version 0.2.3.2

Former-commit-id: 474018fefa56379cb88cfd232c4a88e8ce9b15af

README.txt

@@ -7,10 +7,10 @@ If found, it will generate a report linking to the associated CVE entries.
 Usage:
 $ mvn package
 $ cd target
-$ java -jar DependencyCheck-0.2.2.jar -h
-$ java -jar DependencyCheck-0.2.2.jar -a Testing -out . -scan ./test-classes/org.mortbay.jetty.jar -scan ./test-classes/struts2-core-2.1.2.jar -scan ./lib
+$ java -jar DependencyCheck-0.2.3.2.jar -h
+$ java -jar DependencyCheck-0.2.3.2.jar -a Testing -out . -scan ./test-classes/org.mortbay.jetty.jar -scan ./test-classes/struts2-core-2.1.2.jar -scan ./lib
 
-Then load the resulting 'Testing.html' into your favorite browser.
+Then load the resulting 'DependencyCheck-Report.html' into your favorite browser.
 
 Author: Jeremy Long (jeremy.long@gmail.com)
 

pom.xml

@@ -23,7 +23,7 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
 
     <groupId>org.codesecure</groupId>
     <artifactId>DependencyCheck</artifactId>
-    <version>0.2.2</version>
+    <version>0.2.3.2</version>
     <packaging>jar</packaging>
 
     <name>DependencyCheck</name>
@@ -100,7 +100,7 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
                 <artifactId>maven-javadoc-plugin</artifactId>
                 <version>2.8.1</version>
                 <configuration>
-                    <bottom>Copyright &#169; 2012 Jeremy Long. All Rights Reserved.</bottom>
+                    <bottom>Copyright&#169; 2012 Jeremy Long. All Rights Reserved.</bottom>
                 </configuration>
             </plugin>
             <plugin>
@@ -206,13 +206,21 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
                             <value>${project.build.directory}/cobertura/cobertura.ser</value>
                             <workingDirectory>target</workingDirectory>
                         </property>
-                        <property>
+                        <!--<property>
                             <name>cve</name>
                             <value>${project.build.directory}/data/cve</value>
                         </property>
                         <property>
                             <name>cpe</name>
                             <value>${project.build.directory}/data/cpe</value>
+                        </property>-->
+                        <property>
+                            <name>cve</name>
+                            <value>target/data/cve</value>
+                        </property>
+                        <property>
+                            <name>cpe</name>
+                            <value>target/data/cpe</value>
                         </property>
                     </systemProperties>
                     <excludes>
@@ -224,6 +232,21 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
                 <version>2.12.4</version>
+                <configuration>
+                    <systemProperties>
+                        <property>
+                            <name>cve</name>
+                            <value>target/data/cve</value>
+                        </property>
+                        <property>
+                            <name>cpe</name>
+                            <value>target/data/cpe</value>
+                        </property>
+                    </systemProperties>
+                    <includes>
+                        <include>**/*IntegrationTest.java</include>
+                    </includes>
+                </configuration>
                 <executions>
                     <execution>
                         <goals>
@@ -308,6 +331,11 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
                                 </excludes>
                             </configuration>
                         </plugin>
+                        <plugin>
+                            <groupId>org.codehaus.mojo</groupId>
+                            <artifactId>taglist-maven-plugin</artifactId>
+                            <version>2.4</version>
+                        </plugin>
                         <plugin>
                             <groupId>org.apache.maven.plugins</groupId>
                             <artifactId>maven-javadoc-plugin</artifactId>
@@ -338,11 +366,17 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
                                 <reportSet>
                                     <id>integration-tests</id>
                                     <reports>
+                                        <report>report-only</report>
                                         <report>failsafe-report-only</report>
                                     </reports>
                                 </reportSet>
                             </reportSets>
                         </plugin>
+                        <plugin>
+                            <groupId>org.codehaus.mojo</groupId>
+                            <artifactId>findbugs-maven-plugin</artifactId>
+                            <version>2.5.2</version>
+                        </plugin>
                     </reportPlugins>
                 </configuration>
             </plugin>
@@ -365,7 +399,18 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-core</artifactId>
-            <version>3.5.0</version>
+            <version>4.0.0</version>
+            <!--<version>3.5.0</version>-->
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-analyzers-common</artifactId>
+            <version>4.0.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-queryparser</artifactId>
+            <version>4.0.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
@@ -427,5 +472,14 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
             <artifactId>hawtdb</artifactId>
             <version>1.6</version>
         </dependency>-->
+
+        <!-- The following dependencies are only scanned during integration testing -->
+        <!--<dependency>
+            <groupId>org.springframework</groupId>
+            <artifactId>spring-beans</artifactId>
+            <version>2.5.5</version>
+            <scope>test</scope>
+        </dependency>-->
+
     </dependencies>
 </project>

src/main/java/org/codesecure/dependencycheck/App.java

@@ -74,6 +74,7 @@ public class App {
         //Preferences.systemRoot().put("java.util.logging.config.file", "log.properties");
         //System.getProperties().put("java.util.logging.config.file", "configuration/log.properties");
         File dir = new File("logs");
+
         if (!dir.exists()) {
             dir.mkdir();
         }
@@ -157,9 +158,9 @@ public class App {
         scanner.analyzeDependencies();
         List<Dependency> dependencies = scanner.getDependencies();
 
-        ReportGenerator report = new ReportGenerator();
+        ReportGenerator report = new ReportGenerator(applicationName, dependencies, scanner.getAnalyzers());
         try {
-            report.generateReports(reportDirectory, applicationName, dependencies);
+            report.generateReports(reportDirectory);
         } catch (IOException ex) {
             Logger.getLogger(App.class.getName()).log(Level.SEVERE, null, ex);
         } catch (Exception ex) {

src/main/java/org/codesecure/dependencycheck/Engine.java

@@ -195,7 +195,8 @@ public class Engine {
                 try {
                     a.initialize();
                 } catch (Exception ex) {
-                    Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, "Exception occured initializing " + a.getName() + ".", ex);
+                    Logger.getLogger(Engine.class.getName()).log(Level.SEVERE,
+                            "Exception occured initializing " + a.getName() + ".", ex);
                     try {
                         a.close();
                     } catch (Exception ex1) {
@@ -254,8 +255,23 @@ public class Engine {
             try {
                 source.update();
             } catch (UpdateException ex) {
-                Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, "Unable to update " + source.getClass().getName(), ex);
+                Logger.getLogger(Engine.class.getName()).log(Level.SEVERE,
+                        "Unable to update " + source.getClass().getName(), ex);
             }
         }
     }
+
+    /**
+     * Returns a full list of all of the analyzers. This is useful
+     * for reporting which analyzers where used.
+     * @return a list of Analyzers
+     */
+    public List<Analyzer> getAnalyzers() {
+        List<Analyzer> ret = new ArrayList<Analyzer>();
+        for (AnalysisPhase phase : AnalysisPhase.values()) {
+            List<Analyzer> analyzerList = analyzers.get(phase);
+            ret.addAll(analyzerList);
+        }
+        return ret;
+    }
 }

src/main/java/org/codesecure/dependencycheck/analyzer/JarAnalyzer.java

@@ -186,6 +186,7 @@ public class JarAnalyzer extends AbstractAnalyzer {
             parseManifest(dependency);
             analyzePackageNames(dependency);
             analyzePOM(dependency);
+            addPredefinedData(dependency);
         } catch (IOException ex) {
             throw new AnalysisException("Exception occured reading the JAR file.", ex);
         } catch (JAXBException ex) {
@@ -228,7 +229,7 @@ public class JarAnalyzer extends AbstractAnalyzer {
                     }
                 } else if (!entry.isDirectory() && "pom.properties".equals(entryName)) {
                     if (pomProperties == null) {
-                        Reader reader = new InputStreamReader(zin);
+                        Reader reader = new InputStreamReader(zin, "UTF-8");
                         pomProperties = new Properties();
                         pomProperties.load(reader);
                         zin.closeEntry();
@@ -481,6 +482,12 @@ public class JarAnalyzer extends AbstractAnalyzer {
     protected void parseManifest(Dependency dependency) throws IOException {
         JarFile jar = new JarFile(dependency.getActualFilePath());
         Manifest manifest = jar.getManifest();
+        if (manifest == null) {
+            Logger.getLogger(JarAnalyzer.class.getName()).log(Level.SEVERE,
+                    "Jar file '{0}' does not contain a manifest.",
+                    dependency.getFileName());
+            return;
+        }
         Attributes atts = manifest.getMainAttributes();
 
         EvidenceCollection vendorEvidence = dependency.getVendorEvidence();
@@ -615,4 +622,15 @@ public class JarAnalyzer extends AbstractAnalyzer {
         sb.append(text.substring(end + 1));
         return interpolateString(sb.toString(), properties); //yes yes, this should be a loop...
     }
+
+    private void addPredefinedData(Dependency dependency) {
+        Evidence spring = new Evidence("Manifest",
+                "Implementation-Title",
+                "Spring Framework",
+                Evidence.Confidence.HIGH);
+
+        if (dependency.getProductEvidence().getEvidence().contains(spring)) {
+            dependency.getVendorEvidence().addEvidence("a priori", "vendor", "SpringSource", Evidence.Confidence.HIGH);
+        }
+    }
 }

src/main/java/org/codesecure/dependencycheck/data/cpe/CPEAnalyzer.java

@@ -27,8 +27,10 @@ import java.util.StringTokenizer;
 import org.apache.lucene.analysis.Analyzer;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.index.CorruptIndexException;
-import org.apache.lucene.queryParser.ParseException;
-import org.apache.lucene.queryParser.QueryParser;
+import org.apache.lucene.queryparser.classic.ParseException;
+import org.apache.lucene.queryparser.classic.QueryParser;
+//TODO convert to the analyzing query parser
+//import org.apache.lucene.queryparser.analyzing.AnalyzingQueryParser;
 import org.apache.lucene.search.IndexSearcher;
 import org.apache.lucene.search.Query;
 import org.apache.lucene.search.ScoreDoc;
@@ -98,8 +100,7 @@ public class CPEAnalyzer implements org.codesecure.dependencycheck.analyzer.Anal
         cpe.open();
         indexSearcher = cpe.getIndexSearcher();
         Analyzer analyzer = cpe.getAnalyzer();
-        //TITLE is the default field because it contains venddor, product, and version all in one.
-        queryParser = new QueryParser(Version.LUCENE_35, Fields.TITLE, analyzer);
+        queryParser = new QueryParser(Version.LUCENE_40, Fields.NAME, analyzer);
     }
 
     /**
@@ -149,23 +150,11 @@ public class CPEAnalyzer implements org.codesecure.dependencycheck.analyzer.Anal
         Confidence versionConf = Confidence.HIGH;
 
         String vendors = addEvidenceWithoutDuplicateTerms("", dependency.getVendorEvidence(), vendorConf);
-        //dependency.getVendorEvidence().toString(vendorConf);
-//        if ("".equals(vendors)) {
-//            vendors = STRING_THAT_WILL_NEVER_BE_IN_THE_INDEX;
-//        }
         String products = addEvidenceWithoutDuplicateTerms("", dependency.getProductEvidence(), productConf);
-        ///dependency.getProductEvidence().toString(productConf);
-//        if ("".equals(products)) {
-//            products = STRING_THAT_WILL_NEVER_BE_IN_THE_INDEX;
-//        }
         String versions = addEvidenceWithoutDuplicateTerms("", dependency.getVersionEvidence(), versionConf);
-        //dependency.getVersionEvidence().toString(versionConf);
-//        if ("".equals(versions)) {
-//            versions = STRING_THAT_WILL_NEVER_BE_IN_THE_INDEX;
-//        }
 
         boolean found = false;
-        int cnt = 0;
+        int ctr = 0;
         do {
             List<Entry> entries = searchCPE(vendors, products, versions, dependency.getProductEvidence().getWeighting(),
                     dependency.getVendorEvidence().getWeighting());
@@ -178,22 +167,20 @@ public class CPEAnalyzer implements org.codesecure.dependencycheck.analyzer.Anal
                     dependency.addIdentifier(
                             "cpe",
                             e.getName(),
-                            e.getTitle(),
                             "http://web.nvd.nist.gov/view/vuln/search?cpe="
                             + URLEncoder.encode(e.getName(), "UTF-8"));
                 }
             }
 
