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~

README.md

@@ -29,7 +29,7 @@ On Windows
 
 ### Maven Plugin
 
-More detailed instructions can be found on the [dependency-check-maven github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-maven/installation.html).
+More detailed instructions can be found on the [dependency-check-maven github pages](http://jeremylong.github.io/DependencyCheck/dependency-check-maven/usage.html).
 The plugin can be configured using the following:
 
 ```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>1.1.0</version>
+        <version>1.1.4</version>
     </parent>
 
     <artifactId>dependency-check-ant</artifactId>
@@ -237,8 +237,11 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>cobertura-maven-plugin</artifactId>
-                <version>2.5.2</version>
+                <version>2.6</version>
                 <configuration>
+                    <instrumentation>
+                        <ignoreTrivial>true</ignoreTrivial>
+                    </instrumentation>
                     <check>
                         <branchRate>85</branchRate>
                         <lineRate>85</lineRate>
@@ -270,11 +273,6 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
                 <version>2.16</version>
                 <configuration>
                     <systemProperties>
-                        <property>
-                            <name>net.sourceforge.cobertura.datafile</name>
-                            <value>${project.build.directory}/cobertura/cobertura.ser</value>
-                            <workingDirectory>target</workingDirectory>
-                        </property>
                         <property>
                             <name>data.directory</name>
                             <value>${project.build.directory}/dependency-check-data</value>
@@ -356,7 +354,7 @@ Copyright (c) 2013 - Jeremy Long. All Rights Reserved.
                         <plugin>
                             <groupId>org.codehaus.mojo</groupId>
                             <artifactId>cobertura-maven-plugin</artifactId>
-                            <version>2.5.2</version>
+                            <version>2.6</version>
                         </plugin>
                         <plugin>
                             <groupId>org.apache.maven.plugins</groupId>

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.
      */
@@ -502,6 +577,28 @@ public class DependencyCheckTask extends Task {
     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.
@@ -616,6 +713,144 @@ public class DependencyCheckTask extends Task {
         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;
+    }
+
     @Override
     public void execute() throws BuildException {
         final InputStream in = DependencyCheckTask.class.getClassLoader().getResourceAsStream(LOG_PROPERTIES_FILE);
@@ -625,46 +860,60 @@ public class DependencyCheckTask extends Task {
         validateConfiguration();
         populateSettings();
 
-        final Engine engine = new Engine();
-        for (Resource resource : path) {
-            final FileProvider provider = resource.as(FileProvider.class);
-            if (provider != null) {
-                final File file = provider.getFile();
-                if (file != null && file.exists()) {
-                    engine.scan(file);
-                }
-            }
-        }
+        Engine engine = null;
         try {
-            engine.analyzeDependencies();
-            DatabaseProperties prop = null;
-            CveDB cve = null;
-            try {
-                cve = new CveDB();
-                cve.open();
-                prop = cve.getDatabaseProperties();
-            } catch (DatabaseException ex) {
-                Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE, "Unable to retrieve DB Properties", ex);
-            } finally {
-                if (cve != null) {
-                    cve.close();
+            engine = new Engine();
+
+            for (Resource resource : path) {
+                final FileProvider provider = resource.as(FileProvider.class);
+                if (provider != null) {
+                    final File file = provider.getFile();
+                    if (file != null && file.exists()) {
+                        engine.scan(file);
+                    }
                 }
             }
-            final ReportGenerator reporter = new ReportGenerator(applicationName, engine.getDependencies(), engine.getAnalyzers(), prop);
-            reporter.generateReports(reportOutputDirectory, reportFormat);
+            try {
+                engine.analyzeDependencies();
+                DatabaseProperties prop = null;
+                CveDB cve = null;
+                try {
+                    cve = new CveDB();
+                    cve.open();
+                    prop = cve.getDatabaseProperties();
+                } catch (DatabaseException ex) {
+                    Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE, "Unable to retrieve DB Properties", ex);
+                } finally {
+                    if (cve != null) {
+                        cve.close();
+                    }
+                }
+                final ReportGenerator reporter = new ReportGenerator(applicationName, engine.getDependencies(), engine.getAnalyzers(), prop);
+                reporter.generateReports(reportOutputDirectory, reportFormat);
 
-            if (this.failBuildOnCVSS <= 10) {
-                checkForFailure(engine.getDependencies());
+                if (this.failBuildOnCVSS <= 10) {
+                    checkForFailure(engine.getDependencies());
+                }
+                if (this.showSummary) {
+                    showSummary(engine.getDependencies());
+                }
+            } catch (IOException ex) {
+                Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE,
+                        "Unable to generate dependency-check report", ex);
+                throw new BuildException("Unable to generate dependency-check report", ex);
+            } catch (Exception ex) {
+                Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE,
+                        "An exception occurred; unable to continue task", ex);
+                throw new BuildException("An exception occurred; unable to continue task", ex);
             }
-            if (this.showSummary) {
-                showSummary(engine.getDependencies());
+        } catch (DatabaseException ex) {
+            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.SEVERE,
+                    "Unable to connect to the dependency-check database; analysis has stopped");
+            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE, "", ex);
+        } finally {
+            if (engine != null) {
+                engine.cleanup();
             }
-        } catch (IOException ex) {
-            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE, "Unable to generate dependency-check report", ex);
-            throw new BuildException("Unable to generate dependency-check report", ex);
-        } catch (Exception ex) {
-            Logger.getLogger(DependencyCheckTask.class.getName()).log(Level.FINE, "An exception occurred; unable to continue task", ex);
-            throw new BuildException("An exception occurred; unable to continue task", ex);
         }
     }
 
@@ -733,10 +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);
         }
@@ -752,6 +1020,18 @@ public class DependencyCheckTask extends Task {
         if (databasePassword != null && !databasePassword.isEmpty()) {
             Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
         }
+        if (cveUrl12Modified != null && !cveUrl12Modified.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
+        }
+        if (cveUrl20Modified != null && !cveUrl20Modified.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
+        }
+        if (cveUrl12Base != null && !cveUrl12Base.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
+        }
+        if (cveUrl20Base != null && !cveUrl20Base.isEmpty()) {
+            Settings.setString(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
+        }
     }
 
     /**
@@ -843,4 +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

@@ -18,29 +18,60 @@ the project's dependencies.
     </dependency-check>
 </target>
 ```
-The following table lists the configurable properties:
 
-Property              | Description | Requirement
-----------------------|-------------|---------
-ApplicationName       | The name of the application to use in the generated report. | Required
-ReportFormat          | The format of the report to be generated. Allowed values are: HTML, XML, VULN, or ALL. The default value is HTML.| Optional
-ReportOutputDirectory | The directory where dependency-check will store data used for analysis. Defaults to the current working directory. | Optional
-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
-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. The default value is true. | Optional
-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
-LogFile               | The file path to write verbose logging information. | Optional
-SuppressionFile       | An XML file conforming to the suppression schema that suppresses findings; this is used to hide [false positives](../suppression.html). | Optional
-ProxyUrl              | Defines the proxy used to connect to the Internet. | Optional
-ProxyPort             | Defines the port for the proxy. | Optional
-ProxyUsername         | Defines the proxy user name. | Optional
-ProxyPassword         | Defines the proxy password. | Optional
-ConnectionTimeout     | The connection timeout used when downloading data files from the Internet. | Optional
-nexusAnalyzerEnabled  | The connection timeout used when downloading data files from the Internet. | Optional
-nexusUrl              | The connection timeout used when downloading data files from the Internet. | Optional
-databaseDriverName    | The name of the database driver. Example: org.h2.Driver. | Optional
-databaseDriverPath    | The path to the database driver JAR file; only used if the driver is not in the class path. | Optional
-connectionString      | The connection string used to connect to the database. | Optional
-databaseUser          | The username used when connecting to the database. | Optional
-databasePassword      | The password used when connecting to the database. | Optional
+Configuration
+====================
+The following properties can be set on the dependency-check-maven plugin.
 
+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. | &nbsp;
+suppressionFile      | The file path to the XML suppression file \- used to suppress [false positives](../suppression.html) | &nbsp;
+proxyUrl             | The Proxy URL.                     | &nbsp;
+proxyPort            | The Proxy Port.                    | &nbsp;
+proxyUsername        | Defines the proxy user name.       | &nbsp;
+proxyPassword        | Defines the proxy password.        | &nbsp;
+connectionTimeout    | The URL Connection Timeout.        | &nbsp;
 
+Analyzer Configuration
+====================
+The following properties are used to configure the various file type analyzers.
+These properties can be used to turn off specific analyzers if it is not needed.
+Note, that specific analyzers will automatically disable themselves if no file
+types that they support are detected - so specifically disabling them may not
+be needed.
+
+Property                | Description                        | Default Value
+------------------------|------------------------------------|------------------
+archiveAnalyzerEnabled  | Sets whether the Archive Analyzer will be used.                    | true
+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>1.1.0</version>
+        <version>1.1.4</version>
     </parent>
 
     <artifactId>dependency-check-cli</artifactId>
@@ -77,8 +77,11 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>cobertura-maven-plugin</artifactId>
-                <version>2.5.2</version>
+                <version>2.6</version>
                 <configuration>
+                    <instrumentation>
+                        <ignoreTrivial>true</ignoreTrivial>
+                    </instrumentation>
                     <check>
                         <branchRate>85</branchRate>
                         <lineRate>85</lineRate>
@@ -115,11 +118,6 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                 <version>2.16</version>
                 <configuration>
                     <systemProperties>
-                        <property>
-                            <name>net.sourceforge.cobertura.datafile</name>
-                            <value>${project.build.directory}/cobertura/cobertura.ser</value>
-                            <workingDirectory>target</workingDirectory>
-                        </property>
                         <property>
                             <name>cpe</name>
                             <value>data/cpe</value>
@@ -206,7 +204,7 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                         <plugin>
                             <groupId>org.codehaus.mojo</groupId>
                             <artifactId>cobertura-maven-plugin</artifactId>
-                            <version>2.5.2</version>
+                            <version>2.6</version>
                         </plugin>
                         <plugin>
                             <groupId>org.apache.maven.plugins</groupId>

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

@@ -98,36 +98,46 @@ public class App {
      * @param files the files/directories to scan
      */
     private void runScan(String reportDirectory, String outputFormat, String applicationName, String[] files) {
-        final Engine scanner = new Engine();
-
-        for (String file : files) {
-            scanner.scan(file);
-        }
-
-        scanner.analyzeDependencies();
-        final List<Dependency> dependencies = scanner.getDependencies();
-        DatabaseProperties prop = null;
-        CveDB cve = null;
+        Engine scanner = null;
         try {
-            cve = new CveDB();
-            cve.open();
-            prop = cve.getDatabaseProperties();
-        } catch (DatabaseException ex) {
-            Logger.getLogger(App.class.getName()).log(Level.FINE, "Unable to retrieve DB Properties", ex);
-        } finally {
-            if (cve != null) {
-                cve.close();
+            scanner = new Engine();
+
+            for (String file : files) {
+                scanner.scan(file);
+            }
+
+            scanner.analyzeDependencies();
+            final List<Dependency> dependencies = scanner.getDependencies();
+            DatabaseProperties prop = null;
+            CveDB cve = null;
+            try {
+                cve = new CveDB();
+                cve.open();
+                prop = cve.getDatabaseProperties();
+            } catch (DatabaseException ex) {
+                Logger.getLogger(App.class.getName()).log(Level.FINE, "Unable to retrieve DB Properties", ex);
+            } finally {
+                if (cve != null) {
+                    cve.close();
+                }
+            }
+            final ReportGenerator report = new ReportGenerator(applicationName, dependencies, scanner.getAnalyzers(), prop);
+            try {
+                report.generateReports(reportDirectory, outputFormat);
+            } catch (IOException ex) {
+                Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an IO error while attempting to generate the report.");
+                Logger.getLogger(App.class.getName()).log(Level.FINE, null, ex);
+            } catch (Throwable ex) {
+                Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an error while attempting to generate the report.");
+                Logger.getLogger(App.class.getName()).log(Level.FINE, null, ex);
+            }
+        } catch (DatabaseException ex) {
+            Logger.getLogger(App.class.getName()).log(Level.SEVERE, "Unable to connect to the dependency-check database; analysis has stopped");
+            Logger.getLogger(App.class.getName()).log(Level.FINE, "", ex);
+        } finally {
+            if (scanner != null) {
+                scanner.cleanup();
             }
-        }
-        final ReportGenerator report = new ReportGenerator(applicationName, dependencies, scanner.getAnalyzers(), prop);
-        try {
-            report.generateReports(reportDirectory, outputFormat);
-        } catch (IOException ex) {
-            Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an IO error while attempting to generate the report.");
-            Logger.getLogger(App.class.getName()).log(Level.INFO, null, ex);
-        } catch (Exception ex) {
-            Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an error while attempting to generate the report.");
-            Logger.getLogger(App.class.getName()).log(Level.INFO, null, ex);
         }
     }
 
@@ -148,6 +158,10 @@ 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 String databaseDriverName = cli.getDatabaseDriverName();
@@ -155,6 +169,8 @@ public class App {
         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 {
@@ -169,6 +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) {
@@ -200,11 +220,18 @@ 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);
         }
-
+        Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY, nexusUsesProxy);
         if (databaseDriverName != null && !databaseDriverName.isEmpty()) {
             Settings.setString(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
         }
@@ -220,5 +247,11 @@ public class App {
         if (databasePassword != null && !databasePassword.isEmpty()) {
             Settings.setString(Settings.KEYS.DB_PASSWORD, databasePassword);
         }
+        if (additionalZipExtensions != null && !additionalZipExtensions.isEmpty()) {
+            Settings.setString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, additionalZipExtensions);
+        }
+        if (pathToMono != null && !pathToMono.isEmpty()) {
+            Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
+        }
     }
 }

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(getReportDirectory(), "out");
+            validatePathExists(getScanFiles(), ArgumentName.SCAN);
+            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 {
-        final File f = new File(path);
-        if (!f.exists()) {
-            isValid = false;
-            final String msg = String.format("Invalid '%s' argument: '%s'", optType, path);
-            throw new FileNotFoundException(msg);
-        }
+    private void validatePathExists(String path, String argumentName) throws FileNotFoundException {
+        if (!path.contains("*.")) {
+            final File f = new File(path);
+            if (!f.exists()) {
+                isValid = false;
+                final String msg = String.format("Invalid '%s' argument: '%s'", argumentName, path);
+                throw new FileNotFoundException(msg);
+            }
+        } // 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)
@@ -196,14 +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();
-
         //This is an option group because it can be specified more then once.
         final OptionGroup og = new OptionGroup();
         og.addOption(path);
@@ -218,9 +217,7 @@ public final class CliParser {
                 .addOption(noUpdate)
                 .addOption(props)
                 .addOption(verboseLog)
-                .addOption(suppressionFile)
-                .addOption(disableNexusAnalyzer)
-                .addOption(nexusUrl);
+                .addOption(suppressionFile);
     }
 
     /**
@@ -260,19 +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)
@@ -283,7 +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);
     }
 
     /**
@@ -313,6 +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.
      *
@@ -335,6 +416,26 @@ public final class CliParser {
         }
     }
 
+    /**
+     * Returns true if the Nexus Analyzer should use the configured proxy to connect to Nexus; otherwise false is
+     * returned.
+     *
+     * @return true if the Nexus Analyzer should use the configured proxy to connect to Nexus; otherwise false
+     */
+    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)) {
+            try {
+                return Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY);
+            } catch (InvalidSettingException ise) {
+                return true;
+            }
+        } else {
+            return Boolean.parseBoolean(line.getOptionValue(ArgumentName.NEXUS_USES_PROXY));
+        }
+    }
+
     /**
      * Displays the command line help message to the standard output.
      */
@@ -377,6 +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.
      *
@@ -548,6 +658,15 @@ public final class CliParser {
         return line.getOptionValue(ArgumentName.DB_PASSWORD);
     }
 
+    /**
+     * Returns the additional Extensions if specified; otherwise null is returned.
+     *
+     * @return the additional Extensions; otherwise null is returned
+     */
+    public String getAdditionalZipExtensions() {
+        return line.getOptionValue(ArgumentName.ADDITIONAL_ZIP_EXTENSIONS);
+    }
+
     /**
      * A collection of static final strings that represent the possible command line arguments.
      */
@@ -648,7 +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.
          */
@@ -673,6 +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.
          */
@@ -681,6 +816,10 @@ public final class CliParser {
          * The URL of the nexus server.
          */
         public static final String NEXUS_URL = "nexus";
+        /**
+         * Whether or not the defined proxy should be used when connecting to Nexus.
+         */
+        public static final String NEXUS_USES_PROXY = "nexusUsesProxy";
         /**
          * The CLI argument name for setting the connection string.
          */
@@ -701,5 +840,13 @@ 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.
+         */
+        public static final String ADDITIONAL_ZIP_EXTENSIONS = "zipExtensions";
     }
 }

