Fixed merge conflict

Former-commit-id: 4a4bfd553bd5b91c53e87f7e327beb0a605bc21f

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

@@ -127,7 +127,7 @@ public class App {
             } catch (IOException ex) {
                 Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an IO error while attempting to generate the report.");
                 Logger.getLogger(App.class.getName()).log(Level.FINE, null, ex);
-            } catch (Exception ex) {
+            } catch (Throwable ex) {
                 Logger.getLogger(App.class.getName()).log(Level.SEVERE, "There was an error while attempting to generate the report.");
                 Logger.getLogger(App.class.getName()).log(Level.FINE, null, ex);
             }

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

@@ -299,13 +299,13 @@ public class Engine {
                     final String msg = String.format("Initializing %s", a.getName());
                     Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
                     a.initialize();
-                } catch (Exception ex) {
+                } catch (Throwable ex) {
                     final String msg = String.format("Exception occurred initializing %s.", a.getName());
                     Logger.getLogger(Engine.class.getName()).log(Level.SEVERE, msg);
                     Logger.getLogger(Engine.class.getName()).log(Level.FINE, null, ex);
                     try {
                         a.close();
-                    } catch (Exception ex1) {
+                    } catch (Throwable ex1) {
                         Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex1);
                     }
                 }
@@ -354,7 +354,7 @@ public class Engine {
                 Logger.getLogger(Engine.class.getName()).log(Level.FINE, msg);
                 try {
                     a.close();
-                } catch (Exception ex) {
+                } catch (Throwable ex) {
                     Logger.getLogger(Engine.class.getName()).log(Level.FINEST, null, ex);
                 }
             }

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

@@ -175,9 +175,10 @@ public class ArchiveAnalyzer extends AbstractAnalyzer implements Analyzer {
     public void close() throws Exception {
         if (tempFileLocation != null && tempFileLocation.exists()) {
             Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.FINE, "Attempting to delete temporary files");
-            boolean success = FileUtils.delete(tempFileLocation);
+            final boolean success = FileUtils.delete(tempFileLocation);
             if (!success) {
-                Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING, "Failed to delete some temporary files, see the log for more details");
+                Logger.getLogger(ArchiveAnalyzer.class.getName()).log(Level.WARNING,
+                        "Failed to delete some temporary files, see the log for more details");
             }
         }
     }

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

@@ -180,14 +180,14 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
             if (fos != null) {
                 try {
                     fos.close();
-                } catch (Exception e) {
+                } catch (Throwable e) {
                     LOG.fine("Error closing output stream");
                 }
             }
             if (is != null) {
                 try {
                     is.close();
-                } catch (Exception e) {
+                } catch (Throwable e) {
                     LOG.fine("Error closing input stream");
                 }
             }
@@ -206,9 +206,10 @@ public class AssemblyAnalyzer extends AbstractAnalyzer {
                 grokAssemblyExe = null;
                 throw new AnalysisException("Could not execute .NET AssemblyAnalyzer");
             }
-        } catch (Exception e) {
+        } catch (Throwable e) {
-            LOG.warning("An error occured with the .NET AssemblyAnalyzer, please see the log for more details.");
+            LOG.warning("An error occured with the .NET AssemblyAnalyzer; "
-            LOG.fine("Could not execute GrokAssembly " + e.getMessage());
+                    + "this can be ignored unless you are scanning .NET dlls. Please see the log for more details.");
+            LOG.log(Level.FINE, "Could not execute GrokAssembly {0}", e.getMessage());
             throw new AnalysisException("An error occured with the .NET AssemblyAnalyzer", e);
         }
 