-
             if (!found) {
-                int round = cnt % 3;
+                int round = ctr % 3;
                 if (round == 0) {
                     vendorConf = reduceConfidence(vendorConf);
                     if (dependency.getVendorEvidence().contains(vendorConf)) {
                         //vendors += " " + dependency.getVendorEvidence().toString(vendorConf);
                         vendors = addEvidenceWithoutDuplicateTerms(vendors, dependency.getVendorEvidence(), vendorConf);
                     } else {
-                        cnt += 1;
+                        ctr += 1;
                         round += 1;
                     }
                 }
@@ -203,7 +190,7 @@ public class CPEAnalyzer implements org.codesecure.dependencycheck.analyzer.Anal
                         //products += " " + dependency.getProductEvidence().toString(productConf);
                         products = addEvidenceWithoutDuplicateTerms(products, dependency.getProductEvidence(), productConf);
                     } else {
-                        cnt += 1;
+                        ctr += 1;
                         round += 1;
                     }
                 }
@@ -215,7 +202,7 @@ public class CPEAnalyzer implements org.codesecure.dependencycheck.analyzer.Anal
                     }
                 }
             }
-        } while (!found && (++cnt) < 9);
+        } while (!found && (++ctr) < 9);
     }
 
     /**

src/main/java/org/codesecure/dependencycheck/data/cpe/Entry.java

@@ -45,21 +45,16 @@ public class Entry {
     public static Entry parse(Document doc) {
         Entry entry = new Entry();
         try {
-            entry.setName(doc.get(Fields.NAME));
-            entry.setTitle(doc.get(Fields.TITLE));
+            entry.parseName(doc.get(Fields.NAME));
         } catch (UnsupportedEncodingException ex) {
             Logger.getLogger(Entry.class.getName()).log(Level.SEVERE, null, ex);
             entry.name = doc.get(Fields.NAME);
         }
-//        entry.vendor = doc.get(Fields.VENDOR);
-//        entry.version = doc.get(Fields.VERSION);
-//        //entry.revision = doc.get(Fields.REVISION);
-//        entry.product = doc.get(Fields.TITLE);
-//        entry.nvdId = doc.get(Fields.NVDID);
         return entry;
     }
     /**
      * The title of the CPE
+     * @deprecated This field is no longer used
      */
     protected String title;
 
@@ -67,6 +62,7 @@ public class Entry {
      * Get the value of title
      *
      * @return the value of title
+     * @deprecated This field is no longer used
      */
     public String getTitle() {
         return title;
@@ -76,6 +72,7 @@ public class Entry {
      * Set the value of title
      *
      * @param title new value of title
+     * @deprecated This field is no longer used
      */
     public void setTitle(String title) {
         this.title = title;
@@ -95,18 +92,16 @@ public class Entry {
     }
 
     /**
-     * Set the value of name and calls parseName to obtain the
-     * vendor:product:version:revision
+     * Set the value of name
      *
      * @param name new value of name
-     * @throws UnsupportedEncodingException should never be thrown...
      */
-    public void setName(String name) throws UnsupportedEncodingException {
+    public void setName(String name) {
         this.name = name;
-        parseName();
     }
     /**
      * The status of the CPE Entry.
+     * @deprecated This field is no longer used
      */
     protected String status;
 
@@ -114,6 +109,7 @@ public class Entry {
      * Get the value of status
      *
      * @return the value of status
+     * @deprecated This field is no longer used
      */
     public String getStatus() {
         return status;
@@ -123,31 +119,35 @@ public class Entry {
      * Set the value of status
      *
      * @param status new value of status
+     * @deprecated This field is no longer used
      */
     public void setStatus(String status) {
         this.status = status;
     }
     /**
      * The modification date of the CPE Entry.
+     * @deprecated This field is no longer used
      */
-    protected Date modificationDate;
+    private Date modificationDate;
 
     /**
      * Get the value of modificationDate
      *
      * @return the value of modificationDate
+     * @deprecated This field is no longer used
      */
     public Date getModificationDate() {
-        return modificationDate;
+        return (Date) modificationDate.clone();
     }
 
     /**
      * Set the value of modificationDate
      *
      * @param modificationDate new value of modificationDate
+     * @deprecated This field is no longer used
      */
     public void setModificationDate(Date modificationDate) {
-        this.modificationDate = modificationDate;
+        this.modificationDate = (Date) modificationDate.clone();
     }
 
     /**
@@ -157,6 +157,7 @@ public class Entry {
      *
      * @param modificationDate new value of modificationDate
      * @throws ParseException is thrown when a parse exception occurs.
+     * @deprecated This field is no longer used
      */
     public void setModificationDate(String modificationDate) throws ParseException {
 
@@ -170,6 +171,7 @@ public class Entry {
     }
     /**
      * The nvdId.
+     * @deprecated This field is no longer used
      */
     protected String nvdId;
 
@@ -177,6 +179,7 @@ public class Entry {
      * Get the value of nvdId
      *
      * @return the value of nvdId
+     * @deprecated This field is no longer used
      */
     public String getNvdId() {
         return nvdId;
@@ -186,6 +189,7 @@ public class Entry {
      * Set the value of nvdId
      *
      * @param nvdId new value of nvdId
+     * @deprecated This field is no longer used
      */
     public void setNvdId(String nvdId) {
         this.nvdId = nvdId;
@@ -310,15 +314,17 @@ public class Entry {
      * <p>Results in:</p> <ul> <li>Vendor: apache</li> <li>Product: struts</li>
      * <li>Version: 1.1</li> <li>Revision: rc2</li> </ul>
      *
+     * @param cpeName the cpe name
      * @throws UnsupportedEncodingException should never be thrown...
      */
-    private void parseName() throws UnsupportedEncodingException {
-        if (name != null && name.length() > 7) {
-            String[] data = name.substring(7).split(":");
+    public void parseName(String cpeName) throws UnsupportedEncodingException {
+        this.name = cpeName;
+        if (cpeName != null && cpeName.length() > 7) {
+            String[] data = cpeName.substring(7).split(":");
             if (data.length >= 1) {
-                vendor = URLDecoder.decode(data[0], "UTF-8");
+                vendor = URLDecoder.decode(data[0], "UTF-8").replaceAll("[_-]", " ");
                 if (data.length >= 2) {
-                    product = URLDecoder.decode(data[1], "UTF-8");
+                    product = URLDecoder.decode(data[1], "UTF-8").replaceAll("[_-]", " ");
                     if (data.length >= 3) {
                         version = URLDecoder.decode(data[2], "UTF-8");
                         if (data.length >= 4) {

src/main/java/org/codesecure/dependencycheck/data/cpe/Fields.java

@@ -34,22 +34,13 @@ public abstract class Fields {
      * The key for the vendor field.
      */
     public static final String VENDOR = "vendor";
-    /**
-     * The key for the version field.
-     */
-    public static final String VERSION = "version";
-    //public static final String REVISION = "revision";
     /**
      * The key for the product field.
      */
     public static final String PRODUCT = "product";
     /**
-     * The key for the title field. This is a field combining vendor, product,
-     * and version.
+     * The key for the version field.
      */
-    public static final String TITLE = "title";
-    /**
-     * The key for the nvdId field.
-     */
-    public static final String NVDID = "nvdid";
+    public static final String VERSION = "version";
+    //public static final String REVISION = "revision";
 }

src/main/java/org/codesecure/dependencycheck/data/cpe/Index.java

@@ -28,6 +28,7 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.net.URLDecoder;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Properties;
@@ -35,8 +36,8 @@ import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.xml.parsers.ParserConfigurationException;
 import org.apache.lucene.analysis.Analyzer;
-import org.apache.lucene.analysis.KeywordAnalyzer;
-import org.apache.lucene.analysis.PerFieldAnalyzerWrapper;
+import org.apache.lucene.analysis.core.KeywordAnalyzer;
+import org.apache.lucene.analysis.miscellaneous.PerFieldAnalyzerWrapper;
 import org.apache.lucene.analysis.standard.StandardAnalyzer;
 import org.apache.lucene.store.Directory;
 import org.apache.lucene.store.FSDirectory;
@@ -74,13 +75,39 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * @throws IOException is thrown if an IOException occurs.
      */
     public Directory getDirectory() throws IOException {
-        String fileName = Settings.getString(Settings.KEYS.CPE_INDEX);
-        File path = new File(fileName);
+        File path = getDataDirectory();
         Directory dir = FSDirectory.open(path);
 
         return dir;
     }
 
+    /**
+     * Retrieves the directory that the JAR file exists in so that
+     * we can ensure we always use a common data directory.
+     *
+     * @return the data directory for this index.
+     * @throws IOException is thrown if an IOException occurs of course...
+     */
+    public File getDataDirectory() throws IOException {
+        String fileName = Settings.getString(Settings.KEYS.CPE_INDEX);
+        String filePath = Index.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (exePath.getName().toLowerCase().endsWith(".jar")) {
+            exePath = exePath.getParentFile();
+        } else {
+            exePath = new File(".");
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        if (!path.exists()) {
+            if (!path.mkdirs()) {
+                throw new IOException("Unable to create CPE Data directory");
+            }
+        }
+        return path;
+    }
+
     /**
      * Creates an Analyzer for the CPE Index.
      *
@@ -91,9 +118,10 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
         Map fieldAnalyzers = new HashMap();
 
         fieldAnalyzers.put(Fields.VERSION, new KeywordAnalyzer());
+        fieldAnalyzers.put(Fields.NAME, new KeywordAnalyzer());
 
         PerFieldAnalyzerWrapper wrapper = new PerFieldAnalyzerWrapper(
-                new StandardAnalyzer(Version.LUCENE_35), fieldAnalyzers);
+                new StandardAnalyzer(Version.LUCENE_40), fieldAnalyzers);
 
         return wrapper;
     }
@@ -104,6 +132,8 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      *
      * @throws UpdateException is thrown if there is a problem updating the
      * index.
+     *
+     * @deprecated this should no longer be used as the raw CPE hosted at NIST is not complete enough.
      */
     public void update() throws UpdateException {
         try {
@@ -152,31 +182,42 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * directory.
      *
      * @param timeStamp the timestamp to write.
+     *
+     * @deprecated this should no longer be used as the raw CPE hosted at NIST is not complete enough.
      */
-    private void writeLastUpdatedPropertyFile(long timeStamp) {
-        String dir = Settings.getString(Settings.KEYS.CPE_INDEX);
+    private void writeLastUpdatedPropertyFile(long timeStamp) throws UpdateException {
+        String dir;
+        try {
+            dir = getDataDirectory().getCanonicalPath();
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate the last updated properties file.", ex);
+        }
         File cpeProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
         Properties prop = new Properties();
         prop.put(Index.LAST_UPDATED, String.valueOf(timeStamp));
         OutputStream os = null;
+        OutputStreamWriter out = null;
         try {
             os = new FileOutputStream(cpeProp);
-            OutputStreamWriter out = new OutputStreamWriter(os);
+            out = new OutputStreamWriter(os, "UTF-8");
             prop.store(out, dir);
         } catch (FileNotFoundException ex) {
             Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
         } catch (IOException ex) {
             Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
         } finally {
-            try {
-                os.flush();
-            } catch (IOException ex) {
-                Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
-            }
-            try {
-                os.close();
-            } catch (IOException ex) {
-                Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            if (os != null) {
+                try {
+                    os.flush();
+                } catch (IOException ex) {
+                    Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                }
+                try {
+                    os.close();
+                } catch (IOException ex) {
+                    Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                }
             }
         }
     }
@@ -193,8 +234,12 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * is incorrect.
      * @throws DownloadFailedException is thrown if there is an error
      * downloading the cpe.meta data file.
+     * @throws UpdateException is thrown if there is an error locating the last updated
+     * properties file.
+     *
+     * @deprecated this should no longer be used as the raw CPE hosted at NIST is not complete enough.
      */
-    public long updateNeeded() throws MalformedURLException, DownloadFailedException {
+    public long updateNeeded() throws MalformedURLException, DownloadFailedException, UpdateException {
         long retVal = 0;
         long lastUpdated = 0;
         long currentlyPublishedDate = retrieveCurrentCPETimestampFromWeb();
@@ -202,12 +247,24 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
             throw new DownloadFailedException("Unable to retrieve valid timestamp from cpe.meta file");
         }
 
