 = File.createTempFile("cve" + nvdCveInfo.getId() + "_", ".xml", Settings.getTempDirectory());
-            file2 = File.createTempFile("cve_1_2_" + nvdCveInfo.getId() + "_", ".xml");
+            file2 = File.createTempFile("cve_1_2_" + nvdCveInfo.getId() + "_", ".xml", Settings.getTempDirectory());
         } catch (IOException ex) {
             return;
         }

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

@@ -106,16 +106,26 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Returns the file name of the dependency.
      *
-     * @return the file name of the dependency.
+     * @return the file name of the dependency
      */
     public String getFileName() {
         return this.fileName;
     }
 
+    /**
+     * Returns the file name of the dependency with the backslash escaped for use in JavaScript. This is a complete hack
+     * as I could not get the replace to work in the template itself.
+     *
+     * @return the file name of the dependency with the backslash escaped for use in JavaScript
+     */
+    public String getFileNameForJavaScript() {
+        return this.fileName.replace("\\", "\\\\");
+    }
+
     /**
      * Sets the file name of the dependency.
      *
-     * @param fileName the file name of the dependency.
+     * @param fileName the file name of the dependency
      */
     public void setFileName(String fileName) {
         this.fileName = fileName;
@@ -124,7 +134,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Sets the actual file path of the dependency on disk.
      *
-     * @param actualFilePath the file path of the dependency.
+     * @param actualFilePath the file path of the dependency
      */
     public void setActualFilePath(String actualFilePath) {
         this.actualFilePath = actualFilePath;
@@ -137,7 +147,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Gets the file path of the dependency.
      *
-     * @return the file path of the dependency.
+     * @return the file path of the dependency
      */
     public String getActualFilePath() {
         return this.actualFilePath;
@@ -146,7 +156,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Gets a reference to the File object.
      *
-     * @return the File object.
+     * @return the File object
      */
     public File getActualFile() {
         return new File(this.actualFilePath);
@@ -155,7 +165,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Sets the file path of the dependency.
      *
-     * @param filePath the file path of the dependency.
+     * @param filePath the file path of the dependency
      */
     public void setFilePath(String filePath) {
         this.filePath = filePath;
@@ -168,7 +178,7 @@ public class Dependency implements Comparable<Dependency> {
      * <b>NOTE:</b> This may not be the actual path of the file on disk. The actual path of the file on disk can be
      * obtained via the getActualFilePath().</p>
      *
-     * @return the file path of the dependency.
+     * @return the file path of the dependency
      */
     public String getFilePath() {
         return this.filePath;
@@ -177,7 +187,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Sets the file name of the dependency.
      *
-     * @param fileExtension the file name of the dependency.
+     * @param fileExtension the file name of the dependency
      */
     public void setFileExtension(String fileExtension) {
         this.fileExtension = fileExtension;
@@ -186,7 +196,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Gets the file extension of the dependency.
      *
-     * @return the file extension of the dependency.
+     * @return the file extension of the dependency
      */
     public String getFileExtension() {
         return this.fileExtension;
@@ -231,7 +241,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Returns a List of Identifiers.
      *
-     * @return an ArrayList of Identifiers.
+     * @return an ArrayList of Identifiers
      */
     public Set<Identifier> getIdentifiers() {
         return this.identifiers;
@@ -240,7 +250,7 @@ public class Dependency implements Comparable<Dependency> {
     /**
      * Sets a List of Identifiers.
      *
-     * @param identifiers A list of Identifiers.
+     * @param identifiers A list of Identifiers
      */
     public void setIdentifiers(Set<Identifier> identifiers) {
         this.identifiers = identifiers;

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

@@ -0,0 +1,68 @@
+/*
+ * 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.exception;
+
+import java.io.IOException;
+
+/**
+ * An exception used when using @{link DependencyCheckScanAgent} to conduct a scan and the scan fails.
+ *
+ * @author Steve Springett <steve.springett@owasp.org>
+ */
+public class ScanAgentException extends IOException {
+
+    /**
+     * The serial version uid.
+     */
+    private static final long serialVersionUID = 1L;
+
+    /**
+     * Creates a new ScanAgentException.
+     */
+    public ScanAgentException() {
+        super();
+    }
+
+    /**
+     * Creates a new ScanAgentException.
+     *
+     * @param msg a message for the exception.
+     */
+    public ScanAgentException(String msg) {
+        super(msg);
+    }
+
+    /**
+     * Creates a new NoDataException.
+     *
+     * @param ex the cause of the exception.
+     */
+    public ScanAgentException(Throwable ex) {
+        super(ex);
+    }
+
+    /**
+     * Creates a new ScanAgentException.
+     *
+     * @param msg a message for the exception.
+     * @param ex the cause of the exception.
+     */
+    public ScanAgentException(String msg, Throwable ex) {
+        super(msg, ex);
+    }
+}

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

@@ -140,13 +140,13 @@ public class ReportGenerator {
      */
     public void generateReports(String outputDir, Format format) throws IOException, Exception {
         if (format == Format.XML || format == Format.ALL) {
-            generateReport("XmlReport", outputDir + File.separator + "DependencyCheck-Report.xml");
+            generateReport("XmlReport", outputDir + File.separator + "dependency-check-report.xml");
         }
         if (format == Format.HTML || format == Format.ALL) {
-            generateReport("HtmlReport", outputDir + File.separator + "DependencyCheck-Report.html");
+            generateReport("HtmlReport", outputDir + File.separator + "dependency-check-report.html");
         }
         if (format == Format.VULN || format == Format.ALL) {
-            generateReport("VulnerabilityReport", outputDir + File.separator + "DependencyCheck-Vulnerability.html");
+            generateReport("VulnerabilityReport", outputDir + File.separator + "dependency-check-vulnerability.html");
         }
     }
 

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

@@ -46,68 +46,101 @@ public final class Downloader {
     /**
      * Retrieves a file from a given URL and saves it to the outputPath.
      *
-     * @param url the URL of the file to download.
+     * @param url the URL of the file to download
-     * @param outputPath the path to the save the file to.
+     * @param outputPath the path to the save the file to
-     * @throws DownloadFailedException is thrown if there is an error downloading the file.
+     * @throws DownloadFailedException is thrown if there is an error downloading the file
      */
     public static void fetchFile(URL url, File outputPath) throws DownloadFailedException {
-        HttpURLConnection conn = null;
+        fetchFile(url, outputPath, true);
-        try {
+    }
-            conn = URLConnectionFactory.createHttpURLConnection(url);
-            conn.setRequestProperty("Accept-Encoding", "gzip, deflate");
-            conn.connect();
-        } catch (IOException ex) {
-            try {
-                if (conn != null) {
-                    conn.disconnect();
-                }
-            } finally {
-                conn = null;
-            }
-            throw new DownloadFailedException("Error downloading file.", ex);
-        }
-        final String encoding = conn.getContentEncoding();
 