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

@@ -25,6 +25,7 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.io.OutputStream;
 import java.io.Reader;
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
@@ -393,11 +394,9 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
         } catch (IOException ex) {
             Logger.getLogger(JarAnalyzer.class.getName()).log(Level.SEVERE, null, ex);
         } finally {
-            try {
+            closeStream(bos);
-                input.close();
+            closeStream(fos);
-            } catch (IOException ex) {
+            closeStream(input);
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.SEVERE, null, ex);
-            }
         }
         Model model = null;
         FileInputStream fis = null;
@@ -423,17 +422,41 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
             Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, null, ex);
             throw ex;
         } finally {
-            if (fis != null) {
+            closeStream(fis);
-                try {
-                    fis.close();
-                } catch (IOException ex) {
-                    Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, null, ex);
-                }
-            }
         }
         return model;
     }
 
+    /**
+     * Silently closes an input stream ignoring errors.
+     *
+     * @param stream an input stream to close
+     */
+    private void closeStream(InputStream stream) {
+        if (stream != null) {
+            try {
+                stream.close();
+            } catch (IOException ex) {
+                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+            }
+        }
+    }
+
+    /**
+     * Silently closes an output stream ignoring errors.
+     *
+     * @param stream an output stream to close
+     */
+    private void closeStream(OutputStream stream) {
+        if (stream != null) {
+            try {
+                stream.close();
+            } catch (IOException ex) {
+                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINEST, null, ex);
+            }
+        }
+    }
+
     /**
      * Retrieves the specified POM from a jar file and converts it to a Model.
      *
@@ -938,9 +961,10 @@ public class JarAnalyzer extends AbstractAnalyzer implements Analyzer {
     public void close() {
         if (tempFileLocation != null && tempFileLocation.exists()) {
             Logger.getLogger(JarAnalyzer.class.getName()).log(Level.FINE, "Attempting to delete temporary files");
-            boolean success = FileUtils.delete(tempFileLocation);
+            final boolean success = FileUtils.delete(tempFileLocation);
             if (!success) {
-                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING, "Failed to delete some temporary files, see the log for more details");
+                Logger.getLogger(JarAnalyzer.class.getName()).log(Level.WARNING,
+                        "Failed to delete some temporary files, see the log for more details");
             }
         }
     }

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

@@ -17,13 +17,12 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import java.io.FileInputStream;
 import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
-
 import org.owasp.dependencycheck.Engine;
+import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
 import org.owasp.dependencycheck.data.nuget.NugetPackage;
 import org.owasp.dependencycheck.data.nuget.NuspecParser;
 import org.owasp.dependencycheck.data.nuget.XPathNuspecParser;
@@ -128,7 +127,7 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
                 if (fis != null) {
                     try {
                         fis.close();
-                    } catch (Exception e) {
+                    } catch (Throwable e) {
                         LOGGER.fine("Error closing input stream");
                     }
                 }
@@ -143,7 +142,7 @@ public class NuspecAnalyzer extends AbstractAnalyzer {
             if (np.getTitle() != null) {
                 dependency.getProductEvidence().addEvidence("nuspec", "title", np.getTitle(), Confidence.MEDIUM);
             }
-        } catch (Exception e) {
+        } catch (Throwable e) {
             throw new AnalysisException(e);
         }
     }

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

@@ -137,7 +137,7 @@ public class NexusSearch {
              * Nexus. This is useful upstream for recovery, so we just re-throw it
              */
             throw fnfe;
-        } catch (Exception e) {
+        } catch (Throwable e) {
             // Anything else is jacked-up XML stuff that we really can't recover
             // from well
             throw new IOException(e.getMessage(), e);
@@ -151,7 +151,7 @@ public class NexusSearch {
      */
     public boolean preflightRequest() {
         try {
-            HttpURLConnection conn = URLConnectionFactory.createHttpURLConnection(new URL(rootURL, "status"));
+            final HttpURLConnection conn = URLConnectionFactory.createHttpURLConnection(new URL(rootURL, "status"));
             conn.addRequestProperty("Accept", "application/xml");
             conn.connect();
             if (conn.getResponseCode() != 200) {
@@ -164,7 +164,7 @@ public class NexusSearch {
                 LOGGER.warning("Expected root node name of status, got " + doc.getDocumentElement().getNodeName());
                 return false;
             }
-        } catch (Exception e) {
+        } catch (Throwable e) {
             return false;
         }
 

