/*
    * This file is part of dependency-check-maven.
    *
    * Licensed under the Apache License, Version 2.0 (the "License");
    * you may not use this file except in compliance with the License.
    * You may obtain a copy of the License at
    *
    *     http://www.apache.org/licenses/LICENSE-2.0
    *
   * Unless required by applicable law or agreed to in writing, software
   * distributed under the License is distributed on an "AS IS" BASIS,
   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   * See the License for the specific language governing permissions and
   * limitations under the License.
   *
   * Copyright (c) 2014 Jeremy Long. All Rights Reserved.
   */
  package org.owasp.dependencycheck.maven;
  
  import java.io.BufferedOutputStream;
  import java.io.File;
  import java.io.FileInputStream;
  import java.io.FileNotFoundException;
  import java.io.FileOutputStream;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.ObjectOutputStream;
  import java.util.List;
  import java.util.Locale;
  import org.eclipse.aether.artifact.Artifact;
  import org.apache.maven.doxia.sink.Sink;
  import org.apache.maven.plugin.AbstractMojo;
  import org.apache.maven.plugin.MojoExecutionException;
  import org.apache.maven.plugin.MojoFailureException;
  import org.apache.maven.plugins.annotations.Component;
  import org.apache.maven.plugins.annotations.Parameter;
  import org.apache.maven.project.MavenProject;
  import org.apache.maven.reporting.MavenReport;
  import org.apache.maven.reporting.MavenReportException;
  import org.apache.maven.settings.Proxy;
  import org.apache.maven.settings.Server;
  import org.apache.maven.shared.dependency.graph.DependencyGraphBuilder;
  import org.apache.maven.shared.dependency.graph.DependencyGraphBuilderException;
  import org.apache.maven.shared.dependency.graph.DependencyNode;
  import org.eclipse.aether.RepositorySystem;
  import org.eclipse.aether.RepositorySystemSession;
  import org.eclipse.aether.artifact.DefaultArtifact;
  import org.eclipse.aether.repository.RemoteRepository;
  import org.eclipse.aether.resolution.ArtifactRequest;
  import org.eclipse.aether.resolution.ArtifactResolutionException;
  import org.eclipse.aether.resolution.ArtifactResult;
  import org.owasp.dependencycheck.data.nexus.MavenArtifact;
  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.Confidence;
  import org.owasp.dependencycheck.dependency.Dependency;
  import org.owasp.dependencycheck.dependency.Identifier;
  import org.owasp.dependencycheck.dependency.Vulnerability;
  import org.owasp.dependencycheck.exception.ExceptionCollection;
  import org.owasp.dependencycheck.exception.ReportException;
  import org.owasp.dependencycheck.reporting.ReportGenerator;
  import org.owasp.dependencycheck.utils.ExpectedOjectInputStream;
  import org.owasp.dependencycheck.utils.Settings;
  import org.sonatype.plexus.components.sec.dispatcher.DefaultSecDispatcher;
  import org.sonatype.plexus.components.sec.dispatcher.SecDispatcher;
  import org.sonatype.plexus.components.sec.dispatcher.SecDispatcherException;
  
  /**
   *
   * @author Jeremy Long
   */
  public abstract class BaseDependencyCheckMojo extends AbstractMojo implements MavenReport {
  
      //<editor-fold defaultstate="collapsed" desc="Private fields">
      /**
       * The properties file location.
       */
      private static final String PROPERTIES_FILE = "mojo.properties";
      /**
       * System specific new line character.
       */
      private static final String NEW_LINE = System.getProperty("line.separator", "\n").intern();
      //</editor-fold>
      // <editor-fold defaultstate="collapsed" desc="Maven bound parameters and components">
      /**
       * Sets whether or not the external report format should be used.
       */
      @Parameter(property = "metaFileName", defaultValue = "dependency-check.ser", required = true)
      private String dataFileName;
      /**
       * Sets whether or not the external report format should be used.
       */
      @Parameter(property = "failOnError", defaultValue = "true", required = true)
      private boolean failOnError;
  
      /**
       * Returns if the mojo should fail the build if an exception occurs.
       *
      * @return whether or not the mojo should fail the build
      */
     protected boolean isFailOnError() {
         return failOnError;
     }
 
     /**
      * The Maven Project Object.
      */
     @Parameter(property = "project", required = true, readonly = true)
     private MavenProject project;
     /**
      * List of Maven project of the current build
      */
     @Parameter(readonly = true, required = true, property = "reactorProjects")
     private List<MavenProject> reactorProjects;
     /**
      * The entry point to Aether, i.e. the component doing all the work.
      */
     @Component
     private RepositorySystem repoSystem;
 
     /**
      * The current repository/network configuration of Maven.
      */
     @Parameter(defaultValue = "${repositorySystemSession}", readonly = true)
     private RepositorySystemSession repoSession;
 
     /**
      * The project's remote repositories to use for the resolution of plug-ins
      * and their dependencies.
      */
     @Parameter(defaultValue = "${project.remotePluginRepositories}", readonly = true)
     private List<RemoteRepository> remoteRepos;
 
     /**
      * Component within Maven to build the dependency graph.
      */
     @Component
     private DependencyGraphBuilder dependencyGraphBuilder;
 