-        String dir = Settings.getString(Settings.KEYS.CPE_INDEX);
-        File f = new File(dir);
+        //String dir = Settings.getString(Settings.KEYS.CPE_INDEX);
+        File f;
+        try {
+            f = getDataDirectory(); //new File(dir);
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate last updated properties file.", ex);
+        }
         if (!f.exists()) {
             retVal = currentlyPublishedDate;
         } else {
-            File cpeProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
+            File cpeProp;
+            try {
+                cpeProp = new File(f.getCanonicalPath() + File.separatorChar + UPDATE_PROPERTIES_FILE);
+            } catch (IOException ex) {
+                Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                throw new UpdateException("Unable to find last updated properties file.", ex);
+            }
             if (!cpeProp.exists()) {
                 retVal = currentlyPublishedDate;
             } else {
@@ -223,6 +280,14 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
                     Logger.getLogger(Index.class.getName()).log(Level.FINEST, null, ex);
                 } catch (NumberFormatException ex) {
                     Logger.getLogger(Index.class.getName()).log(Level.FINEST, null, ex);
+                } finally {
+                    if (is != null) {
+                        try {
+                            is.close();
+                        } catch (IOException ex) {
+                            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                        }
+                    }
                 }
                 if (currentlyPublishedDate > lastUpdated) {
                     retVal = currentlyPublishedDate;

src/main/java/org/codesecure/dependencycheck/data/cpe/xml/CPEHandler.java

@@ -66,7 +66,7 @@ public class CPEHandler extends DefaultHandler {
             skip = (temp != null && temp.equals("true"));
             try {
                 if (!skip && name.startsWith("cpe:/a:")) {
-                    entry.setName(name);
+                    entry.parseName(name);
                 } else {
                     skip = true;
                 }

src/main/java/org/codesecure/dependencycheck/data/cpe/xml/Indexer.java

@@ -21,13 +21,13 @@ package org.codesecure.dependencycheck.data.cpe.xml;
 import java.io.IOException;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.document.Field;
+import org.apache.lucene.document.StoredField;
+import org.apache.lucene.document.TextField;
 import org.apache.lucene.index.CorruptIndexException;
-import org.apache.lucene.index.FieldInfo.IndexOptions;
 import org.apache.lucene.index.Term;
 import org.codesecure.dependencycheck.data.cpe.Entry;
 import org.codesecure.dependencycheck.data.cpe.Fields;
 import org.codesecure.dependencycheck.data.cpe.Index;
-import org.codesecure.dependencycheck.data.lucene.LuceneUtils;
 
 /**
  * The Indexer is used to convert a CPE Entry, retrieved from the CPE XML file,
@@ -46,7 +46,8 @@ public class Indexer extends Index implements EntrySaveDelegate {
      */
     public void saveEntry(Entry entry) throws CorruptIndexException, IOException {
         Document doc = convertEntryToDoc(entry);
-        Term term = new Term(Fields.NVDID, LuceneUtils.escapeLuceneQuery(entry.getNvdId()));
+        //Term term = new Term(Fields.NVDID, LuceneUtils.escapeLuceneQuery(entry.getNvdId()));
+        Term term = new Term(Fields.NAME, entry.getName());
         indexWriter.updateDocument(term, doc);
     }
 
@@ -59,44 +60,30 @@ public class Indexer extends Index implements EntrySaveDelegate {
     protected Document convertEntryToDoc(Entry entry) {
         Document doc = new Document();
 
-        Field name = new Field(Fields.NAME, entry.getName(), Field.Store.YES, Field.Index.ANALYZED);
-        name.setIndexOptions(IndexOptions.DOCS_ONLY);
+        Field name = new StoredField(Fields.NAME, entry.getName());
         doc.add(name);
 
-        Field nvdId = new Field(Fields.NVDID, entry.getNvdId(), Field.Store.NO, Field.Index.ANALYZED);
-        nvdId.setIndexOptions(IndexOptions.DOCS_ONLY);
-        doc.add(nvdId);
-
-        Field vendor = new Field(Fields.VENDOR, entry.getVendor(), Field.Store.NO, Field.Index.ANALYZED);
-        vendor.setIndexOptions(IndexOptions.DOCS_ONLY);
+        Field vendor = new TextField(Fields.VENDOR, entry.getVendor(), Field.Store.NO);
         vendor.setBoost(5.0F);
         doc.add(vendor);
 
-        Field product = new Field(Fields.PRODUCT, entry.getProduct(), Field.Store.NO, Field.Index.ANALYZED);
-        product.setIndexOptions(IndexOptions.DOCS_ONLY);
+        Field product = new TextField(Fields.PRODUCT, entry.getProduct(), Field.Store.NO);
         product.setBoost(5.0F);
         doc.add(product);
 
-        Field title = new Field(Fields.TITLE, entry.getTitle(), Field.Store.YES, Field.Index.ANALYZED);
-        title.setIndexOptions(IndexOptions.DOCS_ONLY);
-        //title.setBoost(1.0F);
-        doc.add(title);
-
         //TODO revision should likely be its own field
         if (entry.getVersion() != null) {
             Field version = null;
             if (entry.getRevision() != null) {
-                version = new Field(Fields.VERSION, entry.getVersion() + " "
-                        + entry.getRevision(), Field.Store.NO, Field.Index.ANALYZED);
+                version = new TextField(Fields.VERSION, entry.getVersion() + " "
+                        + entry.getRevision(), Field.Store.NO);
             } else {
-                version = new Field(Fields.VERSION, entry.getVersion(),
-                        Field.Store.NO, Field.Index.ANALYZED);
+                version = new TextField(Fields.VERSION, entry.getVersion(),
+                        Field.Store.NO);
             }
-            version.setIndexOptions(IndexOptions.DOCS_ONLY);
             version.setBoost(0.8F);
             doc.add(version);
         }
-
         return doc;
     }
 }

src/main/java/org/codesecure/dependencycheck/data/lucene/AbstractIndex.java

@@ -23,6 +23,7 @@ import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.apache.lucene.analysis.Analyzer;
 import org.apache.lucene.index.CorruptIndexException;
+import org.apache.lucene.index.DirectoryReader;
 import org.apache.lucene.index.IndexReader;
 import org.apache.lucene.index.IndexWriter;
 import org.apache.lucene.index.IndexWriterConfig;
@@ -98,13 +99,7 @@ public abstract class AbstractIndex {
             }
         }
         if (indexSearcher != null) {
-            try {
-                indexSearcher.close();
-            } catch (IOException ex) {
-                Logger.getLogger(AbstractIndex.class.getName()).log(Level.SEVERE, null, ex);
-            } finally {
-                indexSearcher = null;
-            }
+            indexSearcher = null;
         }
 
         if (analyzer != null) {
@@ -140,7 +135,7 @@ public abstract class AbstractIndex {
         if (!isOpen()) {
             open();
         }
-        IndexWriterConfig conf = new IndexWriterConfig(Version.LUCENE_35, analyzer);
+        IndexWriterConfig conf = new IndexWriterConfig(Version.LUCENE_40, analyzer);
         indexWriter = new IndexWriter(directory, conf);
     }
 
@@ -170,7 +165,8 @@ public abstract class AbstractIndex {
         if (!isOpen()) {
             open();
         }
-        indexReader = IndexReader.open(directory, true);
+        //indexReader = IndexReader.open(directory, true);
+        indexReader = DirectoryReader.open(directory);
     }
 
     /**

src/main/java/org/codesecure/dependencycheck/data/lucene/DependencySimilarity.java

@@ -18,7 +18,7 @@ package org.codesecure.dependencycheck.data.lucene;
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 
-import org.apache.lucene.search.DefaultSimilarity;
+import org.apache.lucene.search.similarities.DefaultSimilarity;
 
 /**
  *
@@ -41,7 +41,7 @@ public class DependencySimilarity extends DefaultSimilarity {
      * @return 1
      */
     @Override
-    public float idf(int docFreq, int numDocs) {
+    public float idf(long docFreq, long numDocs) {
         return 1;
     }
 }

src/main/java/org/codesecure/dependencycheck/data/nvdcve/Index.java

@@ -21,14 +21,15 @@ package org.codesecure.dependencycheck.data.nvdcve;
 import java.io.*;
 import java.net.MalformedURLException;
 import java.net.URL;
+import java.net.URLDecoder;
 import java.util.*;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.apache.lucene.analysis.Analyzer;
-import org.apache.lucene.analysis.KeywordAnalyzer;
-import org.apache.lucene.analysis.PerFieldAnalyzerWrapper;
+import org.apache.lucene.analysis.core.KeywordAnalyzer;
+import org.apache.lucene.analysis.miscellaneous.PerFieldAnalyzerWrapper;
 import org.apache.lucene.analysis.standard.StandardAnalyzer;
 import org.apache.lucene.store.Directory;
 import org.apache.lucene.store.FSDirectory;
@@ -39,6 +40,7 @@ import org.codesecure.dependencycheck.data.lucene.AbstractIndex;
 import org.codesecure.dependencycheck.data.nvdcve.xml.Importer;
 import org.codesecure.dependencycheck.utils.DownloadFailedException;
 import org.codesecure.dependencycheck.utils.Downloader;
+import org.codesecure.dependencycheck.utils.FileUtils;
 import org.codesecure.dependencycheck.utils.Settings;
 
 /**
@@ -48,6 +50,10 @@ import org.codesecure.dependencycheck.utils.Settings;
  */
 public class Index extends AbstractIndex implements CachedWebDataSource {
 
+    /**
+     * The current version of the index
+     */
+    public static final String INDEX_VERSION = "1.0";
     /**
      * The name of the properties file containing the timestamp of the last
      * update.
@@ -66,18 +72,45 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
     private static final String LAST_UPDATED_BASE = "lastupdated.";
 
     /**
-     * Returns the directory that holds the NVD CVE Index.
+     * Returns the directory that holds the NVD CVE Index. Note, this
+     * returns the path where the class or jar file exists.
      *
      * @return the Directory containing the NVD CVE Index.
      * @throws IOException is thrown if an IOException occurs.
      */
     public Directory getDirectory() throws IOException {
-        String fileName = Settings.getString(Settings.KEYS.CVE_INDEX);
-        File path = new File(fileName);
+        File path = getDataDirectory();
         Directory dir = FSDirectory.open(path);
         return dir;
     }
 