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

@@ -1,30 +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. |
- \-c   | \-\-connectiontimeout | \<timeout\> | The connection timeout (in milliseconds) to use when downloading resources. | Optional
- \-d   | \-\-data              | \<path\>    | The location of the data directory used to store persistent data. This option should generally not be set. | Optional
- \-f   | \-\-format            | \<format\>  | The output format to write to (XML, HTML, VULN, ALL). The default is HTML. |
- \-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. |
-       | \-\-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
- \-v   | \-\-version           |             | Print the version information. | Optional
-       | \-\-advancedHelp      |             | Print the advanced help message. | Optional
-       | \-\-connectionString  | \<connStr\> | The connection string to the database. | 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
-       | \-\-dbPassword        | \<password\>| The password for connecting to the database. | Optional
-       | \-\-dbUser            | \<user\>    | The username used to connect to the database. | Optional
-       | \-\-disableNexus      |             | Disable the Nexus Analyzer. | Optional
-       | \-\-nexus             | \<url\>     | The url to the Nexus Server. | Optional
+Short  | Argument Name         | Parameter       | Description | Requirement
+-------|-----------------------|-----------------|-------------|------------
+ \-a   | \-\-app               | \<name\>        | The name of the application being scanned. This is a required argument. | Required
+ \-s   | \-\-scan              | \<path\>        | The path to scan \- this option can be specified multiple times. It is also possible to specify specific file types that should be scanned by supplying a scan path of '[path]/[to]/[scan]/*.zip'. The wild card can only be used to denote any file-name with a specific extension. | Required
+ \-o   | \-\-out               | \<folder\>      | The folder to write reports to. This defaults to the current directory. | Optional
+ \-f   | \-\-format            | \<format\>      | The output format to write to (XML, HTML, VULN, ALL). The default is HTML. | Required
+ \-l   | \-\-log               | \<file\>        | The file path to write verbose logging information. | Optional
+ \-n   | \-\-noupdate          |                 | Disables the automatic updating of the CPE data. | Optional
+       | \-\-suppression       | \<file\>        | The file path to the suppression XML file; used to suppress [false positives](../suppression.html). | Optional
+ \-h   | \-\-help              |                 | Print the help message. | Optional
+       | \-\-advancedHelp      |                 | Print the advanced help message. | Optional
+ \-v   | \-\-version           |                 | Print the version information. | Optional
+
+Advanced Options
+================
+Short  | Argument Name         | Parameter       | Description | Default Value
+-------|-----------------------|-----------------|-------------|---------------
+       | \-\-disableArchive    |                 | Sets whether the Archive Analyzer will be used.                      | false
+       | \-\-zipExtensions     | \<strings\>     | A comma-separated list of additional file extensions to be treated like a ZIP file, the contents will be extracted and analyzed. | &nbsp;
+       | \-\-disableJar        |                 | Sets whether Jar Analyzer will be used.                              | false
+       | \-\-disableNexus      |                 | Sets whether Nexus Analyzer will be used.                            | false
+       | \-\-disableNexus      |                 | Disable the Nexus Analyzer.                                          | &nbsp;
+       | \-\-nexus             | \<url\>         | The url to the Nexus Server. | https://repository.sonatype.org/service/local/
+       | \-\-nexusUsesProxy    | \<true\|false\> | Whether or not the defined proxy should be used when connecting to Nexus. | true
+       | \-\-disableNuspec     |                 | Sets whether or not the .NET Nuget Nuspec Analyzer will be used.     | false
+       | \-\-disableAssembly   |                 | Sets whether or not the .NET Assembly Analyzer should be used.       | false
+       | \-\-pathToMono        | \<path\>        | The path to Mono for .NET Assembly analysis on non-windows systems.  | &nbsp;
+       | \-\-proxyurl          | \<url\>         | The proxy url to use when downloading resources. | &nbsp;
+       | \-\-proxyport         | \<port\>        | The proxy port to use when downloading resources. | &nbsp;
+       | \-\-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

@@ -1,5 +1,5 @@
 Installation & Usage
---------------------
+====================
 Download the dependency-check command line tool [here](http://dl.bintray.com/jeremy-long/owasp/dependency-check-${project.version}-release.zip).
 Extract the zip file to a location on your computer and put the 'bin' directory into the
 path environment variable. On \*nix systems you will likely need to make the shell
@@ -8,16 +8,18 @@ script executable:
     $ chmod +777 dependency-check.sh
 
 To scan a folder on the system you can run:
+#set( $H = '#' )
 
-<h3>Windows</h3>
+$H$H$H Windows
     dependency-check.bat --app "My App Name" --scan "c:\java\application\lib"
 
-<h3>\*nix</h3>
+$H$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:
-<h3>Windows</h3>
+
+$H$H$H Windows
     dependency-check.bat --help
 
-<h3>\*nix</h3>
+$H$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>1.1.0</version>
+        <version>1.1.4</version>
     </parent>
 
     <artifactId>dependency-check-core</artifactId>
@@ -144,6 +144,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 <version>2.6</version>
                 <configuration>
                     <instrumentation>
+                        <ignoreTrivial>true</ignoreTrivial>
                         <ignores>
                             <ignore>.*\$KEYS\.class</ignore>
                             <ignore>.*\$Element\.class</ignore>
@@ -580,6 +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>
@@ -635,5 +643,40 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                 </plugins>
             </build>
         </profile>
+        <profile>
+            <!-- The following profile adds additional
+            dependencies that are only used during testing.
+            Additionally, these are only added when using "allTests" to
+            make the build slightly faster in most cases. -->
+            <id>False Positive Tests</id>
+            <!--activation>
+                <property>
+                    <name>allTests</name>
+                </property>
+            </activation-->
+            <dependencies>
+                <dependency>
+                    <groupId>org.apache.xmlgraphics</groupId>
+                    <artifactId>batik-util</artifactId>
+                    <version>1.7</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>com.thoughtworks.xstream</groupId>
+                    <artifactId>xstream</artifactId>
+                    <version>1.4.2</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+                <dependency>
+                    <groupId>org.apache.ws.security</groupId>
+                    <artifactId>wss4j</artifactId>
+                    <version>1.5.7</version>
+                    <scope>provided</scope>
+                    <optional>true</optional>
+                </dependency>
+            </dependencies>
+        </profile>
     </profiles>
 </project>

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

@@ -26,12 +26,14 @@ import java.util.List;
 import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-import org.owasp.dependencycheck.analyzer.AnalysisException;
 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;
+import org.owasp.dependencycheck.data.nvdcve.ConnectionFactory;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
 import org.owasp.dependencycheck.data.update.CachedWebDataSource;
@@ -55,23 +57,27 @@ 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.
+     *
+     * @throws DatabaseException thrown if there is an error connecting to the database
      */
-    public Engine() {
-        this.extensions = new HashSet<String>();
+    public Engine() throws DatabaseException {
         this.dependencies = new ArrayList<Dependency>();
         this.analyzers = new EnumMap<AnalysisPhase, List<Analyzer>>(AnalysisPhase.class);
+        this.fileTypeAnalyzers = new HashSet<FileTypeAnalyzer>();
+
+        ConnectionFactory.initialize();
 
         boolean autoUpdate = true;
         try {
@@ -85,6 +91,13 @@ public class Engine {
         loadAnalyzers();
     }
 
+    /**
+     * Properly cleans up resources allocated during analysis.
+     */
+    public void cleanup() {
+        ConnectionFactory.cleanup();
+    }
+
     /**
      * Loads the analyzers specified in the configuration file (or system properties).
      */
@@ -99,8 +112,8 @@ public class Engine {
         while (iterator.hasNext()) {
             final Analyzer a = iterator.next();
             analyzers.get(a.getAnalysisPhase()).add(a);
-            if (a.getSupportedExtensions() != null) {
-                extensions.addAll(a.getSupportedExtensions());
+            if (a instanceof FileTypeAnalyzer) {
+                this.fileTypeAnalyzers.add((FileTypeAnalyzer) a);
             }
         }
     }
@@ -124,6 +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.
@@ -146,8 +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);
-        scan(file);
+        if (path.matches("^.*[\\/]\\*\\.[^\\/:*|?<>\"]+$")) {
+            final String[] parts = path.split("\\*\\.");
+            final String[] ext = new String[]{parts[parts.length - 1]};
+            final File dir = new File(path.substring(0, path.length() - ext[0].length() - 2));
+            if (dir.isDirectory()) {
+                final List<File> files = (List<File>) org.apache.commons.io.FileUtils.listFiles(dir, ext, true);
+                scan(files);
+            } else {
+                final String msg = String.format("Invalid file path provided to scan '%s'", path);
+                Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, msg);
+            }
+        } else {
+            final File file = new File(path);
+            scan(file);
+        }
     }
 
     /**
@@ -242,7 +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);
             }
@@ -280,32 +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 (Exception 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.INFO, null, ex);
-                    try {
-                        a.close();
-                    } catch (Exception 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.
@@ -315,36 +329,35 @@ 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 {
                             a.analyze(d, this);
                         } catch (AnalysisException ex) {
-                            d.addAnalysisException(ex);
+                            final String exMsg = String.format("An error occured while analyzing '%s'.", d.getActualFilePath());
+                            Logger.getLogger(Engine.class.getName()).log(Level.WARNING, exMsg);
+                            Logger.getLogger(Engine.class.getName()).log(Level.FINE, "", ex);
                         } catch (Throwable ex) {
                             final String axMsg = String.format("An unexpected error occurred during analysis of '%s'", d.getActualFilePath());
-                            final AnalysisException ax = new AnalysisException(axMsg, ex);
-                            d.addAnalysisException(ax);
-                            Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, axMsg);
-                            Logger.getLogger(Engine.class.getName()).log(Level.FINE, axMsg, ex);
+                            //final AnalysisException ax = new AnalysisException(axMsg, ex);
+                            Logger.getLogger(Engine.class.getName()).log(Level.WARNING, axMsg);
+                            Logger.getLogger(Engine.class.getName()).log(Level.FINE, "", ex);
                         }
                     }
                 }
             }
         }
-
-        //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());
-                Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
-                try {
-                    a.close();
-                } catch (Exception ex) {
-                    Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex);
-                }
+                closeAnalyzer(a);
             }
         }
 
@@ -356,6 +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.
      */
@@ -399,15 +449,13 @@ public class Engine {
         if (ext == null) {
             return false;
         }
-        for (AnalysisPhase phase : AnalysisPhase.values()) {
-            final List<Analyzer> analyzerList = analyzers.get(phase);
-            for (Analyzer a : analyzerList) {
-                if (a.getSupportedExtensions() != null && a.supportsExtension(ext)) {
-                    return true;
-                }
-            }
+        boolean scan = false;
+        for (FileTypeAnalyzer a : this.fileTypeAnalyzers) {
+            /* note, we can't break early on this loop as the analyzers need to know if
+             they have files to work on prior to initialization */
+            scan |= a.supportsExtension(ext);
         }
-        return false;
+        return scan;
     }
 
     /**
@@ -435,4 +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);
-        if (file != null) {
-            final SuppressionParser parser = new SuppressionParser();
-            try {
-                rules = parser.parseSuppressionRules(file);
-            } 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, null, ex);
-                throw ex;
+        final String suppressionFilePath = Settings.getString(Settings.KEYS.SUPPRESSION_FILE);
+        if (suppressionFilePath == null) {
+            return;
+        }
+        File file = null;
+        boolean deleteTempFile = false;
+        try {
+            final Pattern uriRx = Pattern.compile("^(https?|file)\\:.*", Pattern.CASE_INSENSITIVE);
+            if (uriRx.matcher(suppressionFilePath).matches()) {
+                deleteTempFile = true;
+                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

@@ -17,8 +17,8 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.util.Set;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Dependency;
 
 /**
@@ -41,22 +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.
      *
@@ -64,14 +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

@@ -25,6 +25,7 @@ import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -38,9 +39,11 @@ import org.apache.commons.compress.archivers.zip.ZipArchiveInputStream;
 import org.apache.commons.compress.compressors.CompressorInputStream;
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.apache.commons.compress.compressors.gzip.GzipUtils;
-import org.h2.store.fs.FileUtils;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.analyzer.exception.ArchiveExtractionException;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.utils.FileUtils;
 import org.owasp.dependencycheck.utils.Settings;
 
 /**
@@ -50,8 +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.
      */
@@ -72,6 +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.
@@ -82,15 +90,30 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
      */
     private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INITIAL;
     /**
-     * The set of file extensions supported by this analyzer.
+     * The set of things we can handle with Zip methods
      */
-    private static final Set<String> EXTENSIONS = newHashSet("zip", "ear", "war", "tar", "gz", "tgz");
+    private static final Set<String> ZIPPABLES = newHashSet("zip", "ear", "war", "nupkg");
+    /**
+     * The set of file extensions supported by this analyzer. Note for developers, any additions to this list will need
+     * to be explicitly handled in extractFiles().
+     */
+    private static final Set<String> EXTENSIONS = newHashSet("tar", "gz", "tgz");
+
+    static {
+        final String additionalZipExt = Settings.getString(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS);
+        if (additionalZipExt != null) {
+            final HashSet ext = new HashSet<String>(Arrays.asList(additionalZipExt));
+            ZIPPABLES.addAll(ext);
+        }
+        EXTENSIONS.addAll(ZIPPABLES);
+    }
 
     /**
      * Returns a list of file EXTENSIONS supported by this analyzer.
      *
      * @return a list of file EXTENSIONS supported by this analyzer.
      */
+    @Override
     public Set<String> getSupportedExtensions() {
         return EXTENSIONS;
     }
@@ -100,37 +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()) {
@@ -150,14 +175,18 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
     }
 
     /**
-     * The close method does nothing for this Analyzer.
+     * The close method deletes any temporary files and directories created during analysis.
      *
      * @throws Exception thrown if there is an exception deleting temporary files
      */
     @Override
     public void close() throws Exception {
         if (tempFileLocation != null && tempFileLocation.exists()) {
-            FileUtils.deleteRecursive(tempFileLocation.getAbsolutePath(), true);
+            LOGGER.log(Level.FINE, "Attempting to delete temporary files");
+            final boolean success = FileUtils.delete(tempFileLocation);
+            if (!success) {
+                LOGGER.log(Level.WARNING, "Failed to delete some temporary files, see the log for more details");
+            }
         }
     }
 
@@ -170,7 +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);
@@ -246,35 +275,35 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
         try {
             fis = new FileInputStream(archive);
         } catch (FileNotFoundException ex) {
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.INFO, null, ex);
+            LOGGER.log(Level.FINE, null, ex);
             throw new AnalysisException("Archive file was not found.", ex);
         }
-        final String archiveExt = org.owasp.dependencycheck.utils.FileUtils.getFileExtension(archive.getName()).toLowerCase();
+        final String archiveExt = FileUtils.getFileExtension(archive.getName()).toLowerCase();
         try {
-            if ("zip".equals(archiveExt) || "war".equals(archiveExt) || "ear".equals(archiveExt)) {
+            if (ZIPPABLES.contains(archiveExt)) {
                 extractArchive(new ZipArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
             } else if ("tar".equals(archiveExt)) {
                 extractArchive(new TarArchiveInputStream(new BufferedInputStream(fis)), destination, engine);
             } else if ("gz".equals(archiveExt) || "tgz".equals(archiveExt)) {
                 final String uncompressedName = GzipUtils.getUncompressedFilename(archive.getName());
-                final String uncompressedExt = org.owasp.dependencycheck.utils.FileUtils.getFileExtension(uncompressedName).toLowerCase();
+                final String uncompressedExt = FileUtils.getFileExtension(uncompressedName).toLowerCase();
                 if (engine.supportsExtension(uncompressedExt)) {
                     decompressFile(new GzipCompressorInputStream(new BufferedInputStream(fis)), new File(destination, uncompressedName));
                 }
             }
         } catch (ArchiveExtractionException ex) {
             final String msg = String.format("Exception extracting archive '%s'.", archive.getName());
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING, msg);
-            Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.WARNING, msg);
+            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.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.WARNING, msg);
+            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);
             }
         }
     }
@@ -301,7 +330,7 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
                     }
                 } else {
                     final File file = new File(destination, entry.getName());
-                    final String ext = org.owasp.dependencycheck.utils.FileUtils.getFileExtension(file.getName());
+                    final String ext = FileUtils.getFileExtension(file.getName());
                     if (engine.supportsExtension(ext)) {
                         BufferedOutputStream bos = null;
                         FileOutputStream fos;
@@ -353,7 +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);
                 }
             }
         }
@@ -376,17 +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