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

@@ -18,12 +18,10 @@
 package org.owasp.dependencycheck.data.nuget;
 
 import java.io.InputStream;
-
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.xpath.XPath;
 import javax.xml.xpath.XPathConstants;
 import javax.xml.xpath.XPathFactory;
-
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 
@@ -33,6 +31,7 @@ import org.w3c.dom.Node;
  * @author colezlaw
  */
 public class XPathNuspecParser implements NuspecParser {
+
     /**
      * Gets the string value of a node or null if it's not present
      *
@@ -71,11 +70,11 @@ public class XPathNuspecParser implements NuspecParser {
             nuspec.setId(xpath.evaluate("/package/metadata/id", d));
             nuspec.setVersion(xpath.evaluate("/package/metadata/version", d));
             nuspec.setAuthors(xpath.evaluate("/package/metadata/authors", d));
-            nuspec.setOwners(getOrNull((Node) xpath.evaluate("/package/metadata/owners",  d, XPathConstants.NODE)));
+            nuspec.setOwners(getOrNull((Node) xpath.evaluate("/package/metadata/owners", d, XPathConstants.NODE)));
-            nuspec.setLicenseUrl(getOrNull((Node) xpath.evaluate("/package/metadata/licenseUrl",  d, XPathConstants.NODE)));
+            nuspec.setLicenseUrl(getOrNull((Node) xpath.evaluate("/package/metadata/licenseUrl", d, XPathConstants.NODE)));
-            nuspec.setTitle(getOrNull((Node) xpath.evaluate("/package/metadata/title",  d, XPathConstants.NODE)));
+            nuspec.setTitle(getOrNull((Node) xpath.evaluate("/package/metadata/title", d, XPathConstants.NODE)));
             return nuspec;
-        } catch (Exception e) {
+        } catch (Throwable e) {
             throw new NuspecParseException("Unable to parse nuspec", e);
         }
     }

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

@@ -300,7 +300,7 @@ public class CveDB {
      * @throws DatabaseException thrown when there is an error retrieving the data from the DB
      */
     public Set<Pair<String, String>> getVendorProductList() throws DatabaseException {
-        HashSet data = new HashSet<Pair<String, String>>();
+        final HashSet data = new HashSet<Pair<String, String>>();
         ResultSet rs = null;
         PreparedStatement ps = null;
         try {

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

@@ -116,7 +116,7 @@ class DriverShim implements Driver {
         Method m = null;
         try {
             m = driver.getClass().getMethod("getParentLogger");
-        } catch (Exception e) {
+        } catch (Throwable e) {
             throw new SQLFeatureNotSupportedException();
         }
         if (m != null) {

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

@@ -292,7 +292,7 @@ public class StandardUpdate {
         if (cveDB != null) {
             try {
                 cveDB.close();
-            } catch (Exception ignore) {
+            } catch (Throwable ignore) {
                 Logger.getLogger(StandardUpdate.class.getName()).log(Level.FINEST, "Error closing the cveDB", ignore);
             }
         }

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

@@ -85,13 +85,13 @@ public final class Downloader {
             while ((bytesRead = reader.read(buffer)) > 0) {
                 writer.write(buffer, 0, bytesRead);
             }
-        } catch (Exception ex) {
+        } catch (Throwable ex) {
             throw new DownloadFailedException("Error saving downloaded file.", ex);
         } finally {
             if (writer != null) {
                 try {
                     writer.close();
-                } catch (Exception ex) {
+                } catch (Throwable ex) {
                     Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
                             "Error closing the writer in Downloader.", ex);
                 }
@@ -99,7 +99,7 @@ public final class Downloader {
             if (reader != null) {
                 try {
                     reader.close();
-                } catch (Exception ex) {
+                } catch (Throwable ex) {
                     Logger.getLogger(Downloader.class.getName()).log(Level.FINEST,
                             "Error closing the reader in Downloader.", ex);
                 }