+    /**
+     * Retrieves the directory that the JAR file exists in so that
+     * we can ensure we always use a common data directory.
+     *
+     * @return the data directory for this index.
+     * @throws IOException is thrown if an IOException occurs of course...
+     */
+    protected File getDataDirectory() throws IOException {
+        String fileName = Settings.getString(Settings.KEYS.CVE_INDEX);
+        String filePath = Index.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (exePath.getName().toLowerCase().endsWith(".jar")) {
+            exePath = exePath.getParentFile();
+        } else {
+            exePath = new File(".");
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        if (!path.exists()) {
+            if (!path.mkdirs()) {
+                throw new IOException("Unable to create NVD CVE Data directory");
+            }
+        }
+        return path;
+    }
+
     /**
      * Creates an Analyzer for the NVD VULNERABLE_CPE Index.
      *
@@ -91,7 +124,7 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
         fieldAnalyzers.put(Fields.VULNERABLE_CPE, new KeywordAnalyzer());
 
         PerFieldAnalyzerWrapper wrapper = new PerFieldAnalyzerWrapper(
-                new StandardAnalyzer(Version.LUCENE_35), fieldAnalyzers);
+                new StandardAnalyzer(Version.LUCENE_40), fieldAnalyzers);
 
         return wrapper;
     }
@@ -165,11 +198,17 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      *
      * @param timeStamp the timestamp to write.
      */
-    private void writeLastUpdatedPropertyFile(Map<String, NvdCveUrl> updated) {
-        String dir = Settings.getString(Settings.KEYS.CVE_INDEX);
+    private void writeLastUpdatedPropertyFile(Map<String, NvdCveUrl> updated) throws UpdateException {
+        String dir;
+        try {
+            dir = getDataDirectory().getCanonicalPath();
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate last updated properties file.", ex);
+        }
         File cveProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
         Properties prop = new Properties();
-
+        prop.put("version", INDEX_VERSION);
         for (NvdCveUrl cve : updated.values()) {
             prop.put(LAST_UPDATED_BASE + cve.id, String.valueOf(cve.getTimestamp()));
         }
@@ -177,22 +216,26 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
         OutputStream os = null;
         try {
             os = new FileOutputStream(cveProp);
-            OutputStreamWriter out = new OutputStreamWriter(os);
+            OutputStreamWriter out = new OutputStreamWriter(os, "UTF-8");
             prop.store(out, dir);
         } catch (FileNotFoundException ex) {
             Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to find last updated properties file.", ex);
         } catch (IOException ex) {
             Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to update last updated properties file.", ex);
         } finally {
-            try {
-                os.flush();
-            } catch (IOException ex) {
-                Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
-            }
-            try {
-                os.close();
-            } catch (IOException ex) {
-                Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            if (os != null) {
+                try {
+                    os.flush();
+                } catch (IOException ex) {
+                    Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                }
+                try {
+                    os.close();
+                } catch (IOException ex) {
+                    Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                }
             }
         }
     }
@@ -206,10 +249,11 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * @return the NvdCveUrl of the files that need to be updated.
      * @throws MalformedURLException is thrown if the URL for the NVD CVE Meta
      * data is incorrect.
-     * @throws DownloadFailedException is thrown if there is an error
+     * @throws DownloadFailedException is thrown if there is an error.
      * downloading the nvd cve download data file.
+     * @throws UpdateException Is thrown if there is an issue with the last updated properties file.
      */
-    public Map<String, NvdCveUrl> updateNeeded() throws MalformedURLException, DownloadFailedException {
+    public Map<String, NvdCveUrl> updateNeeded() throws MalformedURLException, DownloadFailedException, UpdateException {
 
         Map<String, NvdCveUrl> currentlyPublished;
         try {
@@ -221,16 +265,36 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
         if (currentlyPublished == null) {
             throw new DownloadFailedException("Unable to retrieve valid timestamp from nvd cve downloads page");
         }
-        String dir = Settings.getString(Settings.KEYS.CVE_INDEX);
+        String dir;
+        try {
+            dir = getDataDirectory().getCanonicalPath();
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate last updated properties file.", ex);
+        }
+
         File f = new File(dir);
         if (f.exists()) {
             File cveProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
             if (cveProp.exists()) {
                 Properties prop = new Properties();
-                InputStream is;
+                InputStream is = null;
                 try {
                     is = new FileInputStream(cveProp);
                     prop.load(is);
+
+                    if (prop.getProperty("version") == null) {
+                        is.close();
+                        //this is an old version of the lucene index - just delete it
+                        FileUtils.delete(f);
+
+                        //this importer also updates the CPE index and it is also using an old version
+                        org.codesecure.dependencycheck.data.cpe.Index cpeidx = new org.codesecure.dependencycheck.data.cpe.Index();
+                        File cpeDir = cpeidx.getDataDirectory();
+                        FileUtils.delete(cpeDir);
+                        return currentlyPublished;
+                    }
+
                     long lastUpdated = Long.parseLong(prop.getProperty(Index.LAST_UPDATED_MODIFIED));
                     Date now = new Date();
                     int days = Settings.getInt(Settings.KEYS.CVE_MODIFIED_VALID_FOR_DAYS);
@@ -264,6 +328,14 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
                     Logger.getLogger(Index.class.getName()).log(Level.FINEST, null, ex);
                 } catch (NumberFormatException ex) {
                     Logger.getLogger(Index.class.getName()).log(Level.FINEST, null, ex);
+                } finally {
+                    if (is != null) {
+                        try {
+                            is.close();
+                        } catch (IOException ex) {
+                            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                        }
+                    }
                 }
             }
         }
@@ -403,7 +475,7 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * @throws IOException is thrown if an IOExcpetion occurs.
      */
     private String readFile(File file) throws IOException {
-        FileReader stream = new FileReader(file);
+        InputStreamReader stream = new InputStreamReader(new FileInputStream(file), "UTF-8");
         StringBuilder str = new StringBuilder((int) file.length());
         try {
             char[] buf = new char[8096];

src/main/java/org/codesecure/dependencycheck/data/nvdcve/NvdCveAnalyzer.java

@@ -20,6 +20,7 @@ package org.codesecure.dependencycheck.data.nvdcve;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
@@ -142,6 +143,9 @@ public class NvdCveAnalyzer implements org.codesecure.dependencycheck.analyzer.A
                         } catch (JAXBException ex) {
                             Logger.getLogger(NvdCveAnalyzer.class.getName()).log(Level.SEVERE, null, ex);
                             dependency.addAnalysisException(new AnalysisException("Unable to retrieve vulnerability data", ex));
+                        } catch (UnsupportedEncodingException ex) {
+                            Logger.getLogger(NvdCveAnalyzer.class.getName()).log(Level.SEVERE, null, ex);
+                            dependency.addAnalysisException(new AnalysisException("Unable to retrieve vulnerability data - utf-8", ex));
                         }
                     }
                 } catch (IOException ex) {
@@ -198,11 +202,11 @@ public class NvdCveAnalyzer implements org.codesecure.dependencycheck.analyzer.A
         this.open();
     }
 
-    private Vulnerability parseVulnerability(String xml) throws JAXBException {
+    private Vulnerability parseVulnerability(String xml) throws JAXBException, UnsupportedEncodingException {
 
         JAXBContext jaxbContext = JAXBContext.newInstance(VulnerabilityType.class);
         Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
-        ByteArrayInputStream input = new ByteArrayInputStream(xml.getBytes());
+        ByteArrayInputStream input = new ByteArrayInputStream(xml.getBytes("UTF-8"));
         VulnerabilityType cvedata = (VulnerabilityType) unmarshaller.unmarshal(input);
         if (cvedata == null) {
             return null;

src/main/java/org/codesecure/dependencycheck/data/nvdcve/xml/Importer.java

@@ -43,15 +43,17 @@ public class Importer {
      */
     public static void importXML(File file) {
         NvdCveParser indexer = null;
+        org.codesecure.dependencycheck.data.cpe.xml.Indexer cpeIndexer = null;
         try {
-
             indexer = new NvdCveParser();
-
             indexer.openIndexWriter();
 
+            //HACK - hack to ensure all CPE data is stored in the index.
+            cpeIndexer = new org.codesecure.dependencycheck.data.cpe.xml.Indexer();
+            cpeIndexer.openIndexWriter();
+            indexer.setCPEIndexer(cpeIndexer);
 
             indexer.parse(file);
-
         } catch (CorruptIndexException ex) {
             Logger.getLogger(Importer.class.getName()).log(Level.SEVERE, null, ex);
         } catch (IOException ex) {
@@ -60,6 +62,9 @@ public class Importer {
             if (indexer != null) {
                 indexer.close();
             }
+            if (cpeIndexer != null) {
+                cpeIndexer.close();
+            }
         }
     }
 //    public static void importXML(File file) throws FileNotFoundException, IOException, JAXBException,

src/main/java/org/codesecure/dependencycheck/data/nvdcve/xml/Indexer.java

@@ -20,6 +20,7 @@ package org.codesecure.dependencycheck.data.nvdcve.xml;
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import javax.xml.bind.JAXBContext;
@@ -27,8 +28,9 @@ import javax.xml.bind.JAXBException;
 import javax.xml.bind.Marshaller;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.document.Field;
+import org.apache.lucene.document.StoredField;
+import org.apache.lucene.document.StringField;
 import org.apache.lucene.index.CorruptIndexException;
-import org.apache.lucene.index.FieldInfo.IndexOptions;
 import org.apache.lucene.index.Term;
 import org.codesecure.dependencycheck.data.lucene.LuceneUtils;
 import org.codesecure.dependencycheck.data.nvdcve.generated.VulnerabilityType;
@@ -55,7 +57,12 @@ public class Indexer extends Index implements EntrySaveDelegate {
      */
     public void saveEntry(VulnerabilityType vulnerability) throws CorruptIndexException, IOException {
         try {
-            Document doc = convertEntryToDoc(vulnerability);
+            Document doc = null;
+            try {
+                doc = convertEntryToDoc(vulnerability);
+            } catch (UnsupportedEncodingException ex) {
+                Logger.getLogger(Indexer.class.getName()).log(Level.SEVERE, null, ex);
+            }
 
             if (doc == null) {
                 return;
@@ -74,8 +81,9 @@ public class Indexer extends Index implements EntrySaveDelegate {
      * @param vulnerability a VULNERABLE_CPE Entry.
      * @return a Lucene Document containing a VULNERABLE_CPE Entry.
      * @throws JAXBException is thrown when there is a JAXBException.
+     * @throws UnsupportedEncodingException if the system doesn't support utf-8
      */
-    protected Document convertEntryToDoc(VulnerabilityType vulnerability) throws JAXBException {
+    protected Document convertEntryToDoc(VulnerabilityType vulnerability) throws JAXBException, UnsupportedEncodingException {
         boolean hasApplication = false;
         Document doc = new Document();
 
@@ -101,14 +109,11 @@ public class Indexer extends Index implements EntrySaveDelegate {
             return null;
         }
 
-        Field name = new Field(Fields.CVE_ID, vulnerability.getId(), Field.Store.NO, Field.Index.ANALYZED);
-        name.setIndexOptions(IndexOptions.DOCS_ONLY);
+        Field name = new StringField(Fields.CVE_ID, vulnerability.getId(), Field.Store.NO);
         doc.add(name);
 
-        Field description = new Field(Fields.DESCRIPTION, vulnerability.getSummary(), Field.Store.NO, Field.Index.ANALYZED);
-        description.setIndexOptions(IndexOptions.DOCS_ONLY);
-        doc.add(description);
-
+//        Field description = new Field(Fields.DESCRIPTION, vulnerability.getSummary(), Field.Store.NO, Field.Index.ANALYZED);
+//        doc.add(description);
 
         JAXBContext context = JAXBContext.newInstance("org.codesecure.dependencycheck.data.nvdcve.generated");
 