@@ -0,0 +1,315 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import java.io.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;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathExpressionException;
+import javax.xml.xpath.XPathFactory;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.utils.Settings;
+import org.w3c.dom.Document;
+import org.xml.sax.SAXException;
+
+/**
+ * Analyzer for getting company, product, and version information from a .NET assembly.
+ *
+ * @author colezlaw
+ *
+ */
+public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
+
+    /**
+     * The analyzer name
+     */
+    private static final String ANALYZER_NAME = "Assembly Analyzer";
+    /**
+     * The analysis phase
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+    /**
+     * The list of supported extensions
+     */
+    private static final Set<String> SUPORTED_EXTENSIONS = newHashSet("dll", "exe");
+    /**
+     * The temp value for GrokAssembly.exe
+     */
+    private File grokAssemblyExe = null;
+    /**
+     * The DocumentBuilder for parsing the XML
+     */
+    private DocumentBuilder builder;
+    /**
+     * Logger
+     */
+    private static final Logger LOG = Logger.getLogger(AssemblyAnalyzer.class.getName());
+
+    /**
+     * Builds the beginnings of a List for ProcessBuilder
+     *
+     * @return the list of arguments to begin populating the ProcessBuilder
+     */
+    private List<String> buildArgumentList() {
+        // Use file.separator as a wild guess as to whether this is Windows
+        final List<String> args = new ArrayList<String>();
+        if (!"\\".equals(System.getProperty("file.separator"))) {
+            if (Settings.getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH) != null) {
+                args.add(Settings.getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH));
+            } else {
+                args.add("mono");
+            }
+        }
+        args.add(grokAssemblyExe.getPath());
+
+        return args;
+    }
+
+    /**
+     * Performs the analysis on a single Dependency.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine to perform the analysis under
+     * @throws AnalysisException if anything goes sideways
+     */
+    @Override
+    public void analyzeFileType(Dependency dependency, Engine engine)
+            throws AnalysisException {
+        if (grokAssemblyExe == null) {
+            LOG.warning("GrokAssembly didn't get deployed");
+            return;
+        }
+
+        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();
+
+            // First, see if there was an error
+            final String error = xpath.evaluate("/assembly/error", doc);
+            if (error != null && !"".equals(error)) {
+                throw new AnalysisException(error);
+            }
+
+            final String version = xpath.evaluate("/assembly/version", doc);
+            if (version != null) {
+                dependency.getVersionEvidence().addEvidence(new Evidence("grokassembly", "version",
+                        version, Confidence.HIGHEST));
+            }
+
+            final String vendor = xpath.evaluate("/assembly/company", doc);
+            if (vendor != null) {
+                dependency.getVendorEvidence().addEvidence(new Evidence("grokassembly", "vendor",
+                        vendor, Confidence.HIGH));
+            }
+
+            final String product = xpath.evaluate("/assembly/product", doc);
+            if (product != null) {
+                dependency.getProductEvidence().addEvidence(new Evidence("grokassembly", "product",
+                        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) {
+            throw new AnalysisException("Couldn't parse GrokAssembly result", saxe);
+        } catch (XPathExpressionException xpe) {
+            // This shouldn't happen
+            throw new AnalysisException(xpe);
+        } finally {
+            if (rdr != null) {
+                try {
+                    rdr.close();
+                } catch (IOException ex) {
+                    Logger.getLogger(AssemblyAnalyzer.class.getName()).log(Level.FINEST, "ignore", ex);
+                }
+            }
+        }
+    }
+
+    /**
+     * Initialize the analyzer. In this case, extract GrokAssembly.exe to a temporary location.
+     *
+     * @throws Exception if anything goes wrong
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+        final File tempFile = File.createTempFile("GKA", ".exe", Settings.getTempDirectory());
+        FileOutputStream fos = null;
+        InputStream is = null;
+        try {
+            fos = new FileOutputStream(tempFile);
+            is = AssemblyAnalyzer.class.getClassLoader().getResourceAsStream("GrokAssembly.exe");
+            final byte[] buff = new byte[4096];
+            int bread = -1;
+            while ((bread = is.read(buff)) >= 0) {
+                fos.write(buff, 0, bread);
+            }
+            grokAssemblyExe = tempFile;
+            // Set the temp file to get deleted when we're done
+            grokAssemblyExe.deleteOnExit();
+            LOG.log(Level.FINE, "Extracted GrokAssembly.exe to {0}", grokAssemblyExe.getPath());
+        } catch (IOException ioe) {
+            LOG.log(Level.WARNING, "Could not extract GrokAssembly.exe: {0}", ioe.getMessage());
+            throw new AnalysisException("Could not extract GrokAssembly.exe", ioe);
+        } finally {
+            if (fos != null) {
+                try {
+                    fos.close();
+                } catch (Throwable e) {
+                    LOG.fine("Error closing output stream");
+                }
+            }
+            if (is != null) {
+                try {
+                    is.close();
+                } catch (Throwable e) {
+                    LOG.fine("Error closing input stream");
+                }
+            }
+        }
+
+        // Now, need to see if GrokAssembly actually runs from this location.
+        final List<String> args = buildArgumentList();
+        BufferedReader rdr = null;
+        try {
+            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);
+            if (p.waitFor() != 1 || error == null || "".equals(error)) {
+                LOG.warning("An error occured with the .NET AssemblyAnalyzer, please see the log for more details.");
+                LOG.fine("GrokAssembly.exe is not working properly");
+                grokAssemblyExe = null;
+                throw new AnalysisException("Could not execute .NET AssemblyAnalyzer");
+            }
+        } catch (Throwable e) {
+            LOG.warning("An error occured with the .NET AssemblyAnalyzer; "
+                    + "this can be ignored unless you are scanning .NET dlls. Please see the log for more details.");
+            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();
+    }
+
+    @Override
+    public void close() throws Exception {
+        super.close();
+        try {
+            if (grokAssemblyExe != null && !grokAssemblyExe.delete()) {
+                grokAssemblyExe.deleteOnExit();
+            }
+        } catch (SecurityException se) {
+            LOG.fine("Can't delete temporary GrokAssembly.exe");
+        }
+    }
+
+    /**
+     * Gets the set of extensions supported by this analyzer.
+     *
+     * @return the list of supported extensions
+     */
+    @Override
+    public Set<String> getSupportedExtensions() {
+        return SUPORTED_EXTENSIONS;
+    }
+
+    /**
+     * Gets this analyzer's name.
+     *
+     * @return the analyzer name
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the phase this analyzer runs under.
+     *
+     * @return the phase this runs under
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
+     *
+     * @return the analyzer's enabled property setting key
+     */
+    @Override
+    protected String getAnalyzerEnabledSettingKey() {
+        return Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED;
+    }
+}

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

@@ -33,6 +33,7 @@ import org.apache.lucene.queryparser.classic.ParseException;
 import org.apache.lucene.search.ScoreDoc;
 import org.apache.lucene.search.TopDocs;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.data.cpe.CpeMemoryIndex;
 import org.owasp.dependencycheck.data.cpe.Fields;
 import org.owasp.dependencycheck.data.cpe.IndexEntry;
@@ -86,6 +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.
      *
@@ -460,57 +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/CpeSuppressionAnalyzer.java

@@ -17,6 +17,7 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.suppression.SuppressionRule;

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

@@ -27,6 +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;
@@ -56,10 +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.
      */
@@ -69,15 +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.
      *
@@ -87,16 +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

@@ -30,6 +30,7 @@ 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.dependency.VulnerableSoftware;
@@ -42,10 +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.
      */
@@ -55,15 +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.
      *
@@ -73,16 +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.
      *
@@ -281,6 +259,12 @@ public class FalsePositiveAnalyzer extends AbstractAnalyzer {
                 } else if (i.getValue().startsWith("cpe:/a:apache:maven")
                         && !dependency.getFileName().toLowerCase().matches("maven-core-[\\d\\.]+\\.jar")) {
                     itr.remove();
+                } else if (i.getValue().startsWith("cpe:/a:m-core:m-core")
+                        && !dependency.getEvidenceUsed().containsUsedString("m-core")) {
+                    itr.remove();
+                } else if (i.getValue().startsWith("cpe:/a:jboss:jboss")
+                        && !dependency.getFileName().toLowerCase().matches("jboss-[\\d\\.]+(GA)?\\.jar")) {
+                    itr.remove();
                 }
             }
         }

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

@@ -18,8 +18,8 @@
 package org.owasp.dependencycheck.analyzer;
 
 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;
@@ -42,19 +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.
@@ -65,16 +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

@@ -21,6 +21,7 @@ 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;
@@ -40,44 +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

@@ -25,6 +25,7 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.OutputStream;
 import java.io.Reader;
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
@@ -53,9 +54,9 @@ import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.parsers.SAXParser;
 import javax.xml.parsers.SAXParserFactory;
 import javax.xml.transform.sax.SAXSource;
-import org.h2.store.fs.FileUtils;
 import org.jsoup.Jsoup;
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.dependency.Confidence;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.EvidenceCollection;
@@ -64,6 +65,7 @@ import org.owasp.dependencycheck.jaxb.pom.generated.License;
 import org.owasp.dependencycheck.jaxb.pom.generated.Model;
 import org.owasp.dependencycheck.jaxb.pom.generated.Organization;
 import org.owasp.dependencycheck.jaxb.pom.generated.Parent;
+import org.owasp.dependencycheck.utils.FileUtils;
 import org.owasp.dependencycheck.utils.NonClosingStream;
 import org.owasp.dependencycheck.utils.Settings;
 import org.xml.sax.InputSource;
@@ -77,9 +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.
      */
@@ -109,9 +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",
@@ -123,7 +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.
      */
@@ -158,10 +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.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.SEVERE, "Unable to load parser. See the log for more details.");
+            LOGGER.log(Level.FINE, null, ex);
         }
     }
+
     //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
     /**
      * The name of the analyzer.
@@ -181,6 +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;
     }
@@ -190,20 +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.
      *
@@ -214,6 +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.
@@ -223,7 +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();
@@ -260,10 +278,9 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             jar = new JarFile(dependency.getActualFilePath());
         } catch (IOException ex) {
             final String msg = String.format("Unable to read JarFile '%s'.", dependency.getActualFilePath());
-            final AnalysisException ax = new AnalysisException(msg, ex);
-            dependency.getAnalysisExceptions().add(ax);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            //final AnalysisException ax = new AnalysisException(msg, ex);
+            LOGGER.log(Level.WARNING, msg);
+            LOGGER.log(Level.FINE, "", ex);
             return false;
         }
         List<String> pomEntries;
@@ -271,10 +288,9 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             pomEntries = retrievePomListing(jar);
         } 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);
-            dependency.getAnalysisExceptions().add(ax);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
-            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.INFO, msg, ex);
+            //final AnalysisException ax = new AnalysisException(msg, ex);
+            LOGGER.log(Level.WARNING, msg);
+            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 {
@@ -313,7 +329,9 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
                     foundSomething |= setPomEvidence(dependency, pom, pomProperties, classes);
                 }
             } catch (AnalysisException ex) {
-                dependency.addAnalysisException(ex);
+                final String msg = String.format("An error occured while analyzing '%s'.", dependency.getActualFilePath());
+                LOGGER.log(Level.WARNING, msg);
+                LOGGER.log(Level.FINE, "", ex);
             }
         }
         return foundSomething;
@@ -390,13 +408,13 @@ 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 {
-            try {
-                input.close();
-            } catch (IOException ex) {
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.SEVERE, null, ex);
-            }
+            closeStream(bos);
+            closeStream(fos);
+            closeStream(input);
         }
         Model model = null;
         FileInputStream fis = null;
@@ -408,31 +426,55 @@ 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.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.WARNING, msg);
+            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.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.WARNING, msg);
+            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.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+            LOGGER.log(Level.WARNING, msg);
+            LOGGER.log(Level.FINE, "", ex);
             throw ex;
         } finally {
-            if (fis != null) {
-                try {
-                    fis.close();
-                } catch (IOException ex) {
-                    Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, null, ex);
-                }
-            }
+            closeStream(fis);
         }
         return model;
     }
 
+    /**
+     * Silently closes an input stream ignoring errors.
+     *
+     * @param stream an input stream to close
+     */
+    private void closeStream(InputStream stream) {
+        if (stream != null) {
+            try {
+                stream.close();
+            } catch (IOException ex) {
+                LOGGER.log(Level.FINEST, null, ex);
+            }
+        }
+    }
+
+    /**
+     * Silently closes an output stream ignoring errors.
+     *
+     * @param stream an output stream to close
+     */
+    private void closeStream(OutputStream stream) {
+        if (stream != null) {
+            try {
+                stream.close();
+            } catch (IOException ex) {
+                LOGGER.log(Level.FINEST, null, ex);
+            }
+        }
+    }
+
     /**
      * Retrieves the specified POM from a jar file and converts it to a Model.
      *
@@ -462,13 +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.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+                LOGGER.log(Level.WARNING, msg);
+                LOGGER.log(Level.FINE, "", ex);
                 throw new AnalysisException(ex);
             } catch (Throwable ex) {
                 final String msg = String.format("Unexpected error during parsing of the pom '%s' in jar '%s'", path, jar.getName());
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, msg);
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
+                LOGGER.log(Level.WARNING, msg);
+                LOGGER.log(Level.FINE, "", ex);
                 throw new AnalysisException(ex);
             }
         }
@@ -575,43 +617,12 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             foundSomething = true;
             final String description = interpolateString(pom.getDescription(), pomProperties);
             if (description != null && !description.isEmpty()) {
-                addDescription(dependency, description, "pom", "description");
-                addMatchingValues(classes, description, dependency.getVendorEvidence());
-                addMatchingValues(classes, description, dependency.getProductEvidence());
-            }
-        }
-
-        //license
-        if (pom.getLicenses() != null) {
-            String license = null;
-            for (License lic : pom.getLicenses().getLicense()) {
-                String tmp = null;
-                if (lic.getName() != null) {
-                    tmp = interpolateString(lic.getName(), pomProperties);
-                }
-                if (lic.getUrl() != null) {
-                    if (tmp == null) {
-                        tmp = interpolateString(lic.getUrl(), pomProperties);
-                    } else {
-                        tmp += ": " + interpolateString(lic.getUrl(), pomProperties);
-                    }
-                }
-                if (tmp == null) {
-                    continue;
-                }
-                if (HTML_DETECTION_PATTERN.matcher(tmp).find()) {
-                    tmp = Jsoup.parse(tmp).text();
-                }
-                if (license == null) {
-                    license = tmp;
-                } else {
-                    license += "\n" + tmp;
-                }
-            }
-            if (license != null) {
-                dependency.setLicense(license);
+                final String trimmedDescription = addDescription(dependency, description, "pom", "description");
+                addMatchingValues(classes, trimmedDescription, dependency.getVendorEvidence());
+                addMatchingValues(classes, trimmedDescription, dependency.getProductEvidence());
             }
         }
+        extractLicense(pom, pomProperties, dependency);
         return foundSomething;
     }
 
@@ -767,7 +778,16 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
                             } else {
                                 versionEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                             }
-
+                        } else if ("build-id".equals(key)) {
+                            int pos = value.indexOf('(');
+                            if (pos >= 0) {
+                                value = value.substring(0, pos - 1);
+                            }
+                            pos = value.indexOf('[');
+                            if (pos >= 0) {
+                                value = value.substring(0, pos - 1);
+                            }
+                            versionEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                         } else if (key.contains("title")) {
                             productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                             addMatchingValues(classInformation, value, productEvidence);
@@ -816,14 +836,18 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
     }
 
     /**
-     * Adds a description to the given dependency.
+     * Adds a description to the given dependency. If the description contains one of the following strings beyond 100
+     * characters, then the description used will be trimmed to that position:
+     * <ul><li>"such as"</li><li>"like "</li><li>"will use "</li><li>"* uses "</li></ul>
      *
      * @param dependency a dependency
      * @param description the description
      * @param source the source of the evidence
      * @param key the "name" of the evidence
+     * @return if the description is trimmed, the trimmed version is returned; otherwise the original description is
+     * returned
      */
-    private void addDescription(Dependency dependency, String description, String source, String key) {
+    private String addDescription(Dependency dependency, String description, String source, String key) {
         if (dependency.getDescription() == null) {
             dependency.setDescription(description);
         }
@@ -835,29 +859,42 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
         }
         dependency.setDescription(desc);
         if (desc.length() > 100) {
+            desc = desc.replaceAll("\\s\\s+", " ");
             final int posSuchAs = desc.toLowerCase().indexOf("such as ", 100);
             final int posLike = desc.toLowerCase().indexOf("like ", 100);
+            final int posWillUse = desc.toLowerCase().indexOf("will use ", 100);
+            final int posUses = desc.toLowerCase().indexOf(" uses ", 100);
             int pos = -1;
-            if (posLike > 0 && posSuchAs > 0) {
-                pos = posLike > posSuchAs ? posLike : posSuchAs;
-            } else if (posLike > 0) {
-                pos = posLike;
-            } else if (posSuchAs > 0) {
-                pos = posSuchAs;
+            pos = Math.max(pos, posSuchAs);
+            if (pos >= 0 && posLike >= 0) {
+                pos = Math.min(pos, posLike);
+            } else {
+                pos = Math.max(pos, posLike);
             }
-            String descToUse = desc;
+            if (pos >= 0 && posWillUse >= 0) {
+                pos = Math.min(pos, posWillUse);
+            } else {
+                pos = Math.max(pos, posWillUse);
+            }
+            if (pos >= 0 && posUses >= 0) {
+                pos = Math.min(pos, posUses);
+            } else {
+                pos = Math.max(pos, posUses);
+            }
+
             if (pos > 0) {
                 final StringBuilder sb = new StringBuilder(pos + 3);
                 sb.append(desc.substring(0, pos));
                 sb.append("...");
-                descToUse = sb.toString();
+                desc = sb.toString();
             }
-            dependency.getProductEvidence().addEvidence(source, key, descToUse, Confidence.LOW);
-            dependency.getVendorEvidence().addEvidence(source, key, descToUse, Confidence.LOW);
+            dependency.getProductEvidence().addEvidence(source, key, desc, Confidence.LOW);
+            dependency.getVendorEvidence().addEvidence(source, key, desc, Confidence.LOW);
         } else {
             dependency.getProductEvidence().addEvidence(source, key, desc, Confidence.MEDIUM);
             dependency.getVendorEvidence().addEvidence(source, key, desc, Confidence.MEDIUM);
         }
+        return desc;
     }
 
     /**
@@ -880,12 +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()) {
@@ -910,7 +947,12 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
     @Override
     public void close() {
         if (tempFileLocation != null && tempFileLocation.exists()) {
-            FileUtils.deleteRecursive(tempFileLocation.getAbsolutePath(), true);
+            LOGGER.log(Level.FINE, "Attempting to delete temporary files");
+            final boolean success = FileUtils.delete(tempFileLocation);
+            if (!success) {
+                LOGGER.log(Level.WARNING,
+                        "Failed to delete some temporary files, see the log for more details");
+            }
         }
     }
 
@@ -979,11 +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*)+$");
-        if (packageRx.matcher(value).matches()) {
-            return (key.contains("import") || key.contains("include"));
-        }
-        return false;
+        final Pattern packageRx = Pattern.compile("^([a-zA-Z0-9_#\\$\\*\\.]+\\s*[,;]\\s*)+([a-zA-Z0-9_#\\$\\*\\.]+\\s*)?$");
+        final boolean matches = packageRx.matcher(value).matches();
+        return matches && (key.contains("import") || key.contains("include") || value.length() > 10);
     }
 
     /**
@@ -1020,7 +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);
                 }
             }
         }
@@ -1195,7 +1235,17 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
                 addDescription(dependency, description, "pom", "description");
             }
         }
+        extractLicense(pom, pomProperties, dependency);
+    }
 
+    /**
+     * Extracts the license information from the pom and adds it to the dependency.
+     *
+     * @param pom the pom object
+     * @param pomProperties the properties, used for string interpolation
+     * @param dependency the dependency to add license information too
+     */
+    private void extractLicense(Model pom, Properties pomProperties, Dependency dependency) {
         //license
         if (pom.getLicenses() != null) {
             String license = null;

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

@@ -13,22 +13,36 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *
- * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
 import java.util.Set;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 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;
 
 /**
  *
- * Used to load a JAR file and collect information that can be used to determine the associated CPE.
+ * Used to analyze a JavaScript file to gather information to aid in identification of a CPE identifier.
  *
  * @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">
     /**
@@ -49,6 +63,7 @@ public class JavaScriptAnalyzer extends AbstractAnalyzer implements Analyzer {
      *
      * @return a list of file EXTENSIONS supported by this analyzer.
      */
+    @Override
     public Set<String> getSupportedExtensions() {
         return EXTENSIONS;
     }
@@ -58,61 +73,69 @@ public class JavaScriptAnalyzer 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_JAVASCRIPT_ENABLED;
+    }
 