-        BufferedOutputStream writer = null;
+    /**
-        InputStream reader = null;
+     * Retrieves a file from a given URL and saves it to the outputPath.
-        try {
+     *
-            if (encoding != null && "gzip".equalsIgnoreCase(encoding)) {
+     * @param url the URL of the file to download
-                reader = new GZIPInputStream(conn.getInputStream());
+     * @param outputPath the path to the save the file to
-            } else if (encoding != null && "deflate".equalsIgnoreCase(encoding)) {
+     * @param useProxy whether to use the configured proxy when downloading files
-                reader = new InflaterInputStream(conn.getInputStream());
+     * @throws DownloadFailedException is thrown if there is an error downloading the file
+     */
+    public static void fetchFile(URL url, File outputPath, boolean useProxy) throws DownloadFailedException {
+        if ("file".equalsIgnoreCase(url.getProtocol())) {
+            File file;
+            try {
+                file = new File(url.toURI());
+            } catch (URISyntaxException ex) {
+                final String msg = String.format("Download failed, unable to locate '%s'", url.toString());
+                throw new DownloadFailedException(msg);
+            }
+            if (file.exists()) {
+                try {
+                    org.apache.commons.io.FileUtils.copyFile(file, outputPath);
+                } catch (IOException ex) {
+                    final String msg = String.format("Download failed, unable to copy '%s'", url.toString());
+                    throw new DownloadFailedException(msg);
+                }
             } else {
-                reader = conn.getInputStream();
+                final String msg = String.format("Download failed, file does not exist '%s'", url.toString());
-            }
+                throw new DownloadFailedException(msg);
-
-            writer = new BufferedOutputStream(new FileOutputStream(outputPath));
-            final byte[] buffer = new byte[4096];
-            int bytesRead;
-            while ((bytesRead = reader.read(buffer)) > 0) {
-                writer.write(buffer, 0, bytesRead);
-            }
-        } catch (Throwable ex) {
-            throw new DownloadFailedException("Error saving downloaded file.", ex);
-        } finally {
-            if (writer != null) {
-                try {
-                    writer.close();
-                } catch (Throwable ex) {
-                    Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
-                            "Error closing the writer in Downloader.", ex);
-                }
-            }
-            if (reader != null) {
-                try {
-                    reader.close();
-                } catch (Throwable ex) {
-                    Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
-                            "Error closing the reader in Downloader.", ex);
-                }
             }
+        } else {
+            HttpURLConnection conn = null;
             try {
-                conn.disconnect();
+                conn = URLConnectionFactory.createHttpURLConnection(url, useProxy);
+                conn.setRequestProperty("Accept-Encoding", "gzip, deflate");
+                conn.connect();
+            } catch (IOException ex) {
+                try {
+                    if (conn != null) {
+                        conn.disconnect();
+                    }
+                } finally {
+                    conn = null;
+                }
+                throw new DownloadFailedException("Error downloading file.", ex);
+            }
+            final String encoding = conn.getContentEncoding();
+
+            BufferedOutputStream writer = null;
+            InputStream reader = null;
+            try {
+                if (encoding != null && "gzip".equalsIgnoreCase(encoding)) {
+                    reader = new GZIPInputStream(conn.getInputStream());
+                } else if (encoding != null && "deflate".equalsIgnoreCase(encoding)) {
+                    reader = new InflaterInputStream(conn.getInputStream());
+                } else {
+                    reader = conn.getInputStream();
+                }
+
+                writer = new BufferedOutputStream(new FileOutputStream(outputPath));
+                final byte[] buffer = new byte[4096];
+                int bytesRead;
+                while ((bytesRead = reader.read(buffer)) > 0) {
+                    writer.write(buffer, 0, bytesRead);
+                }
+            } catch (Throwable ex) {
+                throw new DownloadFailedException("Error saving downloaded file.", ex);
             } finally {
-                conn = null;
+                if (writer != null) {
+                    try {
+                        writer.close();
+                    } catch (Throwable ex) {
+                        Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
+                                "Error closing the writer in Downloader.", ex);
+                    }
+                }
+                if (reader != null) {
+                    try {
+                        reader.close();
+                    } catch (Throwable ex) {
+                        Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
+                                "Error closing the reader in Downloader.", ex);
+                    }
+                }
+                try {
+                    conn.disconnect();
+                } finally {
+                    conn = null;
+                }
             }
         }
     }
@@ -122,20 +155,11 @@ public final class Downloader {
      */
     public static long getLastModified(URL url) throws DownloadFailedException {
         long timestamp = 0;
-        //TODO add the FPR protocol?
+        //TODO add the FTP protocol?
         if ("file".equalsIgnoreCase(url.getProtocol())) {
             File lastModifiedFile;
             try {
-//                if (System.getProperty("os.name").toLowerCase().startsWith("windows")) {
-//                    String filePath = url.toString();
-//                    if (filePath.matches("file://[a-zA-Z]:.*")) {
-//                        f = new File(filePath.substring(7));
-//                    } else {
-//                        f = new File(url.toURI());
-//                    }
-//                } else {
                 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());
                 throw new DownloadFailedException(msg);

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

@@ -26,6 +26,7 @@ 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;
@@ -39,6 +40,16 @@ import org.owasp.dependencycheck.Engine;
  */
 public final class FileUtils {
 
+    /**
+     * Bit bucket for non-Windows systems
+     */
+    private static final String BIT_BUCKET_UNIX = "/dev/null";
+
+    /**
+     * Bit bucket for Windows systems (yes, only one 'L')
+     */
+    private static final String BIT_BUCKET_WIN = "NUL";
+
     /**
      * The buffer size to use when extracting files from the archive.
      */
@@ -73,19 +84,38 @@ public final class FileUtils {
      */
     public static boolean delete(File file) {
         boolean success = true;
-        if (file.isDirectory()) { //some of this may duplicative of deleteQuietly....
-            for (File f : file.listFiles()) {
-                success &= delete(f);
-            }
-        }
         if (!org.apache.commons.io.FileUtils.deleteQuietly(file)) {
             success = false;
-            final String msg = String.format("Failed to delete file: %s", file.getPath());
+            final String msg = String.format("Failed to delete file: %s; attempting to delete on exit.", file.getPath());
             Logger.getLogger(FileUtils.class.getName()).log(Level.FINE, msg);
+            file.deleteOnExit();
         }
         return success;
     }
 
+    /**
+     * Generates a new temporary file name that is guaranteed to be unique.
+     *
+     * @param prefix the prefix for the file name to generate
+     * @param extension the extension of the generated file name
+     * @return a temporary File
+     * @throws java.io.IOException thrown if the temporary folder could not be created
+     */
+    public static File getTempFile(String prefix, String extension) throws IOException {
+        final File dir = Settings.getTempDirectory();
+        if (!dir.exists()) {
+            if (!dir.mkdirs()) {
+                throw new IOException("Unable to create temporary folder");
+            }
+        }
+        final String tempFileName = String.format("%s%s.%s", prefix, UUID.randomUUID().toString(), extension);
+        final File tempFile = new File(dir, tempFileName);
+        if (tempFile.exists()) {
+            return getTempFile(prefix, extension);
+        }
+        return tempFile;
+    }
+
     /**
      * Returns the data directory. If a path was specified in dependencycheck.properties or was specified using the
      * Settings object, and the path exists, that path will be returned as a File object. If it does not exist, then a
@@ -218,4 +248,17 @@ public final class FileUtils {
             }
         }
     }
+
+    /**
+     * Return the bit bucket for the OS. '/dev/null' for Unix and 'NUL' for Windows
+     *
+     * @return a String containing the bit bucket
+     */
+    public static String getBitBucket() {
+        if (System.getProperty("os.name").startsWith("Windows")) {
+            return BIT_BUCKET_WIN;
+        } else {
+            return BIT_BUCKET_UNIX;
+        }
+    }
 }

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

@@ -145,6 +145,26 @@ public final class Settings {
          * The key for a list of suppression files.
          */
         public static final String SUPPRESSION_FILE = "suppression.file";
+        /**
+         * The properties key for whether the Jar Analyzer is enabled.
+         */
+        public static final String ANALYZER_JAR_ENABLED = "analyzer.jar.enabled";
+        /**
+         * The properties key for whether the Archive analyzer is enabled.
+         */
+        public static final String ANALYZER_ARCHIVE_ENABLED = "analyzer.archive.enabled";
+        /**
+         * The properties key for whether the .NET Assembly analyzer is enabled.
+         */
+        public static final String ANALYZER_ASSEMBLY_ENABLED = "analyzer.assembly.enabled";
+        /**
+         * The properties key for whether the .NET Nuspec analyzer is enabled.
+         */
+        public static final String ANALYZER_NUSPEC_ENABLED = "analyzer.nuspec.enabled";
+        /**
+         * The properties key for whether the JavaScript analyzer is enabled.
+         */
+        public static final String ANALYZER_JAVASCRIPT_ENABLED = "analyzer.javascript.enabled";
         /**
          * The properties key for whether the Nexus analyzer is enabled.
          */
@@ -511,4 +531,28 @@ public final class Settings {
         }
         return value;
     }
+
+    /**
+     * Returns a boolean value from the properties file. If the value was specified as a system property or passed in
+     * via the <code>-Dprop=value</code> argument this method will return the value from the system properties before
+     * the values in the contained configuration file.
+     *
+     * @param key the key to lookup within the properties file
+     * @param defaultValue the default value to return if the setting does not exist
+     * @return the property from the properties file
+     * @throws InvalidSettingException is thrown if there is an error retrieving the setting
+     */
+    public static boolean getBoolean(String key, boolean defaultValue) throws InvalidSettingException {
+        boolean value;
+        try {
+            final String strValue = Settings.getString(key);
+            if (strValue == null) {
+                return defaultValue;
+            }
+            value = Boolean.parseBoolean(strValue);
+        } catch (NumberFormatException ex) {
+            throw new InvalidSettingException("Could not convert property '" + key + "' to an int.", ex);
+        }
+        return value;
+    }
 }