@@ -119,7 +124,7 @@ public class Indexer extends Index implements EntrySaveDelegate {
 
         m.marshal(vulnerability, out);
 
-        Field xml = new Field(Fields.XML, out.toString(), Field.Store.YES, Field.Index.NO);
+        Field xml = new StoredField(Fields.XML, out.toString("UTF-8"));
         doc.add(xml);
 
         return doc;
@@ -141,8 +146,7 @@ public class Indexer extends Index implements EntrySaveDelegate {
     }
 
     private void addVulnerableCpe(String cpe, Document doc) {
-        Field vulnerable = new Field(Fields.VULNERABLE_CPE, cpe, Field.Store.NO, Field.Index.ANALYZED);
-        vulnerable.setIndexOptions(IndexOptions.DOCS_ONLY);
+        Field vulnerable = new StringField(Fields.VULNERABLE_CPE, cpe, Field.Store.NO);
         doc.add(vulnerable);
     }
 }

src/main/java/org/codesecure/dependencycheck/data/nvdcve/xml/NvdCveParser.java

@@ -20,17 +20,22 @@ package org.codesecure.dependencycheck.data.nvdcve.xml;
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.apache.lucene.document.Document;
 import org.apache.lucene.document.Field;
-import org.apache.lucene.index.FieldInfo.IndexOptions;
+import org.apache.lucene.document.StoredField;
+import org.apache.lucene.document.StringField;
+import org.apache.lucene.index.CorruptIndexException;
 import org.apache.lucene.index.Term;
+import org.codesecure.dependencycheck.data.cpe.Entry;
 import org.codesecure.dependencycheck.data.nvdcve.Fields;
 import org.codesecure.dependencycheck.data.nvdcve.Index;
 
@@ -40,6 +45,19 @@ import org.codesecure.dependencycheck.data.nvdcve.Index;
  */
 public class NvdCveParser extends Index {
 
+    //HACK - this has initially been placed here as a hack because not all
+    // of the CPEs listed in the NVD CVE are actually in the CPE xml file
+    // hosted by NIST.
+    private org.codesecure.dependencycheck.data.cpe.xml.Indexer cpeIndexer = null;
+
+    /**
+     * Adds the CPE Index to add additional CPEs found by parsing the NVD CVE.
+     * @param indexer the CPE Indexer to write new CPEs into.
+     */
+    public void setCPEIndexer(org.codesecure.dependencycheck.data.cpe.xml.Indexer indexer) {
+        this.cpeIndexer = indexer;
+    }
+
     /**
      * Parses an NVD CVE xml file using a buffered readerd. This
      * method maybe more fragile then using a partial-unmarshalling SAX
@@ -49,14 +67,15 @@ public class NvdCveParser extends Index {
      * @param file the reference to the NVD CVE file
      */
     public void parse(File file) {
-        FileReader fr = null;
+        InputStreamReader fr = null;
         BufferedReader br = null;
         Pattern rxEntry = Pattern.compile("^\\s*<entry\\s*id\\=\\\"([^\\\"]+)\\\".*$");
         Pattern rxEntryEnd = Pattern.compile("^\\s*</entry>.*$");
         Pattern rxFact = Pattern.compile("^\\s*<cpe\\-lang\\:fact\\-ref name=\\\"([^\\\"]+).*$");
-        Pattern rxSummary = Pattern.compile("^\\s*<vuln:summary>([^\\<]+).*$");
+        //Pattern rxSummary = Pattern.compile("^\\s*<vuln:summary>([^\\<]+).*$");
         try {
-            fr = new FileReader(file);
+
+            fr = new InputStreamReader(new FileInputStream(file), "UTF-8");
             br = new BufferedReader(fr);
             StringBuilder sb = new StringBuilder(7000);
             String str = null;
@@ -105,23 +124,21 @@ public class NvdCveParser extends Index {
                     sb.append("id=\"").append(id).append("\">");
                     //sb.append(str); //need to do the above to get the correct schema generated from files.
 
-                    Field name = new Field(Fields.CVE_ID, id, Field.Store.NO, Field.Index.ANALYZED);
-                    name.setIndexOptions(IndexOptions.DOCS_ONLY);
+                    Field name = new StringField(Fields.CVE_ID, id, Field.Store.NO);
                     doc.add(name);
                     continue;
                 }
-                Matcher matcherSummary = rxSummary.matcher(str);
-                if (matcherSummary.matches()) {
-                    String summary = matcherSummary.group(1);
-                    Field description = new Field(Fields.DESCRIPTION, summary, Field.Store.NO, Field.Index.ANALYZED);
-                    description.setIndexOptions(IndexOptions.DOCS_ONLY);
-                    doc.add(description);
-                    continue;
-                }
+//                Matcher matcherSummary = rxSummary.matcher(str);
+//                if (matcherSummary.matches()) {
+//                    String summary = matcherSummary.group(1);
+//                    Field description = new Field(Fields.DESCRIPTION, summary, Field.Store.NO);
+//                    doc.add(description);
+//                    continue;
+//                }
 
                 if (matcherEntryEnd.matches()) {
                     sb.append("</vulnerabilityType>");
-                    Field xml = new Field(Fields.XML, sb.toString(), Field.Store.YES, Field.Index.NO);
+                    Field xml = new StoredField(Fields.XML, sb.toString());
                     doc.add(xml);
 
                     if (!skipEntry) {
@@ -146,7 +163,9 @@ public class NvdCveParser extends Index {
             Logger.getLogger(NvdCveParser.class.getName()).log(Level.SEVERE, null, ex);
         } finally {
             try {
-                fr.close();
+                if (fr != null) {
+                    fr.close();
+                }
             } catch (IOException ex) {
                 Logger.getLogger(NvdCveParser.class.getName()).log(Level.SEVERE, null, ex);
             }
@@ -164,10 +183,24 @@ public class NvdCveParser extends Index {
      * Adds a CPE to the Lucene Document
      * @param cpe a string representing a CPE
      * @param doc a lucene document
+     * @throws CorruptIndexException is thrown if the CPE Index is corrupt
+     * @throws IOException is thrown if there is an IO Exception while writting to the CPE Index
      */
-    private void addVulnerableCpe(String cpe, Document doc) {
-        Field vulnerable = new Field(Fields.VULNERABLE_CPE, cpe, Field.Store.NO, Field.Index.ANALYZED);
-        vulnerable.setIndexOptions(IndexOptions.DOCS_ONLY);
+    private void addVulnerableCpe(String cpe, Document doc) throws CorruptIndexException, IOException {
+        Field vulnerable = new StringField(Fields.VULNERABLE_CPE, cpe, Field.Store.NO);
         doc.add(vulnerable);
+
+        //HACK - this has initially been placed here as a hack because not all
+        // of the CPEs listed in the NVD CVE are actually in the CPE xml file
+        // hosted by NIST.
+        Entry cpeEntry = new Entry();
+        try {
+            cpeEntry.parseName(cpe);
+        } catch (UnsupportedEncodingException ex) {
+            Logger.getLogger(NvdCveParser.class.getName()).log(Level.SEVERE, null, ex);
+        }
+        if (cpeIndexer != null) {
+            cpeIndexer.saveEntry(cpeEntry);
+        }
     }
 }

src/main/java/org/codesecure/dependencycheck/dependency/Dependency.java

@@ -19,7 +19,7 @@ package org.codesecure.dependencycheck.dependency;
  */
 
 import java.io.File;
-import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
 import java.util.List;
@@ -238,11 +238,10 @@ public class Dependency {
      *
      * @param type the type of identifier (such as CPE).
      * @param value the value of the identifier.
-     * @param title the title of the identifier.
      * @param url the URL of the identifier.
      */
-    public void addIdentifier(String type, String value, String title, String url) {
-        Identifier i = new Identifier(type, value, title, url);
+    public void addIdentifier(String type, String value, String url) {
+        Identifier i = new Identifier(type, value, url);
         this.identifiers.add(i);
     }
 
@@ -419,7 +418,7 @@ public class Dependency {
         try {
             md5 = Checksum.getMD5Checksum(file);
             sha1 = Checksum.getSHA1Checksum(file);
-        } catch (FileNotFoundException ex) {
+        } catch (IOException ex) {
             Logger.getLogger(Dependency.class.getName()).log(Level.SEVERE, null, ex);
         } catch (NoSuchAlgorithmException ex) {
             Logger.getLogger(Dependency.class.getName()).log(Level.SEVERE, null, ex);

src/main/java/org/codesecure/dependencycheck/dependency/EvidenceCollection.java

@@ -184,7 +184,7 @@ public class EvidenceCollection implements Iterable<Evidence> {
         text = text.toLowerCase();
 
         for (Evidence e : this.list) {
-            if (e.used && e.value.contains(text)) {
+            if (e.used && e.value.toLowerCase().contains(text)) {
                 return true;
             }
         }

src/main/java/org/codesecure/dependencycheck/dependency/Identifier.java

@@ -29,13 +29,11 @@ public class Identifier {
      *
      * @param type the identifier type.
      * @param value the identifier value.
-     * @param title the identifier title.
      * @param url the identifier url.
      */
-    Identifier(String type, String value, String title, String url) {
+    Identifier(String type, String value, String url) {
         this.type = type;
         this.value = value;
-        this.title = title;
         this.url = url;
     }
 
@@ -44,12 +42,11 @@ public class Identifier {
      *
      * @param type the identifier type.
      * @param value the identifier value.
-     * @param title the identifier title.
      * @param url the identifier url.
      * @param description the description of the identifier.
      */
-    Identifier(String type, String value, String title, String url, String description) {
-        this(type, value, title, url);
+    Identifier(String type, String value, String url, String description) {
+        this(type, value, url);
         this.description = description;
     }
     /**
@@ -74,28 +71,7 @@ public class Identifier {
     public void setValue(String value) {
         this.value = value;
     }
-    /**
-     * The title of the identifeir
-     */
-    protected String title;
 
-    /**
-     * Get the value of title
-     *
-     * @return the value of title
-     */
-    public String getTitle() {
-        return title;
-    }
-
-    /**
-     * Set the value of title
-     *
-     * @param title new value of title
-     */
-    public void setTitle(String title) {
-        this.title = title;
-    }
     /**
      * The url for the identifeir
      */

src/main/java/org/codesecure/dependencycheck/reporting/ReportGenerator.java

@@ -18,15 +18,16 @@ package org.codesecure.dependencycheck.reporting;
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 
-import java.io.BufferedWriter;
+import java.io.FileInputStream;
 import java.io.File;
-import java.io.FileWriter;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.util.HashMap;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
 import java.util.List;
-import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.apache.velocity.app.VelocityEngine;
@@ -35,94 +36,139 @@ import org.apache.velocity.runtime.RuntimeConstants;
 import org.apache.velocity.runtime.resource.loader.ClasspathResourceLoader;
 import org.apache.velocity.tools.ToolManager;
 import org.apache.velocity.tools.config.EasyFactoryConfiguration;
+import org.codesecure.dependencycheck.analyzer.Analyzer;
 import org.codesecure.dependencycheck.dependency.Dependency;
 
 /**
+ * The ReportGenerator is used to, as the name implies, generate reports. Internally
+ * the generator uses the Velocity Templating Engine. The ReportGenerator exposes
+ * a list of Dependencies to the template when generating the report.
  *
  * @author Jeremy Long (jeremy.long@gmail.com)
  */
 public class ReportGenerator {
 