     /**
-     * Loads a specified JAR file and collects information from the manifest and checksums to identify the correct CPE
-     * information.
+     * Loads a specified JavaScript file and collects information from the copyright information contained within.
      *
      * @param dependency the dependency to analyze.
      * @param engine the engine that is scanning the dependencies
-     * @throws AnalysisException is thrown if there is an error reading the JAR file.
+     * @throws AnalysisException is thrown if there is an error reading the JavaScript file.
      */
     @Override
-    public void analyze(Dependency dependency, Engine engine) throws AnalysisException {
-        final Pattern extractComments = Pattern.compile("(/\\*([^*]|[\\r\\n]|(\\*+([^*/]|[\\r\\n])))*\\*+/)|(//.*)");
-
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        BufferedReader fin = null;;
+        try {
+            //  /\*([^\*][^/]|[\r\n\f])+?\*/
+            final Pattern extractComments = Pattern.compile("(/\\*([^*]|[\\r\\n]|(\\*+([^*/]|[\\r\\n])))*\\*+/)|(//.*)", Pattern.MULTILINE);
+            File file = dependency.getActualFile();
+            fin = new BufferedReader(new FileReader(file));
+            StringBuilder sb = new StringBuilder(2000);
+            String text;
+            while ((text = fin.readLine()) != null) {
+                sb.append(text);
+            }
+        } catch (FileNotFoundException ex) {
+            final String msg = String.format("Dependency file not found: '%s'", dependency.getActualFilePath());
+            throw new AnalysisException(msg, ex);
+        } catch (IOException ex) {
+            LOGGER.log(Level.SEVERE, null, ex);
+        } finally {
+            if (fin != null) {
+                try {
+                    fin.close();
+                } catch (IOException ex) {
+                    LOGGER.log(Level.FINEST, null, ex);
+                }
+            }
+        }
     }
 
-    /**
-     * The initialize method does nothing for this Analyzer.
-     *
-     * @throws Exception thrown if there is an exception
-     */
     @Override
-    public void initialize() throws Exception {
-        //do nothing
-    }
+    protected void initializeFileTypeAnalyzer() throws Exception {
 
-    /**
-     * The close method does nothing for this Analyzer.
-     *
-     * @throws Exception thrown if there is an exception
-     */
-    @Override
-    public void close() throws Exception {
-        //do nothing
     }
 }

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

@@ -25,6 +25,7 @@ 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.nexus.MavenArtifact;
 import org.owasp.dependencycheck.data.nexus.NexusSearch;
 import org.owasp.dependencycheck.dependency.Confidence;
@@ -45,20 +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;
 
@@ -67,11 +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.
      */
@@ -83,20 +79,23 @@ public class NexusAnalyzer extends AbstractAnalyzer {
      * @throws Exception if there's an error during initialization
      */
     @Override
-    public void initialize() throws Exception {
-        enabled = Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED);
+    public void initializeFileTypeAnalyzer() throws Exception {
         LOGGER.fine("Initializing Nexus Analyzer");
-        LOGGER.fine(String.format("Nexus Analyzer enabled: %s", enabled));
-        if (enabled) {
+        LOGGER.fine(String.format("Nexus Analyzer enabled: %s", isEnabled()));
+        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.");
+                    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);
             }
         }
     }
@@ -111,6 +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.
      *
@@ -131,17 +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.
      *
@@ -150,12 +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 {
-        // Make a quick exit if this analyzer is disabled
-        if (!enabled) {
-            return;
-        }
-
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
         try {
             final MavenArtifact ma = searcher.searchSha1(dependency.getSha1sum());
             if (ma.getGroupId() != null && !"".equals(ma.getGroupId())) {
@@ -183,5 +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

@@ -0,0 +1,156 @@
+/*
+ * 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.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 AbstractFileTypeAnalyzer {
+
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(NuspecAnalyzer.class.getName());
+
+    /**
+     * The name of the analyzer.
+     */
+    private static final String ANALYZER_NAME = "Nuspec Analyzer";
+
+    /**
+     * The phase in which the analyzer runs.
+     */
+    private static final AnalysisPhase ANALYSIS_PHASE = AnalysisPhase.INFORMATION_COLLECTION;
+
+    /**
+     * The types of files on which this will work.
+     */
+    private static final Set<String> SUPPORTED_EXTENSIONS = newHashSet("nuspec");
+
+    /**
+     * Initializes the analyzer once before any analysis is performed.
+     *
+     * @throws Exception if there's an error during initialization
+     */
+    @Override
+    public void initializeFileTypeAnalyzer() throws Exception {
+    }
+
+    /**
+     * Returns the analyzer's name.
+     *
+     * @return the name of the analyzer
+     */
+    @Override
+    public String getName() {
+        return ANALYZER_NAME;
+    }
+
+    /**
+     * Returns the key used in the properties file to 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.
+     *
+     * @return the phase under which this analyzer runs
+     */
+    @Override
+    public AnalysisPhase getAnalysisPhase() {
+        return ANALYSIS_PHASE;
+    }
+
+    /**
+     * Returns the extensions for which this Analyzer runs.
+     *
+     * @return the extensions for which this Analyzer runs
+     */
+    @Override
+    public Set<String> getSupportedExtensions() {
+        return SUPPORTED_EXTENSIONS;
+    }
+
+    /**
+     * Performs the analysis.
+     *
+     * @param dependency the dependency to analyze
+     * @param engine the engine
+     * @throws AnalysisException when there's an exception during analysis
+     */
+    @Override
+    public void analyzeFileType(Dependency dependency, Engine engine) throws AnalysisException {
+        LOGGER.log(Level.FINE, "Checking Nuspec file {0}", dependency.toString());
+        try {
+            final NuspecParser parser = new XPathNuspecParser();
+            NugetPackage np = null;
+            FileInputStream fis = null;
+            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 (IOException e) {
+                        LOGGER.fine("Error closing input stream");
+                    }
+                }
+            }
+
+            if (np.getOwners() != null) {
+                dependency.getVendorEvidence().addEvidence("nuspec", "owners", np.getOwners(), Confidence.HIGHEST);
+            }
+            dependency.getVendorEvidence().addEvidence("nuspec", "authors", np.getAuthors(), Confidence.HIGH);
+            dependency.getVersionEvidence().addEvidence("nuspec", "version", np.getVersion(), Confidence.HIGHEST);
+            dependency.getProductEvidence().addEvidence("nuspec", "id", np.getId(), Confidence.HIGHEST);
+            if (np.getTitle() != null) {
+                dependency.getProductEvidence().addEvidence("nuspec", "title", np.getTitle(), Confidence.MEDIUM);
+            }
+        } catch (Throwable e) {
+            throw new AnalysisException(e);
+        }
+    }
+}

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

@@ -20,8 +20,8 @@ package org.owasp.dependencycheck.analyzer;
 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;
@@ -61,6 +61,7 @@ public class NvdCveAnalyzer implements Analyzer {
     /**
      * Closes the data source.
      */
+    @Override
     public void close() {
         cveDB.close();
         cveDB = null;
@@ -95,6 +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())) {
@@ -109,48 +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/analyzer/VulnerabilitySuppressionAnalyzer.java

@@ -17,6 +17,7 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.Engine;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.suppression.SuppressionRule;

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

@@ -15,7 +15,7 @@
  *
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
-package org.owasp.dependencycheck.analyzer;
+package org.owasp.dependencycheck.analyzer.exception;
 
 /**
  * An exception thrown when the analysis of a dependency fails.

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

@@ -15,7 +15,7 @@
  *
  * Copyright (c) 2013 Jeremy Long. All Rights Reserved.
  */
-package org.owasp.dependencycheck.analyzer;
+package org.owasp.dependencycheck.analyzer.exception;
 
 /**
  * An exception thrown when files in an archive cannot be extracted.

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

@@ -0,0 +1,12 @@
+/**
+ * <html>
+ * <head>
+ * <title>org.owasp.dependencycheck.analyzer.exception</title>
+ * </head>
+ * <body>
+ * <p>
+ * A collection of exception classes used within the analyzers.</p>
+ * </body>
+ * </html>
+ */
+package org.owasp.dependencycheck.analyzer.exception;

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

@@ -18,10 +18,9 @@
 package org.owasp.dependencycheck.data.cpe;
 
 import java.io.IOException;
-import java.sql.ResultSet;
-import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.apache.lucene.analysis.Analyzer;
@@ -45,6 +44,8 @@ import org.owasp.dependencycheck.data.lucene.FieldAnalyzer;
 import org.owasp.dependencycheck.data.lucene.LuceneUtils;
 import org.owasp.dependencycheck.data.lucene.SearchFieldAnalyzer;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.utils.Pair;
 
 /**
  * An in memory lucene index that contains the vendor/product combinations from the CPE (application) identifiers within
@@ -210,7 +211,7 @@ public final class CpeMemoryIndex {
     }
 
     /**
-     * Builds the lucene index based off of the data within the CveDB.
+     * Builds the CPE Lucene Index based off of the data within the CveDB.
      *
      * @param cve the data base containing the CPE data
      * @throws IndexException thrown if there is an issue creating the index
@@ -222,15 +223,12 @@ public final class CpeMemoryIndex {
             analyzer = createIndexingAnalyzer();
             final IndexWriterConfig conf = new IndexWriterConfig(LuceneUtils.CURRENT_VERSION, analyzer);
             indexWriter = new IndexWriter(index, conf);
-            final ResultSet rs = cve.getVendorProductList();
-            if (rs == null) {
-                throw new IndexException("No data exists");
-            }
             try {
-                while (rs.next()) {
-                    saveEntry(rs.getString(1), rs.getString(2), indexWriter);
+                final Set<Pair<String, String>> data = cve.getVendorProductList();
+                for (Pair<String, String> pair : data) {
+                    saveEntry(pair.getLeft(), pair.getRight(), indexWriter);
                 }
-            } catch (SQLException ex) {
+            } catch (DatabaseException ex) {
                 Logger.getLogger(CpeMemoryIndex.class.getName()).log(Level.FINE, null, ex);
                 throw new IndexException("Error reading CPE data", ex);
             }

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

@@ -67,7 +67,7 @@ public final class UrlTokenizingFilter extends AbstractTokenizingFilter {
                             final List<String> data = UrlStringUtils.extractImportantUrlData(part);
                             tokens.addAll(data);
                         } catch (MalformedURLException ex) {
-                            Logger.getLogger(UrlTokenizingFilter.class.getName()).log(Level.INFO, "error parsing " + part, ex);
+                            Logger.getLogger(UrlTokenizingFilter.class.getName()).log(Level.FINE, "error parsing " + part, ex);
                             tokens.add(part);
                         }
                     } else {

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

@@ -19,13 +19,18 @@ package org.owasp.dependencycheck.data.nexus;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.net.HttpURLConnection;
 import java.net.URL;
 import java.net.URLConnection;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.xpath.XPath;
 import javax.xml.xpath.XPathFactory;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
+import org.owasp.dependencycheck.utils.Settings;
+import org.owasp.dependencycheck.utils.URLConnectionFactory;
 import org.w3c.dom.Document;
 
 /**
@@ -40,10 +45,16 @@ public class NexusSearch {
      */
     private final URL rootURL;
 
+    /**
+     * Whether to use the Proxy when making requests
+     */
+    private boolean useProxy;
+
     /**
      * Used for logging.
      */
-    private static final Logger LOGGER = Logger.getLogger(NexusSearch.class.getName());
+    private static final Logger LOGGER = Logger.getLogger(NexusSearch.class
+            .getName());
 
     /**
      * Creates a NexusSearch for the given repository URL.
@@ -53,6 +64,18 @@ public class NexusSearch {
      */
     public NexusSearch(URL rootURL) {
         this.rootURL = rootURL;
+        try {
+            if (null != Settings.getString(Settings.KEYS.PROXY_URL)
+                    && Settings.getBoolean(Settings.KEYS.ANALYZER_NEXUS_PROXY)) {
+                useProxy = true;
+                LOGGER.fine("Using proxy");
+            } else {
+                useProxy = false;
+                LOGGER.fine("Not using proxy");
+            }
+        } catch (InvalidSettingException ise) {
+            useProxy = false;
+        }
     }
 
     /**
@@ -69,11 +92,19 @@ public class NexusSearch {
             throw new IllegalArgumentException("Invalid SHA1 format");
         }
 
-        final URL url = new URL(rootURL, String.format("identify/sha1/%s", sha1.toLowerCase()));
+        final URL url = new URL(rootURL, String.format("identify/sha1/%s",
+                sha1.toLowerCase()));
 
         LOGGER.fine(String.format("Searching Nexus url %s", url.toString()));
 
-        final URLConnection conn = url.openConnection();
+        // Determine if we need to use a proxy. The rules:
+        // 1) If the proxy is set, AND the setting is set to true, use the proxy
+        // 2) Otherwise, don't use the proxy (either the proxy isn't configured,
+        // or proxy is specifically
+        // set to false
+        URLConnection conn = null;
+        conn = URLConnectionFactory.createHttpURLConnection(url, useProxy);
+
         conn.setDoOutput(true);
 
         // JSON would be more elegant, but there's not currently a dependency
@@ -82,23 +113,64 @@ public class NexusSearch {
         conn.connect();
 
         try {
-            final DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+            final DocumentBuilder builder = DocumentBuilderFactory
+                    .newInstance().newDocumentBuilder();
             final Document doc = builder.parse(conn.getInputStream());
             final XPath xpath = XPathFactory.newInstance().newXPath();
-            final String groupId = xpath.evaluate("/org.sonatype.nexus.rest.model.NexusArtifact/groupId", doc);
-            final String artifactId = xpath.evaluate("/org.sonatype.nexus.rest.model.NexusArtifact/artifactId", doc);
-            final String version = xpath.evaluate("/org.sonatype.nexus.rest.model.NexusArtifact/version", doc);
-            final String link = xpath.evaluate("/org.sonatype.nexus.rest.model.NexusArtifact/artifactLink", doc);
+            final String groupId = xpath
+                    .evaluate(
+                            "/org.sonatype.nexus.rest.model.NexusArtifact/groupId",
+                            doc);
+            final String artifactId = xpath.evaluate(
+                    "/org.sonatype.nexus.rest.model.NexusArtifact/artifactId",
+                    doc);
+            final String version = xpath
+                    .evaluate(
+                            "/org.sonatype.nexus.rest.model.NexusArtifact/version",
+                            doc);
+            final String link = xpath
+                    .evaluate(
+                            "/org.sonatype.nexus.rest.model.NexusArtifact/artifactLink",
+                            doc);
             return new MavenArtifact(groupId, artifactId, version, link);
         } catch (FileNotFoundException fnfe) {
-            // This is what we get when the SHA1 they sent doesn't exist in Nexus. This
-            // is useful upstream for recovery, so we just re-throw it
+            /* This is what we get when the SHA1 they sent doesn't exist in
+             * Nexus. This is useful upstream for recovery, so we just re-throw it
+             */
             throw fnfe;
-        } catch (Exception e) {
-            // Anything else is jacked-up XML stuff that we really can't recover from well
+        } catch (Throwable e) {
+            // Anything else is jacked-up XML stuff that we really can't recover
+            // from well
             throw new IOException(e.getMessage(), e);
         }
     }
+
+    /**
+     * Do a preflight request to see if the repository is actually working.
+     *
+     * @return whether the repository is listening and returns the /status URL correctly
+     */
+    public boolean preflightRequest() {
+        try {
+            final HttpURLConnection conn = URLConnectionFactory.createHttpURLConnection(new URL(rootURL, "status"), useProxy);
+            conn.addRequestProperty("Accept", "application/xml");
+            conn.connect();
+            if (conn.getResponseCode() != 200) {
+                LOGGER.log(Level.WARNING, "Expected 200 result from Nexus, got {0}", conn.getResponseCode());
+                return false;
+            }
+            final DocumentBuilder builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+            final Document doc = builder.parse(conn.getInputStream());
+            if (!"status".equals(doc.getDocumentElement().getNodeName())) {
+                LOGGER.log(Level.WARNING, "Expected root node name of status, got {0}", doc.getDocumentElement().getNodeName());
+                return false;
+            }
+        } catch (Throwable e) {
+            return false;
+        }
+
+        return true;
+    }
 }
 
 // vim: cc=120:sw=4:ts=4:sts=4

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

@@ -0,0 +1,186 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.data.nuget;
+
+/**
+ * Represents the contents of a Nuspec manifest.
+ *
+ * @author colezlaw
+ */
+public class NugetPackage {
+    /**
+     * The id.
+     */
+    private String id;
+
+    /**
+     * The version.
+     */
+    private String version;
+
+    /**
+     * The title.
+     */
+    private String title;
+
+    /**
+     * The authors.
+     */
+    private String authors;
+
+    /**
+     * The owners.
+     */
+    private String owners;
+
+    /**
+     * The licenseUrl.
+     */
+    private String licenseUrl;
+
+    /**
+     * Creates an empty NugetPackage.
+     */
+    public NugetPackage() {
+    }
+
+    /**
+     * Sets the id.
+     * @param id the id
+     */
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    /**
+     * Gets the id.
+     * @return the id
+     */
+    public String getId() {
+        return id;
+    }
+
+    /**
+     * Sets the version.
+     * @param version the version
+     */
+    public void setVersion(String version) {
+        this.version = version;
+    }
+
+    /**
+     * Gets the version.
+     * @return the version
+     */
+    public String getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the title.
+     * @param title the title
+     */
+    public void setTitle(String title) {
+        this.title = title;
+    }
+
+    /**
+     * Gets the title.
+     * @return the title
+     */
+    public String getTitle() {
+        return title;
+    }
+
+    /**
+     * Sets the authors.
+     * @param authors the authors
+     */
+    public void setAuthors(String authors) {
+        this.authors = authors;
+    }
+
+    /**
+     * Gets the authors.
+     * @return the authors
+     */
+    public String getAuthors() {
+        return authors;
+    }
+
+    /**
+     * Sets the owners.
+     * @param owners the owners
+     */
+    public void setOwners(String owners) {
+        this.owners = owners;
+    }
+
+    /**
+     * Gets the owners.
+     * @return the owners
+     */
+    public String getOwners() {
+        return owners;
+    }
+
+    /**
+     * Sets the licenseUrl.
+     * @param licenseUrl the licenseUrl
+     */
+    public void setLicenseUrl(String licenseUrl) {
+        this.licenseUrl = licenseUrl;
+    }
+
+    /**
+     * Gets the licenseUrl.
+     * @return the licenseUrl
+     */
+    public String getLicenseUrl() {
+        return licenseUrl;
+    }
+
+    @Override
+    public boolean equals(Object other) {
+        if (this == other) {
+            return true;
+        }
+        if (other == null || other.getClass() != this.getClass()) {
+            return false;
+        }
+        final NugetPackage o = (NugetPackage) other;
+        return o.getId().equals(id)
+                && o.getVersion().equals(version)
+                && o.getTitle().equals(title)
+                && o.getAuthors().equals(authors)
+                && o.getOwners().equals(owners)
+                && o.getLicenseUrl().equals(licenseUrl);
+    }
+
+    @Override
+    public int hashCode() {
+        int hash = 7;
+        hash = 31 * hash + (null == id ? 0 : id.hashCode());
+        hash = 31 * hash + (null == version ? 0 : version.hashCode());
+        hash = 31 * hash + (null == title ? 0 : title.hashCode());
+        hash = 31 * hash + (null == authors ? 0 : authors.hashCode());
+        hash = 31 * hash + (null == owners ? 0 : owners.hashCode());
+        hash = 31 * hash + (null == licenseUrl ? 0 : licenseUrl.hashCode());
+        return hash;
+    }
+}