     /**
      * The output directory. This generally maps to "target".
      */
     @Parameter(defaultValue = "${project.build.directory}", required = true)
     private File outputDirectory;
     /**
      * Specifies the destination directory for the generated Dependency-Check
      * report. This generally maps to "target/site".
      */
     @Parameter(property = "project.reporting.outputDirectory", required = true)
     private File reportOutputDirectory;
     /**
      * Specifies if the build should be failed if a CVSS score above a specified
      * level is identified. The default is 11 which means since the CVSS scores
      * are 0-10, by default the build will never fail.
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "failBuildOnCVSS", defaultValue = "11", required = true)
     private float failBuildOnCVSS = 11;
     /**
      * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not
      * recommended that this be turned to false. Default is true.
      */
     @Parameter(property = "autoUpdate")
     private Boolean autoUpdate;
     /**
      * Sets whether Experimental analyzers are enabled. Default is false.
      */
     @Parameter(property = "enableExperimental")
     private Boolean enableExperimental;
     /**
      * Generate aggregate reports in multi-module projects.
      *
      * @deprecated use the aggregate goal instead
      */
     @Parameter(property = "aggregate")
     @Deprecated
     private Boolean aggregate;
     /**
      * The report format to be generated (HTML, XML, VULN, ALL). This
      * configuration option has no affect if using this within the Site plug-in
      * unless the externalReport is set to true. Default is HTML.
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "format", defaultValue = "HTML", required = true)
     private String format = "HTML";
     /**
      * The Maven settings.
      */
     @Parameter(property = "mavenSettings", defaultValue = "${settings}", required = false)
     private org.apache.maven.settings.Settings mavenSettings;
 
     /**
      * The maven settings proxy id.
      */
     @Parameter(property = "mavenSettingsProxyId", required = false)
     private String mavenSettingsProxyId;
 
     /**
      * The Connection Timeout.
      */
     @Parameter(property = "connectionTimeout", defaultValue = "", required = false)
     private String connectionTimeout;
     /**
      * The path to the suppression file.
      */
     @Parameter(property = "suppressionFile", defaultValue = "", required = false)
     private String suppressionFile;
     /**
      * Flag indicating whether or not to show a summary in the output.
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "showSummary", defaultValue = "true", required = false)
     private boolean showSummary = true;
 
     /**
      * Whether or not the Jar Analyzer is enabled.
      */
     @Parameter(property = "jarAnalyzerEnabled", required = false)
     private Boolean jarAnalyzerEnabled;
 
     /**
      * Whether or not the Archive Analyzer is enabled.
      */
     @Parameter(property = "archiveAnalyzerEnabled", required = false)
     private Boolean archiveAnalyzerEnabled;
 
     /**
      * Sets whether the Python Distribution Analyzer will be used.
      */
     @Parameter(property = "pyDistributionAnalyzerEnabled", required = false)
     private Boolean pyDistributionAnalyzerEnabled;
     /**
      * Sets whether the Python Package Analyzer will be used.
      */
     @Parameter(property = "pyPackageAnalyzerEnabled", required = false)
     private Boolean pyPackageAnalyzerEnabled;
     /**
      * Sets whether the Ruby Gemspec Analyzer will be used.
      */
     @Parameter(property = "rubygemsAnalyzerEnabled", required = false)
     private Boolean rubygemsAnalyzerEnabled;
     /**
      * Sets whether or not the openssl Analyzer should be used.
      */
     @Parameter(property = "opensslAnalyzerEnabled", required = false)
     private Boolean opensslAnalyzerEnabled;
     /**
      * Sets whether or not the CMake Analyzer should be used.
      */
     @Parameter(property = "cmakeAnalyzerEnabled", required = false)
     private Boolean cmakeAnalyzerEnabled;
     /**
      * Sets whether or not the autoconf Analyzer should be used.
      */
     @Parameter(property = "autoconfAnalyzerEnabled", required = false)
     private Boolean autoconfAnalyzerEnabled;
     /**
      * Sets whether or not the PHP Composer Lock File Analyzer should be used.
      */
     @Parameter(property = "composerAnalyzerEnabled", required = false)
     private Boolean composerAnalyzerEnabled;
     /**
      * Sets whether or not the Node.js Analyzer should be used.
      */
     @Parameter(property = "nodeAnalyzerEnabled", required = false)
     private Boolean nodeAnalyzerEnabled;
 
     /**
      * Whether or not the .NET Assembly Analyzer is enabled.
      */
     @Parameter(property = "assemblyAnalyzerEnabled", required = false)
     private Boolean assemblyAnalyzerEnabled;
 
     /**
      * Whether or not the .NET Nuspec Analyzer is enabled.
      */
     @Parameter(property = "nuspecAnalyzerEnabled", required = false)
     private Boolean nuspecAnalyzerEnabled;
 
     /**
      * Whether or not the Central Analyzer is enabled.
      */
     @Parameter(property = "centralAnalyzerEnabled", required = false)
     private Boolean centralAnalyzerEnabled;
 
     /**
      * Whether or not the Nexus Analyzer is enabled.
      */
     @Parameter(property = "nexusAnalyzerEnabled", required = false)
     private Boolean nexusAnalyzerEnabled;
 
     /**
      * The URL of a Nexus server's REST API end point
      * (http://domain/nexus/service/local).
      */
     @Parameter(property = "nexusUrl", required = false)
     private String nexusUrl;
     /**
      * Whether or not the configured proxy is used to connect to Nexus.
      */
     @Parameter(property = "nexusUsesProxy", required = false)
     private Boolean nexusUsesProxy;
     /**
      * The database connection string.
      */
     @Parameter(property = "connectionString", defaultValue = "", required = false)
     private String connectionString;
 