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

@@ -42,9 +42,15 @@ cve.startyear=2002
 cve.url-2.0.base=http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
 cve.url-1.2.base=http://nvd.nist.gov/download/nvdcve-%d.xml
 
+# file type analyzer settings:
+analyzer.archive.enabled=true
+analyzer.jar.enabled=true
+analyzer.nuspec.enabled=true
+analyzer.assembly.enabled=true
+
 # the URL for searching Nexus for SHA-1 hashes and whether it's enabled
 analyzer.nexus.enabled=true
-analyzer.nexus.url=http://repository.sonatype.org/service/local/
+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-core/src/main/resources/templates/HtmlReport.vsl

@@ -448,6 +448,11 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 color: blue;
                 float:right;
             }
+            .disclaimer {
+                color: #888888;
+                font: 9px "Droid Sans",Arial,"Helvetica Neue","Lucida Grande",sans-serif
+            }
+
         </style>
     </head>
     <body>
@@ -459,6 +464,12 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
         </div>
         <div class="wrapper">
             <h1>Dependency-Check Report</h1>
+<p class="disclaimer">Dependency-Check is an open source tool performing a best effort analysis of 3rd party dependencies;
+false positives and false negatives may exist in the analysis performed by the tool. Use of the tool and
+the reporting provided constitutes acceptance for use in an AS IS condition, and there are NO warranties,
+implied or otherwise, with regard to the analysis or its use. Any use of the tool and the reporting provided
+is at the user’s risk. In no event shall the copyright holder or OWASP be held liable for any damages whatsoever
+arising out of or in connection with the use of this tool, the analysis performed, or the resulting report.</p>
 ]]#
             <h2 class="">Project:&nbsp;$esc.html($applicationName)</h2>
             <div class="">
@@ -586,7 +597,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                                 #end
                                 #if ($id.type=="cpe")
                                     ##yes, we are HTML Encoding into JavaScript... the escape utils don't have a JS Encode and I haven't written one yet
-                                    &nbsp;&nbsp;<button class="copybutton" onclick="copyText('$esc.html($dependency.FileName)', '$esc.html($dependency.Sha1sum)', 'cpe', '$esc.html($id.value)')">suppress</button>
+                                    &nbsp;&nbsp;<button class="copybutton" onclick="copyText('$esc.html($dependency.FileNameForJavaScript)', '$esc.html($dependency.Sha1sum)', 'cpe', '$esc.html($id.value)')">suppress</button>
                                 #end
                                 #if ($id.description)
                                     <br/>$esc.html($id.description)
@@ -602,7 +613,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                     <div id="content$cnt" class="subsectioncontent standardsubsection">
                         #foreach($vuln in $dependency.getVulnerabilities())
                             #set($vsctr=$vsctr+1)
-                            <p><b><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/detail?vulnId=$esc.url($vuln.name)">$esc.html($vuln.name)</a></b>&nbsp;&nbsp;<button class="copybutton" onclick="copyText('$esc.html($dependency.FileName)', '$esc.html($dependency.Sha1sum)', 'cve', '$esc.html($vuln.name)')">suppress</button></p>
+                            <p><b><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/detail?vulnId=$esc.url($vuln.name)">$esc.html($vuln.name)</a></b>&nbsp;&nbsp;<button class="copybutton" onclick="copyText('$esc.html($dependency.FileNameForJavaScript)', '$esc.html($dependency.Sha1sum)', 'cve', '$esc.html($vuln.name)')">suppress</button></p>
                             <p>Severity:
                             #if ($vuln.cvssScore<4.0)
                                 Low

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

@@ -161,11 +161,22 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
                 margin-top:3px;
                 margin-bottom:3px;
             }
+            .disclaimer {
+                color: #888888;
+                font: 9px "Droid Sans",Arial,"Helvetica Neue","Lucida Grande",sans-serif
+            }
+
         </style>
     </head>
     <body>
         <div>
             <h1 class="sectionheader">Vulnerability Report</h1>
+<p class="disclaimer">Dependency-Check is an open source tool performing a best effort analysis of 3rd party dependencies;
+false positives and false negatives may exist in the analysis performed by the tool. Use of the tool and
+the reporting provided constitutes acceptance for use in an AS IS condition, and there are NO warranties,
+implied or otherwise, with regard to the analysis or its use. Any use of the tool and the reporting provided
+is at the user’s risk. In no event shall the copyright holder or OWASP be held liable for any damages whatsoever
+arising out of or in connection with the use of this tool, the analysis performed, or the resulting report.</p>
 ]]#
             <h2 class="sectionheader white">Project:&nbsp;$esc.html($applicationName)</h2>
             <div class="sectioncontent">Report Generated On: $date<br/><br/>

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

@@ -25,7 +25,9 @@ import org.junit.BeforeClass;
 import org.junit.Test;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
+import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.reporting.ReportGenerator;
+import org.owasp.dependencycheck.utils.Settings;
 
 /**
  *
@@ -57,6 +59,26 @@ public class EngineIntegrationTest {
      */
     @Test
     public void testScan() throws Exception {
+        String testClasses = "target/test-classes/*.zip";
+        boolean autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
+        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+        Engine instance = new Engine();
+        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
+        instance.scan(testClasses);
+        assertTrue(instance.getDependencies().size() > 0);
+        for (Dependency d : instance.getDependencies()) {
+            assertTrue("non-zip file collected " + d.getFileName(), d.getFileName().toLowerCase().endsWith(".zip"));
+        }
+        instance.cleanup();
+    }
+
+    /**
+     * Test running the entire engine.
+     *
+     * @throws Exception is thrown when an exception occurs.
+     */
+    @Test
+    public void testEngine() throws Exception {
         String testClasses = "target/test-classes";
         Engine instance = new Engine();
         instance.scan(testClasses);

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

@@ -30,9 +30,9 @@ import org.junit.Test;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class AbstractAnalyzerTest {
+public class AbstractFileTypeAnalyzerTest {
 
-    public AbstractAnalyzerTest() {
+    public AbstractFileTypeAnalyzerTest() {
     }
 
     @BeforeClass
@@ -56,7 +56,7 @@ public class AbstractAnalyzerTest {
      */
     @Test
     public void testNewHashSet() {
-        Set result = AbstractAnalyzer.newHashSet("one", "two");
+        Set result = AbstractFileTypeAnalyzer.newHashSet("one", "two");
         assertEquals(2, result.size());
         assertTrue(result.contains("one"));
         assertTrue(result.contains("two"));

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

@@ -0,0 +1,121 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.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 org.junit.After;
+import org.junit.AfterClass;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.suppression.SuppressionRule;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public class AbstractSuppressionAnalyzerTest {
+
+    public AbstractSuppressionAnalyzerTest() {
+    }
+
+    @BeforeClass
+    public static void setUpClass() {
+    }
+
+    @AfterClass
+    public static void tearDownClass() {
+    }
+
+    @Before
+    public void setUp() {
+        try {
+            final String uri = this.getClass().getClassLoader().getResource("suppressions.xml").toURI().toURL().toString();
+            Settings.setString(Settings.KEYS.SUPPRESSION_FILE, uri);
+        } catch (URISyntaxException ex) {
+            Logger.getLogger(AbstractSuppressionAnalyzerTest.class.getName()).log(Level.SEVERE, null, ex);
+        } catch (MalformedURLException ex) {
+            Logger.getLogger(AbstractSuppressionAnalyzerTest.class.getName()).log(Level.SEVERE, null, ex);
+        }
+    }
+
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * 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
+        public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
+            throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+        }
+
+        @Override
+        public String getName() {
+            throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+        }
+
+        @Override
+        public AnalysisPhase getAnalysisPhase() {
+            throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
+        }
+    }
+
+}