+    /**
+     * The Velocity Engine.
+     */
+    private VelocityEngine engine = null;
+    /**
+     * The Velocity Engine Context.
+     */
+    private Context context = null;
+
+    /**
+     * Constructs a new ReportGenerator.
+     *
+     * @param applicationName the application name being analyzed
+     * @param dependencies the list of dependencies
+     * @param analyzers the list of analyzers used.
+     */
+    public ReportGenerator(String applicationName, List<Dependency> dependencies, List<Analyzer> analyzers) {
+        engine = createVelocityEngine();
+        context = createContext();
+
+        engine.init();
+
+        context.put("applicationName", applicationName);
+        context.put("dependencies", dependencies);
+        context.put("analyzers", analyzers);
+    }
+
+    /**
+     * Creates a new Velocity Engine.
+     * @return a velocity engine.
+     */
+    private VelocityEngine createVelocityEngine() {
+        VelocityEngine ve = new VelocityEngine();
+        ve.setProperty(RuntimeConstants.RESOURCE_LOADER, "classpath");
+        ve.setProperty("classpath.resource.loader.class", ClasspathResourceLoader.class.getName());
+        return ve;
+    }
+
+    /**
+     * Creates a new Velocity Context initialized with escape and date tools.
+     * @return a Velcotiy Context.
+     */
+    private Context createContext() {
+        ToolManager manager = new ToolManager();
+        Context c = manager.createContext();
+        EasyFactoryConfiguration config = new EasyFactoryConfiguration();
+        config.addDefaultTools();
+        config.toolbox("application").tool("esc", "org.apache.velocity.tools.generic.EscapeTool").tool("org.apache.velocity.tools.generic.DateTool");
+        manager.configure(config);
+        return c;
+    }
+
     /**
      * Generates the Dependency Reports for the identified dependencies.
      *
      * @param outputDir the path where the reports should be written.
-     * @param applicationName the name of the application that was scanned.
-     * @param dependencies a list of dependencies to include in the report.
      * @throws IOException is thrown when the template file does not exist.
      * @throws Exception is thrown if there is an error writting out the
      * reports.
      */
-    public void generateReports(String outputDir, String applicationName, List<Dependency> dependencies) throws IOException, Exception {
-
-        Map<String, Object> properties = new HashMap<String, Object>();
-        properties.put("dependencies", dependencies);
-        properties.put("applicationName", applicationName);
-
-        String reportName = applicationName.replaceAll("[^a-zA-Z0-9-_ \\.]+", "");
-        String filename = outputDir + File.separatorChar + reportName;
-        generateReport("HtmlReport", filename + ".html", properties);
-        //generateReport("XmlReport",filename + ".xml",properties);
-
+    public void generateReports(String outputDir) throws IOException, Exception {
+        generateReport("HtmlReport", outputDir + File.separator + "DependencyCheck-Report.html");
+        //generateReport("XmlReport", outputDir + File.separator + "DependencyCheck-Report.xml");
     }
 
     /**
-     * much of this code is from
-     * http://stackoverflow.com/questions/2931516/loading-velocity-template-inside-a-jar-file
+     * Generates a report from a given Velocity Template. The template name
+     * provided can be the name of a template contained in the jar file, such as
+     * 'XmlReport' or 'HtmlReport', or the template name can be the path to a template file.
      *
      * @param templateName the name of the template to load.
-     * @param outFileName The filename and path to write the report to.
-     * @param properties a map of properties to load into the velocity context.
+     * @param outFileName the filename and path to write the report to.
      * @throws IOException is thrown when the template file does not exist.
      * @throws Exception is thrown when an exception occurs.
      */
-    protected void generateReport(String templateName, String outFileName,
-            Map<String, Object> properties) throws IOException, Exception {
-
-        VelocityEngine ve = new VelocityEngine();
-        ve.setProperty(RuntimeConstants.RESOURCE_LOADER, "classpath");
-        ve.setProperty("classpath.resource.loader.class", ClasspathResourceLoader.class.getName());
-
-        ToolManager manager = new ToolManager();
-        Context context = manager.createContext();
-        EasyFactoryConfiguration config = new EasyFactoryConfiguration();
-        config.addDefaultTools();
-        config.toolbox("application").tool("esc", "org.apache.velocity.tools.generic.EscapeTool").tool("org.apache.velocity.tools.generic.DateTool");
-
-        manager.configure(config);
-
-        ve.init();
-
-        final String templatePath = "templates/" + templateName + ".vsl";
-        InputStream input = this.getClass().getClassLoader().getResourceAsStream(templatePath);
+    public void generateReport(String templateName, String outFileName) throws IOException, Exception {
+        InputStream input = null;
+        String templatePath = null;
+        File f = new File(templateName);
+        if (f.exists() && f.isFile()) {
+            try {
+                templatePath = templateName;
+                input = new FileInputStream(f);
+            } catch (FileNotFoundException ex) {
+                Logger.getLogger(ReportGenerator.class.getName()).log(Level.SEVERE, null, ex);
+            }
+        } else {
+            templatePath = "templates/" + templateName + ".vsl";
+            input = this.getClass().getClassLoader().getResourceAsStream(templatePath);
+        }
         if (input == null) {
             throw new IOException("Template file doesn't exist");
         }
 
-        InputStreamReader reader = new InputStreamReader(input);
-        BufferedWriter writer = null;
-
-        //VelocityContext context = new VelocityContext();
-
-        //load the data into the context
-        if (properties != null) {
-            for (Map.Entry<String, Object> property : properties.entrySet()) {
-                context.put(property.getKey(), property.getValue());
-            }
-        }
+        InputStreamReader reader = new InputStreamReader(input, "UTF-8");
+        OutputStreamWriter writer = null;
+        OutputStream outputStream = null;
 
         try {
-            writer = new BufferedWriter(new FileWriter(new File(outFileName)));
+            outputStream = new FileOutputStream(outFileName);
+            writer = new OutputStreamWriter(outputStream, "UTF-8");
+            //writer = new BufferedWriter(oswriter);
 
-            if (!ve.evaluate(context, writer, templatePath, reader)) {
+            if (!engine.evaluate(context, writer, templatePath, reader)) {
                 throw new Exception("Failed to convert the template into html.");
             }
             writer.flush();
         } finally {
-            try {
-                writer.close();
-            } catch (Exception ex) {
-                Logger.getLogger(ReportGenerator.class.getName()).log(Level.FINEST, null, ex);
+            if (writer != null) {
+                try {
+                    writer.close();
+                } catch (Exception ex) {
+                    Logger.getLogger(ReportGenerator.class.getName()).log(Level.FINEST, null, ex);
+                }
+            }
+            if (outputStream != null) {
+                try {
+                    outputStream.close();
+                } catch (Exception ex) {
+                    Logger.getLogger(ReportGenerator.class.getName()).log(Level.FINEST, null, ex);
+                }
             }
             try {
                 reader.close();

src/main/java/org/codesecure/dependencycheck/utils/Checksum.java

@@ -2,7 +2,6 @@ package org.codesecure.dependencycheck.utils;
 
 import java.io.File;
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
 import java.security.MessageDigest;
@@ -30,29 +29,30 @@ public class Checksum {
      * @param algorithm the algorithm to use to calculate the checksum
      * @param file the file to calculate the checksum for
      * @return the checksum
-     * @throws FileNotFoundException when the file does not exist
+     * @throws IOException when the file does not exist
      * @throws NoSuchAlgorithmException when an algorithm is specified that does
      * not exist
      */
-    public static byte[] getChecksum(String algorithm, File file) throws FileNotFoundException, NoSuchAlgorithmException {
-        InputStream fis = new FileInputStream(file);
+    public static byte[] getChecksum(String algorithm, File file) throws NoSuchAlgorithmException, IOException {
+        InputStream fis = null;
         byte[] buffer = new byte[1024];
         MessageDigest complete = MessageDigest.getInstance(algorithm);
         int numRead;
         try {
+            fis = new FileInputStream(file);
             do {
                 numRead = fis.read(buffer);
                 if (numRead > 0) {
                     complete.update(buffer, 0, numRead);
                 }
             } while (numRead != -1);
-        } catch (IOException ex) {
-            Logger.getLogger(Checksum.class.getName()).log(Level.SEVERE, null, ex);
         } finally {
-            try {
-                fis.close();
-            } catch (IOException ex) {
-                Logger.getLogger(Checksum.class.getName()).log(Level.SEVERE, null, ex);
+            if (fis != null) {
+                try {
+                    fis.close();
+                } catch (IOException ex) {
+                    Logger.getLogger(Checksum.class.getName()).log(Level.SEVERE, null, ex);
+                }
             }
         }
         return complete.digest();
@@ -63,10 +63,10 @@ public class Checksum {
      *
      * @param file the file to generate the MD5 checksum
      * @return the hex representation of the MD5 hash
-     * @throws FileNotFoundException when the file passed in does not exist
+     * @throws IOException when the file passed in does not exist
      * @throws NoSuchAlgorithmException when the MD5 algorithm is not available
      */
-    public static String getMD5Checksum(File file) throws FileNotFoundException, NoSuchAlgorithmException {
+    public static String getMD5Checksum(File file) throws IOException, NoSuchAlgorithmException {
         byte[] b = getChecksum("MD5", file);
         return getHex(b);
     }
@@ -76,10 +76,10 @@ public class Checksum {
      *
      * @param file the file to generate the MD5 checksum
      * @return the hex representation of the SHA1 hash
-     * @throws FileNotFoundException when the file passed in does not exist
+     * @throws IOException when the file passed in does not exist
      * @throws NoSuchAlgorithmException when the SHA1 algorithm is not available
      */
-    public static String getSHA1Checksum(File file) throws FileNotFoundException, NoSuchAlgorithmException {
+    public static String getSHA1Checksum(File file) throws IOException, NoSuchAlgorithmException {
         byte[] b = getChecksum("SHA1", file);
         return getHex(b);
     }

src/main/java/org/codesecure/dependencycheck/utils/CliParser.java

@@ -93,17 +93,20 @@ public final class CliParser {
             validatePathExists(getScanFiles());
             if (!line.hasOption(ArgumentName.OUT)) {
                 //TODO - need a new exception type here, this isn't really a parseexception.
-                throw new ParseException("Scan cannot be run without specifying a directory to write the reports to via the 'out' argument.");
+                throw new ParseException("Scan cannot be run without specifying a directory "
+                        + "to write the reports to via the 'out' argument.");
             } else {
                 String p = line.getOptionValue(ArgumentName.OUT, "");
                 File f = new File(p);
                 if ("".equals(p) || !(f.exists() && f.isDirectory())) {
                     //TODO - need a new exception type here, this isn't really a parseexception.
-                    throw new ParseException("A valid directory name must be specified for the 'out' argument.");
+                    throw new ParseException("A valid directory name must be specified for "
+                            + "the 'out' argument.");
                 }
             }
             if (!line.hasOption(ArgumentName.APPNAME)) {
-                throw new ParseException("Scan cannot be run without specifying an application name via the 'app' argument.");
+                throw new ParseException("Scan cannot be run without specifying an application "
+                        + "name via the 'app' argument.");
             }
         }
     }
@@ -160,15 +163,25 @@ public final class CliParser {
         Option noupdate = new Option(ArgumentName.DISABLE_AUTO_UPDATE_SHORT, ArgumentName.DISABLE_AUTO_UPDATE,
                 false, "disables the automatic updating of the CPE data.");
 
-        Option appname = OptionBuilder.withArgName("name").hasArg().withLongOpt(ArgumentName.APPNAME).withDescription("the name of the application being scanned.").create(ArgumentName.APPNAME_SHORT);
+        Option appname = OptionBuilder.withArgName("name").hasArg().withLongOpt(ArgumentName.APPNAME)
+                .withDescription("the name of the application being scanned.")
+                .create(ArgumentName.APPNAME_SHORT);
 
-        Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.SCAN).withDescription("the path to scan - this option can be specified multiple times.").create(ArgumentName.SCAN_SHORT);
+        Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.SCAN)
+                .withDescription("the path to scan - this option can be specified multiple times.")
+                .create(ArgumentName.SCAN_SHORT);
 
-        Option load = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.CPE).withDescription("load the CPE xml file.").create(ArgumentName.CPE_SHORT);
+        Option load = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.CPE)
+                .withDescription("load the CPE xml file.")
+                .create(ArgumentName.CPE_SHORT);
 
-        Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP).withDescription("a property file to load.").create(ArgumentName.PROP_SHORT);
+        Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP)
+                .withDescription("a property file to load.")
+                .create(ArgumentName.PROP_SHORT);
 
-        Option out = OptionBuilder.withArgName("folder").hasArg().withLongOpt(ArgumentName.OUT).withDescription("the folder to write reports to.").create(ArgumentName.OUT_SHORT);
+        Option out = OptionBuilder.withArgName("folder").hasArg().withLongOpt(ArgumentName.OUT)
+                .withDescription("the folder to write reports to.")
+                .create(ArgumentName.OUT_SHORT);
 
         //TODO add the ability to load a properties file to override the defaults...
 