     /**
      * Returns the connection string.
      *
      * @return the connection string
      */
     protected String getConnectionString() {
         return connectionString;
     }
     /**
      * The database driver name. An example would be org.h2.Driver.
      */
     @Parameter(property = "databaseDriverName", defaultValue = "", required = false)
     private String databaseDriverName;
     /**
      * The path to the database driver if it is not on the class path.
      */
     @Parameter(property = "databaseDriverPath", defaultValue = "", required = false)
     private String databaseDriverPath;
     /**
      * The server id in the settings.xml; used to retrieve encrypted passwords
      * from the settings.xml.
      */
     @Parameter(property = "serverId", defaultValue = "", required = false)
     private String serverId;
     /**
      * A reference to the settings.xml settings.
      */
     @Parameter(defaultValue = "${settings}", readonly = true, required = true)
     private org.apache.maven.settings.Settings settingsXml;
     /**
      * The security dispatcher that can decrypt passwords in the settings.xml.
      */
     @Component(role = SecDispatcher.class, hint = "default")
     private SecDispatcher securityDispatcher;
     /**
      * The database user name.
      */
     @Parameter(property = "databaseUser", defaultValue = "", required = false)
     private String databaseUser;
     /**
      * The password to use when connecting to the database.
      */
     @Parameter(property = "databasePassword", defaultValue = "", required = false)
     private String databasePassword;
     /**
      * A comma-separated list of file extensions to add to analysis next to jar,
      * zip, ....
      */
     @Parameter(property = "zipExtensions", required = false)
     private String zipExtensions;
     /**
      * Skip Dependency Check altogether.
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "dependency-check.skip", defaultValue = "false", required = false)
     private boolean skip = false;
     /**
      * Skip Analysis for Test Scope Dependencies.
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "skipTestScope", defaultValue = "true", required = false)
     private boolean skipTestScope = true;
     /**
      * Skip Analysis for Runtime Scope Dependencies.
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "skipRuntimeScope", defaultValue = "false", required = false)
     private boolean skipRuntimeScope = false;
     /**
      * Skip Analysis for Provided Scope Dependencies.
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "skipProvidedScope", defaultValue = "false", required = false)
     private boolean skipProvidedScope = false;
     /**
      * The data directory, hold DC SQL DB.
      */
     @Parameter(property = "dataDirectory", defaultValue = "", required = false)
     private String dataDirectory;
     /**
      * Data Mirror URL for CVE 1.2.
      */
     @Parameter(property = "cveUrl12Modified", defaultValue = "", required = false)
     private String cveUrl12Modified;
     /**
      * Data Mirror URL for CVE 2.0.
      */
     @Parameter(property = "cveUrl20Modified", defaultValue = "", required = false)
     private String cveUrl20Modified;
     /**
      * Base Data Mirror URL for CVE 1.2.
      */
     @Parameter(property = "cveUrl12Base", defaultValue = "", required = false)
     private String cveUrl12Base;
     /**
      * Data Mirror URL for CVE 2.0.
      */
     @Parameter(property = "cveUrl20Base", defaultValue = "", required = false)
     private String cveUrl20Base;
     /**
      * Optionally skip excessive CVE update checks for a designated duration in
      * hours.
      */
     @Parameter(property = "cveValidForHours", defaultValue = "", required = false)
     private Integer cveValidForHours;
 
     /**
      * The path to mono for .NET Assembly analysis on non-windows systems.
      */
     @Parameter(property = "pathToMono", defaultValue = "", required = false)
     private String pathToMono;
 
     /**
      * The Proxy URL.
      *
      * @deprecated Please use mavenSettings instead
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "proxyUrl", defaultValue = "", required = false)
     @Deprecated
     private String proxyUrl = null;
     /**
      * Sets whether or not the external report format should be used.
      *
      * @deprecated the internal report is no longer supported
      */
     @SuppressWarnings("CanBeFinal")
     @Parameter(property = "externalReport")
     @Deprecated
     private String externalReport = null;
     // </editor-fold>
     //<editor-fold defaultstate="collapsed" desc="Base Maven implementation">
 
     /**
      * Executes dependency-check.
      *
      * @throws MojoExecutionException thrown if there is an exception executing
      * the mojo
      * @throws MojoFailureException thrown if dependency-check failed the build
      */
     @Override
     public void execute() throws MojoExecutionException, MojoFailureException {
         generatingSite = false;
         if (skip) {
             getLog().info("Skipping " + getName(Locale.US));
         } else {
             validateAggregate();
             project.setContextValue(getOutputDirectoryContextKey(), this.outputDirectory);
             runCheck();
         }
     }
 
     /**
      * Checks if the aggregate configuration parameter has been set to true. If
      * it has a MojoExecutionException is thrown because the aggregate
      * configuration parameter is no longer supported.
      *
      * @throws MojoExecutionException thrown if aggregate is set to true
      */
     private void validateAggregate() throws MojoExecutionException {
         if (aggregate != null && aggregate) {
             final String msg = "Aggregate configuration detected - as of dependency-check 1.2.8 this no longer supported. "
                     + "Please use the aggregate goal instead.";
             throw new MojoExecutionException(msg);
         }
     }
 
