/*
    * 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.File;
  import java.io.FileFilter;
  import java.io.FileOutputStream;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.InputStreamReader;
  import java.io.Reader;
  import java.io.UnsupportedEncodingException;
  import java.util.ArrayList;
  import java.util.Enumeration;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  import java.util.Map.Entry;
  import java.util.Properties;
  import java.util.Set;
  import java.util.StringTokenizer;
  import java.util.concurrent.atomic.AtomicInteger;
  import java.util.jar.Attributes;
  import java.util.jar.JarEntry;
  import java.util.jar.JarFile;
  import java.util.jar.Manifest;
  import java.util.regex.Pattern;
  import java.util.zip.ZipEntry;
  import org.apache.commons.compress.utils.IOUtils;
  import org.apache.commons.io.FilenameUtils;
  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;
  import org.owasp.dependencycheck.exception.InitializationException;
  import org.owasp.dependencycheck.utils.FileFilterBuilder;
  import org.owasp.dependencycheck.xml.pom.License;
  import org.owasp.dependencycheck.xml.pom.PomUtils;
  import org.owasp.dependencycheck.xml.pom.Model;
  import org.owasp.dependencycheck.utils.FileUtils;
  import org.owasp.dependencycheck.utils.Settings;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  /**
   * Used to load a JAR file and collect information that can be used to determine
   * the associated CPE.
   *
   * @author Jeremy Long
   */
  public class JarAnalyzer extends AbstractFileTypeAnalyzer {
  
      //<editor-fold defaultstate="collapsed" desc="Constants and Member Variables">
      /**
       * The logger.
       */
      private static final Logger LOGGER = LoggerFactory.getLogger(JarAnalyzer.class);
      /**
       * The count of directories created during analysis. This is used for
       * creating temporary directories.
       */
      private static final AtomicInteger DIR_COUNT = new AtomicInteger(0);
      /**
       * The system independent newline character.
       */
      private static final String NEWLINE = System.getProperty("line.separator");
      /**
       * A list of values in the manifest to ignore as they only result in false
       * positives.
       */
      private static final Set<String> IGNORE_VALUES = newHashSet(
              "Sun Java System Application Server");
      /**
       * A list of elements in the manifest to ignore.
       */
      private static final Set<String> IGNORE_KEYS = newHashSet(
              "built-by",
              "created-by",
              "builtby",
              "createdby",
              "build-jdk",
              "buildjdk",
             "ant-version",
             "antversion",
             "dynamicimportpackage",
             "dynamicimport-package",
             "dynamic-importpackage",
             "dynamic-import-package",
             "import-package",
             "ignore-package",
             "export-package",
             "importpackage",
             "ignorepackage",
             "exportpackage",
             "sealed",
             "manifest-version",
             "archiver-version",
             "manifestversion",
             "archiverversion",
             "classpath",
             "class-path",
             "tool",
             "bundle-manifestversion",
             "bundlemanifestversion",
             "bundle-vendor",
             "include-resource",
             "embed-dependency",
             "ipojo-components",
             "ipojo-extension",
             "eclipse-sourcereferences");
     /**
      * Deprecated Jar manifest attribute, that is, nonetheless, useful for
      * analysis.
      */
     @SuppressWarnings("deprecation")
     private static final String IMPLEMENTATION_VENDOR_ID = Attributes.Name.IMPLEMENTATION_VENDOR_ID
             .toString();
     /**
      * item in some manifest, should be considered medium confidence.
      */
     private static final String BUNDLE_VERSION = "Bundle-Version"; //: 2.1.2
     /**
      * item in some manifest, should be considered medium confidence.
      */
     private static final String BUNDLE_DESCRIPTION = "Bundle-Description"; //: Apache Struts 2
     /**
      * item in some manifest, should be considered medium confidence.
      */
     private static final String BUNDLE_NAME = "Bundle-Name"; //: Struts 2 Core
     /**
      * A pattern to detect HTML within text.
      */
     private static final Pattern HTML_DETECTION_PATTERN = Pattern.compile("\\<[a-z]+.*/?\\>", Pattern.CASE_INSENSITIVE);
 
     //</editor-fold>
     /**
      * Constructs a new JarAnalyzer.
      */
     public JarAnalyzer() {
     }
 
     //<editor-fold defaultstate="collapsed" desc="All standard implmentation details of Analyzer">
     /**
      * The name of the analyzer.
      */
     private static final String ANALYZER_NAME = "Jar 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 String[] EXTENSIONS = {"jar", "war"};
 
     /**
      * The file filter used to determine which files this analyzer supports.
      */
     private static final FileFilter FILTER = FileFilterBuilder.newInstance().addExtensions(EXTENSIONS).build();
 
     /**
      * Returns the FileFilter.
      *
      * @return the FileFilter
      */
     @Override
     protected FileFilter getFileFilter() {
         return FILTER;
     }
 
     /**
      * Returns the name of the analyzer.
      *
      * @return the name of the analyzer.
      */
     @Override
     public String getName() {
         return ANALYZER_NAME;
     }
 