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

@@ -18,7 +18,6 @@
 package org.owasp.dependencycheck.analyzer;
 
 import java.util.Iterator;
-import java.util.Set;
 import org.junit.After;
 import org.junit.AfterClass;
 import static org.junit.Assert.assertTrue;
@@ -62,8 +61,7 @@ public class AnalyzerServiceTest {
         boolean found = false;
         while (result.hasNext()) {
             Analyzer a = result.next();
-            Set<String> e = a.getSupportedExtensions();
+            if ("Jar Analyzer".equals(a.getName())) {
-            if (e != null && e.contains("jar")) {
                 found = true;
             }
         }

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

@@ -26,7 +26,7 @@ import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.owasp.dependencycheck.Engine;
-import org.owasp.dependencycheck.data.cpe.BaseIndexTestCase;
+import org.owasp.dependencycheck.data.cpe.AbstractDatabaseTestCase;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.utils.Settings;
 
@@ -34,7 +34,7 @@ import org.owasp.dependencycheck.utils.Settings;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class ArchiveAnalyzerTest extends BaseIndexTestCase {
+public class ArchiveAnalyzerTest extends AbstractDatabaseTestCase {
 
     public ArchiveAnalyzerTest() {
     }
@@ -147,6 +147,8 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
     @Test
     public void testAnalyze() throws Exception {
         ArchiveAnalyzer instance = new ArchiveAnalyzer();
+        //trick the analyzer into thinking it is active.
+        instance.supportsExtension("ear");
         try {
             instance.initialize();
 
@@ -175,6 +177,8 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
     @Test
     public void testAnalyzeTar() throws Exception {
         ArchiveAnalyzer instance = new ArchiveAnalyzer();
+        //trick the analyzer into thinking it is active so that it will initialize
+        instance.supportsExtension("tar");
         try {
             instance.initialize();
 
@@ -203,6 +207,7 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
     @Test
     public void testAnalyzeTarGz() throws Exception {
         ArchiveAnalyzer instance = new ArchiveAnalyzer();
+        instance.supportsExtension("zip"); //ensure analyzer is "enabled"
         try {
             instance.initialize();
 
@@ -252,6 +257,7 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
     @Test
     public void testAnalyzeTgz() throws Exception {
         ArchiveAnalyzer instance = new ArchiveAnalyzer();
+        instance.supportsExtension("zip"); //ensure analyzer is "enabled"
         try {
             instance.initialize();
 

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

@@ -17,14 +17,17 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+import static org.junit.Assume.assumeFalse;
+
 import java.io.File;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.junit.After;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
 import org.junit.Assume;
-import static org.junit.Assume.assumeFalse;
 import org.junit.Before;
 import org.junit.Test;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
@@ -54,6 +57,7 @@ public class AssemblyAnalyzerTest {
     public void setUp() {
         try {
             analyzer = new AssemblyAnalyzer();
+            analyzer.supportsExtension("dll");
             analyzer.initialize();
         } catch (Exception e) {
             LOGGER.log(Level.WARNING, "Exception setting up AssemblyAnalyzer. Tests will be incomplete", e);
@@ -74,7 +78,21 @@ public class AssemblyAnalyzerTest {
         File f = new File(AssemblyAnalyzerTest.class.getClassLoader().getResource("GrokAssembly.exe").getPath());
         Dependency d = new Dependency(f);
         analyzer.analyze(d, null);
-        assertTrue(d.getVersionEvidence().getEvidence().contains(new Evidence("grokassembly", "version", "1.0.5140.29700", Confidence.HIGHEST)));
+        boolean foundVendor = false;
+        for (Evidence e : d.getVendorEvidence().getEvidence("grokassembly", "vendor")) {
+            if ("OWASP".equals(e.getValue())) {
+                foundVendor = true;
+            }
+        }
+        assertTrue(foundVendor);
+        
+        boolean foundProduct = false;
+        for (Evidence e : d.getProductEvidence().getEvidence("grokassembly", "product")) {
+            if ("GrokAssembly".equals(e.getValue())) {
+                foundProduct = true;
+            }
+        }
+        assertTrue(foundProduct);
     }
 
     @Test
@@ -87,15 +105,29 @@ public class AssemblyAnalyzerTest {
         assertTrue(d.getProductEvidence().getEvidence().contains(new Evidence("grokassembly", "product", "log4net", Confidence.HIGH)));
     }
 
-    @Test(expected = AnalysisException.class)
+    @Test
-    public void testNonexistent() throws Exception {
+    public void testNonexistent() {
+        Level oldLevel = Logger.getLogger(AssemblyAnalyzer.class.getName()).getLevel();
+        Level oldDependency = Logger.getLogger(Dependency.class.getName()).getLevel();
+        // Tweak the log level so the warning doesn't show in the console
+        Logger.getLogger(AssemblyAnalyzer.class.getName()).setLevel(Level.OFF);
+        Logger.getLogger(Dependency.class.getName()).setLevel(Level.OFF);
         File f = new File(AssemblyAnalyzerTest.class.getClassLoader().getResource("log4net.dll").getPath());
         File test = new File(f.getParent(), "nonexistent.dll");
         Dependency d = new Dependency(test);
-        analyzer.analyze(d, null);
+
+        try {
+            analyzer.analyze(d, null);
+            fail("Expected an AnalysisException");
+        } catch (AnalysisException ae) {
+            assertEquals("File does not exist", ae.getMessage());
+        } finally {
+            Logger.getLogger(AssemblyAnalyzer.class.getName()).setLevel(oldLevel);
+            Logger.getLogger(Dependency.class.getName()).setLevel(oldDependency);
+        }
     }
 
-    @Test(expected = AnalysisException.class)
+    @Test
     public void testWithSettingMono() throws Exception {
 
         //This test doesn't work on Windows.
@@ -112,11 +144,20 @@ public class AssemblyAnalyzerTest {
             Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, "/yooser/bine/mono");
         }
 
+        Level oldLevel = Logger.getLogger(AssemblyAnalyzer.class.getName()).getLevel();
         try {
+            // Tweak the logging to swallow the warning when testing
+            Logger.getLogger(AssemblyAnalyzer.class.getName()).setLevel(Level.OFF);
             // Have to make a NEW analyzer because during setUp, it would have gotten the correct one
             AssemblyAnalyzer aanalyzer = new AssemblyAnalyzer();
+            aanalyzer.supportsExtension("dll");
             aanalyzer.initialize();
+            fail("Expected an AnalysisException");
+        } catch (AnalysisException ae) {
+            assertEquals("An error occured with the .NET AssemblyAnalyzer", ae.getMessage());
         } finally {
+            // Recover the logger
+            Logger.getLogger(AssemblyAnalyzer.class.getName()).setLevel(oldLevel);
             // Now recover the way we came in. If we had to set a System property, delete it. Otherwise,
             // reset the old value
             if (oldValue == null) {

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

@@ -30,7 +30,7 @@ import org.junit.Assert;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
-import org.owasp.dependencycheck.data.cpe.BaseIndexTestCase;
+import org.owasp.dependencycheck.data.cpe.AbstractDatabaseTestCase;
 import org.owasp.dependencycheck.data.cpe.IndexEntry;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Identifier;
@@ -39,7 +39,7 @@ import org.owasp.dependencycheck.dependency.Identifier;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class CPEAnalyzerTest extends BaseIndexTestCase {
+public class CPEAnalyzerTest extends AbstractDatabaseTestCase {
 
     @BeforeClass
     public static void setUpClass() throws Exception {

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

@@ -17,11 +17,9 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.util.Set;
 import org.junit.After;
 import org.junit.AfterClass;
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -52,16 +50,6 @@ public class DependencyBundlingAnalyzerTest {
     public void tearDown() {
     }
 