     /**
      * Generates the Dependency-Check Site Report.
      *
      * @param sink the sink to write the report to
      * @param locale the locale to use when generating the report
      * @throws MavenReportException if a maven report exception occurs
      * @deprecated use
      * {@link #generate(org.apache.maven.doxia.sink.Sink, java.util.Locale)}
      * instead.
      */
     @Override
     @Deprecated
     public final void generate(@SuppressWarnings("deprecation") org.codehaus.doxia.sink.Sink sink, Locale locale) throws MavenReportException {
         generate((Sink) sink, locale);
     }
 
     /**
      * A flag indicating whether or not the maven site is being generated.
      */
     private boolean generatingSite = false;
 
     /**
      * Returns true if the Maven site is being generated.
      *
      * @return true if the Maven site is being generated
      */
     protected boolean isGeneratingSite() {
         return generatingSite;
     }
 
     /**
      * Generates the Dependency-Check Site Report.
      *
      * @param sink the sink to write the report to
      * @param locale the locale to use when generating the report
      * @throws MavenReportException if a maven report exception occurs
      */
     public void generate(Sink sink, Locale locale) throws MavenReportException {
         generatingSite = true;
         try {
             validateAggregate();
         } catch (MojoExecutionException ex) {
             throw new MavenReportException(ex.getMessage());
         }
         project.setContextValue(getOutputDirectoryContextKey(), getReportOutputDirectory());
         try {
             runCheck();
         } catch (MojoExecutionException ex) {
             throw new MavenReportException(ex.getMessage(), ex);
         } catch (MojoFailureException ex) {
             getLog().warn("Vulnerabilities were identifies that exceed the CVSS threshold for failing the build");
         }
     }
 
     /**
      * Returns the correct output directory depending on if a site is being
      * executed or not.
      *
      * @return the directory to write the report(s)
      * @throws MojoExecutionException thrown if there is an error loading the
      * file path
      */
     protected File getCorrectOutputDirectory() throws MojoExecutionException {
         return getCorrectOutputDirectory(this.project);
     }
 
     /**
      * Returns the correct output directory depending on if a site is being
      * executed or not.
      *
      * @param current the Maven project to get the output directory from
      * @return the directory to write the report(s)
      */
     protected File getCorrectOutputDirectory(MavenProject current) {
         final Object obj = current.getContextValue(getOutputDirectoryContextKey());
         if (obj != null && obj instanceof File) {
             return (File) obj;
         }
         File target = new File(current.getBuild().getDirectory());
         if (target.getParentFile() != null && "target".equals(target.getParentFile().getName())) {
             target = target.getParentFile();
         }
         return target;
     }
 
     /**
      * Returns the correct output directory depending on if a site is being
      * executed or not.
      *
      * @param current the Maven project to get the output directory from
      * @return the directory to write the report(s)
      */
     protected File getDataFile(MavenProject current) {
         if (getLog().isDebugEnabled()) {
             getLog().debug(String.format("Getting data filefor %s using key '%s'", current.getName(), getDataFileContextKey()));
         }
         final Object obj = current.getContextValue(getDataFileContextKey());
         if (obj != null) {
             if (obj instanceof String) {
                 final File f = new File((String) obj);
                 return f;
             }
         } else if (getLog().isDebugEnabled()) {
             getLog().debug("Context value not found");
         }
         return null;
     }
 
     /**
      * Scans the project's artifacts and adds them to the engine's dependency
      * list.
      *
      * @param project the project to scan the dependencies of
      * @param engine the engine to use to scan the dependencies
      * @return a collection of exceptions that may have occurred while resolving
      * and scanning the dependencies
      */
     protected ExceptionCollection scanArtifacts(MavenProject project, MavenEngine engine) {
         // <editor-fold defaultstate="collapsed" desc="old implementation">
         /*
             for (Artifact a : project.getArtifacts()) {
             if (excludeFromScan(a)) {
             continue;
             }
             final List<Dependency> deps = engine.scan(a.getFile().getAbsoluteFile());
             if (deps != null) {
             if (deps.size() == 1) {
             final Dependency d = deps.get(0);
             if (d != null) {
             final MavenArtifact ma = new MavenArtifact(a.getGroupId(), a.getArtifactId(), a.getVersion());
             d.addAsEvidence("pom", ma, Confidence.HIGHEST);
             d.addProjectReference(project.getName());
             if (getLog().isDebugEnabled()) {
             getLog().debug(String.format("Adding project reference %s on dependency %s", project.getName(),
             d.getDisplayFileName()));
             }
             }
             } else if (getLog().isDebugEnabled()) {
             final String msg = String.format("More then 1 dependency was identified in first pass scan of '%s:%s:%s'",
             a.getGroupId(), a.getArtifactId(), a.getVersion());
             getLog().debug(msg);
             }
             }
             }
          */
         // </editor-fold>
         try {
             final DependencyNode dn = dependencyGraphBuilder.buildDependencyGraph(project, null, reactorProjects);
             return collectDependencies(engine, project, dn.getChildren());
         } catch (DependencyGraphBuilderException ex) {
             final String msg = String.format("Unable to build dependency graph on project %s", project.getName());
             getLog().debug(msg, ex);
             return new ExceptionCollection(msg, ex);
         }
     }
 