     /**
      * 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_JAR_ENABLED;
     }
 
     /**
      * Loads a specified JAR file and collects information from the manifest and
      * checksums to identify the correct CPE information.
      *
      * @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.
      */
     @Override
     public void analyzeDependency(Dependency dependency, Engine engine) throws AnalysisException {
         try {
             final List<ClassNameInformation> classNames = collectClassNames(dependency);
             final String fileName = dependency.getFileName().toLowerCase();
             if (classNames.isEmpty()
                     && (fileName.endsWith("-sources.jar")
                     || fileName.endsWith("-javadoc.jar")
                     || fileName.endsWith("-src.jar")
                     || fileName.endsWith("-doc.jar"))) {
                 engine.getDependencies().remove(dependency);
             }
             final boolean hasManifest = parseManifest(dependency, classNames);
             final boolean hasPOM = analyzePOM(dependency, classNames, engine);
             final boolean addPackagesAsEvidence = !(hasManifest && hasPOM);
             analyzePackageNames(classNames, dependency, addPackagesAsEvidence);
         } catch (IOException ex) {
             throw new AnalysisException("Exception occurred reading the JAR file (" + dependency.getFileName() + ").", ex);
         }
     }
 
     /**
      * Attempts to find a pom.xml within the JAR file. If found it extracts
      * information and adds it to the evidence. This will attempt to interpolate
      * the strings contained within the pom.properties if one exists.
      *
      * @param dependency the dependency being analyzed
      * @param classes a collection of class name information
      * @param engine the analysis engine, used to add additional dependencies
      * @throws AnalysisException is thrown if there is an exception parsing the
      * pom
      * @return whether or not evidence was added to the dependency
      */
     protected boolean analyzePOM(Dependency dependency, List<ClassNameInformation> classes, Engine engine) throws AnalysisException {
         JarFile jar = null;
         List<String> pomEntries = null;
         try {
             jar = new JarFile(dependency.getActualFilePath());
             pomEntries = retrievePomListing(jar);
         } catch (IOException ex) {
             LOGGER.warn("Unable to read JarFile '{}'.", dependency.getActualFilePath());
             LOGGER.trace("", ex);
             if (jar != null) {
                 try {
                     jar.close();
                 } catch (IOException ex1) {
                     LOGGER.trace("", ex1);
                 }
             }
             return false;
         }
         if (pomEntries != null && pomEntries.size() <= 1) {
             try {
                 String path = null;
                 Properties pomProperties = null;
                 File pomFile = null;
                 if (pomEntries.size() == 1) {
                     path = pomEntries.get(0);
                     pomFile = extractPom(path, jar);
                     pomProperties = retrievePomProperties(path, jar);
                 } else {
                     path = FilenameUtils.removeExtension(dependency.getActualFilePath()) + ".pom";
                     pomFile = new File(path);
                 }
                 if (pomFile.isFile()) {
                     final Model pom = PomUtils.readPom(pomFile);
                     if (pom != null && pomProperties != null) {
                         pom.processProperties(pomProperties);
                     }
                     if (pom != null) {
                         return setPomEvidence(dependency, pom, classes);
                     }
                     return false;
                 } else {
                     return false;
                 }
             } finally {
                 try {
                     jar.close();
                 } catch (IOException ex) {
                     LOGGER.trace("", ex);
                 }
             }
         }
 
         //reported possible null dereference on pomEntries is on a non-feasible path
         for (String path : pomEntries) {
             //TODO - one of these is likely the pom for the main JAR we are analyzing
             LOGGER.debug("Reading pom entry: {}", path);
             try {
                 //extract POM to its own directory and add it as its own dependency
                 final Properties pomProperties = retrievePomProperties(path, jar);
                 final File pomFile = extractPom(path, jar);
                 final Model pom = PomUtils.readPom(pomFile);
                 pom.processProperties(pomProperties);
 
                 final String displayPath = String.format("%s%s%s",
                         dependency.getFilePath(),
                         File.separator,
                         path);
                 final String displayName = String.format("%s%s%s",
                         dependency.getFileName(),
                         File.separator,
                         path);
                 final Dependency newDependency = new Dependency();
                 newDependency.setActualFilePath(pomFile.getAbsolutePath());
                 newDependency.setFileName(displayName);
                 newDependency.setFilePath(displayPath);
                 setPomEvidence(newDependency, pom, null);
                 engine.getDependencies().add(newDependency);
             } catch (AnalysisException ex) {
                 LOGGER.warn("An error occurred while analyzing '{}'.", dependency.getActualFilePath());
                 LOGGER.trace("", ex);
             }
         }
         try {
             jar.close();
         } catch (IOException ex) {
             LOGGER.trace("", ex);
         }
         return false;
     }
 