-    /**
-     * Test of getSupportedExtensions method, of class DependencyBundlingAnalyzer.
-     */
-    @Test
-    public void testGetSupportedExtensions() {
-        DependencyBundlingAnalyzer instance = new DependencyBundlingAnalyzer();
-        Set<String> result = instance.getSupportedExtensions();
-        assertNull(result);
-    }
-
     /**
      * Test of getName method, of class DependencyBundlingAnalyzer.
      */
@@ -73,18 +61,6 @@ public class DependencyBundlingAnalyzerTest {
         assertEquals(expResult, result);
     }
 
-    /**
-     * Test of supportsExtension method, of class DependencyBundlingAnalyzer.
-     */
-    @Test
-    public void testSupportsExtension() {
-        String extension = "jar";
-        DependencyBundlingAnalyzer instance = new DependencyBundlingAnalyzer();
-        boolean expResult = true;
-        boolean result = instance.supportsExtension(extension);
-        assertEquals(expResult, result);
-    }
-
     /**
      * Test of getAnalysisPhase method, of class DependencyBundlingAnalyzer.
      */

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

@@ -15,11 +15,9 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.util.Set;
 import org.junit.After;
 import org.junit.AfterClass;
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertTrue;
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -52,17 +50,6 @@ public class FalsePositiveAnalyzerTest {
     public void tearDown() {
     }
 
-    /**
-     * Test of getSupportedExtensions method, of class FalsePositiveAnalyzer.
-     */
-    @Test
-    public void testGetSupportedExtensions() {
-        FalsePositiveAnalyzer instance = new FalsePositiveAnalyzer();
-        Set<String> result = instance.getSupportedExtensions();
-        assertNull(result);
-
-    }
-
     /**
      * Test of getName method, of class FalsePositiveAnalyzer.
      */
@@ -74,18 +61,6 @@ public class FalsePositiveAnalyzerTest {
         assertEquals(expResult, result);
     }
 
-    /**
-     * Test of supportsExtension method, of class FalsePositiveAnalyzer.
-     */
-    @Test
-    public void testSupportsExtension() {
-        String extension = "any";
-        FalsePositiveAnalyzer instance = new FalsePositiveAnalyzer();
-        boolean expResult = true;
-        boolean result = instance.supportsExtension(extension);
-        assertEquals(expResult, result);
-    }
-
     /**
      * Test of getAnalysisPhase method, of class FalsePositiveAnalyzer.
      */

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

@@ -18,7 +18,6 @@
 package org.owasp.dependencycheck.analyzer;
 
 import java.io.File;
-import java.util.Set;
 import org.junit.After;
 import org.junit.AfterClass;
 import static org.junit.Assert.assertEquals;
@@ -53,17 +52,6 @@ public class FileNameAnalyzerTest {
     public void tearDown() {
     }
 
-    /**
-     * Test of getSupportedExtensions method, of class FileNameAnalyzer.
-     */
-    @Test
-    public void testGetSupportedExtensions() {
-        FileNameAnalyzer instance = new FileNameAnalyzer();
-        Set expResult = null;
-        Set result = instance.getSupportedExtensions();
-        assertEquals(expResult, result);
-    }
-
     /**
      * Test of getName method, of class FileNameAnalyzer.
      */
@@ -75,18 +63,6 @@ public class FileNameAnalyzerTest {
         assertEquals(expResult, result);
     }
 
-    /**
-     * Test of supportsExtension method, of class FileNameAnalyzer.
-     */
-    @Test
-    public void testSupportsExtension() {
-        String extension = "any";
-        FileNameAnalyzer instance = new FileNameAnalyzer();
-        boolean expResult = true;
-        boolean result = instance.supportsExtension(extension);
-        assertEquals(expResult, result);
-    }
-
     /**
      * Test of getAnalysisPhase method, of class FileNameAnalyzer.
      */

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

@@ -17,39 +17,43 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 import org.junit.Before;
 import org.junit.Test;
-import static org.junit.Assert.*;
 
 public class NuspecAnalyzerTest {
-  private NuspecAnalyzer instance;
 
-  @Before
+    private NuspecAnalyzer instance;
-  public void setUp() {
-    instance = new NuspecAnalyzer();
-  }
 
-  @Test
+    @Before
-  public void testGetAnalyzerName() {
+    public void setUp() {
-    assertEquals("Nuspec Analyzer", instance.getName());
+        instance = new NuspecAnalyzer();
-  }
+        instance.setEnabled(true);
+    }
 
-  @Test
+    @Test
-  public void testGetSupportedExtensions() {
+    public void testGetAnalyzerName() {
-    assertTrue(instance.getSupportedExtensions().contains("nuspec"));
+        assertEquals("Nuspec Analyzer", instance.getName());
-    assertFalse(instance.getSupportedExtensions().contains("nupkg"));
+    }
-  }
 
-  @Test
+    @Test
-  public void testSupportsExtension() {
+    public void testGetSupportedExtensions() {
-    assertTrue(instance.supportsExtension("nuspec"));
+        assertTrue(instance.getSupportedExtensions().contains("nuspec"));
-    assertFalse(instance.supportsExtension("nupkg"));
+        assertFalse(instance.getSupportedExtensions().contains("nupkg"));
-  }
+    }
 
-  @Test
+    @Test
-  public void testGetAnalysisPhaze() {
+    public void testSupportsExtension() {
-    assertEquals(AnalysisPhase.INFORMATION_COLLECTION, instance.getAnalysisPhase());
+        assertTrue(instance.supportsExtension("nuspec"));
-  }
+        assertFalse(instance.supportsExtension("nupkg"));
+    }
+
+    @Test
+    public void testGetAnalysisPhaze() {
+        assertEquals(AnalysisPhase.INFORMATION_COLLECTION, instance.getAnalysisPhase());
+    }
 }
 
 // vim: cc=120:sw=4:ts=4:sts=4

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

@@ -0,0 +1,128 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.File;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.data.cpe.AbstractDatabaseTestCase;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * Testing the vulnerability suppression analyzer.
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public class VulnerabilitySuppressionAnalyzerTest extends AbstractDatabaseTestCase {
+
+    public VulnerabilitySuppressionAnalyzerTest() {
+    }
+
+    @BeforeClass
+    public static void setUpClass() {
+    }
+
+    @AfterClass
+    public static void tearDownClass() {
+    }
+    private boolean update = true;
+    private boolean nexus = false;
+
+    @Before
+    @Override
+    public void setUp() throws Exception {
+        super.setUp();
+        update = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
+        nexus = Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED);
+        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
+    }
+
+    @After
+    @Override
+    public void tearDown() throws Exception {
+        super.tearDown();
+        Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, update);
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexus);
+    }
+
+    /**
+     * Test of getName method, of class VulnerabilitySuppressionAnalyzer.
+     */
+    @Test
+    public void testGetName() {
+        VulnerabilitySuppressionAnalyzer instance = new VulnerabilitySuppressionAnalyzer();
+        String expResult = "Vulnerability Suppression Analyzer";
+        String result = instance.getName();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of getAnalysisPhase method, of class VulnerabilitySuppressionAnalyzer.
+     */
+    @Test
+    public void testGetAnalysisPhase() {
+        VulnerabilitySuppressionAnalyzer instance = new VulnerabilitySuppressionAnalyzer();
+        AnalysisPhase expResult = AnalysisPhase.POST_FINDING_ANALYSIS;;
+        AnalysisPhase result = instance.getAnalysisPhase();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of analyze method, of class VulnerabilitySuppressionAnalyzer.
+     */
+    @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());
+
+        Engine engine = new Engine();
+        engine.scan(file);
+        engine.analyzeDependencies();
+        Dependency dependency = getDependency(engine, file);
+        assertTrue(dependency.getVulnerabilities().size() > 0);
+        Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppression.getAbsolutePath());
+        VulnerabilitySuppressionAnalyzer instance = new VulnerabilitySuppressionAnalyzer();
+        instance.initialize();
+        instance.analyze(dependency, engine);
+        assertTrue(dependency.getVulnerabilities().size() == 0);
+        engine.cleanup();
+    }
+
+    /**
+     * Retrieves a specific dependency from the engine.
+     *
+     * @param engine the engine
+     * @param file the dependency to retrieve
+     * @return the dependency
+     */
+    private Dependency getDependency(Engine engine, File file) {
+        for (Dependency d : engine.getDependencies()) {
+            if (d.getFileName().equals(file.getName())) {
+                return d;
+            }
+        }
+        return null;
+    }
+}