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

@@ -0,0 +1,67 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.data.nuget;
+
+/**
+ * Exception during the parsing of a Nuspec file.
+ *
+ * @author colezlaw
+ */
+public class NuspecParseException extends Exception {
+
+    /**
+     * The serialVersionUID
+     */
+    private static final long serialVersionUID = 1;
+
+    /**
+     * Constructs a new exception with <code>null</code> as its detail message.
+     *
+     * The cause is not initialized, and may subsequently be initialized by a call to
+     * {@link java.lang.Throwable#initCause(java.lang.Throwable)}.
+     */
+    public NuspecParseException() {
+        super();
+    }
+
+    /**
+     * Constructs a new exception with the specified detail message. The cause is not initialized, and may subsequently
+     * be initialized by a call to {@link java.lang.Throwable#initCause(java.lang.Throwable)}.
+     *
+     * @param message the detail message. The detail message is saved for later retrieval by the
+     * {@link java.lang.Throwable#getMessage()} method.
+     */
+    public NuspecParseException(String message) {
+        super(message);
+    }
+
+    /**
+     * Constructs a new exception with the specified detail message and cause.
+     *
+     * Note that the detail message associated with <code>cause</code> is <em>not</em>
+     * automatically incorporated in this exception's detail message.
+     *
+     * @param message the detail message (whcih is saved for later retrieval by the
+     * {@link java.lang.Throwable#getMessage()} method.
+     * @param cause the cause (which is saved for later retrieval by the {@link java.lang.Throwable#getCause()} method).
+     * (A <code>null</code> value is permitted, and indicates that the cause is nonexistent or unknown).
+     */
+    public NuspecParseException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}

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

@@ -0,0 +1,37 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.data.nuget;
+
+import java.io.InputStream;
+
+/**
+ * Interface defining methods for parsing a Nuspec file.
+ *
+ * @author colezlaw
+ *
+ */
+public interface NuspecParser {
+    /**
+     * Parse an input stream and return the resulting {@link NugetPackage}.
+     *
+     * @param stream the input stream to parse
+     * @return the populated bean
+     * @throws NuspecParseException when an exception occurs
+     */
+    NugetPackage parse(InputStream stream) throws NuspecParseException;
+}

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

@@ -0,0 +1,81 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.data.nuget;
+
+import java.io.InputStream;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathFactory;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+
+/**
+ * Parse a Nuspec file using XPath.
+ *
+ * @author colezlaw
+ */
+public class XPathNuspecParser implements NuspecParser {
+
+    /**
+     * Gets the string value of a node or null if it's not present
+     *
+     * @param n the node to test
+     * @return the string content of the node, or null if the node itself is null
+     */
+    private String getOrNull(Node n) {
+        if (n != null) {
+            return n.getTextContent();
+        } else {
+            return null;
+        }
+    }
+
+    /**
+     * Parse an input stream and return the resulting {@link NugetPackage}.
+     *
+     * @param stream the input stream to parse
+     * @return the populated bean
+     * @throws NuspecParseException when an exception occurs
+     */
+    @Override
+    public NugetPackage parse(InputStream stream) throws NuspecParseException {
+        try {
+            final Document d = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(stream);
+            final XPath xpath = XPathFactory.newInstance().newXPath();
+            final NugetPackage nuspec = new NugetPackage();
+
+            if (xpath.evaluate("/package/metadata/id", d, XPathConstants.NODE) == null
+                    || xpath.evaluate("/package/metadata/version", d, XPathConstants.NODE) == null
+                    || xpath.evaluate("/package/metadata/authors", d, XPathConstants.NODE) == null
+                    || xpath.evaluate("/package/metadata/description", d, XPathConstants.NODE) == null) {
+                throw new NuspecParseException("Invalid Nuspec format");
+            }
+
+            nuspec.setId(xpath.evaluate("/package/metadata/id", d));
+            nuspec.setVersion(xpath.evaluate("/package/metadata/version", d));
+            nuspec.setAuthors(xpath.evaluate("/package/metadata/authors", d));
+            nuspec.setOwners(getOrNull((Node) xpath.evaluate("/package/metadata/owners", d, XPathConstants.NODE)));
+            nuspec.setLicenseUrl(getOrNull((Node) xpath.evaluate("/package/metadata/licenseUrl", d, XPathConstants.NODE)));
+            nuspec.setTitle(getOrNull((Node) xpath.evaluate("/package/metadata/title", d, XPathConstants.NODE)));
+            return nuspec;
+        } catch (Throwable e) {
+            throw new NuspecParseException("Unable to parse nuspec", e);
+        }
+    }
+}

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

@@ -0,0 +1,15 @@
+/**
+ * <html>
+ * <head>
+ * <title>org.owasp.dependencycheck.data.nuget</title>
+ * </head>
+ * <body>
+ * <p>
+ * Contains classes related to parsing Nuget related files</p>
+ * <p>
+ * These are used to abstract away Nuget-related handling from Dependency Check
+ * so they can be used elsewhere.</p>
+ * </body>
+ * </html>
+ */
+package org.owasp.dependencycheck.data.nuget;

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

@@ -24,6 +24,7 @@ import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.sql.CallableStatement;
 import java.sql.Connection;
+import java.sql.Driver;
 import java.sql.DriverManager;
 import java.sql.ResultSet;
 import java.sql.SQLException;
@@ -50,6 +51,22 @@ public final class ConnectionFactory {
      * Resource location for SQL file used to create the database schema.
      */
     public static final String DB_STRUCTURE_RESOURCE = "data/initialize.sql";
+    /**
+     * The database driver used to connect to the database.
+     */
+    private static Driver driver = null;
+    /**
+     * The database connection string.
+     */
+    private static String connectionString = null;
+    /**
+     * The username to connect to the database.
+     */
+    private static String userName = null;
+    /**
+     * The password for the database.
+     */
+    private static String password = null;
 
     /**
      * Private constructor for this factory class; no instance is ever needed.
@@ -58,64 +75,135 @@ public final class ConnectionFactory {
     }
 
     /**
-     * Constructs a new database connection object per the database configuration. This will load the appropriate
-     * database driver, via the DriverManager, if configured.
+     * Initializes the connection factory. Ensuring that the appropriate drivers are loaded and that a connection can be
+     * made successfully.
      *
-     * @return a database connection object
-     * @throws DatabaseException thrown if there is an exception loading the database connection
+     * @throws DatabaseException thrown if we are unable to connect to the database
      */
-    public static Connection getConnection() throws DatabaseException {
+    public static synchronized void initialize() throws DatabaseException {
+        //this only needs to be called once.
+        if (connectionString != null) {
+            return;
+        }
         Connection conn = null;
         try {
-            Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Loading database connection");
-
-            final String connStr = getConnectionString();
-            final String user = Settings.getString(Settings.KEYS.DB_USER, "dcuser");
-            //yes, yes - hard-coded password - only if there isn't one in the properties file.
-            final String pass = Settings.getString(Settings.KEYS.DB_PASSWORD, "DC-Pass1337!");
-            Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Connection String: {0}", connStr);
-            Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Database User: {0}", user);
-            boolean createTables = false;
-            if (connStr.startsWith("jdbc:h2:file:")) { //H2
-                createTables = needToCreateDatabaseStructure();
-                Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Need to create DB Structure: {0}", createTables);
-            }
+            //load the driver if necessary
             final String driverName = Settings.getString(Settings.KEYS.DB_DRIVER_NAME, "");
             if (!driverName.isEmpty()) { //likely need to load the correct driver
                 Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Loading driver: {0}", driverName);
                 final String driverPath = Settings.getString(Settings.KEYS.DB_DRIVER_PATH, "");
-                if (!driverPath.isEmpty()) { //ugh, driver is not on classpath?
-                    Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Loading driver from: {0}", driverPath);
-                    DriverLoader.load(driverName, driverPath);
+                try {
+                    if (!driverPath.isEmpty()) {
+                        Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Loading driver from: {0}", driverPath);
+                        driver = DriverLoader.load(driverName, driverPath);
+                    } else {
+                        driver = DriverLoader.load(driverName);
+                    }
+                } catch (DriverLoadException ex) {
+                    Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, "Unable to load database driver", ex);
+                    throw new DatabaseException("Unable to load database driver");
+                }
+            }
+            userName = Settings.getString(Settings.KEYS.DB_USER, "dcuser");
+            //yes, yes - hard-coded password - only if there isn't one in the properties file.
+            password = Settings.getString(Settings.KEYS.DB_PASSWORD, "DC-Pass1337!");
+            try {
+                connectionString = getConnectionString();
+            } catch (IOException ex) {
+                Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE,
+                        "Unable to retrieve the database connection string", ex);
+                throw new DatabaseException("Unable to retrieve the database connection string");
+            }
+            boolean shouldCreateSchema = false;
+            try {
+                if (connectionString.startsWith("jdbc:h2:file:")) { //H2
+                    shouldCreateSchema = !dbSchemaExists();
+                    Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Need to create DB Structure: {0}", shouldCreateSchema);
+                }
+            } catch (IOException ioex) {
+                Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, "Unable to verify database exists", ioex);
+                throw new DatabaseException("Unable to verify database exists");
+            }
+            Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Loading database connection");
+            Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Connection String: {0}", connectionString);
+            Logger.getLogger(CveDB.class.getName()).log(Level.FINE, "Database User: {0}", userName);
+
+            try {
+                conn = DriverManager.getConnection(connectionString, userName, password);
+            } catch (SQLException ex) {
+                if (ex.getMessage().contains("java.net.UnknownHostException") && connectionString.contains("AUTO_SERVER=TRUE;")) {
+                    connectionString = connectionString.replace("AUTO_SERVER=TRUE;", "");
+                    try {
+                        conn = DriverManager.getConnection(connectionString, userName, password);
+                        Settings.setString(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
+                        Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE,
+                                "Unable to start the database in server mode; reverting to single user mode");
+                    } catch (SQLException sqlex) {
+                        Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, "Unable to connect to the database", ex);
+                        throw new DatabaseException("Unable to connect to the database");
+                    }
                 } else {
-                    DriverLoader.load(driverName);
+                    Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, "Unable to connect to the database", ex);
+                    throw new DatabaseException("Unable to connect to the database");
                 }
             }
 
-            //JDBC4 drivers don't need this call.
-            //Class.forName("org.h2.Driver");
-            conn = DriverManager.getConnection(connStr, user, pass);
-            if (createTables) {
+            if (shouldCreateSchema) {
                 try {
                     createTables(conn);
-                } catch (DatabaseException ex) {
-                    Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, null, ex);
+                } catch (DatabaseException dex) {
+                    Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, null, dex);
                     throw new DatabaseException("Unable to create the database structure");
                 }
             } else {
                 try {
                     ensureSchemaVersion(conn);
-                } catch (DatabaseException ex) {
-                    Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, null, ex);
+                } catch (DatabaseException dex) {
+                    Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, null, dex);
                     throw new DatabaseException("Database schema does not match this version of dependency-check");
                 }
             }
-        } catch (IOException ex) {
-            Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, null, ex);
-            throw new DatabaseException("Unable to load database");
-        } catch (DriverLoadException ex) {
-            Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, null, ex);
-            throw new DatabaseException("Unable to load database driver");
+        } finally {
+            if (conn != null) {
+                try {
+                    conn.close();
+                } catch (SQLException ex) {
+                    Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, "An error occured closing the connection", ex);
+                }
+            }
+        }
+    }
+
+    /**
+     * Cleans up resources and unloads any registered database drivers. This needs to be called to ensure the driver is
+     * unregistered prior to the finalize method being called as during shutdown the class loader used to load the
+     * driver may be unloaded prior to the driver being de-registered.
+     */
+    public static synchronized void cleanup() {
+        if (driver != null) {
+            try {
+                DriverManager.deregisterDriver(driver);
+            } catch (SQLException ex) {
+                Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, "An error occured unloading the databse driver", ex);
+            }
+            driver = null;
+        }
+        connectionString = null;
+        userName = null;
+        password = null;
+    }
+
+    /**
+     * Constructs a new database connection object per the database configuration.
+     *
+     * @return a database connection object
+     * @throws DatabaseException thrown if there is an exception loading the database connection
+     */
+    public static Connection getConnection() throws DatabaseException {
+        initialize();
+        Connection conn = null;
+        try {
+            conn = DriverManager.getConnection(connectionString, userName, password);
         } catch (SQLException ex) {
             Logger.getLogger(ConnectionFactory.class.getName()).log(Level.FINE, null, ex);
             throw new DatabaseException("Unable to connect to the database");
@@ -164,11 +252,11 @@ public final class ConnectionFactory {
      * @return true if the H2 database file does not exist; otherwise false
      * @throws IOException thrown if the data directory does not exist and cannot be created
      */
-    private static boolean needToCreateDatabaseStructure() throws IOException {
+    private static boolean dbSchemaExists() throws IOException {
         final File dir = getDataDirectory();
         final String name = String.format("cve.%s.h2.db", DB_SCHEMA_VERSION);
         final File file = new File(dir, name);
-        return !file.exists();
+        return file.exists();
     }
 
     /**

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

@@ -38,6 +38,7 @@ import org.owasp.dependencycheck.dependency.VulnerableSoftware;
 import org.owasp.dependencycheck.utils.DBUtils;
 import org.owasp.dependencycheck.utils.DependencyVersion;
 import org.owasp.dependencycheck.utils.DependencyVersionUtil;
+import org.owasp.dependencycheck.utils.Pair;
 
 /**
  * The database holding information about the NVD CVE data.
@@ -96,6 +97,10 @@ public class CveDB {
                 final String msg = "There was an error attempting to close the CveDB, see the log for more details.";
                 Logger.getLogger(DBUtils.class.getName()).log(Level.SEVERE, msg);
                 Logger.getLogger(DBUtils.class.getName()).log(Level.FINE, null, ex);
+            } catch (Throwable ex) {
+                final String msg = "There was an exception attempting to close the CveDB, see the log for more details.";
+                Logger.getLogger(DBUtils.class.getName()).log(Level.SEVERE, msg);
+                Logger.getLogger(DBUtils.class.getName()).log(Level.FINE, null, ex);
             }
             conn = null;
         }
@@ -128,7 +133,9 @@ public class CveDB {
      * @throws Throwable thrown if there is a problem
      */
     @Override
+    @SuppressWarnings("FinalizeDeclaration")
     protected void finalize() throws Throwable {
+        Logger.getLogger(DBUtils.class.getName()).log(Level.FINE, "Entering finalize");
         close();
         super.finalize();
     }
@@ -289,19 +296,27 @@ public class CveDB {
     /**
      * Returns the entire list of vendor/product combinations.
      *
-     * @return the entire list of vendor/product combinations.
+     * @return the entire list of vendor/product combinations
+     * @throws DatabaseException thrown when there is an error retrieving the data from the DB
      */
-    public ResultSet getVendorProductList() {
+    public Set<Pair<String, String>> getVendorProductList() throws DatabaseException {
+        final HashSet data = new HashSet<Pair<String, String>>();
         ResultSet rs = null;
+        PreparedStatement ps = null;
         try {
-            final PreparedStatement ps = getConnection().prepareStatement(SELECT_VENDOR_PRODUCT_LIST);
+            ps = getConnection().prepareStatement(SELECT_VENDOR_PRODUCT_LIST);
             rs = ps.executeQuery();
+            while (rs.next()) {
+                data.add(new Pair(rs.getString(1), rs.getString(2)));
+            }
         } catch (SQLException ex) {
             final String msg = "An unexpected SQL Exception occurred; please see the verbose log for more details.";
-            Logger.getLogger(CveDB.class.getName()).log(Level.SEVERE, msg);
-            Logger.getLogger(CveDB.class.getName()).log(Level.FINE, null, ex);
-        } // can't close the statement in the PS as the resultset is returned, closing PS would close the resultset
-        return rs;
+            throw new DatabaseException(msg, ex);
+        } finally {
+            DBUtils.closeResultSet(rs);
+            DBUtils.closeStatement(ps);
+        }
+        return data;
     }
 
     /**

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

@@ -47,11 +47,12 @@ public final class DriverLoader {
      * Loads the specified class using the system class loader and registers the driver with the driver manager.
      *
      * @param className the fully qualified name of the desired class
+     * @return the loaded Driver
      * @throws DriverLoadException thrown if the driver cannot be loaded
      */
-    public static void load(String className) throws DriverLoadException {
+    public static Driver load(String className) throws DriverLoadException {
         final ClassLoader loader = DriverLoader.class.getClassLoader(); //ClassLoader.getSystemClassLoader();
-        load(className, loader);
+        return load(className, loader);
     }
 
