bug fixes

Former-commit-id: a415f5e84dbe7c887a20a8acd18403655c82f9be

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-0.2.3.jar -h
+$ java -jar DependencyCheck-0.2.3.1.jar -h
-$ java -jar DependencyCheck-0.2.3.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-0.2.3.1.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>0.2.3</version>
+    <version>0.2.3.1</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>
@@ -451,5 +451,14 @@ 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

@@ -28,7 +28,6 @@ import java.util.logging.LogManager;
 import java.util.logging.Logger;
 import javax.xml.parsers.ParserConfigurationException;
 import org.apache.commons.cli.ParseException;
-import org.codesecure.dependencycheck.analyzer.AnalysisPhase;
 import org.codesecure.dependencycheck.data.cpe.xml.Importer;
 import org.codesecure.dependencycheck.reporting.ReportGenerator;
 import org.codesecure.dependencycheck.dependency.Dependency;

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

@@ -195,7 +195,7 @@ public class Engine {
                 try {
                     a.initialize();
                 } catch (Exception ex) {
-                    Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, 
+                    Logger.getLogger(Engine.class.getName()).log(Level.SEVERE,
                             "Exception occured initializing " + a.getName() + ".", ex);
                     try {
                         a.close();
@@ -255,7 +255,7 @@ public class Engine {
             try {
                 source.update();
             } catch (UpdateException ex) {
-                Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, 
+                Logger.getLogger(Engine.class.getName()).log(Level.SEVERE,
                         "Unable to update " + source.getClass().getName(), ex);
             }
         }

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) {
@@ -615,4 +616,15 @@ 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

@@ -149,23 +149,11 @@ 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());
@@ -186,14 +174,14 @@ public class CPEAnalyzer implements org.codesecure.dependencycheck.analyzer.Anal
 
 
             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 +191,7 @@ 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 +203,7 @@ 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

@@ -45,17 +45,12 @@ public class Entry {
     public static Entry parse(Document doc) {
         Entry entry = new Entry();
         try {
-            entry.setName(doc.get(Fields.NAME));
+            entry.parseName(doc.get(Fields.NAME));
             entry.setTitle(doc.get(Fields.TITLE));
         } 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;
     }
     /**
@@ -95,15 +90,12 @@ public class Entry {
     }
 
     /**
-     * Set the value of name and calls parseName to obtain the
+     * Set the value of name
-     * vendor:product:version:revision
      *
      * @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.
@@ -310,15 +302,17 @@ 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 {
+    public void parseName(String cpeName) throws UnsupportedEncodingException {
-        if (name != null && name.length() > 7) {
+        this.name = cpeName;
-            String[] data = name.substring(7).split(":");
+        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/Index.java

@@ -100,6 +100,11 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
         }
         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;
     }
 
@@ -113,6 +118,7 @@ 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);

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

@@ -27,7 +27,6 @@ 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 +45,8 @@ 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);
     }
 

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

@@ -98,6 +98,11 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
         }
         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;
     }
 

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/NvdCveParser.java

@@ -23,14 +23,17 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
+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.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.nvdcve.Fields;
 import org.codesecure.dependencycheck.data.nvdcve.Index;
 
@@ -40,6 +43,19 @@ 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
@@ -164,10 +180,27 @@ 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) {
+    private void addVulnerableCpe(String cpe, Document doc) throws CorruptIndexException, IOException {
         Field vulnerable = new Field(Fields.VULNERABLE_CPE, cpe, Field.Store.NO, Field.Index.ANALYZED);
         vulnerable.setIndexOptions(IndexOptions.DOCS_ONLY);
         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);
+            cpeEntry.setNvdId("0");
+            cpeEntry.setTitle(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/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/utils/CliParser.java

@@ -326,7 +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/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);*/
@@ -312,7 +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 $dependency.analysisExceptions)
@@ -340,7 +340,7 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
                             </div>
                         #end
                         #set($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>
@@ -381,7 +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/data/cpe/CPEAnalyzerTest.java

@@ -98,11 +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));
@@ -131,7 +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());