     /**
      * Given a path to a pom.xml within a JarFile, this method attempts to load
      * a sibling pom.properties if one exists.
      *
      * @param path the path to the pom.xml within the JarFile
      * @param jar the JarFile to load the pom.properties from
      * @return a Properties object or null if no pom.properties was found
      * @throws IOException thrown if there is an exception reading the
      * pom.properties
      */
     private Properties retrievePomProperties(String path, final JarFile jar) {
         Properties pomProperties = null;
         final String propPath = path.substring(0, path.length() - 7) + "pom.properies";
         final ZipEntry propEntry = jar.getEntry(propPath);
         if (propEntry != null) {
             Reader reader = null;
             try {
                 reader = new InputStreamReader(jar.getInputStream(propEntry), "UTF-8");
                 pomProperties = new Properties();
                 pomProperties.load(reader);
                 LOGGER.debug("Read pom.properties: {}", propPath);
             } catch (UnsupportedEncodingException ex) {
                 LOGGER.trace("UTF-8 is not supported", ex);
             } catch (IOException ex) {
                 LOGGER.trace("Unable to read the POM properties", ex);
             } finally {
                 if (reader != null) {
                     try {
                         reader.close();
                     } catch (IOException ex) {
                         LOGGER.trace("close error", ex);
                     }
                 }
             }
         }
         return pomProperties;
     }
 
     /**
      * Searches a JarFile for pom.xml entries and returns a listing of these
      * entries.
      *
      * @param jar the JarFile to search
      * @return a list of pom.xml entries
      * @throws IOException thrown if there is an exception reading a JarEntry
      */
     private List<String> retrievePomListing(final JarFile jar) throws IOException {
         final List<String> pomEntries = new ArrayList<String>();
         final Enumeration<JarEntry> entries = jar.entries();
         while (entries.hasMoreElements()) {
             final JarEntry entry = entries.nextElement();
             final String entryName = (new File(entry.getName())).getName().toLowerCase();
             if (!entry.isDirectory() && "pom.xml".equals(entryName)) {
                 LOGGER.trace("POM Entry found: {}", entry.getName());
                 pomEntries.add(entry.getName());
             }
         }
         return pomEntries;
     }
 
     /**
      * Retrieves the specified POM from a jar.
      *
      * @param path the path to the pom.xml file within the jar file
      * @param jar the jar file to extract the pom from
      * @return returns the POM file
      * @throws AnalysisException is thrown if there is an exception extracting
      * the file
      */
     private File extractPom(String path, JarFile jar) throws AnalysisException {
         InputStream input = null;
         FileOutputStream fos = null;
         final File tmpDir = getNextTempDirectory();
         final File file = new File(tmpDir, "pom.xml");
         try {
             final ZipEntry entry = jar.getEntry(path);
             if (entry == null) {
                 throw new AnalysisException(String.format("Pom (%s)does not exist in %s", path, jar.getName()));
             }
             input = jar.getInputStream(entry);
             fos = new FileOutputStream(file);
             IOUtils.copy(input, fos);
         } catch (IOException ex) {
             LOGGER.warn("An error occurred reading '{}' from '{}'.", path, jar.getName());
             LOGGER.error("", ex);
         } finally {
             FileUtils.close(fos);
             FileUtils.close(input);
         }
         return file;
     }
 
     /**
      * Sets evidence from the pom on the supplied dependency.
      *
      * @param dependency the dependency to set data on
      * @param pom the information from the pom
      * @param classes a collection of ClassNameInformation - containing data
      * about the fully qualified class names within the JAR file being analyzed
      * @return true if there was evidence within the pom that we could use;
      * otherwise false
      */
     public static boolean setPomEvidence(Dependency dependency, Model pom, List<ClassNameInformation> classes) {
         boolean foundSomething = false;
         boolean addAsIdentifier = true;
         if (pom == null) {
             return foundSomething;
         }
         String groupid = pom.getGroupId();
         String parentGroupId = pom.getParentGroupId();
         String artifactid = pom.getArtifactId();
         String parentArtifactId = pom.getParentArtifactId();
         String version = pom.getVersion();
         String parentVersion = pom.getParentVersion();
 
         if ("org.sonatype.oss".equals(parentGroupId) && "oss-parent".equals(parentArtifactId)) {
             parentGroupId = null;
             parentArtifactId = null;
             parentVersion = null;
         }
 
         if ((groupid == null || groupid.isEmpty()) && parentGroupId != null && !parentGroupId.isEmpty()) {
             groupid = parentGroupId;
         }
 
         final String originalGroupID = groupid;
         if (groupid != null && (groupid.startsWith("org.") || groupid.startsWith("com."))) {
             groupid = groupid.substring(4);
         }
 
         if ((artifactid == null || artifactid.isEmpty()) && parentArtifactId != null && !parentArtifactId.isEmpty()) {
             artifactid = parentArtifactId;
         }
 
         final String originalArtifactID = artifactid;
         if (artifactid != null && (artifactid.startsWith("org.") || artifactid.startsWith("com."))) {
             artifactid = artifactid.substring(4);
         }
 