     /**
@@ -64,9 +65,10 @@ public final class DriverLoader {
      * @param className the fully qualified name of the desired class
      * @param pathToDriver the path to the JAR file containing the driver; note, this can be a semi-colon separated list
      * of paths
+     * @return the loaded Driver
      * @throws DriverLoadException thrown if the driver cannot be loaded
      */
-    public static void load(String className, String pathToDriver) throws DriverLoadException {
+    public static Driver load(String className, String pathToDriver) throws DriverLoadException {
         final URLClassLoader parent = (URLClassLoader) ClassLoader.getSystemClassLoader();
         final ArrayList<URL> urls = new ArrayList<URL>();
         final String[] paths = pathToDriver.split(File.pathSeparator);
@@ -103,7 +105,7 @@ public final class DriverLoader {
             }
         });
 
-        load(className, loader);
+        return load(className, loader);
     }
 
     /**
@@ -111,15 +113,18 @@ public final class DriverLoader {
      *
      * @param className the fully qualified name of the desired class
      * @param loader the class loader to use when loading the driver
+     * @return the loaded Driver
      * @throws DriverLoadException thrown if the driver cannot be loaded
      */
-    private static void load(String className, ClassLoader loader) throws DriverLoadException {
+    private static Driver load(String className, ClassLoader loader) throws DriverLoadException {
         try {
             final Class c = Class.forName(className, true, loader);
             //final Class c = loader.loadClass(className);
             final Driver driver = (Driver) c.newInstance();
+            final Driver shim = new DriverShim(driver);
             //using the DriverShim to get around the fact that the DriverManager won't register a driver not in the base class path
-            DriverManager.registerDriver(new DriverShim(driver));
+            DriverManager.registerDriver(shim);
+            return shim;
         } catch (ClassNotFoundException ex) {
             final String msg = String.format("Unable to load database driver '%s'", className);
             Logger.getLogger(DriverLoader.class.getName()).log(Level.FINE, msg, ex);

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

@@ -17,12 +17,15 @@
  */
 package org.owasp.dependencycheck.data.nvdcve;
 
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 import java.sql.Connection;
 import java.sql.Driver;
 import java.sql.DriverPropertyInfo;
 import java.sql.SQLException;
 import java.sql.SQLFeatureNotSupportedException;
 import java.util.Properties;
+import java.util.logging.Level;
 import java.util.logging.Logger;
 
 /**
@@ -64,6 +67,20 @@ class DriverShim implements Driver {
         return this.driver.acceptsURL(url);
     }
 
+    /**
+     * Wraps the call to the underlying driver's connect method.
+     *
+     * @param url the URL of the database
+     * @param info a collection of string/value pairs
+     * @return a Connection object
+     * @throws SQLException thrown if there is an error connecting to the database
+     * @see java.sql.Driver#connect(java.lang.String, java.util.Properties)
+     */
+    @Override
+    public Connection connect(String url, Properties info) throws SQLException {
+        return this.driver.connect(url, info);
+    }
+
     /**
      * Returns the wrapped driver's major version number.
      *
@@ -87,28 +104,33 @@ class DriverShim implements Driver {
     }
 
     /**
-     * Returns whether or not the wrapped driver is jdbcCompliant.
+     * Wraps the call to the underlying driver's getParentLogger method.
      *
-     * @return true if the wrapped driver is JDBC compliant; otherwise false
-     * @see java.sql.Driver#jdbcCompliant()
+     * @return the parent's Logger
+     * @throws SQLFeatureNotSupportedException thrown if the feature is not supported
+     * @see java.sql.Driver#getParentLogger()
      */
-    @Override
-    public boolean jdbcCompliant() {
-        return this.driver.jdbcCompliant();
-    }
-
-    /**
-     * Wraps the call to the underlying driver's connect method.
-     *
-     * @param url the URL of the database
-     * @param info a collection of string/value pairs
-     * @return a Connection object
-     * @throws SQLException thrown if there is an error connecting to the database
-     * @see java.sql.Driver#connect(java.lang.String, java.util.Properties)
-     */
-    @Override
-    public Connection connect(String url, Properties info) throws SQLException {
-        return this.driver.connect(url, info);
+    //@Override
+    public Logger getParentLogger() throws SQLFeatureNotSupportedException {
+        //return driver.getParentLogger();
+        Method m = null;
+        try {
+            m = driver.getClass().getMethod("getParentLogger");
+        } catch (Throwable e) {
+            throw new SQLFeatureNotSupportedException();
+        }
+        if (m != null) {
+            try {
+                return (Logger) m.invoke(m);
+            } catch (IllegalAccessException ex) {
+                Logger.getLogger(DriverShim.class.getName()).log(Level.FINER, null, ex);
+            } catch (IllegalArgumentException ex) {
+                Logger.getLogger(DriverShim.class.getName()).log(Level.FINER, null, ex);
+            } catch (InvocationTargetException ex) {
+                Logger.getLogger(DriverShim.class.getName()).log(Level.FINER, null, ex);
+            }
+        }
+        throw new SQLFeatureNotSupportedException();
     }
 
     /**
@@ -126,15 +148,14 @@ class DriverShim implements Driver {
     }
 
     /**
-     * Wraps the call to the underlying driver's getParentLogger method.
+     * Returns whether or not the wrapped driver is jdbcCompliant.
      *
-     * @return the parent's Logger
-     * @throws SQLFeatureNotSupportedException thrown if the feature is not supported
-     * @see java.sql.Driver#getParentLogger()
+     * @return true if the wrapped driver is JDBC compliant; otherwise false
+     * @see java.sql.Driver#jdbcCompliant()
      */
     @Override
-    public Logger getParentLogger() throws SQLFeatureNotSupportedException {
-        return this.driver.getParentLogger();
+    public boolean jdbcCompliant() {
+        return this.driver.jdbcCompliant();
     }
 
     /**

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

@@ -134,20 +134,20 @@ public class StandardUpdate {
                     downloadExecutors.shutdownNow();
                     processExecutor.shutdownNow();
 
-                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interupted during download", ex);
-                    throw new UpdateException("The download was interupted", ex);
+                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interrupted during download", ex);
+                    throw new UpdateException("The download was interrupted", ex);
                 } catch (ExecutionException ex) {
                     downloadExecutors.shutdownNow();
                     processExecutor.shutdownNow();
 
-                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interupted during download execution", ex);
-                    throw new UpdateException("The execution of the download was interupted", ex);
+                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interrupted during download execution", ex);
+                    throw new UpdateException("The execution of the download was interrupted", ex);
                 }
                 if (task == null) {
                     downloadExecutors.shutdownNow();
                     processExecutor.shutdownNow();
-                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interupted during download");
-                    throw new UpdateException("The download was interupted; unable to complete the update");
+                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interrupted during download");
+                    throw new UpdateException("The download was interrupted; unable to complete the update");
                 } else {
                     processFutures.add(task);
                 }
@@ -161,7 +161,7 @@ public class StandardUpdate {
                     }
                 } catch (InterruptedException ex) {
                     processExecutor.shutdownNow();
-                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interupted during processing", ex);
+                    Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "Thread was interrupted during processing", ex);
                     throw new UpdateException(ex);
                 } catch (ExecutionException ex) {
                     processExecutor.shutdownNow();
@@ -245,11 +245,8 @@ public class StandardUpdate {
                 }
             } catch (NumberFormatException ex) {
                 final String msg = "An invalid schema version or timestamp exists in the data.properties file.";
-                Logger
-                        .getLogger(StandardUpdate.class
-                                .getName()).log(Level.WARNING, msg);
-                Logger.getLogger(StandardUpdate.class
-                        .getName()).log(Level.FINE, null, ex);
+                Logger.getLogger(StandardUpdate.class.getName()).log(Level.WARNING, msg);
+                Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINE, "", ex);
             }
         }
         return updates;
@@ -292,7 +289,7 @@ public class StandardUpdate {
         if (cveDB != null) {
             try {
                 cveDB.close();
-            } catch (Exception ignore) {
+            } catch (Throwable ignore) {
                 Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINEST, "Error closing the cveDB", ignore);
             }
         }

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");
-            file2 = File.createTempFile("cve_1_2_" + nvdCveInfo.getId() + "_", ".xml");
+            file1 = File.createTempFile("cve" + nvdCveInfo.getId() + "_", ".xml", Settings.getTempDirectory());
+            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

@@ -20,8 +20,6 @@ package org.owasp.dependencycheck.dependency;
 import java.io.File;
 import java.io.IOException;
 import java.security.NoSuchAlgorithmException;
-import java.util.ArrayList;
-import java.util.List;
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
@@ -108,16 +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;
@@ -126,7 +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;
@@ -139,16 +147,25 @@ 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;
     }
 
+    /**
+     * Gets a reference to the File object.
+     *
+     * @return the File object
+     */
+    public File getActualFile() {
+        return new File(this.actualFilePath);
+    }
+
     /**
      * 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;
@@ -161,7 +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;
@@ -170,7 +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;
@@ -179,7 +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;
@@ -224,7 +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;
@@ -233,7 +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;
@@ -318,37 +335,6 @@ public class Dependency implements Comparable<Dependency> {
     public EvidenceCollection getVersionEvidence() {
         return this.versionEvidence;
     }
-    /**
-     * A list of exceptions that occurred during analysis of this dependency.
-     */
-    private List<Exception> analysisExceptions = new ArrayList<Exception>();
-
-    /**
-     * Get the value of analysisExceptions.
-     *
-     * @return the value of analysisExceptions
-     */
-    public List<Exception> getAnalysisExceptions() {
-        return analysisExceptions;
-    }
-
-    /**
-     * Set the value of analysisExceptions.
-     *
-     * @param analysisExceptions new value of analysisExceptions
-     */
-    public void setAnalysisExceptions(List<Exception> analysisExceptions) {
-        this.analysisExceptions = analysisExceptions;
-    }
-
-    /**
-     * Adds an exception to the analysis exceptions collection.
-     *
-     * @param ex an exception.
-     */
-    public void addAnalysisException(Exception ex) {
-        this.analysisExceptions.add(ex);
-    }
     /**
      * The description of the JAR file.
      */
@@ -535,10 +521,6 @@ public class Dependency implements Comparable<Dependency> {
         if (this.versionEvidence != other.versionEvidence && (this.versionEvidence == null || !this.versionEvidence.equals(other.versionEvidence))) {
             return false;
         }
-        if (this.analysisExceptions != other.analysisExceptions
-                && (this.analysisExceptions == null || !this.analysisExceptions.equals(other.analysisExceptions))) {
-            return false;
-        }
         if ((this.description == null) ? (other.description != null) : !this.description.equals(other.description)) {
             return false;
         }
@@ -573,7 +555,6 @@ public class Dependency implements Comparable<Dependency> {
         hash = 47 * hash + (this.vendorEvidence != null ? this.vendorEvidence.hashCode() : 0);
         hash = 47 * hash + (this.productEvidence != null ? this.productEvidence.hashCode() : 0);
         hash = 47 * hash + (this.versionEvidence != null ? this.versionEvidence.hashCode() : 0);
-        hash = 47 * hash + (this.analysisExceptions != null ? this.analysisExceptions.hashCode() : 0);
         hash = 47 * hash + (this.description != null ? this.description.hashCode() : 0);
         hash = 47 * hash + (this.license != null ? this.license.hashCode() : 0);
         hash = 47 * hash + (this.vulnerabilities != null ? this.vulnerabilities.hashCode() : 0);

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

@@ -360,7 +360,7 @@ public class EvidenceCollection implements Iterable<Evidence> {
                     final List<String> data = UrlStringUtils.extractImportantUrlData(part);
                     sb.append(' ').append(StringUtils.join(data, ' '));
                 } catch (MalformedURLException ex) {
-                    Logger.getLogger(EvidenceCollection.class.getName()).log(Level.INFO, "error parsing " + part, ex);
+                    Logger.getLogger(EvidenceCollection.class.getName()).log(Level.FINE, "error parsing " + part, ex);
                     sb.append(' ').append(part);
                 }
             } else {

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

@@ -184,13 +184,21 @@ public class VulnerableSoftware extends IndexEntry implements Serializable, Comp
                 if (subMax > 0) {
                     for (int x = 0; result == 0 && x < subMax; x++) {
                         if (isPositiveInteger(subLeft[x]) && isPositiveInteger(subRight[x])) {
-                            final int iLeft = Integer.parseInt(subLeft[x]);
-                            final int iRight = Integer.parseInt(subRight[x]);
-                            if (iLeft != iRight) {
-                                if (iLeft > iRight) {
-                                    result = 2;
-                                } else {
-                                    result = -2;
+                            try {
+                                result = Long.valueOf(subLeft[x]).compareTo(Long.valueOf(subRight[x]));
+//                                final long iLeft = Long.parseLong(subLeft[x]);
+//                                final long iRight = Long.parseLong(subRight[x]);
+//                                if (iLeft != iRight) {
+//                                    if (iLeft > iRight) {
+//                                        result = 2;
+//                                    } else {
+//                                        result = -2;
+//                                    }
+//                                }
+                            } catch (NumberFormatException ex) {
+                                //ignore the exception - they obviously aren't numbers
+                                if (!subLeft[x].equalsIgnoreCase(subRight[x])) {
+                                    result = subLeft[x].compareToIgnoreCase(subRight[x]);
                                 }
                             }
                         } else {

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

@@ -22,12 +22,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.net.Authenticator;
 import java.net.HttpURLConnection;
-import java.net.InetSocketAddress;
-import java.net.PasswordAuthentication;
-import java.net.Proxy;
-import java.net.SocketAddress;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.logging.Level;
@@ -51,68 +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 outputPath the path to the save the file to.
-     * @throws DownloadFailedException is thrown if there is an error downloading the file.
+     * @param url the URL of the file to download
+     * @param outputPath the path to the save the file to
+     * @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;
-        try {
-            conn = Downloader.getConnection(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();
+        fetchFile(url, outputPath, true);
+    }
 
-        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());
+    /**
+     * Retrieves a file from a given URL and saves it to the outputPath.
+     *
+     * @param url the URL of the file to download
+     * @param outputPath the path to the save the file to
+     * @param useProxy whether to use the configured proxy when downloading files
+     * @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();
-            }
-
-            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 (Exception ex) {
-            throw new DownloadFailedException("Error saving downloaded file.", ex);
-        } finally {
-            if (writer != null) {
-                try {
-                    writer.close();
-                } catch (Exception ex) {
-                    Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
-                            "Error closing the writer in Downloader.", ex);
-                }
-            }
-            if (reader != null) {
-                try {
-                    reader.close();
-                } catch (Exception ex) {
-                    Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
-                            "Error closing the reader in Downloader.", ex);
-                }
+                final String msg = String.format("Download failed, file does not exist '%s'", url.toString());
+                throw new DownloadFailedException(msg);
             }
+        } 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;
+                }
             }
         }
     }
@@ -127,20 +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);
@@ -149,11 +168,13 @@ public final class Downloader {
         } else {
             HttpURLConnection conn = null;
             try {
-                conn = Downloader.getConnection(url);
+                conn = URLConnectionFactory.createHttpURLConnection(url);
                 conn.setRequestMethod("HEAD");
                 conn.connect();
                 timestamp = conn.getLastModified();
-            } catch (Exception ex) {
+            } catch (URLConnectionFailureException ex) {
+                throw new DownloadFailedException("Error creating URL Connection for HTTP HEAD request.", ex);
+            } catch (IOException ex) {
                 throw new DownloadFailedException("Error making HTTP HEAD request.", ex);
             } finally {
                 if (conn != null) {
@@ -167,56 +188,4 @@ public final class Downloader {
         }
         return timestamp;
     }
-
-    /**
-     * Utility method to get an HttpURLConnection. If the app is configured to use a proxy this method will retrieve the
-     * proxy settings and use them when setting up the connection.
-     *
-     * @param url the url to connect to
-     * @return an HttpURLConnection
-     * @throws DownloadFailedException thrown if there is an exception
-     */
-    private static HttpURLConnection getConnection(URL url) throws DownloadFailedException {
-        HttpURLConnection conn = null;
-        Proxy proxy = null;
-        final String proxyUrl = Settings.getString(Settings.KEYS.PROXY_URL);
-        try {
-            if (proxyUrl != null) {
-                final int proxyPort = Settings.getInt(Settings.KEYS.PROXY_PORT);
-                final SocketAddress addr = new InetSocketAddress(proxyUrl, proxyPort);
-
-                final String username = Settings.getString(Settings.KEYS.PROXY_USERNAME);
-                final String password = Settings.getString(Settings.KEYS.PROXY_PASSWORD);
-                if (username != null && password != null) {
-                    final Authenticator auth = new Authenticator() {
-                        @Override
-                        public PasswordAuthentication getPasswordAuthentication() {
-                            if (getRequestorType().equals(RequestorType.PROXY)) {
-                                return new PasswordAuthentication(username, password.toCharArray());
-                            }
-                            return super.getPasswordAuthentication();
-                        }
-                    };
-                    Authenticator.setDefault(auth);
-                }
-
-                proxy = new Proxy(Proxy.Type.HTTP, addr);
-                conn = (HttpURLConnection) url.openConnection(proxy);
-            } else {
-                conn = (HttpURLConnection) url.openConnection();
-            }
-            final int timeout = Settings.getInt(Settings.KEYS.CONNECTION_TIMEOUT, 60000);
-            conn.setConnectTimeout(timeout);
-        } catch (IOException ex) {
-            if (conn != null) {
-                try {
-                    conn.disconnect();
-                } finally {
-                    conn = null;
-                }
-            }
-            throw new DownloadFailedException("Error getting connection.", ex);
-        }
-        return conn;
-    }
 }

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.
      */
@@ -69,23 +80,40 @@ public final class FileUtils {
      * Deletes a file. If the File is a directory it will recursively delete the contents.
      *
      * @param file the File to delete
-     * @throws IOException is thrown if the file could not be deleted
+     * @return true if the file was deleted successfully, otherwise false
      */
-    public static void delete(File file) throws IOException {
-        if (file.isDirectory()) {
-            for (File c : file.listFiles()) {
-                delete(c);
+    public static boolean delete(File file) {
+        boolean success = true;
+        if (!org.apache.commons.io.FileUtils.deleteQuietly(file)) {
+            success = false;
+            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");
             }
         }
-        if (!org.apache.commons.io.FileUtils.deleteQuietly(file)) {
-            throw new FileNotFoundException("Failed to delete file: " + file);
+        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);
         }
-        /* else {
-         //delete on exit was a bad idea. if for some reason the file can't be deleted
-         // this will cause a newly constructed file to be deleted and a subsequent run may fail.
-         // still not sure why a file fails to be deleted, but can be overwritten... odd.
-         file.deleteOnExit();
-         }*/
+        return tempFile;
     }
 