     /**
      * Resolves the projects artifacts using Aether and scans the resulting
      * dependencies.
      *
      * @param engine the core dependency-check engine
      * @param project the project being scanned
      * @param nodes the list of dependency nodes, generally obtained via the
      * DependencyGraphBuilder
      * @return a collection of exceptions that may have occurred while resolving
      * and scanning the dependencies
      */
     private ExceptionCollection collectDependencies(MavenEngine engine, MavenProject project, List<DependencyNode> nodes) {
         ExceptionCollection exCol = null;
         for (DependencyNode dependencyNode : nodes) {
             exCol = collectDependencies(engine, project, dependencyNode.getChildren());
             if (excludeFromScan(dependencyNode.getArtifact().getScope())) {
                 continue;
             }
             final ArtifactRequest request = new ArtifactRequest();
             request.setArtifact(new DefaultArtifact(dependencyNode.getArtifact().getId()));
             request.setRepositories(remoteRepos);
             try {
                 final ArtifactResult result = repoSystem.resolveArtifact(repoSession, request);
                 if (result.isResolved() && result.getArtifact() != null && result.getArtifact().getFile() != null) {
                     final List<Dependency> deps = engine.scan(result.getArtifact().getFile().getAbsoluteFile());
                     if (deps != null) {
                         if (deps.size() == 1) {
                             final Dependency d = deps.get(0);
                             if (d != null) {
                                 final Artifact a = result.getArtifact();
                                 final MavenArtifact ma = new MavenArtifact(a.getGroupId(), a.getArtifactId(), a.getVersion());
                                 d.addAsEvidence("pom", ma, Confidence.HIGHEST);
                                 d.addProjectReference(project.getName() + ":" + dependencyNode.getArtifact().getScope());
                                 if (getLog().isDebugEnabled()) {
                                     getLog().debug(String.format("Adding project reference %s on dependency %s",
                                             project.getName(), d.getDisplayFileName()));
                                 }
                             }
                         } else if (getLog().isDebugEnabled()) {
                             final String msg = String.format("More then 1 dependency was identified in first pass scan of '%s' in project %s",
                                     dependencyNode.getArtifact().getId(), project.getName());
                             getLog().debug(msg);
                         }
                     } else {
                         final String msg = String.format("Error resolving '%s' in project %s",
                                 dependencyNode.getArtifact().getId(), project.getName());
                         if (exCol == null) {
                             exCol = new ExceptionCollection();
                         }
                         getLog().error(msg);
                         for (Exception ex : result.getExceptions()) {
                             exCol.addException(ex);
                         }
                     }
                 } else {
                     final String msg = String.format("Unable to resolve '%s' in project %s",
                             dependencyNode.getArtifact().getId(), project.getName());
                     getLog().debug(msg);
                     if (exCol == null) {
                         exCol = new ExceptionCollection();
                     }
                     for (Exception ex : result.getExceptions()) {
                         exCol.addException(ex);
                     }
                 }
             } catch (ArtifactResolutionException ex) {
                 if (exCol == null) {
                     exCol = new ExceptionCollection();
                 }
                 exCol.addException(ex);
             }
         }
         return exCol;
     }
 
     /**
      * Executes the dependency-check scan and generates the necassary report.
      *
      * @throws MojoExecutionException thrown if there is an exception running
      * the scan
      * @throws MojoFailureException thrown if dependency-check is configured to
      * fail the build
      */
     public abstract void runCheck() throws MojoExecutionException, MojoFailureException;
 
     /**
      * Sets the Reporting output directory.
      *
      * @param directory the output directory
      */
     @Override
     public void setReportOutputDirectory(File directory) {
         reportOutputDirectory = directory;
     }
 
     /**
      * Returns the report output directory.
      *
      * @return the report output directory
      */
     @Override
     public File getReportOutputDirectory() {
         return reportOutputDirectory;
     }
 
     /**
      * Returns the output directory.
      *
      * @return the output directory
      */
     public File getOutputDirectory() {
         return outputDirectory;
     }
 
     /**
      * Returns whether this is an external report. This method always returns
      * true.
      *
      * @return <code>true</code>
      */
     @Override
     public final boolean isExternalReport() {
         return true;
     }
 
     /**
      * Returns the output name.
      *
      * @return the output name
      */
     @Override
     public String getOutputName() {
         if ("HTML".equalsIgnoreCase(this.format) || "ALL".equalsIgnoreCase(this.format)) {
             return "dependency-check-report";
         } else if ("XML".equalsIgnoreCase(this.format)) {
             return "dependency-check-report.xml#";
         } else if ("VULN".equalsIgnoreCase(this.format)) {
             return "dependency-check-vulnerability";
         } else {
             getLog().warn("Unknown report format used during site generation.");
             return "dependency-check-report";
         }
     }
 
     /**
      * Returns the category name.
      *
      * @return the category name
      */
     @Override
     public String getCategoryName() {
         return MavenReport.CATEGORY_PROJECT_REPORTS;
     }
     //</editor-fold>
 
     /**
      * Initializes a new <code>MavenEngine</code> that can be used for scanning.
      *
      * @return a newly instantiated <code>MavenEngine</code>
      * @throws DatabaseException thrown if there is a database exception
      */
     protected MavenEngine initializeEngine() throws DatabaseException {
         populateSettings();
         return new MavenEngine(this.project, this.reactorProjects);
     }
 