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/cpe/AbstractDatabaseTestCase.java

@@ -25,10 +25,12 @@ import org.junit.BeforeClass;
 import org.owasp.dependencycheck.data.nvdcve.BaseDBTestCase;
 
 /**
+ * An abstract database test case that is used to ensure the H2 DB exists prior to performing tests that utilize the
+ * data contained within.
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public abstract class BaseIndexTestCase extends TestCase {
+public abstract class AbstractDatabaseTestCase extends TestCase {
 
     @BeforeClass
     public static void setUpClass() throws Exception {

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

@@ -73,7 +73,7 @@ public class FileUtilsTest {
     @Test
     public void testDelete() throws Exception {
 
-        File file = File.createTempFile("tmp", "deleteme");
+        File file = File.createTempFile("tmp", "deleteme", Settings.getTempDirectory());
         if (!file.exists()) {
             fail("Unable to create a temporary file.");
         }

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

@@ -155,6 +155,11 @@ public class SettingsTest {
         boolean expResult = false;
         boolean result = Settings.getBoolean(key);
         Assert.assertEquals(expResult, result);
+
+        key = "something that does not exist";
+        expResult = true;
+        result = Settings.getBoolean(key, true);
+        Assert.assertEquals(expResult, result);
     }
 
     /**

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

@@ -0,0 +1,10 @@
+<?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/dependencycheck.properties

@@ -49,7 +49,7 @@ 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=http://repository.sonatype.org/service/local/
+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-jenkins/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.1.2</version>
+        <version>1.1.4</version>
     </parent>
 
     <groupId>org.owasp</groupId>

dependency-check-maven/pom.xml

@@ -23,7 +23,7 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
     <parent>
         <groupId>org.owasp</groupId>
         <artifactId>dependency-check-parent</artifactId>
-        <version>1.1.2</version>
+        <version>1.1.4</version>
     </parent>
 
     <artifactId>dependency-check-maven</artifactId>
@@ -275,6 +275,11 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
             <artifactId>maven-plugin-api</artifactId>
             <version>3.0</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.maven</groupId>
+            <artifactId>maven-settings</artifactId>
+            <version>3.0</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.maven</groupId>
             <artifactId>maven-core</artifactId>

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

@@ -44,6 +44,7 @@ import org.apache.maven.project.MavenProject;
 import org.apache.maven.reporting.MavenMultiPageReport;
 import org.apache.maven.reporting.MavenReport;
 import org.apache.maven.reporting.MavenReportException;
+import org.apache.maven.settings.Proxy;
 import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
@@ -87,48 +88,45 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     @Component
     private MavenProject project;
     /**
-     * The name of the site report destination.
+     * The path to the verbose log.
-     */
-    @Parameter(property = "report-name", defaultValue = "dependency-check-report")
-    private String reportName;
-    /**
-     * The path to the verbose log
      */
     @Parameter(property = "logfile", defaultValue = "")
     private String logFile;
     /**
-     * The name of the report to be displayed in the Maven Generated Reports page
+     * The name of the report to be displayed in the Maven Generated Reports page.
      */
     @Parameter(property = "name", defaultValue = "Dependency-Check")
     private String name;
     /**
-     * The description of the Dependency-Check report to be displayed in the Maven Generated Reports page
+     * The description of the Dependency-Check report to be displayed in the Maven Generated Reports page.
      */
     @Parameter(property = "description", defaultValue = "A report providing details on any published "
             + "vulnerabilities within project dependencies. This report is a best effort but may contain "
             + "false positives and false negatives.")
     private String description;
     /**
-     * Specifies the destination directory for the generated Dependency-Check report.
+     * Specifies the destination directory for the generated Dependency-Check report. This generally maps to
+     * "target/site".
      */
     @Parameter(property = "reportOutputDirectory", defaultValue = "${project.reporting.outputDirectory}", required = true)
     private File reportOutputDirectory;
     /**
-     * Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11
+     * The output directory. This generally maps to "target".
-     * which means since the CVSS scores are 0-10, by default the build will never fail.
-     */
-    @Parameter(property = "failBuildOnCVSS", defaultValue = "11", required = true)
-    private float failBuildOnCVSS = 11;
-    /**
-     * The output directory.
      */
     @Parameter(defaultValue = "${project.build.directory}", required = true)
     private File outputDirectory;
+    /**
+     * Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11
+     * which means since the CVSS scores are 0-10, by default the build will never fail.
+     */
+    @SuppressWarnings("CanBeFinal")
+    @Parameter(property = "failBuildOnCVSS", defaultValue = "11", required = true)
+    private float failBuildOnCVSS = 11;
     /**
      * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to
      * false. Default is true.
      */
-    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @SuppressWarnings("CanBeFinal")
     @Parameter(property = "autoupdate", defaultValue = "true", required = true)
     private boolean autoUpdate = true;
     /**
@@ -146,27 +144,54 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     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.
+     */
+    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @Parameter(property = "mavenSettings", defaultValue = "${settings}", required = false)
+    private org.apache.maven.settings.Settings mavenSettings;
+
+    /**
+     * The maven settings proxy id.
+     */
+    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @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.
@@ -186,6 +211,35 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
     @Parameter(property = "showSummary", defaultValue = "true", required = false)
     private boolean showSummary = true;
+
+    /**
+     * Whether or not the Jar Analyzer is enabled.
+     */
+    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @Parameter(property = "jarAnalyzerEnabled", defaultValue = "true", required = false)
+    private boolean jarAnalyzerEnabled = true;
+
+    /**
+     * Whether or not the Archive Analyzer is enabled.
+     */
+    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @Parameter(property = "archiveAnalyzerEnabled", defaultValue = "true", required = false)
+    private boolean archiveAnalyzerEnabled = true;
+
+    /**
+     * Whether or not the .NET Assembly Analyzer is enabled.
+     */
+    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @Parameter(property = "assemblyAnalyzerEnabled", defaultValue = "true", required = false)
+    private boolean assemblyAnalyzerEnabled = true;
+
+    /**
+     * Whether or not the .NET Nuspec Analyzer is enabled.
+     */
+    @SuppressWarnings({"CanBeFinal", "FieldCanBeLocal"})
+    @Parameter(property = "nuspecAnalyzerEnabled", defaultValue = "true", required = false)
+    private boolean nuspecAnalyzerEnabled = true;
+
     /**
      * Whether or not the Nexus Analyzer is enabled.
      */
@@ -240,18 +294,21 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     @Parameter(property = "zipExtensions", required = false)
     private String zipExtensions;
     /**
-     * Skip Analisys for Test Scope Dependencies
+     * Skip Analisys for Test Scope Dependencies.
      */
+    @SuppressWarnings("CanBeFinal")
     @Parameter(property = "skipTestScope", defaultValue = "true", required = false)
     private boolean skipTestScope = true;
     /**
-     * Skip Analisys for Runtime Scope Dependencies
+     * Skip Analisys for Runtime Scope Dependencies.
      */
+    @SuppressWarnings("CanBeFinal")
     @Parameter(property = "skipRuntimeScope", defaultValue = "false", required = false)
     private boolean skipRuntimeScope = false;
     /**
-     * Skip Analisys for Provided Scope Dependencies
+     * Skip Analisys for Provided Scope Dependencies.
      */
+    @SuppressWarnings("CanBeFinal")
     @Parameter(property = "skipProvidedScope", defaultValue = "false", required = false)
     private boolean skipProvidedScope = false;
     /**
@@ -260,26 +317,32 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     @Parameter(property = "dataDirectory", defaultValue = "", required = false)
     private String dataDirectory;
     /**
-     * Data Mirror URL for CVE 1.2
+     * Data Mirror URL for CVE 1.2.
      */
     @Parameter(property = "cveUrl12Modified", defaultValue = "", required = false)
     private String cveUrl12Modified;
     /**
-     * Data Mirror URL for CVE 2.0
+     * Data Mirror URL for CVE 2.0.
      */
     @Parameter(property = "cveUrl20Modified", defaultValue = "", required = false)
     private String cveUrl20Modified;
     /**
-     * Base Data Mirror URL for CVE 1.2
+     * Base Data Mirror URL for CVE 1.2.
      */
     @Parameter(property = "cveUrl12Base", defaultValue = "", required = false)
     private String cveUrl12Base;
     /**
-     * Data Mirror URL for CVE 2.0
+     * Data Mirror URL for CVE 2.0.
      */
     @Parameter(property = "cveUrl20Base", defaultValue = "", required = false)
     private String cveUrl20Base;
 