     /**
@@ -160,7 +188,7 @@ public final class FileUtils {
         try {
             fis = new FileInputStream(archive);
         } catch (FileNotFoundException ex) {
-            Logger.getLogger(FileUtils.class.getName()).log(Level.INFO, null, ex);
+            Logger.getLogger(FileUtils.class.getName()).log(Level.FINE, null, ex);
             throw new ExtractionException("Archive file was not found.", ex);
         }
         zis = new ZipInputStream(new BufferedInputStream(fis));
@@ -220,4 +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/LogUtils.java

@@ -66,7 +66,7 @@ public final class LogUtils {
             if (in != null) {
                 try {
                     in.close();
-                } catch (Exception ex) {
+                } catch (Throwable ex) {
                     Logger.getLogger(LogUtils.class.getName()).log(Level.FINEST, "Error closing resource stream", ex);
                 }
             }

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

@@ -0,0 +1,127 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.utils;
+
+/**
+ * A generic pair of elements.
+ *
+ * @param <L> the type for the left element in the pair
+ * @param <R> the type for the right element in the pair
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public class Pair<L, R> {
+
+    /**
+     * Constructs a new empty pair.
+     */
+    public Pair() {
+    }
+
+    /**
+     * Constructs a new Pair with the given left and right values.
+     *
+     * @param left the value for the left pair
+     * @param right the value for the right pair
+     */
+    public Pair(L left, R right) {
+        this.left = left;
+        this.right = right;
+    }
+    /**
+     * The left element of the pair.
+     */
+    private L left = null;
+
+    /**
+     * Get the value of left.
+     *
+     * @return the value of left
+     */
+    public L getLeft() {
+        return left;
+    }
+
+    /**
+     * Set the value of left.
+     *
+     * @param left new value of left
+     */
+    public void setLeft(L left) {
+        this.left = left;
+    }
+    /**
+     * The right element of the pair.
+     */
+    private R right = null;
+
+    /**
+     * Get the value of right.
+     *
+     * @return the value of right
+     */
+    public R getRight() {
+        return right;
+    }
+
+    /**
+     * Set the value of right.
+     *
+     * @param right new value of right
+     */
+    public void setRight(R right) {
+        this.right = right;
+    }
+
+    /**
+     * Generates the hash code using the hash codes from the contained objects.
+     *
+     * @return the hash code of the Pair
+     */
+    @Override
+    public int hashCode() {
+        int hash = 3;
+        hash = 53 * hash + (this.left != null ? this.left.hashCode() : 0);
+        hash = 53 * hash + (this.right != null ? this.right.hashCode() : 0);
+        return hash;
+    }
+
+    /**
+     * Determines the equality of this and the provided object.
+     *
+     * @param obj the {@link Object} to check for equality to this
+     * @return true if this and the provided {@link Object} are equal; otherwise false
+     */
+    @Override
+    public boolean equals(Object obj) {
+        if (obj == null) {
+            return false;
+        }
+        if (getClass() != obj.getClass()) {
+            return false;
+        }
+        final Pair<?, ?> other = (Pair<?, ?>) obj;
+        if (this.left != other.left && (this.left == null || !this.left.equals(other.left))) {
+            return false;
+        }
+        if (this.right != other.right && (this.right == null || !this.right.equals(other.right))) {
+            return false;
+        }
+        return true;
+    }
+}

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

@@ -22,8 +22,11 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.PrintWriter;
+import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
 import java.net.URLDecoder;
+import java.util.Enumeration;
 import java.util.Properties;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -35,6 +38,11 @@ import java.util.logging.Logger;
  */
 public final class Settings {
 
+    /**
+     * The logger.
+     */
+    private static final Logger LOGGER = Logger.getLogger(Settings.class.getName());
+
     /**
      * The collection of keys used within the properties file.
      */
@@ -137,6 +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.
          */
@@ -145,6 +173,30 @@ public final class Settings {
          * The properties key for the Nexus search URL.
          */
         public static final String ANALYZER_NEXUS_URL = "analyzer.nexus.url";
+        /**
+         * The properties key for using the proxy to reach Nexus.
+         */
+        public static final String ANALYZER_NEXUS_PROXY = "analyzer.nexus.proxy";
+        /**
+         * The path to mono, if available.
+         */
+        public static final String ANALYZER_ASSEMBLY_MONO_PATH = "analyzer.assembly.mono.path";
+        /**
+         * The additional configured zip file extensions, if available.
+         */
+        public static final String ADDITIONAL_ZIP_EXTENSIONS = "extensions.zip";
+        /**
+         * The properties key for whether Test Scope dependencies should be skipped.
+         */
+        public static final String SKIP_TEST_SCOPE = "skip.test.scope";
+        /**
+         * The properties key for whether Runtime Scope dependencies should be skipped.
+         */
+        public static final String SKIP_RUNTIME_SCOPE = "skip.runtime.scope";
+        /**
+         * The properties key for whether Provided Scope dependencies should be skipped.
+         */
+        public static final String SKIP_PROVIDED_SCOPE = "skip.provided.scope";
     }
     /**
      * The properties file location.
@@ -180,6 +232,43 @@ public final class Settings {
                 }
             }
         }
+        logProperties("Properties loaded", props);
+    }
+
+    /**
+     * Logs the properties. This will not log any properties that contain 'password' in the key.
+     *
+     * @param header the header to print with the log message
+     * @param properties the properties to log
+     */
+    private static void logProperties(String header, Properties properties) {
+        if (LOGGER.isLoggable(Level.FINE)) {
+            final StringWriter sw = new StringWriter();
+            PrintWriter pw = null;
+            try {
+                pw = new PrintWriter(sw);
+                pw.format("%s:%n%n", header);
+                final Enumeration e = properties.propertyNames();
+                while (e.hasMoreElements()) {
+                    final String key = (String) e.nextElement();
+                    if (key.contains("password")) {
+                        pw.format("%s='*****'%n", key);
+                    } else {
+                        final String value = properties.getProperty(key);
+                        if (value != null) {
+                            pw.format("%s='%s'%n", key, value);
+                        }
+                    }
+                }
+                pw.flush();
+                LOGGER.fine(sw.toString());
+            } finally {
+                if (pw != null) {
+                    pw.close();
+                }
+            }
+
+        }
     }
 
     /**
@@ -190,6 +279,9 @@ public final class Settings {
      */
     public static void setString(String key, String value) {
         INSTANCE.props.setProperty(key, value);
+        if (LOGGER.isLoggable(Level.FINE)) {
+            LOGGER.fine(String.format("Setting: %s='%s'", key, value));
+        }
     }
 
     /**
@@ -204,6 +296,9 @@ public final class Settings {
         } else {
             INSTANCE.props.setProperty(key, Boolean.FALSE.toString());
         }
+        if (LOGGER.isLoggable(Level.FINE)) {
+            LOGGER.fine(String.format("Setting: %s='%b'", key, value));
+        }
     }
 
     /**
@@ -244,6 +339,7 @@ public final class Settings {
      */
     public static void mergeProperties(InputStream stream) throws IOException {
         INSTANCE.props.load(stream);
+        logProperties("Properties updated via merge", INSTANCE.props);
     }
 
     /**
@@ -435,4 +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/java/org/owasp/dependencycheck/utils/URLConnectionFactory.java

@@ -0,0 +1,118 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.utils;
+
+import java.io.IOException;
+import java.net.Authenticator;
+import java.net.HttpURLConnection;
+import java.net.InetSocketAddress;
+import java.net.PasswordAuthentication;
+import java.net.Proxy;
+import java.net.SocketAddress;
+import java.net.URL;
+
+/**
+ * A URLConnection Factory to create new connections. This encapsulates several configuration checks to ensure that the
+ * connection uses the correct proxy settings.
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public final class URLConnectionFactory {
+
+    /**
+     * Private constructor for this factory.
+     */
+    private URLConnectionFactory() {
+    }
+
+    /**
+     * Utility method to create an HttpURLConnection. If the application is configured to use a proxy this method will
+     * retrieve the proxy settings and use them when setting up the connection.
+     *
+     * @param url the url to connect to
+     * @return an HttpURLConnection
+     * @throws URLConnectionFailureException thrown if there is an exception
+     */
+    public static HttpURLConnection createHttpURLConnection(URL url) throws URLConnectionFailureException {
+        HttpURLConnection conn = null;
+        Proxy proxy = null;
+        final String proxyUrl = Settings.getString(Settings.KEYS.PROXY_URL);
+        try {
+            if (proxyUrl != null) {
+                final int proxyPort = Settings.getInt(Settings.KEYS.PROXY_PORT);
+                final SocketAddress addr = new InetSocketAddress(proxyUrl, proxyPort);
+
+                final String username = Settings.getString(Settings.KEYS.PROXY_USERNAME);
+                final String password = Settings.getString(Settings.KEYS.PROXY_PASSWORD);
+                if (username != null && password != null) {
+                    final Authenticator auth = new Authenticator() {
+                        @Override
+                        public PasswordAuthentication getPasswordAuthentication() {
+                            if (getRequestorType().equals(Authenticator.RequestorType.PROXY)) {
+                                return new PasswordAuthentication(username, password.toCharArray());
+                            }
+                            return super.getPasswordAuthentication();
+                        }
+                    };
+                    Authenticator.setDefault(auth);
+                }
+
+                proxy = new Proxy(Proxy.Type.HTTP, addr);
+                conn = (HttpURLConnection) url.openConnection(proxy);
+            } else {
+                conn = (HttpURLConnection) url.openConnection();
+            }
+            final int timeout = Settings.getInt(Settings.KEYS.CONNECTION_TIMEOUT, 60000);
+            conn.setConnectTimeout(timeout);
+        } catch (IOException ex) {
+            if (conn != null) {
+                try {
+                    conn.disconnect();
+                } finally {
+                    conn = null;
+                }
+            }
+            throw new URLConnectionFailureException("Error getting connection.", ex);
+        }
+        return conn;
+    }
+
+    /**
+     * Utility method to create an HttpURLConnection. The use of a proxy here is optional as there may be cases where a
+     * proxy is configured but we don't want to use it (for example, if there's an internal repository configured)
+     *
+     * @param url the url to connect to
+     * @param proxy whether to use the proxy (if configured)
+     * @return a newly constructed HttpURLConnection
+     * @throws URLConnectionFailureException thrown if there is an exception
+     */
+    public static HttpURLConnection createHttpURLConnection(URL url, boolean proxy) throws URLConnectionFailureException {
+        if (proxy) {
+            return createHttpURLConnection(url);
+        }
+        HttpURLConnection conn = null;
+        try {
+            conn = (HttpURLConnection) url.openConnection();
+            final int timeout = Settings.getInt(Settings.KEYS.CONNECTION_TIMEOUT, 60000);
+            conn.setConnectTimeout(timeout);
+        } catch (IOException ioe) {
+            throw new URLConnectionFailureException("Error getting connection.", ioe);
+        }
+        return conn;
+    }
+}

dependency-check-core/src/main/java/org/owasp/dependencycheck/utils/URLConnectionFailureException.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.utils;
+
+import java.io.IOException;
+
+/**
+ * An exception used when the creation of an URLConnection fails.
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public class URLConnectionFailureException extends IOException {
+
+    /**
+     * The serial version UID.
+     */
+    private static final long serialVersionUID = 1L;
+
+    /**
+     * Creates a new URLConnectionFailureException.
+     */
+    public URLConnectionFailureException() {
+        super();
+    }
+
+    /**
+     * Creates a new URLConnectionFailureException.
+     *
+     * @param msg a message for the exception.
+     */
+    public URLConnectionFailureException(String msg) {
+        super(msg);
+    }
+
+    /**
+     * Creates a new URLConnectionFailureException.
+     *
+     * @param ex the cause of the download failure.
+     */
+    public URLConnectionFailureException(Throwable ex) {
+        super(ex);
+    }
+
+    /**
+     * Creates a new URLConnectionFailureException.
+     *
+     * @param msg a message for the exception.
+     * @param ex the cause of the download failure.
+     */
+    public URLConnectionFailureException(String msg, Throwable ex) {
+        super(msg, ex);
+    }
+}

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

@@ -9,3 +9,5 @@ org.owasp.dependencycheck.analyzer.DependencyBundlingAnalyzer
 org.owasp.dependencycheck.analyzer.NvdCveAnalyzer
 org.owasp.dependencycheck.analyzer.VulnerabilitySuppressionAnalyzer
 org.owasp.dependencycheck.analyzer.NexusAnalyzer
+org.owasp.dependencycheck.analyzer.NuspecAnalyzer
+org.owasp.dependencycheck.analyzer.AssemblyAnalyzer

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

@@ -30,11 +30,6 @@ data.password=DC-Pass1337!
 data.driver_name=org.h2.Driver
 data.driver_path=
 
-# the path to the cpe xml file
-cpe.url=http://static.nvd.nist.gov/feeds/xml/cpe/dictionary/official-cpe-dictionary_v2.2.xml.gz
-# the path to the cpe meta data file.
-cpe.meta.url=http://static.nvd.nist.gov/feeds/xml/cpe/dictionary/official-cpe-dictionary_v2.2.meta
-
 # the number of days that the modified nvd cve data holds data for. We don't need
 # to update the other files if we are within this timespan. Per NIST this file
 # holds 8 days of updates, we are using 7 just to be safe.
@@ -47,7 +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);
@@ -69,5 +91,6 @@ public class EngineIntegrationTest {
         ReportGenerator rg = new ReportGenerator("DependencyCheck",
                 instance.getDependencies(), instance.getAnalyzers(), dbProp);
         rg.generateReports("./target/", "ALL");
+        instance.cleanup();
     }
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/analyzer/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 (e != null && e.contains("jar")) {
+            if ("Jar Analyzer".equals(a.getName())) {
                 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() {
     }
@@ -69,6 +69,7 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
         expResult.add("zip");
         expResult.add("war");
         expResult.add("ear");
+        expResult.add("nupkg");
         expResult.add("tar");
         expResult.add("gz");
         expResult.add("tgz");
@@ -110,6 +111,10 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
         extension = "zip"; //supported
         result = instance.supportsExtension(extension);
         assertEquals(expResult, result);
+
+        extension = "nupkg"; //supported
+        result = instance.supportsExtension(extension);
+        assertEquals(expResult, result);
     }
 
     /**
@@ -142,18 +147,23 @@ 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();
 
             File file = new File(this.getClass().getClassLoader().getResource("daytrader-ear-2.1.7.ear").getPath());
             Dependency dependency = new Dependency(file);
             Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+            Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
             Engine engine = new Engine();
 
             int initial_size = engine.getDependencies().size();
             instance.analyze(dependency, engine);
             int ending_size = engine.getDependencies().size();
 
+            engine.cleanup();
+
             assertTrue(initial_size < ending_size);
 
         } finally {
@@ -167,6 +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();
 
@@ -174,11 +186,13 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
             File file = new File(this.getClass().getClassLoader().getResource("stagedhttp-modified.tar").getPath());
             Dependency dependency = new Dependency(file);
             Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+            Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
             Engine engine = new Engine();
 
             int initial_size = engine.getDependencies().size();
             instance.analyze(dependency, engine);
             int ending_size = engine.getDependencies().size();
+            engine.cleanup();
 
             assertTrue(initial_size < ending_size);
 
@@ -193,12 +207,14 @@ 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();
 
             File file = new File(this.getClass().getClassLoader().getResource("file.tar.gz").getPath());
             //Dependency dependency = new Dependency(file);
             Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+            Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
             Engine engine = new Engine();
 
             int initial_size = engine.getDependencies().size();
@@ -206,7 +222,7 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
             engine.scan(file);
             engine.analyzeDependencies();
             int ending_size = engine.getDependencies().size();
-
+            engine.cleanup();
             assertTrue(initial_size < ending_size);
 
         } finally {
@@ -214,24 +230,47 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
         }
     }
 
+//    /**
+//     * Test of analyze method, of class ArchiveAnalyzer.
+//     */
+//    @Test
+//    public void testNestedZipFolder() throws Exception {
+//        ArchiveAnalyzer instance = new ArchiveAnalyzer();
+//        try {
+//            instance.initialize();
+//
+//            File file = new File(this.getClass().getClassLoader().getResource("nested.zip").getPath());
+//            Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+//            Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
+//            Engine engine = new Engine();
+//
+//            engine.scan(file);
+//            engine.analyzeDependencies();
+//
+//        } finally {
+//            instance.close();
+//        }
+//    }
     /**
      * Test of analyze method, of class ArchiveAnalyzer.
      */
     @Test
     public void testAnalyzeTgz() throws Exception {
         ArchiveAnalyzer instance = new ArchiveAnalyzer();
+        instance.supportsExtension("zip"); //ensure analyzer is "enabled"
         try {
             instance.initialize();
 
             File file = new File(this.getClass().getClassLoader().getResource("file.tgz").getPath());
             Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+            Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
             Engine engine = new Engine();
 
             int initial_size = engine.getDependencies().size();
             engine.scan(file);
             engine.analyzeDependencies();
             int ending_size = engine.getDependencies().size();
-
+            engine.cleanup();
             assertTrue(initial_size < ending_size);
 
         } finally {
@@ -251,6 +290,7 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
             File file = new File(this.getClass().getClassLoader().getResource("test.zip").getPath());
             Dependency dependency = new Dependency(file);
             Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
+            Settings.setBoolean(Settings.KEYS.ANALYZER_NEXUS_ENABLED, false);
             Engine engine = new Engine();
             int initial_size = engine.getDependencies().size();
 //            boolean failed = false;
@@ -261,6 +301,7 @@ public class ArchiveAnalyzerTest extends BaseIndexTestCase {
 //            }
 //            assertTrue(failed);
             int ending_size = engine.getDependencies().size();
+            engine.cleanup();
             assertEquals(initial_size, ending_size);
         } finally {
             instance.close();