     /**
      * 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.
      */
     protected void populateSettings() {
         Settings.initialize();
         InputStream mojoProperties = null;
         try {
             mojoProperties = this.getClass().getClassLoader().getResourceAsStream(PROPERTIES_FILE);
             Settings.mergeProperties(mojoProperties);
         } catch (IOException ex) {
             getLog().warn("Unable to load the dependency-check ant task.properties file.");
             if (getLog().isDebugEnabled()) {
                 getLog().debug("", ex);
             }
         } finally {
             if (mojoProperties != null) {
                 try {
                     mojoProperties.close();
                 } catch (IOException ex) {
                     if (getLog().isDebugEnabled()) {
                         getLog().debug("", ex);
                     }
                 }
             }
         }
         Settings.setBooleanIfNotNull(Settings.KEYS.AUTO_UPDATE, autoUpdate);
 
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_EXPERIMENTAL_ENABLED, enableExperimental);
 
         if (externalReport != null) {
             getLog().warn("The 'externalReport' option was set; this configuration option has been removed. "
                     + "Please update the dependency-check-maven plugin's configuration");
         }
 
         if (proxyUrl != null && !proxyUrl.isEmpty()) {
             getLog().warn("Deprecated configuration detected, proxyUrl will be ignored; use the maven settings " + "to configure the proxy instead");
         }
         final Proxy proxy = getMavenProxy();
         if (proxy != null) {
             Settings.setString(Settings.KEYS.PROXY_SERVER, proxy.getHost());
             Settings.setString(Settings.KEYS.PROXY_PORT, Integer.toString(proxy.getPort()));
             final String userName = proxy.getUsername();
             final String password = proxy.getPassword();
             Settings.setStringIfNotNull(Settings.KEYS.PROXY_USERNAME, userName);
             Settings.setStringIfNotNull(Settings.KEYS.PROXY_PASSWORD, password);
             Settings.setStringIfNotNull(Settings.KEYS.PROXY_NON_PROXY_HOSTS, proxy.getNonProxyHosts());
         }
 
         Settings.setStringIfNotEmpty(Settings.KEYS.CONNECTION_TIMEOUT, connectionTimeout);
         Settings.setStringIfNotEmpty(Settings.KEYS.SUPPRESSION_FILE, suppressionFile);
 
         //File Type Analyzer Settings
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_JAR_ENABLED, jarAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NUSPEC_ENABLED, nuspecAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_CENTRAL_ENABLED, centralAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_ENABLED, nexusAnalyzerEnabled);
         Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_NEXUS_URL, nexusUrl);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NEXUS_USES_PROXY, nexusUsesProxy);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_ASSEMBLY_ENABLED, assemblyAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_ARCHIVE_ENABLED, archiveAnalyzerEnabled);
         Settings.setStringIfNotEmpty(Settings.KEYS.ADDITIONAL_ZIP_EXTENSIONS, zipExtensions);
         Settings.setStringIfNotEmpty(Settings.KEYS.ANALYZER_ASSEMBLY_MONO_PATH, pathToMono);
 
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_DISTRIBUTION_ENABLED, pyDistributionAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_PYTHON_PACKAGE_ENABLED, pyPackageAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_RUBY_GEMSPEC_ENABLED, rubygemsAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_OPENSSL_ENABLED, opensslAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_CMAKE_ENABLED, cmakeAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_AUTOCONF_ENABLED, autoconfAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_COMPOSER_LOCK_ENABLED, composerAnalyzerEnabled);
         Settings.setBooleanIfNotNull(Settings.KEYS.ANALYZER_NODE_PACKAGE_ENABLED, nodeAnalyzerEnabled);
 
         //Database configuration
         Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_NAME, databaseDriverName);
         Settings.setStringIfNotEmpty(Settings.KEYS.DB_DRIVER_PATH, databaseDriverPath);
         Settings.setStringIfNotEmpty(Settings.KEYS.DB_CONNECTION_STRING, connectionString);
 
         if (databaseUser == null && databasePassword == null && serverId != null) {
             final Server server = settingsXml.getServer(serverId);
             if (server != null) {
                 databaseUser = server.getUsername();
                 try {
                     //The following fix was copied from:
                     //   https://github.com/bsorrentino/maven-confluence-plugin/blob/master/maven-confluence-reporting-plugin/src/main/java/org/bsc/maven/confluence/plugin/AbstractBaseConfluenceMojo.java
                     //
                     // FIX to resolve
                     // org.sonatype.plexus.components.sec.dispatcher.SecDispatcherException:
                     // java.io.FileNotFoundException: ~/.settings-security.xml (No such file or directory)
                     //
                     if (securityDispatcher instanceof DefaultSecDispatcher) {
                         ((DefaultSecDispatcher) securityDispatcher).setConfigurationFile("~/.m2/settings-security.xml");
                     }
 
                     databasePassword = securityDispatcher.decrypt(server.getPassword());
                 } catch (SecDispatcherException ex) {
                     if (ex.getCause() instanceof FileNotFoundException
                             || (ex.getCause() != null && ex.getCause().getCause() instanceof FileNotFoundException)) {
                         //maybe its not encrypted?
                         final String tmp = server.getPassword();
                         if (tmp.startsWith("{") && tmp.endsWith("}")) {
                             getLog().error(String.format(
                                     "Unable to decrypt the server password for server id '%s' in settings.xml%n\tCause: %s",
                                     serverId, ex.getMessage()));
                         } else {
                             databasePassword = tmp;
                         }
                     } else {
                         getLog().error(String.format(
                                 "Unable to decrypt the server password for server id '%s' in settings.xml%n\tCause: %s",
                                 serverId, ex.getMessage()));
                     }
                 }
             } else {
                 getLog().error(String.format("Server '%s' not found in the settings.xml file", serverId));
             }
         }
 