         if ((version == null || version.isEmpty()) && parentVersion != null && !parentVersion.isEmpty()) {
             version = parentVersion;
         }
 
         if (groupid != null && !groupid.isEmpty()) {
             foundSomething = true;
             dependency.getVendorEvidence().addEvidence("pom", "groupid", groupid, Confidence.HIGHEST);
             dependency.getProductEvidence().addEvidence("pom", "groupid", groupid, Confidence.LOW);
             addMatchingValues(classes, groupid, dependency.getVendorEvidence());
             addMatchingValues(classes, groupid, dependency.getProductEvidence());
             if (parentGroupId != null && !parentGroupId.isEmpty() && !parentGroupId.equals(groupid)) {
                 dependency.getVendorEvidence().addEvidence("pom", "parent-groupid", parentGroupId, Confidence.MEDIUM);
                 dependency.getProductEvidence().addEvidence("pom", "parent-groupid", parentGroupId, Confidence.LOW);
                 addMatchingValues(classes, parentGroupId, dependency.getVendorEvidence());
                 addMatchingValues(classes, parentGroupId, dependency.getProductEvidence());
             }
         } else {
             addAsIdentifier = false;
         }
 
         if (artifactid != null && !artifactid.isEmpty()) {
             foundSomething = true;
             dependency.getProductEvidence().addEvidence("pom", "artifactid", artifactid, Confidence.HIGHEST);
             dependency.getVendorEvidence().addEvidence("pom", "artifactid", artifactid, Confidence.LOW);
             addMatchingValues(classes, artifactid, dependency.getVendorEvidence());
             addMatchingValues(classes, artifactid, dependency.getProductEvidence());
             if (parentArtifactId != null && !parentArtifactId.isEmpty() && !parentArtifactId.equals(artifactid)) {
                 dependency.getProductEvidence().addEvidence("pom", "parent-artifactid", parentArtifactId, Confidence.MEDIUM);
                 dependency.getVendorEvidence().addEvidence("pom", "parent-artifactid", parentArtifactId, Confidence.LOW);
                 addMatchingValues(classes, parentArtifactId, dependency.getVendorEvidence());
                 addMatchingValues(classes, parentArtifactId, dependency.getProductEvidence());
             }
         } else {
             addAsIdentifier = false;
         }
 
         if (version != null && !version.isEmpty()) {
             foundSomething = true;
             dependency.getVersionEvidence().addEvidence("pom", "version", version, Confidence.HIGHEST);
             if (parentVersion != null && !parentVersion.isEmpty() && !parentVersion.equals(version)) {
                 dependency.getVersionEvidence().addEvidence("pom", "parent-version", version, Confidence.LOW);
             }
         } else {
             addAsIdentifier = false;
         }
 
         if (addAsIdentifier) {
             dependency.addIdentifier("maven", String.format("%s:%s:%s", originalGroupID, originalArtifactID, version), null, Confidence.HIGH);
         }
 
         // org name
         final String org = pom.getOrganization();
         if (org != null && !org.isEmpty()) {
             dependency.getVendorEvidence().addEvidence("pom", "organization name", org, Confidence.HIGH);
             dependency.getProductEvidence().addEvidence("pom", "organization name", org, Confidence.LOW);
             addMatchingValues(classes, org, dependency.getVendorEvidence());
             addMatchingValues(classes, org, dependency.getProductEvidence());
         }
         //pom name
         final String pomName = pom.getName();
         if (pomName
                 != null && !pomName.isEmpty()) {
             foundSomething = true;
             dependency.getProductEvidence().addEvidence("pom", "name", pomName, Confidence.HIGH);
             dependency.getVendorEvidence().addEvidence("pom", "name", pomName, Confidence.HIGH);
             addMatchingValues(classes, pomName, dependency.getVendorEvidence());
             addMatchingValues(classes, pomName, dependency.getProductEvidence());
         }
 
         //Description
         final String description = pom.getDescription();
         if (description != null && !description.isEmpty() && !description.startsWith("POM was created by")) {
             foundSomething = true;
             final String trimmedDescription = addDescription(dependency, description, "pom", "description");
             addMatchingValues(classes, trimmedDescription, dependency.getVendorEvidence());
             addMatchingValues(classes, trimmedDescription, dependency.getProductEvidence());
         }
 
         final String projectURL = pom.getProjectURL();
         if (projectURL != null && !projectURL.trim().isEmpty()) {
             dependency.getVendorEvidence().addEvidence("pom", "url", projectURL, Confidence.HIGHEST);
         }
 
         extractLicense(pom, dependency);
         return foundSomething;
     }
 
     /**
      * Analyzes the path information of the classes contained within the
      * JarAnalyzer to try and determine possible vendor or product names. If any
      * are found they are stored in the packageVendor and packageProduct
      * hashSets.
      *
      * @param classNames a list of class names
      * @param dependency a dependency to analyze
      * @param addPackagesAsEvidence a flag indicating whether or not package
      * names should be added as evidence.
      */
     protected void analyzePackageNames(List<ClassNameInformation> classNames,
             Dependency dependency, boolean addPackagesAsEvidence) {
         final Map<String, Integer> vendorIdentifiers = new HashMap<String, Integer>();
         final Map<String, Integer> productIdentifiers = new HashMap<String, Integer>();
         analyzeFullyQualifiedClassNames(classNames, vendorIdentifiers, productIdentifiers);
 