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

@@ -0,0 +1,175 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.analyzer;
+
+import 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 org.junit.Assume;
+import org.junit.Before;
+import org.junit.Test;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
+import org.owasp.dependencycheck.dependency.Confidence;
+import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.dependency.Evidence;
+import org.owasp.dependencycheck.utils.Settings;
+
+/**
+ * Tests for the AssemblyAnalyzer.
+ *
+ * @author colezlaw
+ *
+ */
+public class AssemblyAnalyzerTest {
+
+    private static final Logger LOGGER = Logger.getLogger(AssemblyAnalyzerTest.class.getName());
+
+    AssemblyAnalyzer analyzer;
+
+    /**
+     * Sets up the analyzer.
+     *
+     * @throws Exception if anything goes sideways
+     */
+    @Before
+    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);
+            Assume.assumeNoException("Is mono installed? TESTS WILL BE INCOMPLETE", e);
+        }
+    }
+
+    /**
+     * Tests to make sure the name is correct.
+     */
+    @Test
+    public void testGetName() {
+        assertEquals("Assembly Analyzer", analyzer.getName());
+    }
+
+    @Test
+    public void testAnalysis() throws Exception {
+        File f = new File(AssemblyAnalyzerTest.class.getClassLoader().getResource("GrokAssembly.exe").getPath());
+        Dependency d = new Dependency(f);
+        analyzer.analyze(d, null);
+        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
+    public void testLog4Net() throws Exception {
+        File f = new File(AssemblyAnalyzerTest.class.getClassLoader().getResource("log4net.dll").getPath());
+        Dependency d = new Dependency(f);
+        analyzer.analyze(d, null);
+        assertTrue(d.getVersionEvidence().getEvidence().contains(new Evidence("grokassembly", "version", "1.2.13.0", Confidence.HIGHEST)));
+        assertTrue(d.getVendorEvidence().getEvidence().contains(new Evidence("grokassembly", "vendor", "The Apache Software Foundation", Confidence.HIGH)));
+        assertTrue(d.getProductEvidence().getEvidence().contains(new Evidence("grokassembly", "product", "log4net", Confidence.HIGH)));
+    }
+
+    @Test
+    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);
+
+        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
+    public void testWithSettingMono() throws Exception {
+
+        //This test doesn't work on Windows.
+        assumeFalse(System.getProperty("os.name").startsWith("Windows"));
+
+        String oldValue = Settings.getString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH);
+        // if oldValue is null, that means that neither the system property nor the setting has
+        // been set. If that's the case, then we have to make it such that when we recover,
+        // null still comes back. But you can't put a null value in a HashMap, so we have to set
+        // the system property rather than the setting.
+        if (oldValue == null) {
+            System.setProperty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, "/yooser/bine/mono");
+        } else {
+            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) {
+                System.getProperties().remove(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH);
+            } else {
+                Settings.setString(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, oldValue);
+            }
+        }
+    }
+
+    @After
+    public void tearDown() throws Exception {
+        analyzer.close();
+    }
+}

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/JavaScriptAnalyzerTest.java

@@ -0,0 +1,145 @@
+/*
+ * 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 java.util.HashSet;
+import java.util.Set;
+import org.junit.After;
+import org.junit.AfterClass;
+import static org.junit.Assert.assertEquals;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.dependency.Dependency;
+
+/**
+ *
+ * @author Jeremy Long <jeremy.long@owasp.org>
+ */
+public class JavaScriptAnalyzerTest {
+
+    public JavaScriptAnalyzerTest() {
+    }
+
+    @BeforeClass
+    public static void setUpClass() {
+    }
+
+    @AfterClass
+    public static void tearDownClass() {
+    }
+
+    @Before
+    public void setUp() {
+    }
+
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * Test of getSupportedExtensions method, of class JavaScriptAnalyzer.
+     */
+    @Test
+    public void testGetSupportedExtensions() {
+        JavaScriptAnalyzer instance = new JavaScriptAnalyzer();
+        Set expResult = new HashSet<String>();
+        expResult.add("js");
+        Set result = instance.getSupportedExtensions();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of getName method, of class JavaScriptAnalyzer.
+     */
+    @Test
+    public void testGetName() {
+        System.out.println("getName");
+        JavaScriptAnalyzer instance = new JavaScriptAnalyzer();
+        String expResult = "JavaScript Analyzer";
+        String result = instance.getName();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of supportsExtension method, of class JavaScriptAnalyzer.
+     */
+    @Test
+    public void testSupportsExtension() {
+        String extension = "js";
+        JavaScriptAnalyzer instance = new JavaScriptAnalyzer();
+        boolean expResult = true;
+        boolean result = instance.supportsExtension(extension);
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of getAnalysisPhase method, of class JavaScriptAnalyzer.
+     */
+    @Test
+    public void testGetAnalysisPhase() {
+        JavaScriptAnalyzer instance = new JavaScriptAnalyzer();
+        AnalysisPhase expResult = AnalysisPhase.INFORMATION_COLLECTION;
+        AnalysisPhase result = instance.getAnalysisPhase();
+        assertEquals(expResult, result);
+    }
+
+    /**
+     * Test of analyze method, of class JavaScriptAnalyzer.
+     */
+    @Test
+    public void testAnalyze() throws Exception {
+        File jq6 = new File(this.getClass().getClassLoader().getResource("jquery-1.6.2.min.js").getPath());
+        File jq10 = new File(this.getClass().getClassLoader().getResource("jquery-1.10.2.js").getPath());
+        File jq10min = new File(this.getClass().getClassLoader().getResource("jquery-1.10.2.min.js").getPath());
+        Dependency depJQ6 = new Dependency(jq6);
+        Dependency depJQ10 = new Dependency(jq10);
+        Dependency depJQ10min = new Dependency(jq10min);
+        Engine engine = null;
+        JavaScriptAnalyzer instance = new JavaScriptAnalyzer();
+
+//        assertTrue(depJQ6.getEvidence().size() == 0);
+//        assertTrue(depJQ10.getEvidence().size() == 0);
+//        assertTrue(depJQ10min.getEvidence().size() == 0);
+//
+//        instance.analyze(depJQ6, engine);
+//        instance.analyze(depJQ10, engine);
+//        instance.analyze(depJQ10min, engine);
+//        //TODO improve the assertions
+//        assertTrue(depJQ6.getEvidence().size() > 0);
+//        assertTrue(depJQ10.getEvidence().size() > 0);
+//        assertTrue(depJQ10min.getEvidence().size() > 0);
+    }
+
+    /**
+     * Test of initialize method, of class JavaScriptAnalyzer.
+     */
+    @Test
+    public void testInitialize() throws Exception {
+    }
+
+    /**
+     * Test of close method, of class JavaScriptAnalyzer.
+     */
+    @Test
+    public void testClose() throws Exception {
+
+    }
+}

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

@@ -0,0 +1,59 @@
+/*
+ * 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 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;
+
+public class NuspecAnalyzerTest {
+
+    private NuspecAnalyzer instance;
+
+    @Before
+    public void setUp() {
+        instance = new NuspecAnalyzer();
+        instance.setEnabled(true);
+    }
+
+    @Test
+    public void testGetAnalyzerName() {
+        assertEquals("Nuspec Analyzer", instance.getName());
+    }
+
+    @Test
+    public void testGetSupportedExtensions() {
+        assertTrue(instance.getSupportedExtensions().contains("nuspec"));
+        assertFalse(instance.getSupportedExtensions().contains("nupkg"));
+    }
+
+    @Test
+    public void testSupportsExtension() {
+        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/data/cwe/CweDBTest.java

@@ -59,11 +59,26 @@ public class CweDBTest {
 //        SAXParser saxParser = factory.newSAXParser();
 //
 //        CweHandler handler = new CweHandler();
-//        File file = new File(this.getClass().getClassLoader().getResource("cwe.2000.xml").getPath());
+//        //File file = new File(this.getClass().getClassLoader().getResource("cwe.2000.xml").getPath());
+//        File file = new File(this.getClass().getClassLoader().getResource("cwec_v2.5.xml").getPath());
 //
 //        saxParser.parse(file, handler);
 //        System.out.println("Found " + handler.getCwe().size() + " cwe entries.");
-//        Map<String,String> cwe = handler.getCwe();
+//        Map<String, String> cwe = handler.getCwe();
+////        FileOutputStream fout = new FileOutputStream("target/current.csv");
+////        //FileOutputStream fout = new FileOutputStream("target/new.csv");
+////        PrintWriter writer = new PrintWriter(fout);
+////        for (Map.Entry<String, String> entry : cwe.entrySet()) {
+////            writer.print('"');
+////            writer.print(entry.getKey());
+////            writer.print('"');
+////            writer.print(',');
+////            writer.print('"');
+////            writer.print(entry.getValue());
+////            writer.println('"');
+////        }
+////        writer.close();
+//
 //        FileOutputStream fout = new FileOutputStream("src/main/resources/data/cwe.hashmap.serialized");
 //        ObjectOutputStream objOut = new ObjectOutputStream(fout);
 //        objOut.writeObject(cwe);

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/nexus/NexusSearchTest.java

@@ -17,13 +17,15 @@
  */
 package org.owasp.dependencycheck.data.nexus;
 
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
 import java.io.FileNotFoundException;
 import java.net.URL;
 import java.util.logging.Logger;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
+
+import org.junit.Assume;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.owasp.dependencycheck.utils.Settings;
 
@@ -37,6 +39,7 @@ public class NexusSearchTest {
         String nexusUrl = Settings.getString(Settings.KEYS.ANALYZER_NEXUS_URL);
         LOGGER.fine(nexusUrl);
         searcher = new NexusSearch(new URL(nexusUrl));
+        Assume.assumeTrue(searcher.preflightRequest());
     }
 
     @Test(expected = IllegalArgumentException.class)
@@ -52,7 +55,6 @@ public class NexusSearchTest {
     // This test does generate network traffic and communicates with a host
     // you may not be able to reach. Remove the @Ignore annotation if you want to
     // test it anyway
-    @Ignore
     @Test
     public void testValidSha1() throws Exception {
         MavenArtifact ma = searcher.searchSha1("9977a8d04e75609cf01badc4eb6a9c7198c4c5ea");
@@ -65,7 +67,6 @@ public class NexusSearchTest {
     // This test does generate network traffic and communicates with a host
     // you may not be able to reach. Remove the @Ignore annotation if you want to
     // test it anyway
-    @Ignore
     @Test(expected = FileNotFoundException.class)
     public void testMissingSha1() throws Exception {
         searcher.searchSha1("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/nuget/XPathNuspecParserTest.java

@@ -0,0 +1,73 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.data.nuget;
+
+import java.io.InputStream;
+
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+
+/**
+ * 
+ * @author colezlaw
+ *
+ */
+public class XPathNuspecParserTest {
+    /**
+     * Test all the valid components.
+     * 
+     * @throws Exception if anything goes sideways.
+     */
+    @Test
+    public void testGoodDocument() throws Exception {
+        NuspecParser parser = new XPathNuspecParser();
+        InputStream is = XPathNuspecParserTest.class.getClassLoader().getResourceAsStream("log4net.2.0.3.nuspec");
+        NugetPackage np = parser.parse(is);
+        assertEquals("log4net", np.getId());
+        assertEquals("2.0.3", np.getVersion());
+        assertEquals("log4net [1.2.13]", np.getTitle());
+        assertEquals("Apache Software Foundation", np.getAuthors());
+        assertEquals("Apache Software Foundation", np.getOwners());
+        assertEquals("http://logging.apache.org/log4net/license.html", np.getLicenseUrl());
+    }
+    
+    /**
+     * Expect a NuspecParseException when what we pass isn't even XML.
+     * 
+     * @throws Exception we expect this.
+     */
+    @Test(expected=NuspecParseException.class)
+    public void testMissingDocument() throws Exception {
+        NuspecParser parser = new XPathNuspecParser();
+        InputStream is = XPathNuspecParserTest.class.getClassLoader().getResourceAsStream("dependencycheck.properties");
+        NugetPackage np = parser.parse(is);
+    }
+    
+    /**
+     * Expect a NuspecParseException when it's valid XML, but not a Nuspec.
+     * 
+     * @throws Exception we expect this.
+     */
+    @Test(expected=NuspecParseException.class)
+    public void testNotNuspec() throws Exception {
+        NuspecParser parser = new XPathNuspecParser();
+        InputStream is = XPathNuspecParserTest.class.getClassLoader().getResourceAsStream("suppressions.xml");
+        NugetPackage np = parser.parse(is);
+    }
+}

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

@@ -73,7 +73,7 @@ public abstract class BaseDBTestCase extends TestCase {
                         while ((count = zin.read(data, 0, BUFFER_SIZE)) != -1) {
                             dest.write(data, 0, count);
                         }
-                    } catch (Exception ex) {
+                    } catch (Throwable ex) {
                         Logger.getLogger(BaseDBTestCase.class.getName()).log(Level.SEVERE, null, ex);
                     } finally {
                         try {

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

@@ -59,7 +59,14 @@ public class DriverLoaderTest {
     @Test
     public void testLoad_String() throws Exception {
         String className = "org.h2.Driver";
-        DriverLoader.load(className);
+        Driver d = null;
+        try {
+            d = DriverLoader.load(className);
+        } finally {
+            if (d != null) {
+                DriverManager.deregisterDriver(d);
+            }
+        }
     }
 
     /**
@@ -68,7 +75,7 @@ public class DriverLoaderTest {
     @Test(expected = DriverLoadException.class)
     public void testLoad_String_ex() throws Exception {
         String className = "bad.Driver";
-        DriverLoader.load(className);
+        Driver d = DriverLoader.load(className);
     }
 
     /**
@@ -82,9 +89,16 @@ public class DriverLoaderTest {
         File driver = new File(testClassPath, "../../src/test/resources/mysql-connector-java-5.1.27-bin.jar");
         assertTrue("MySQL Driver JAR file not found in src/test/resources?", driver.isFile());
 
-        DriverLoader.load(className, driver.getAbsolutePath());
-        Driver d = DriverManager.getDriver("jdbc:mysql://localhost:3306/dependencycheck");
-        assertNotNull(d);
+        Driver d = null;
+        try {
+            d = DriverLoader.load(className, driver.getAbsolutePath());
+            d = DriverManager.getDriver("jdbc:mysql://localhost:3306/dependencycheck");
+            assertNotNull(d);
+        } finally {
+            if (d != null) {
+                DriverManager.deregisterDriver(d);
+            }
+        }
     }
 
     /**
@@ -99,7 +113,14 @@ public class DriverLoaderTest {
         final File dir2 = new File(testClassPath, "../../src/test/resources/");
         final String paths = String.format("%s" + File.pathSeparator + "%s", dir1.getAbsolutePath(), dir2.getAbsolutePath());
 
-        DriverLoader.load(className, paths);
+        Driver d = null;
+        try {
+            d = DriverLoader.load(className, paths);
+        } finally {
+            if (d != null) {
+                DriverManager.deregisterDriver(d);
+            }
+        }
     }
 
     /**
@@ -113,7 +134,7 @@ public class DriverLoaderTest {
         File driver = new File(testClassPath, "../../src/test/resources/mysql-connector-java-5.1.27-bin.jar");
         assertTrue("MySQL Driver JAR file not found in src/test/resources?", driver.isFile());
 
-        DriverLoader.load(className, driver.getAbsolutePath());
+        Driver d = DriverLoader.load(className, driver.getAbsolutePath());
     }
 
     /**
@@ -125,6 +146,6 @@ public class DriverLoaderTest {
         //we know this is in target/test-classes
         File testClassPath = (new File(this.getClass().getClassLoader().getResource("org.mortbay.jetty.jar").getPath())).getParentFile();
         File driver = new File(testClassPath, "../../src/test/bad/mysql-connector-java-5.1.27-bin.jar");
-        DriverLoader.load(className, driver.getAbsolutePath());
+        Driver d = DriverLoader.load(className, driver.getAbsolutePath());
     }
 }

dependency-check-core/src/test/java/org/owasp/dependencycheck/data/update/xml/NvdCve_2_0_HandlerTest.java

@@ -54,7 +54,7 @@ public class NvdCve_2_0_HandlerTest {
 
     @Test
     public void testParse() {
-        Exception results = null;
+        Throwable results = null;
         try {
             SAXParserFactory factory = SAXParserFactory.newInstance();
             SAXParser saxParser = factory.newSAXParser();
@@ -64,7 +64,7 @@ public class NvdCve_2_0_HandlerTest {
             NvdCve20Handler instance = new NvdCve20Handler();
 
             saxParser.parse(file, instance);
-        } catch (Exception ex) {
+        } catch (Throwable ex) {
             results = ex;
         }
         assertTrue("Exception thrown during parse of 2012 CVE version 2.0?", results == null);

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

@@ -87,5 +87,13 @@ public class VulnerableSoftwareTest {
         int expResult = -2;
         int result = instance.compareTo(vs);
         assertEquals(expResult, result);
+
+        vs = new VulnerableSoftware();
+        vs.setCpe("cpe:/a:yahoo:toolbar:3.1.0.20130813024103");
+        instance = new VulnerableSoftware();
+        instance.setCpe("cpe:/a:yahoo:toolbar:3.1.0.20130813024104");
+        expResult = 1;
+        result = instance.compareTo(vs);
+        assertEquals(expResult, result);
     }
 }

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

@@ -150,6 +150,8 @@ public class ReportGeneratorTest {
         ReportGenerator generator = new ReportGenerator("Test Report", engine.getDependencies(), engine.getAnalyzers(), dbProp);
         generator.generateReport(templateName, writeTo);
 
+        engine.cleanup();
+
         InputStream xsdStream = ReportGenerator.class.getClassLoader().getResourceAsStream("schema/DependencyCheck.xsd");
         StreamSource xsdSource = new StreamSource(xsdStream);
         StreamSource xmlSource = new StreamSource(new File(writeTo));

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

@@ -22,6 +22,7 @@ import org.junit.After;
 import org.junit.AfterClass;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -72,11 +73,12 @@ 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.");
         }
-        FileUtils.delete(file);
+        boolean status = FileUtils.delete(file);
+        assertTrue("delete returned a failed status", status);
         assertFalse("Temporary file exists after attempting deletion", file.exists());
     }
 }

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

@@ -49,4 +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