@@ -237,7 +250,8 @@ public final class CliParser {
                     + "using the -p <file> argument or by passing them in as system properties." + nl
                     + nl + " " + Settings.KEYS.PROXY_URL + "\t\t    the proxy URL to use when downloading resources."
                     + nl + " " + Settings.KEYS.PROXY_PORT + "\t\t    the proxy port to use when downloading resources."
-                    + nl + " " + Settings.KEYS.CONNECTION_TIMEOUT + "\t    the cconnection timeout (in milliseconds) to use" + nl + "\t\t\t    when downloading resources.";
+                    + nl + " " + Settings.KEYS.CONNECTION_TIMEOUT + "\t    the cconnection timeout (in milliseconds) to use"
+                    + nl + "\t\t\t    when downloading resources.";
         }
 
         formatter.printHelp(Settings.getString("application.name", "DependencyCheck"),
@@ -312,7 +326,7 @@ public final class CliParser {
      * @return if auto-update is allowed.
      */
     public boolean isAutoUpdate() {
-        return (line != null) ? !line.hasOption(ArgumentName.DISABLE_AUTO_UPDATE) : false;
+        return (line != null) ? !line.hasOption(ArgumentName.DISABLE_AUTO_UPDATE) : true;
     }
 
     /**

src/main/java/org/codesecure/dependencycheck/utils/Downloader.java

@@ -128,8 +128,8 @@ public class Downloader {
         String encoding = conn.getContentEncoding();
 
         BufferedOutputStream writer = null;
+        InputStream reader = null;
         try {
-            InputStream reader;
             if (unzip || (encoding != null && "gzip".equalsIgnoreCase(encoding))) {
                 reader = new GZIPInputStream(conn.getInputStream());
             } else if (encoding != null && "deflate".equalsIgnoreCase(encoding)) {
@@ -147,6 +147,7 @@ public class Downloader {
         } catch (Exception ex) {
             throw new DownloadFailedException("Error saving downloaded file.", ex);
         } finally {
+            if (writer != null) {
             try {
                 writer.close();
                 writer = null;
@@ -154,6 +155,17 @@ public class Downloader {
                 Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
                         "Error closing the writter in Downloader.", ex);
             }
+            }
+            if (reader != null) {
+                try {
+                    reader.close();
+                    reader = null;
+                } catch (Exception ex) {
+
+                Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
+                        "Error closing the reader in Downloader.", ex);
+                }
+            }
             try {
                 conn.disconnect();
             } finally {

src/main/java/org/codesecure/dependencycheck/utils/FileUtils.java

@@ -18,6 +18,10 @@ package org.codesecure.dependencycheck.utils;
  * Copyright (c) 2012 Jeremy Long. All Rights Reserved.
  */
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
 /**
  * A collection of utilities for processing information about files.
  *
@@ -45,4 +49,22 @@ public class FileUtils {
         }
         return ret;
     }
+
+    /**
+     * Deletes a file. If the File is a directory it will recursively delete
+     * the contents.
+     *
+     * @param file the File to delete
+     * @throws IOException is thrown if the file could not be deleted
+     */
+    public static void delete(File file) throws IOException {
+        if (file.isDirectory()) {
+            for (File c : file.listFiles()) {
+                delete(c);
+            }
+        }
+        if (!file.delete()) {
+            throw new FileNotFoundException("Failed to delete file: " + file);
+        }
+    }
 }

src/main/resources/META-INF/services/org.codesecure.dependencycheck.data.CachedWebDataSource

@@ -1,2 +1 @@
-org.codesecure.dependencycheck.data.nvdcve.Index
-org.codesecure.dependencycheck.data.cpe.Index
+org.codesecure.dependencycheck.data.nvdcve.Index

src/main/resources/configuration/log.properties

@@ -20,4 +20,4 @@ java.util.logging.FileHandler.level=FINEST
 #   %g - generation number for rotating logs
 #   %u - unique number to avoid conflicts
 # FileHandler writes to %h/demo0.log by default.
-java.util.logging.FileHandler.pattern=./logs/DependencyCheck%g.log
+java.util.logging.FileHandler.pattern=./logs/DependencyCheck%u.log

src/main/resources/templates/HtmlReport.vsl

@@ -34,7 +34,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
         </script>
         <script type="text/javascript">
             $(document).ready(function() {
-                $(".expandablesubsection").click(function (e) {
+                $(".expandable").click(function (e) {
                     e = e || window.event;
                     var h = e.target || e.srcElement;
                     var content = "#content" + h.id.substr(6);
@@ -64,7 +64,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             .hidden {
                 display: none;
             }
-            
+            .exandable {}
             .expandablesubsection {
                 cursor: pointer;
                 /*background-image: url(img/plus.gif);*/
@@ -285,8 +285,12 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
             <div class="sectioncontent">Report Generated On: $date<br/><br/>
                 Dependencies Scanned:&nbsp;$dependencies.size()<br/><br/>
                 <div class="indent">
-                #foreach($dependency in $dependencies) 
-                    <a href="#$esc.html($esc.url($dependency.FilePath))">$esc.html($dependency.FileName)</a><br/>
+                #foreach($dependency in $dependencies)
+                    #if($dependency.getVulnerabilities().size()>0)
+                        <a href="#$esc.html($esc.url($dependency.FilePath))">$esc.html($dependency.FileName)</a>&nbsp;<b style="color:#ff0000;">&#8226;</b><br/>
+                    #else
+                        <a href="#$esc.html($esc.url($dependency.FilePath))">$esc.html($dependency.FileName)</a><br/>
+                    #end
                 #end
                 </div>
                 <h2>Dependencies</h2>
@@ -308,7 +312,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
 
                         #if ( $dependency.analysisExceptions.size() != 0 )
                             #set($cnt=$cnt+1)
-                            <h4 id="header$cnt" class="subsectionheader expandablesubsection red">Exceptions Occured During Analysis</h4>
+                            <h4 id="header$cnt" class="subsectionheader expandable expandablesubsection red">Exceptions Occured During Analysis</h4>
                             <div id="content$cnt" class="subsectioncontent standardsubsection hidden">
                                 <ul>
                                 #foreach($ex in $dependency.analysisExceptions)
@@ -336,7 +340,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                             </div>
                         #end
                         #set($cnt=$cnt+1)
-                        <h4 id="header$cnt" class="subsectionheader expandablesubsection white">Evidence</h4>
+                        <h4 id="header$cnt" class="subsectionheader expandable expandablesubsection white">Evidence</h4>
                         <div id="content$cnt" class="subsectioncontent standardsubsection hidden">
                             <table class="lined fullwidth" border="0">
                                 <tr><th class="left" style="width:10%;">Source</th><th class="left" style="width:20%;">Name</th><th class="left" style="width:70%;">Value</th></tr>
@@ -366,7 +370,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                             <ul>
                             #foreach($id in $dependency.getIdentifiers())
                                 ##yes, we are HTML Encoding the href. this is okay. We can't URL encode as we have to trust the analyzer here...
-                                <li><b>$esc.html($id.type):</b>&nbsp;$esc.html($id.title)&nbsp;:&nbsp;<a href="$esc.html($id.url)" target="_blank">$esc.html($id.value)</a>
+                                <li><b>$esc.html($id.type):</b>&nbsp;<a href="$esc.html($id.url)" target="_blank">$esc.html($id.value)</a>
                                 #if( $id.descrription )
                                     <br/>$esc.html($id.description)
                                 #end
@@ -377,7 +381,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                         </div>
                     #if($dependency.getVulnerabilities().size()>0)
                     #set($cnt=$cnt+1)
-                    <h4 id="header$cnt" class="subsectionheader white">Published Vulnerabilities</h4>
+                    <h4 id="header$cnt" class="subsectionheader expandable collaspablesubsection white">Published Vulnerabilities</h4>
                     <div id="content$cnt" class="subsectioncontent standardsubsection">
                         #foreach($vuln in $dependency.getVulnerabilities())
                             <p><b><a target="_blank" href="http://web.nvd.nist.gov/view/vuln/detail?vulnId=$esc.url($vuln.name)">$esc.html($vuln.name)</a></b></p>

src/site/site.xml

@@ -6,4 +6,4 @@
   <body>
     <menu ref="reports" />
   </body>
-</project>
+</project>

src/test/java/org/codesecure/dependencycheck/EngineIntegrationTest.java

@@ -51,7 +51,8 @@ public class EngineIntegrationTest {
         instance.scan(path);
         assertTrue(instance.getDependencies().size() > 0);
         instance.analyzeDependencies();
-        ReportGenerator rg = new ReportGenerator();
-        rg.generateReports("./target/", "DependencyCheck", instance.getDependencies());
+        ReportGenerator rg = new ReportGenerator("DependencyCheck",
+                instance.getDependencies(), instance.getAnalyzers());
+        rg.generateReports("./target/");
     }
 }

src/test/java/org/codesecure/dependencycheck/analyzer/JarAnalyzerTest.java

@@ -63,7 +63,8 @@ public class JarAnalyzerTest {
         instance.analyze(result);
         boolean found = false;
         for (Evidence e : result.getProductEvidence()) {
-            if (e.getName().equals("package-title") && e.getValue().equals("org.mortbay.http")) {
+            if (e.getName().equalsIgnoreCase("package-title")
+                    && e.getValue().equalsIgnoreCase("org.mortbay.http")) {
                 found = true;
                 break;
             }
@@ -72,7 +73,8 @@ public class JarAnalyzerTest {
 
         found = false;
         for (Evidence e : result.getVendorEvidence()) {
-            if (e.getName().equals("implementation-url") && e.getValue().equals("http://jetty.mortbay.org")) {
+            if (e.getName().equalsIgnoreCase("implementation-url")
+                    && e.getValue().equalsIgnoreCase("http://jetty.mortbay.org")) {
                 found = true;
                 break;
             }
@@ -81,7 +83,8 @@ public class JarAnalyzerTest {
 
         found = false;
         for (Evidence e : result.getVersionEvidence()) {
-            if (e.getName().equals("Implementation-Version") && e.getValue().equals("4.2.27")) {
+            if (e.getName().equalsIgnoreCase("Implementation-Version")
+                    && e.getValue().equalsIgnoreCase("4.2.27")) {
                 found = true;
                 break;
             }

src/test/java/org/codesecure/dependencycheck/data/cpe/BaseIndexTestCase.java

@@ -9,6 +9,8 @@ import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.URLDecoder;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 import junit.framework.TestCase;
@@ -30,8 +32,24 @@ public abstract class BaseIndexTestCase extends TestCase {
         ensureIndexExists();        
     }
     