         final int classCount = classNames.size();
         final EvidenceCollection vendor = dependency.getVendorEvidence();
         final EvidenceCollection product = dependency.getProductEvidence();
 
         for (Map.Entry<String, Integer> entry : vendorIdentifiers.entrySet()) {
             final float ratio = entry.getValue() / (float) classCount;
             if (ratio > 0.5) {
                 //TODO remove weighting
                 vendor.addWeighting(entry.getKey());
                 if (addPackagesAsEvidence && entry.getKey().length() > 1) {
                     vendor.addEvidence("jar", "package name", entry.getKey(), Confidence.LOW);
                 }
             }
         }
         for (Map.Entry<String, Integer> entry : productIdentifiers.entrySet()) {
             final float ratio = entry.getValue() / (float) classCount;
             if (ratio > 0.5) {
                 product.addWeighting(entry.getKey());
                 if (addPackagesAsEvidence && entry.getKey().length() > 1) {
                     product.addEvidence("jar", "package name", entry.getKey(), Confidence.LOW);
                 }
             }
         }
     }
 
     /**
      * <p>
      * Reads the manifest from the JAR file and collects the entries. Some
      * vendorKey entries are:</p>
      * <ul><li>Implementation Title</li>
      * <li>Implementation Version</li> <li>Implementation Vendor</li>
      * <li>Implementation VendorId</li> <li>Bundle Name</li> <li>Bundle
      * Version</li> <li>Bundle Vendor</li> <li>Bundle Description</li> <li>Main
      * Class</li> </ul>
      * However, all but a handful of specific entries are read in.
      *
      * @param dependency A reference to the dependency
      * @param classInformation a collection of class information
      * @return whether evidence was identified parsing the manifest
      * @throws IOException if there is an issue reading the JAR file
      */
     protected boolean parseManifest(Dependency dependency, List<ClassNameInformation> classInformation)
             throws IOException {
         boolean foundSomething = false;
         JarFile jar = null;
         try {
             jar = new JarFile(dependency.getActualFilePath());
             final Manifest manifest = jar.getManifest();
             if (manifest == null) {
                 if (!dependency.getFileName().toLowerCase().endsWith("-sources.jar")
                         && !dependency.getFileName().toLowerCase().endsWith("-javadoc.jar")
                         && !dependency.getFileName().toLowerCase().endsWith("-src.jar")
                         && !dependency.getFileName().toLowerCase().endsWith("-doc.jar")) {
                     LOGGER.debug("Jar file '{}' does not contain a manifest.",
                             dependency.getFileName());
                 }
                 return false;
             }
             final EvidenceCollection vendorEvidence = dependency.getVendorEvidence();
             final EvidenceCollection productEvidence = dependency.getProductEvidence();
             final EvidenceCollection versionEvidence = dependency.getVersionEvidence();
             String source = "Manifest";
             String specificationVersion = null;
             boolean hasImplementationVersion = false;
             Attributes atts = manifest.getMainAttributes();
             for (Entry<Object, Object> entry : atts.entrySet()) {
                 String key = entry.getKey().toString();
                 String value = atts.getValue(key);
                 if (HTML_DETECTION_PATTERN.matcher(value).find()) {
                     value = Jsoup.parse(value).text();
                 }
                 if (IGNORE_VALUES.contains(value)) {
                     continue;
                 } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_TITLE.toString())) {
                     foundSomething = true;
                     productEvidence.addEvidence(source, key, value, Confidence.HIGH);
                     addMatchingValues(classInformation, value, productEvidence);
                 } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VERSION.toString())) {
                     hasImplementationVersion = true;
                     foundSomething = true;
                     versionEvidence.addEvidence(source, key, value, Confidence.HIGH);
                 } else if ("specification-version".equalsIgnoreCase(key)) {
                     specificationVersion = value;
                 } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VENDOR.toString())) {
                     foundSomething = true;
                     vendorEvidence.addEvidence(source, key, value, Confidence.HIGH);
                     addMatchingValues(classInformation, value, vendorEvidence);
                 } else if (key.equalsIgnoreCase(IMPLEMENTATION_VENDOR_ID)) {
                     foundSomething = true;
                     vendorEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                     addMatchingValues(classInformation, value, vendorEvidence);
                 } else if (key.equalsIgnoreCase(BUNDLE_DESCRIPTION)) {
                     foundSomething = true;
                     addDescription(dependency, value, "manifest", key);
                     addMatchingValues(classInformation, value, productEvidence);
                 } else if (key.equalsIgnoreCase(BUNDLE_NAME)) {
                     foundSomething = true;
                     productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                     addMatchingValues(classInformation, value, productEvidence);
 //                //the following caused false positives.
 //                } else if (key.equalsIgnoreCase(BUNDLE_VENDOR)) {
                 } else if (key.equalsIgnoreCase(BUNDLE_VERSION)) {
                     foundSomething = true;
                     versionEvidence.addEvidence(source, key, value, Confidence.HIGH);
                 } else if (key.equalsIgnoreCase(Attributes.Name.MAIN_CLASS.toString())) {
                     continue;
                     //skipping main class as if this has important information to add it will be added during class name analysis...
                 } else {
                     key = key.toLowerCase();
                     if (!IGNORE_KEYS.contains(key)
                             && !key.endsWith("jdk")
                             && !key.contains("lastmodified")
                             && !key.endsWith("package")
                             && !key.endsWith("classpath")