+    /**
+     * The path to mono for .NET Assembly analysis on non-windows systems.
+     */
+    @Parameter(property = "pathToMono", defaultValue = "", required = false)
+    private String pathToMono;
+
     // </editor-fold>
     /**
      * Executes the Dependency-Check on the dependent libraries.
@@ -325,8 +388,9 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
      * Generates the reports for a given dependency-check engine.
      *
      * @param engine a dependency-check engine
+     * @param outDirectory the directory to write the reports to
      */
-    private void generateExternalReports(Engine engine) {
+    private void generateExternalReports(Engine engine, File outDirectory) {
         DatabaseProperties prop = null;
         CveDB cve = null;
         try {
@@ -342,7 +406,7 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
         }
         final ReportGenerator r = new ReportGenerator(project.getName(), engine.getDependencies(), engine.getAnalyzers(), prop);
         try {
-            r.generateReports(outputDirectory.getCanonicalPath(), format);
+            r.generateReports(outDirectory.getCanonicalPath(), format);
         } catch (IOException ex) {
             Logger.getLogger(DependencyCheckMojo.class.getName()).log(Level.SEVERE,
                     "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
@@ -711,6 +775,41 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
     }
     // </editor-fold>
 
+    /**
+     * Returns the maven settings proxy url.
+     *
+     * @param proxy the maven proxy
+     * @return the proxy url
+     */
+    private String getMavenSettingsProxyUrl(Proxy proxy) {
+        return new StringBuilder(proxy.getProtocol()).append("://").append(proxy.getHost()).toString();
+    }
+
+    /**
+     * Returns the maven proxy.
+     *
+     * @return the maven proxy
+     */
+    private Proxy getMavenProxy() {
+        if (mavenSettings != null) {
+            final List<Proxy> proxies = mavenSettings.getProxies();
+            if (proxies != null && proxies.size() > 0) {
+                if (mavenSettingsProxyId != null) {
+                    for (Proxy proxy : proxies) {
+                        if (mavenSettingsProxyId.equalsIgnoreCase(proxy.getId())) {
+                            return proxy;
+                        }
+                    }
+                } else if (proxies.size() == 1) {
+                    return proxies.get(0);
+                } else {
+                    throw new IllegalStateException("Ambigous proxy definition");
+                }
+            }
+        }
+        return null;
+    }
+
     /**
      * 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.
@@ -735,6 +834,18 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
 
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
 
+        final Proxy proxy = getMavenProxy();
+        if (proxy != null) {
+            Settings.setString(Settings.KEYS.PROXY_URL, getMavenSettingsProxyUrl(proxy));
+            Settings.setString(Settings.KEYS.PROXY_PORT, Integer.toString(proxy.getPort()));
+            final String userName = proxy.getUsername();
+            final String password = proxy.getPassword();
+            if (userName != null && password != null) {
+                Settings.setString(Settings.KEYS.PROXY_USERNAME, userName);
+                Settings.setString(Settings.KEYS.PROXY_PASSWORD, password);
+            }
+        }
+
         if (proxyUrl != null && !proxyUrl.isEmpty()) {
             Settings.setString(Settings.KEYS.PROXY_URL, proxyUrl);
         }
@@ -753,11 +864,30 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
         if (suppressionFile != null && !suppressionFile.isEmpty()) {
             Settings.setString(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
         }
+
+        //File Type Analyzer Settings
+        //JAR ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_JAR_ENABLED, jarAnalyzerEnabled);
+        //NUSPEC ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, nuspecAnalyzerEnabled);
+        //NEXUS ANALYZER
         Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
         if (nexusUrl != null && !nexusUrl.isEmpty()) {
             Settings.setString(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
         }
         Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY, nexusUsesProxy);
+        //ARCHIVE ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, archiveAnalyzerEnabled);
+        if (zipExtensions != null && !zipExtensions.isEmpty()) {
+            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
+        }
+        //ASSEMBLY ANALYZER
+        Settings.setBoolean(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, assemblyAnalyzerEnabled);
+        if (pathToMono != null && !pathToMono.isEmpty()) {
+            Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+        }
+
+        //Database configuration
         if (databaseDriverName != null && !databaseDriverName.isEmpty()) {
             Settings.setString(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
         }
@@ -773,8 +903,9 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
         if (databasePassword != null && !databasePassword.isEmpty()) {
             Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
         }
-        if (zipExtensions != null && !zipExtensions.isEmpty()) {
+        // Data Directory
-            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
+        if (dataDirectory != null && !dataDirectory.isEmpty()) {
+            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
         }
 
         // Scope Exclusion
@@ -782,11 +913,6 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
         Settings.setBoolean(Settings.KEYS.SKIP_RUNTIME_SCOPE, skipRuntimeScope);
         Settings.setBoolean(Settings.KEYS.SKIP_PROVIDED_SCOPE, skipProvidedScope);
 
-        // Data Directory
-        if (dataDirectory != null && !dataDirectory.isEmpty()) {
-            Settings.setString(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
-        }
-
         // CVE Data Mirroring
         if (cveUrl12Modified != null && !cveUrl12Modified.isEmpty()) {
             Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
@@ -800,6 +926,7 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
         if (cveUrl20Base != null && !cveUrl20Base.isEmpty()) {
             Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
         }
+
     }
 
     /**
@@ -812,7 +939,7 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
         Engine engine = null;
         try {
             engine = executeDependencyCheck();
-            generateExternalReports(engine);
+            generateExternalReports(engine, outputDirectory);
             if (this.showSummary) {
                 showSummary(engine.getDependencies());
             }
@@ -854,7 +981,11 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
         Engine engine = null;
         try {
             engine = executeDependencyCheck();
-            generateMavenSiteReport(engine, sink);
+            if (this.externalReport) {
+                generateExternalReports(engine, reportOutputDirectory);
+            } else {
+                generateMavenSiteReport(engine, sink);
+            }
         } catch (DatabaseException ex) {
             Logger.getLogger(DependencyCheckMojo.class.getName()).log(Level.SEVERE,
                     "Unable to connect to the dependency-check database; analysis has stopped");
@@ -873,7 +1004,18 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
      * @return the output name
      */
     public String getOutputName() {
-        return reportName;
+        if ("HTML".equalsIgnoreCase(this.format)
+                || "ALL".equalsIgnoreCase(this.format)) {
+            return "dependency-check-report";
+        } else if ("XML".equalsIgnoreCase(this.format)) {
+            return "dependency-check-report.xml#";
+        } else if ("VULN".equalsIgnoreCase(this.format)) {
+            return "dependency-check-vulnerability";
+        } else {
+            Logger.getLogger(DependencyCheckMojo.class
+                    .getName()).log(Level.WARNING, "Unknown report format used during site generatation.");
+            return "dependency-check-report";
+        }
     }
 
     /**
@@ -1009,7 +1151,9 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
             final String msg = String.format("%n%n"
                     + "One or more dependencies were identified with known vulnerabilities:%n%n%s"
                     + "%n%nSee the dependency-check report for more details.%n%n", summary.toString());
-            Logger.getLogger(DependencyCheckMojo.class.getName()).log(Level.WARNING, msg);
+            Logger
+                    .getLogger(DependencyCheckMojo.class
+                            .getName()).log(Level.WARNING, msg);
         }
     }
 }