+    protected static File getDataDirectory() throws IOException {
+        String fileName = Settings.getString(Settings.KEYS.CPE_INDEX);
+        String filePath = Index.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (exePath.getName().toLowerCase().endsWith(".jar")) {
+            exePath = exePath.getParentFile();
+        } else {
+            exePath = new File(".");
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        return path;
+    }
+    
     public static void ensureIndexExists() throws Exception {
-        String indexPath = Settings.getString(Settings.KEYS.CPE_INDEX);
+        //String indexPath = Settings.getString(Settings.KEYS.CPE_INDEX);
+        String indexPath = getDataDirectory().getCanonicalPath();
         java.io.File f = new File(indexPath);
         if (!f.exists()) {
             f.mkdirs();

src/test/java/org/codesecure/dependencycheck/data/cpe/CPEAnalyzerTest.java

@@ -10,11 +10,9 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import org.apache.lucene.index.CorruptIndexException;
-import org.apache.lucene.queryParser.ParseException;
+import org.apache.lucene.queryparser.classic.ParseException;
 import org.codesecure.dependencycheck.dependency.Dependency;
 import org.codesecure.dependencycheck.analyzer.JarAnalyzer;
-import org.codesecure.dependencycheck.dependency.Evidence;
-import org.codesecure.dependencycheck.dependency.Evidence.Confidence;
 import org.junit.Test;
 
 /**
@@ -100,11 +98,16 @@ public class CPEAnalyzerTest extends BaseIndexTestCase {
         JarAnalyzer jarAnalyzer = new JarAnalyzer();
         Dependency depends = new Dependency(file);
         jarAnalyzer.analyze(depends);
-        
+
+        File fileSpring = new File(this.getClass().getClassLoader().getResource("spring-core-2.5.5.jar").getPath());
+        Dependency spring = new Dependency(fileSpring);
+        jarAnalyzer.analyze(spring);
+
         CPEAnalyzer instance = new CPEAnalyzer();
         instance.open();
         String expResult = "cpe:/a:apache:struts:2.1.2";
         instance.determineCPE(depends);
+        instance.determineCPE(spring);
         instance.close();
         assertTrue("Incorrect match", depends.getIdentifiers().size() == 1);
         assertTrue("Incorrect match", depends.getIdentifiers().get(0).getValue().equals(expResult));
@@ -133,6 +136,7 @@ public class CPEAnalyzerTest extends BaseIndexTestCase {
         expResult = "cpe:/a:apache:struts:2.3.1.2";
         result = instance.searchCPE(vendor, product, version);
         assertEquals(expResult, result.get(0).getName());
+
         instance.close();
     }
 

src/test/java/org/codesecure/dependencycheck/data/cpe/EntryTest.java

@@ -35,7 +35,7 @@ public class EntryTest extends TestCase {
         String name = "cpe:/a:apache:struts:1.1:rc2";
         
         Entry instance = new Entry();
-        instance.setName(name);
+        instance.parseName(name);
         
         assertEquals(name,instance.getName());
         assertEquals("apache", instance.getVendor());

src/test/java/org/codesecure/dependencycheck/data/cpe/IndexIntegrationTest.java

@@ -40,43 +40,15 @@ public class IndexIntegrationTest extends BaseIndexTestCase {
     public void tearDown() {
     }
 
-    /**
-     * Test of open method, of class Index.
-     */
-    @Test
-    public void testOpen() {
-        System.out.println("open");
-        Index instance = new Index();
-        try {
-            instance.open();
-        } catch (IOException ex) {
-            fail(ex.getMessage());
-        }
-        instance.close();
-    }
-
-    /**
-     * Test of getDirectory method, of class Index.
-     */
-    @Test
-    public void testGetDirectory() throws Exception {
-        System.out.println("getDirectory");
-        Index index = new Index();
-        Directory result = index.getDirectory();
-        
-        String exp = File.separatorChar + "target" + File.separatorChar + "data" + File.separatorChar + "cpe";
-        // TODO review the generated test code and remove the default call to fail.
-        assertTrue(result.toString().contains(exp));
-    }
-
     /**
      * Test of update method, of class Index.
      */
     @Test
     public void testUpdate() throws Exception {
         System.out.println("update");
-        Index instance = new Index();
-        instance.update();
+        //deprecated
+        //Index instance = new Index();
+        //instance.update();
     }
 
     /**
@@ -85,8 +57,9 @@ public class IndexIntegrationTest extends BaseIndexTestCase {
     @Test
     public void testUpdateNeeded() throws Exception {
         System.out.println("updateNeeded");
-        Index instance = new Index();
-        instance.updateNeeded();
+        //deprecated
+        //Index instance = new Index();
+        //instance.updateNeeded();
         //if an exception is thrown this test fails. However, because it depends on the
         //  order of the tests what this will return I am just testing for the exception.
         //assertTrue(expResult < result);

src/test/java/org/codesecure/dependencycheck/data/cpe/IndexTest.java

@@ -0,0 +1,71 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.codesecure.dependencycheck.data.cpe;
+
+import java.io.File;
+import java.io.IOException;
+import org.apache.lucene.store.Directory;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+/**
+ *
+ * @author Jeremy Long (jeremy.long@gmail.com)
+ */
+public class IndexTest extends BaseIndexTestCase {
+
+    public IndexTest(String testCase) {
+        super(testCase);
+    }
+
+    @BeforeClass
+    public static void setUpClass() throws Exception {
+    }
+
+    @AfterClass
+    public static void tearDownClass() throws Exception {
+    }
+
+    @Before
+    public void setUp() {
+    }
+
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * Test of open method, of class Index.
+     */
+    @Test
+    public void testOpen() {
+        System.out.println("open");
+        Index instance = new Index();
+        try {
+            instance.open();
+        } catch (IOException ex) {
+            fail(ex.getMessage());
+        }
+        instance.close();
+    }
+
+    /**
+     * Test of getDirectory method, of class Index.
+     */
+    @Test
+    public void testGetDirectory() throws Exception {
+        System.out.println("getDirectory");
+        Index index = new Index();
+        Directory result = index.getDirectory();
+
+        String exp = File.separatorChar + "target" + File.separatorChar + "data" + File.separatorChar + "cpe";
+        // TODO review the generated test code and remove the default call to fail.
+        assertTrue(result.toString().contains(exp));
+    }
+}

src/test/java/org/codesecure/dependencycheck/data/nvdcve/BaseIndexTestCase.java

@@ -10,6 +10,8 @@ import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.URLDecoder;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 import junit.framework.TestCase;
@@ -31,8 +33,25 @@ public abstract class BaseIndexTestCase extends TestCase {
         ensureIndexExists();        
     }
     
+    
+    protected static File getDataDirectory() throws IOException {
+        String fileName = Settings.getString(Settings.KEYS.CVE_INDEX);
+        String filePath = Index.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (exePath.getName().toLowerCase().endsWith(".jar")) {
+            exePath = exePath.getParentFile();
+        } else {
+            exePath = new File( "." );
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        return path;
+    }
+        
     public static void ensureIndexExists() throws Exception {
-        String indexPath = Settings.getString(Settings.KEYS.CVE_INDEX);
+        //String indexPath = Settings.getString(Settings.KEYS.CVE_INDEX);
+        String indexPath = getDataDirectory().getCanonicalPath();
         java.io.File f = new File(indexPath);
         if (!f.exists()) {
             f.mkdirs();

src/test/java/org/codesecure/dependencycheck/data/nvdcve/IndexIntegrationTest.java

@@ -4,11 +4,8 @@
  */
 package org.codesecure.dependencycheck.data.nvdcve;
 
-import java.io.File;
+
 import java.util.Map;
-import org.apache.lucene.store.Directory;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
 import org.junit.*;
 
 /**
@@ -16,7 +13,7 @@ import org.junit.*;
  * @author Jeremy
  */
 public class IndexIntegrationTest extends BaseIndexTestCase {
-    
+
     public IndexIntegrationTest(String testName) {
         super(testName);
     }
@@ -28,11 +25,11 @@ public class IndexIntegrationTest extends BaseIndexTestCase {
     @AfterClass
     public static void tearDownClass() throws Exception {
     }
-    
+
     @Before
     public void setUp() {
     }
-    
+
     @After
     public void tearDown() {
     }
@@ -45,19 +42,7 @@ public class IndexIntegrationTest extends BaseIndexTestCase {
         System.out.println("retrieveCurrentTimestampFromWeb");
         Index instance = new Index();
         Map<String, Index.NvdCveUrl> result = instance.retrieveCurrentTimestampsFromWeb();
-        assertEquals(12, result.size());        
-    }
-
-    /**
-     * Test of getDirectory method, of class Index.
-     */
-    @Test
-    public void testGetDirectory() throws Exception {
-        System.out.println("getDirectory");
-        Index instance = new Index();
-        String exp = File.separatorChar + "target" + File.separatorChar + "data" + File.separatorChar + "cve";
-        Directory result = instance.getDirectory();
-        assertTrue(result.toString().contains(exp));
+        assertEquals(12, result.size());
     }
 
     /**
@@ -81,5 +66,4 @@ public class IndexIntegrationTest extends BaseIndexTestCase {
         //if an exception is thrown this test fails. However, because it depends on the
         //  order of the tests what this will return I am just testing for the exception.
     }
-
 }

src/test/java/org/codesecure/dependencycheck/data/nvdcve/IndexTest.java

@@ -0,0 +1,50 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.codesecure.dependencycheck.data.nvdcve;
+
+import java.io.File;
+import org.apache.lucene.store.Directory;
+import static org.junit.Assert.assertTrue;
+import org.junit.*;
+
+/**
+ *
+ * @author Jeremy
+ */
+public class IndexTest extends BaseIndexTestCase {
+
+    public IndexTest(String testName) {
+        super(testName);
+    }
+
+    @BeforeClass
+    public static void setUpClass() throws Exception {
+    }
+
+    @AfterClass
+    public static void tearDownClass() throws Exception {
+    }
+
+    @Before
+    public void setUp() {
+    }
+
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * Test of getDirectory method, of class Index.
+     */
+    @Test
+    public void testGetDirectory() throws Exception {
+        System.out.println("getDirectory");
+        Index instance = new Index();
+        String exp = File.separatorChar + "target" + File.separatorChar + "data" + File.separatorChar + "cve";
+        Directory result = instance.getDirectory();
+       
+        assertTrue(result.toString().contains(exp));
+    }
+}

src/test/java/org/codesecure/dependencycheck/dependency/DependencyTest.java

@@ -249,15 +249,13 @@ public class DependencyTest {
         System.out.println("addIdentifier");
         String type = "cpe";
         String value = "cpe:/a:apache:struts:2.1.2";
-        String title = "Apache Struts 2.1.2";
         String url = "http://somewhere";
         Dependency instance = new Dependency();
-        instance.addIdentifier(type, value, title, url);
+        instance.addIdentifier(type, value, url);
         assertEquals(1,instance.getIdentifiers().size());
         Identifier i = instance.getIdentifiers().get(0);
         assertEquals(type,i.getType());
         assertEquals(value, i.getValue());
-        assertEquals(title, i.getTitle());
         assertEquals(url, i.getUrl());
     }
 

src/test/java/org/codesecure/dependencycheck/utils/ChecksumTest.java

@@ -5,7 +5,7 @@
 package org.codesecure.dependencycheck.utils;
 
 import java.io.File;
-import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.security.NoSuchAlgorithmException;
 import junit.framework.TestCase;
 import org.junit.Test;
@@ -66,7 +66,7 @@ public class ChecksumTest extends TestCase {
         boolean exceptionThrown = false;
         try {
             byte[] result = Checksum.getChecksum(algorithm, file);
-        } catch (FileNotFoundException ex) {
+        } catch (IOException ex) {
             exceptionThrown = true;
         }
         assertTrue(exceptionThrown);