                             && !key.endsWith("class-path")
                             && !key.endsWith("-scm") //todo change this to a regex?
                             && !key.startsWith("scm-")
                             && !value.trim().startsWith("scm:")
                             && !isImportPackage(key, value)
                             && !isPackage(key, value)) {
                         foundSomething = true;
                         if (key.contains("version")) {
                             if (!key.contains("specification")) {
                                 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);
                         } else if (key.contains("vendor")) {
                             if (key.contains("specification")) {
                                 vendorEvidence.addEvidence(source, key, value, Confidence.LOW);
                             } else {
                                 vendorEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                                 addMatchingValues(classInformation, value, vendorEvidence);
                             }
                         } else if (key.contains("name")) {
                             productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                             vendorEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                             addMatchingValues(classInformation, value, vendorEvidence);
                             addMatchingValues(classInformation, value, productEvidence);
                         } else if (key.contains("license")) {
                             addLicense(dependency, value);
                         } else if (key.contains("description")) {
                             addDescription(dependency, value, "manifest", key);
                         } else {
                             productEvidence.addEvidence(source, key, value, Confidence.LOW);
                             vendorEvidence.addEvidence(source, key, value, Confidence.LOW);
                             addMatchingValues(classInformation, value, vendorEvidence);
                             addMatchingValues(classInformation, value, productEvidence);
                             if (value.matches(".*\\d.*")) {
                                 final StringTokenizer tokenizer = new StringTokenizer(value, " ");
                                 while (tokenizer.hasMoreElements()) {
                                     final String s = tokenizer.nextToken();
                                     if (s.matches("^[0-9.]+$")) {
                                         versionEvidence.addEvidence(source, key, s, Confidence.LOW);
                                     }
                                 }
                             }
                         }
                     }
                 }
             }
             for (Map.Entry<String, Attributes> item : manifest.getEntries().entrySet()) {
                 final String name = item.getKey();
                 source = "manifest: " + name;
                 atts = item.getValue();
                 for (Entry<Object, Object> entry : atts.entrySet()) {
                     final String key = entry.getKey().toString();
                     final String value = atts.getValue(key);
                     if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_TITLE.toString())) {
                         foundSomething = true;
                         productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                         addMatchingValues(classInformation, value, productEvidence);
                     } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VERSION.toString())) {
                         foundSomething = true;
                         versionEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                     } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VENDOR.toString())) {
                         foundSomething = true;
                         vendorEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                         addMatchingValues(classInformation, value, vendorEvidence);
                     } else if (key.equalsIgnoreCase(Attributes.Name.SPECIFICATION_TITLE.toString())) {
                         foundSomething = true;
                         productEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                         addMatchingValues(classInformation, value, productEvidence);
                     }
                 }
             }
             if (specificationVersion != null && !hasImplementationVersion) {
                 foundSomething = true;
                 versionEvidence.addEvidence(source, "specification-version", specificationVersion, Confidence.HIGH);
             }
         } finally {
             if (jar != null) {
                 jar.close();
             }
         }
         return foundSomething;
     }
 
     /**
      * 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
      */
     public static String addDescription(Dependency dependency, String description, String source, String key) {
         if (dependency.getDescription() == null) {
             dependency.setDescription(description);
         }
         String desc;
         if (HTML_DETECTION_PATTERN.matcher(description).find()) {
             desc = Jsoup.parse(description).text();
         } else {
             desc = description;
         }
         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;
             pos = Math.max(pos, posSuchAs);
             if (pos >= 0 && posLike >= 0) {
                 pos = Math.min(pos, posLike);
             } else {
                 pos = Math.max(pos, posLike);
             }
             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) {
                 desc = desc.substring(0, pos) + "...";
             }
             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;
     }
 
     /**
      * Adds a license to the given dependency.
      *
      * @param d a dependency
      * @param license the license
      */
     private void addLicense(Dependency d, String license) {
         if (d.getLicense() == null) {
             d.setLicense(license);
         } else if (!d.getLicense().contains(license)) {
             d.setLicense(d.getLicense() + NEWLINE + license);
         }
     }
 
     /**
      * The parent directory for the individual directories per archive.
      */
     private File tempFileLocation = null;
 