         Settings.setStringIfNotEmpty(Settings.KEYS.DB_USER, databaseUser);
         Settings.setStringIfNotEmpty(Settings.KEYS.DB_PASSWORD, databasePassword);
         Settings.setStringIfNotEmpty(Settings.KEYS.DATA_DIRECTORY, dataDirectory);
 
         Settings.setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_12_URL, cveUrl12Modified);
         Settings.setStringIfNotEmpty(Settings.KEYS.CVE_MODIFIED_20_URL, cveUrl20Modified);
         Settings.setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_1_2, cveUrl12Base);
         Settings.setStringIfNotEmpty(Settings.KEYS.CVE_SCHEMA_2_0, cveUrl20Base);
         Settings.setIntIfNotNull(Settings.KEYS.CVE_CHECK_VALID_FOR_HOURS, cveValidForHours);
 
     }
 
     /**
      * Returns the maven proxy.
      *
      * @return the maven proxy
      */
     private Proxy getMavenProxy() {
         if (mavenSettings != null) {
             final List<Proxy> proxies = mavenSettings.getProxies();
             if (proxies != null && !proxies.isEmpty()) {
                 if (mavenSettingsProxyId != null) {
                     for (Proxy proxy : proxies) {
                         if (mavenSettingsProxyId.equalsIgnoreCase(proxy.getId())) {
                             return proxy;
                         }
                     }
                 } else if (proxies.size() == 1) {
                     return proxies.get(0);
                 } else {
                     getLog().warn("Multiple proxy definitions exist in the Maven settings. In the dependency-check "
                             + "configuration set the mavenSettingsProxyId so that the correct proxy will be used.");
                     throw new IllegalStateException("Ambiguous proxy definition");
                 }
             }
         }
         return null;
     }
 
     /**
      * Tests is the artifact should be included in the scan (i.e. is the
      * dependency in a scope that is being scanned).
      *
      * @param scope the scope of the artifact to test
      * @return <code>true</code> if the artifact is in an excluded scope;
      * otherwise <code>false</code>
      */
     protected boolean excludeFromScan(String scope) {
         if (skipTestScope && org.apache.maven.artifact.Artifact.SCOPE_TEST.equals(scope)) {
             return true;
         }
         if (skipProvidedScope && org.apache.maven.artifact.Artifact.SCOPE_PROVIDED.equals(scope)) {
             return true;
         }
         if (skipRuntimeScope && !org.apache.maven.artifact.Artifact.SCOPE_RUNTIME.equals(scope)) {
             return true;
         }
         return false;
     }
 
     /**
      * Returns a reference to the current project. This method is used instead
      * of auto-binding the project via component annotation in concrete
      * implementations of this. If the child has a
      * <code>@Component MavenProject project;</code> defined then the abstract
      * class (i.e. this class) will not have access to the current project (just
      * the way Maven works with the binding).
      *
      * @return returns a reference to the current project
      */
     protected MavenProject getProject() {
         return project;
     }
 
     /**
      * Returns the list of Maven Projects in this build.
      *
      * @return the list of Maven Projects in this build
      */
     protected List<MavenProject> getReactorProjects() {
         return reactorProjects;
     }
 
     /**
      * Returns the report format.
      *
      * @return the report format
      */
     protected String getFormat() {
         return format;
     }
 
     /**
      * Generates the reports for a given dependency-check engine.
      *
      * @param engine a dependency-check engine
      * @param p the Maven project
      * @param outputDir the directory path to write the report(s)
      * @throws ReportException thrown if there is an error writing the report
      */
     protected void writeReports(MavenEngine engine, MavenProject p, File outputDir) throws ReportException {
         DatabaseProperties prop = null;
         CveDB cve = null;
         try {
             cve = new CveDB();
             cve.open();
             prop = cve.getDatabaseProperties();
         } catch (DatabaseException ex) {
             if (getLog().isDebugEnabled()) {
                 getLog().debug("Unable to retrieve DB Properties", ex);
             }
         } finally {
             if (cve != null) {
                 cve.close();
             }
         }
         final ReportGenerator r = new ReportGenerator(p.getName(), engine.getDependencies(), engine.getAnalyzers(), prop);
         try {
             r.generateReports(outputDir.getAbsolutePath(), format);
         } catch (ReportException ex) {
             final String msg = String.format("Error generating the report for %s", p.getName());
             throw new ReportException(msg, ex);
         }
 
     }
 
     //<editor-fold defaultstate="collapsed" desc="Methods to fail build or show summary">
     /**
      * 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 MojoFailureException thrown if a CVSS score is found that is
      * higher then the threshold set
      */
     protected void checkForFailure(List<Dependency> dependencies) throws MojoFailureException {
         if (failBuildOnCVSS <= 10) {
             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 MojoFailureException(msg);
             }
         }
     }
 