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

@@ -6,29 +6,66 @@ Property             | Description                        | Default Value
 ---------------------|------------------------------------|------------------
 autoUpdate           | Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to false. | true
 externalReport       | When using as a Site plugin this parameter sets whether or not the external report format should be used. | false
+outputDirectory      | The location to write the report(s). Note, this is not used if generating the report as part of a `mvn site` build | 'target'
 failBuildOnCVSS      | Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11 which means since the CVSS scores are 0-10, by default the build will never fail.         | 11
 format               | The report format to be generated (HTML, XML, VULN, ALL). This configuration option has no affect if using this within the Site plugin unless the externalReport is set to true. | HTML
-logFile              | The file path to write verbose logging information. |
+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) |
+suppressionFile      | The file path to the XML suppression file \- used to suppress [false positives](../suppression.html) |  
-connectionTimeout    | The Connection Timeout.            |
+skipTestScope        | Should be skip analysis for artifacts with Test Scope | true
-proxyUrl             | The Proxy URL.                     |
+skipProvidedScope    | Should be skip analysis for artifacts with Provided Scope | false
-proxyPort            | The Proxy Port.                    |
+skipRuntimeScope     | Should be skip analysis for artifacts with Runtime Scope | false
-proxyUsername        | Defines the proxy user name.       |
+
-proxyPassword        | Defines the proxy password.        |
+Analyzer Configuration
-nexusAnalyzerEnabled | Sets whether Nexus Analyzer will be used. |
+====================
-nexusUrl             | Defines the Nexus URL. |
+The following properties are used to configure the various file type analyzers.
-nexusUsesProxy       | Whether or not the defined proxy should be used when connecting to Nexus. | true
+These properties can be used to turn off specific analyzers if it is not needed.
-databaseDriverName   | The name of the database driver. Example: org.h2.Driver. |
+Note, that specific analyzers will automatically disable themselves if no file
-databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path. |
+types that they support are detected - so specifically disabling them may not
-connectionString     | The connection string used to connect to the database. |
+be needed.
-databaseUser         | The username used when connecting to the database. |
+
-databasePassword     | The password used when connecting to the database. |
+Property                | Description                        | Default Value
-zipExtensions        | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. |
+------------------------|------------------------------------|------------------
-skipTestScope | Should be skip analysis for artifacts with Test Scope | true
+archiveAnalyzerEnabled  | Sets whether the Archive Analyzer will be used.                    | true
-skipProvidedScope | Should be skip analysis for artifacts with Provided Scope | false
+zipExtensions           | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. |  
-skipRuntimeScope | Should be skip analysis for artifacts with Runtime Scope | false
+jarAnalyzer             | Sets whether Jar Analyzer will be used.                            | true
-dataDirectory | Data directory to hold SQL CVEs contents. This should generally not be changed. |
+nexusAnalyzerEnabled    | Sets whether Nexus Analyzer will be used.                          | true
-cveUrl12Modified | URL for the modified CVE 1.2 | http://nvd.nist.gov/download/nvdcve-modified.xml
+nexusUrl                | Defines the Nexus URL. | https://repository.sonatype.org/service/local/
-cveUrl20Modified | URL for the modified CVE 2.0 | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+nexusUsesProxy          | Whether or not the defined proxy should be used when connecting to Nexus. | true
-cveUrl12Base | Base URL for each year's CVE 1.2, the %d will be replaced with the year | http://nvd.nist.gov/download/nvdcve-%d.xml
+nuspecAnalyzerEnabled  | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.   | true
-cveUrl20Base | Base URL for each year's CVE 2.0, the %d will be replaced with the year | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+assemblyAnalyzerEnabled | Sets whether or not the .NET Assembly Analyzer should be used.     | true
+pathToMono              | The path to Mono for .NET assembly analysis on non-windows systems |  
+
+Advanced Configuration
+====================
+The following properties can be configured in the plugin. However, they are less frequently changed. One exception
+may be the cvedUrl properties, which can be used to host a mirror of the NVD within an enterprise environment.
+
+Property             | Description                                                             | Default Value
+---------------------|-------------------------------------------------------------------------|------------------
+cveUrl12Modified     | URL for the modified CVE 1.2                                            | http://nvd.nist.gov/download/nvdcve-modified.xml
+cveUrl20Modified     | URL for the modified CVE 2.0                                            | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-modified.xml
+cveUrl12Base         | Base URL for each year's CVE 1.2, the %d will be replaced with the year | http://nvd.nist.gov/download/nvdcve-%d.xml
+cveUrl20Base         | Base URL for each year's CVE 2.0, the %d will be replaced with the year | http://static.nvd.nist.gov/feeds/xml/cve/nvdcve-2.0-%d.xml
+connectionTimeout    | The URL Connection Timeout.                                                                 |  
+dataDirectory        | Data directory to hold SQL CVEs contents. This should generally not be changed.             |  
+databaseDriverName   | The name of the database driver. Example: org.h2.Driver.                                    |  
+databaseDriverPath   | The path to the database driver JAR file; only used if the driver is not in the class path. |  
+connectionString     | The connection string used to connect to the database.                                      |  
+databaseUser         | The username used when connecting to the database.                                          |  
+databasePassword     | The password used when connecting to the database.                                          |  
+
+
+Deprecated Configuration
+====================
+The following properties have been deprecated. These can stell 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.        |  

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

@@ -10,8 +10,9 @@ Vulnerability Database (NVD) hosted by NIST: https://nvd.nist.gov
 After the first batch download, as long as the plugin is executed at least once every
 seven days the update will only take a few seconds.
 
-Example 1:
+#set( $H = '#' )
----------------------
+
+$H$H$H Example 1:
 Create the DependencyCheck-report.html in the target directory
 
 ```xml
@@ -39,8 +40,7 @@ Create the DependencyCheck-report.html in the target directory
 </project>
 ```
 
-Example 2:
+$H$H$H Example 2:
----------------------
 Create the DependencyCheck-report.html and fail the build for CVSS greater then 8
 
 ```xml
@@ -71,8 +71,7 @@ Create the DependencyCheck-report.html and fail the build for CVSS greater then
 </project>
 ```
 
-Example 3:
+$H$H$H Example 3:
----------------------
 Create the dependency-check report within the site
 
 ```xml
@@ -103,8 +102,8 @@ Create the dependency-check report within the site
     ...
 </project>
 ```
-Example 4:
+
----------------------
+$H$H$H Example 4:
 Create the DependencyCheck-report.html and skip artifacts no bundled in distribution (Provided and Runtime scope)
 
 ```xml
@@ -135,8 +134,8 @@ Create the DependencyCheck-report.html and skip artifacts no bundled in distribu
     ...
 </project>
 ```
-Example 5:
+
----------------------
+$H$H$H Example 5:
 Create the DependencyCheck-report.html and use internal mirroring of CVE contents
 
 ```xml
@@ -169,4 +168,3 @@ Create the DependencyCheck-report.html and use internal mirroring of CVE content
     ...
 </project>
 ```
-

pom.xml

@@ -20,7 +20,7 @@ Copyright (c) 2012 - Jeremy Long
 
     <groupId>org.owasp</groupId>
     <artifactId>dependency-check-parent</artifactId>
-    <version>1.1.2</version>
+    <version>1.1.4</version>
     <packaging>pom</packaging>
 
     <modules>

src/site/site.xml

@@ -50,7 +50,7 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
               title="built with maven"
               alt="built with maven"
               img="http://jeremylong.github.io/DependencyCheck/images/logos/maven-feather.png"/>
-        <logo name="IntelliJ" href="http://maven.apache.org/"
+        <logo name="IntelliJ" href="http://www.jetbrains.com/idea/"
               title="developed using" width="170px"
               alt="developed using"
               img="http://jeremylong.github.io/DependencyCheck/images/logos/logo_intellij_idea.png"/>