     /**
      * Initializes the JarAnalyzer.
      *
      * @throws InitializationException is thrown if there is an exception
      * creating a temporary directory
      */
     @Override
     public void initializeFileTypeAnalyzer() throws InitializationException {
         try {
             final File baseDir = Settings.getTempDirectory();
             tempFileLocation = File.createTempFile("check", "tmp", baseDir);
             if (!tempFileLocation.delete()) {
                 final String msg = String.format("Unable to delete temporary file '%s'.", tempFileLocation.getAbsolutePath());
                 setEnabled(false);
                 throw new InitializationException(msg);
             }
             if (!tempFileLocation.mkdirs()) {
                 final String msg = String.format("Unable to create directory '%s'.", tempFileLocation.getAbsolutePath());
                 setEnabled(false);
                 throw new InitializationException(msg);
             }
         } catch (IOException ex) {
             setEnabled(false);
             throw new InitializationException("Unable to create a temporary file", ex);
         }
     }
 
     /**
      * Deletes any files extracted from the JAR during analysis.
      */
     @Override
     public void closeAnalyzer() {
         if (tempFileLocation != null && tempFileLocation.exists()) {
             LOGGER.debug("Attempting to delete temporary files");
             final boolean success = FileUtils.delete(tempFileLocation);
             if (!success && tempFileLocation.exists()) {
                 final String[] l = tempFileLocation.list();
                 if (l != null && l.length > 0) {
                     LOGGER.warn("Failed to delete some temporary files, see the log for more details");
                 }
             }
         }
     }
 
     /**
      * Determines if the key value pair from the manifest is for an "import"
      * type entry for package names.
      *
      * @param key the key from the manifest
      * @param value the value from the manifest
      * @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-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);
     }
 
     /**
      * Cycles through an enumeration of JarEntries, contained within the
      * dependency, and returns a list of the class names. This does not include
      * core Java package names (i.e. java.* or javax.*).
      *
      * @param dependency the dependency being analyzed
      * @return an list of fully qualified class names
      */
     private List<ClassNameInformation> collectClassNames(Dependency dependency) {
         final List<ClassNameInformation> classNames = new ArrayList<ClassNameInformation>();
         JarFile jar = null;
         try {
             jar = new JarFile(dependency.getActualFilePath());
             final Enumeration<JarEntry> entries = jar.entries();
             while (entries.hasMoreElements()) {
                 final JarEntry entry = entries.nextElement();
                 final String name = entry.getName().toLowerCase();
                 //no longer stripping "|com\\.sun" - there are some com.sun jar files with CVEs.
                 if (name.endsWith(".class") && !name.matches("^javax?\\..*$")) {
                     final ClassNameInformation className = new ClassNameInformation(name.substring(0, name.length() - 6));
                     classNames.add(className);
                 }
             }
         } catch (IOException ex) {
             LOGGER.warn("Unable to open jar file '{}'.", dependency.getFileName());
             LOGGER.debug("", ex);
         } finally {
             if (jar != null) {
                 try {
                     jar.close();
                 } catch (IOException ex) {
                     LOGGER.trace("", ex);
                 }
             }
         }
         return classNames;
     }
 
     /**
      * Cycles through the list of class names and places the package levels 0-3
      * into the provided maps for vendor and product. This is helpful when
      * analyzing vendor/product as many times this is included in the package
      * name.
      *
      * @param classNames a list of class names
      * @param vendor HashMap of possible vendor names from package names (e.g.
      * owasp)
      * @param product HashMap of possible product names from package names (e.g.
      * dependencycheck)
      */
     private void analyzeFullyQualifiedClassNames(List<ClassNameInformation> classNames,
             Map<String, Integer> vendor, Map<String, Integer> product) {
         for (ClassNameInformation entry : classNames) {
             final List<String> list = entry.getPackageStructure();
             addEntry(vendor, list.get(0));
 
             if (list.size() == 2) {
                 addEntry(product, list.get(1));
             } else if (list.size() == 3) {
                 addEntry(vendor, list.get(1));
                 addEntry(product, list.get(1));
                 addEntry(product, list.get(2));
             } else if (list.size() >= 4) {
                 addEntry(vendor, list.get(1));
                 addEntry(vendor, list.get(2));
                 addEntry(product, list.get(1));
                 addEntry(product, list.get(2));
                 addEntry(product, list.get(3));
             }
         }
     }
 
     /**
      * Adds an entry to the specified collection and sets the Integer (e.g. the
      * count) to 1. If the entry already exists in the collection then the
      * Integer is incremented by 1.
      *
      * @param collection a collection of strings and their occurrence count
      * @param key the key to add to the collection
      */
     private void addEntry(Map<String, Integer> collection, String key) {
         if (collection.containsKey(key)) {
             collection.put(key, collection.get(key) + 1);
         } else {
             collection.put(key, 1);
         }
     }
 