     /**
      * Generates a warning message listing a summary of dependencies and their
      * associated CPE and CVE entries.
      *
      * @param mp the Maven project for which the summary is shown
      * @param dependencies a list of dependency objects
      */
     protected void showSummary(MavenProject mp, List<Dependency> dependencies) {
         if (showSummary) {
             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 in %s:%n%n%s"
                         + "%n%nSee the dependency-check report for more details.%n%n", mp.getName(), summary.toString());
                 getLog().warn(msg);
             }
         }
     }
 
     //</editor-fold>
     //<editor-fold defaultstate="collapsed" desc="Methods to read/write the serialized data file">
     /**
      * Returns the key used to store the path to the data file that is saved by
      * <code>writeDataFile()</code>. This key is used in the
      * <code>MavenProject.(set|get)ContextValue</code>.
      *
      * @return the key used to store the path to the data file
      */
     protected String getDataFileContextKey() {
         return "dependency-check-path-" + dataFileName;
     }
 
     /**
      * Returns the key used to store the path to the output directory. When
      * generating the report in the <code>executeAggregateReport()</code> the
      * output directory should be obtained by using this key.
      *
      * @return the key used to store the path to the output directory
      */
     protected String getOutputDirectoryContextKey() {
         return "dependency-output-dir-" + dataFileName;
     }
 
     /**
      * Writes the scan data to disk. This is used to serialize the scan data
      * between the "check" and "aggregate" phase.
      *
      * @param mp the mMven project for which the data file was created
      * @param writeTo the directory to write the data file
      * @param dependencies the list of dependencies to serialize
      */
     protected void writeDataFile(MavenProject mp, File writeTo, List<Dependency> dependencies) {
         File file;
         //check to see if this was already written out
         if (mp.getContextValue(this.getDataFileContextKey()) == null) {
             if (writeTo == null) {
                 file = new File(mp.getBuild().getDirectory());
                 file = new File(file, dataFileName);
             } else {
                 file = new File(writeTo, dataFileName);
             }
             final File parent = file.getParentFile();
             if (!parent.isDirectory() && !parent.mkdirs()) {
                 getLog().error(String.format("Directory '%s' does not exist and cannot be created; unable to write data file.",
                         parent.getAbsolutePath()));
             }
 
             ObjectOutputStream out = null;
             try {
                 if (dependencies != null) {
                     out = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(file)));
                     out.writeObject(dependencies);
                 }
                 if (getLog().isDebugEnabled()) {
                     getLog().debug(String.format("Serialized data file written to '%s' for %s, referenced by key %s",
                             file.getAbsolutePath(), mp.getName(), this.getDataFileContextKey()));
                 }
                 mp.setContextValue(this.getDataFileContextKey(), file.getAbsolutePath());
             } catch (IOException ex) {
                 getLog().warn("Unable to create data file used for report aggregation; "
                         + "if report aggregation is being used the results may be incomplete.");
                 if (getLog().isDebugEnabled()) {
                     getLog().debug(ex.getMessage(), ex);
                 }
             } finally {
                 if (out != null) {
                     try {
                         out.close();
                     } catch (IOException ex) {
                         if (getLog().isDebugEnabled()) {
                             getLog().debug("ignore", ex);
                         }
                     }
                 }
             }
         }
     }
 
     /**
      * Reads the serialized scan data from disk. This is used to serialize the
      * scan data between the "check" and "aggregate" phase.
      *
      * @param project the Maven project to read the data file from
      * @return a <code>MavenEngine</code> object populated with dependencies if
      * the serialized data file exists; otherwise <code>null</code> is returned
      */
     protected List<Dependency> readDataFile(MavenProject project) {
         final Object oPath = project.getContextValue(this.getDataFileContextKey());
         if (oPath == null) {
             return null;
         }
         List<Dependency> ret = null;
         final String path = (String) oPath;
         //ObjectInputStream ois = null;
         ExpectedOjectInputStream ois = null;
         try {
             //ois = new ObjectInputStream(new FileInputStream(path));
             ois = new ExpectedOjectInputStream(new FileInputStream(path),
                     "java.util.ArrayList",
                     "java.util.HashSet",
                     "java.util.TreeSet",
                     "java.lang.AbstractSet",
                     "java.lang.AbstractCollection",
                     "java.lang.Enum",
                     "org.owasp.dependencycheck.dependency.Confidence",
                     "org.owasp.dependencycheck.dependency.Dependency",
                     "org.owasp.dependencycheck.dependency.Evidence",
                     "org.owasp.dependencycheck.dependency.EvidenceCollection",
                     "org.owasp.dependencycheck.dependency.Identifier",
                     "org.owasp.dependencycheck.dependency.Reference",
                     "org.owasp.dependencycheck.dependency.Vulnerability",
                     "org.owasp.dependencycheck.dependency.VulnerabilityComparator",
                     "org.owasp.dependencycheck.dependency.VulnerableSoftware",
                     "org.owasp.dependencycheck.data.cpe.IndexEntry");
             @SuppressWarnings("unchecked")
             final List<Dependency> depList = (List<Dependency>) ois.readObject();
             ret = depList;
         } catch (FileNotFoundException ex) {
             //TODO fix logging
             getLog().error("", ex);
         } catch (IOException ex) {
             getLog().error("", ex);
         } catch (ClassNotFoundException ex) {
             getLog().error("", ex);
         } finally {
             if (ois != null) {
                 try {
                     ois.close();
                 } catch (IOException ex) {
                     getLog().error("", ex);
                 }
             }
         }
         return ret;
     }
     //</editor-fold>
 
 }