     /**
      * Cycles through the collection of class name information to see if parts
      * of the package names are contained in the provided value. If found, it
      * will be added as the HIGHEST confidence evidence because we have more
      * then one source corroborating the value.
      *
      * @param classes a collection of class name information
      * @param value the value to check to see if it contains a package name
      * @param evidence the evidence collection to add new entries too
      */
     private static void addMatchingValues(List<ClassNameInformation> classes, String value, EvidenceCollection evidence) {
         if (value == null || value.isEmpty() || classes == null || classes.isEmpty()) {
             return;
         }
         final String text = value.toLowerCase();
         for (ClassNameInformation cni : classes) {
             for (String key : cni.getPackageStructure()) {
                 final Pattern p = Pattern.compile("\b" + key + "\b");
                 if (p.matcher(text).find()) {
                     //if (text.contains(key)) { //note, package structure elements are already lowercase.
                     evidence.addEvidence("jar", "package name", key, Confidence.HIGHEST);
                 }
             }
         }
     }
 
     /**
      * Simple check to see if the attribute from a manifest is just a package
      * name.
      *
      * @param key the key of the value to check
      * @param value the value to check
      * @return true if the value looks like a java package name, otherwise false
      */
     private boolean isPackage(String key, String value) {
 
         return !key.matches(".*(version|title|vendor|name|license|description).*")
                 && value.matches("^([a-zA-Z_][a-zA-Z0-9_\\$]*(\\.[a-zA-Z_][a-zA-Z0-9_\\$]*)*)?$");
 
     }
 
     /**
      * Extracts the license information from the pom and adds it to the
      * dependency.
      *
      * @param pom the pom object
      * @param dependency the dependency to add license information too
      */
     public static void extractLicense(Model pom, Dependency dependency) {
         //license
         if (pom.getLicenses() != null) {
             String license = null;
             for (License lic : pom.getLicenses()) {
                 String tmp = null;
                 if (lic.getName() != null) {
                     tmp = lic.getName();
                 }
                 if (lic.getUrl() != null) {
                     if (tmp == null) {
                         tmp = lic.getUrl();
                     } else {
                         tmp += ": " + lic.getUrl();
                     }
                 }
                 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);
 
             }
         }
     }
 
     /**
      * Stores information about a class name.
      */
     protected static class ClassNameInformation {
 
         /**
          * <p>
          * Stores information about a given class name. This class will keep the
          * fully qualified class name and a list of the important parts of the
          * package structure. Up to the first four levels of the package
          * structure are stored, excluding a leading "org" or "com".
          * Example:</p>
          * <code>ClassNameInformation obj = new ClassNameInformation("org.owasp.dependencycheck.analyzer.JarAnalyzer");
          * System.out.println(obj.getName());
          * for (String p : obj.getPackageStructure())
          *     System.out.println(p);
          * </code>
          * <p>
          * Would result in:</p>
          * <code>org.owasp.dependencycheck.analyzer.JarAnalyzer
          * owasp
          * dependencycheck
          * analyzer
          * jaranalyzer</code>
          *
          * @param className a fully qualified class name
          */
         ClassNameInformation(String className) {
             name = className;
             if (name.contains("/")) {
                 final String[] tmp = className.toLowerCase().split("/");
                 int start = 0;
                 int end = 3;
                 if ("com".equals(tmp[0]) || "org".equals(tmp[0])) {
                     start = 1;
                     end = 4;
                 }
                 if (tmp.length <= end) {
                     end = tmp.length - 1;
                 }
                 for (int i = start; i <= end; i++) {
                     packageStructure.add(tmp[i]);
                 }
             } else {
                 packageStructure.add(name);
             }
         }
         /**
          * The fully qualified class name.
          */
         private String name;
 
         /**
          * Get the value of name
          *
          * @return the value of name
          */
         public String getName() {
             return name;
         }
 
         /**
          * Set the value of name
          *
          * @param name new value of name
          */
         public void setName(String name) {
             this.name = name;
         }
         /**
          * Up to the first four levels of the package structure, excluding a
          * leading "org" or "com".
          */
         private final ArrayList<String> packageStructure = new ArrayList<String>();
 
         /**
          * Get the value of packageStructure
          *
          * @return the value of packageStructure
          */
         public ArrayList<String> getPackageStructure() {
             return packageStructure;
         }
     }
 
     /**
      * Retrieves the next temporary directory to extract an archive too.
      *
      * @return a directory
      * @throws AnalysisException thrown if unable to create temporary directory
      */
     private File getNextTempDirectory() throws AnalysisException {
         final int dirCount = DIR_COUNT.incrementAndGet();
         final File directory = new File(tempFileLocation, String.valueOf(dirCount));
         //getting an exception for some directories not being able to be created; might be because the directory already exists?
         if (directory.exists()) {
             return getNextTempDirectory();
         }
         if (!directory.mkdirs()) {
             final String msg = String.format("Unable to create temp directory '%s'.", directory.getAbsolutePath());
             throw new AnalysisException(msg);
         }
         return directory;
     }
 }