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

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

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

@@ -20,9 +20,12 @@ package org.owasp.dependencycheck.utils;
 /**
  * A generic pair of elements.
  *
+ * @param <L> the type for the left element in the pair
+ * @param <R> the type for the right element in the pair
+ *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class Pair<K, V> {
+public class Pair<L, R> {
 
     /**
      * Constructs a new empty pair.
@@ -36,52 +39,52 @@ public class Pair<K, V> {
      * @param left the value for the left pair
      * @param right the value for the right pair
      */
-    public Pair(K left, V right) {
+    public Pair(L left, R right) {
         this.left = left;
         this.right = right;
     }
     /**
      * The left element of the pair.
      */
-    private K left = null;
+    private L left = null;
 
     /**
-     * Get the value of left
+     * Get the value of left.
      *
      * @return the value of left
      */
-    public K getLeft() {
+    public L getLeft() {
         return left;
     }
 
     /**
-     * Set the value of left
+     * Set the value of left.
      *
      * @param left new value of left
      */
-    public void setLeft(K left) {
+    public void setLeft(L left) {
         this.left = left;
     }
     /**
      * The right element of the pair.
      */
-    private V right = null;
+    private R right = null;
 
     /**
-     * Get the value of right
+     * Get the value of right.
      *
      * @return the value of right
      */
-    public V getRight() {
+    public R getRight() {
         return right;
     }
 
     /**
-     * Set the value of right
+     * Set the value of right.
      *
      * @param right new value of right
      */
-    public void setRight(V right) {
+    public void setRight(R right) {
         this.right = right;
     }
 

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

@@ -146,7 +146,7 @@ public final class Settings {
          */
         public static final String ANALYZER_NEXUS_URL = "analyzer.nexus.url";
         /**
-         * The properties key for using the proxy to reach Nexus
+         * The properties key for using the proxy to reach Nexus.
          */
         public static final String ANALYZER_NEXUS_PROXY = "analyzer.nexus.proxy";
         /**

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

@@ -32,7 +32,7 @@ import java.net.URL;
  *
  * @author Jeremy Long <jeremy.long@owasp.org>
  */
-public class URLConnectionFactory {
+public final class URLConnectionFactory {
 
     /**
      * Private constructor for this factory.

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

@@ -27,6 +27,7 @@ import java.util.logging.Logger;
 
 import org.junit.After;
 import org.junit.Assume;
+import static org.junit.Assume.assumeFalse;
 import org.junit.Before;
 import org.junit.Test;
 import org.owasp.dependencycheck.analyzer.exception.AnalysisException;
@@ -53,7 +54,7 @@ public class AssemblyAnalyzerTest {
      * @throws Exception if anything goes sideways
      */
     @Before
-    public void setUp()  {
+    public void setUp() {
         try {
             analyzer = new AssemblyAnalyzer();
             analyzer.initialize();

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

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

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

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

dependency-check-maven/src/main/java/org/owasp/dependencycheck/maven/DependencyCheckMojo.java

@@ -340,7 +340,7 @@ public class DependencyCheckMojo extends AbstractMojo implements MavenMultiPageR
             Logger.getLogger(DependencyCheckMojo.class.getName()).log(Level.SEVERE,
                     "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
             Logger.getLogger(DependencyCheckMojo.class.getName()).log(Level.FINE, null, ex);
-        } catch (Exception ex) {
+        } catch (Throwable ex) {
             Logger.getLogger(DependencyCheckMojo.class.getName()).log(Level.SEVERE,
                     "Unexpected exception occurred during analysis; please see the verbose error log for more details.");
             Logger.getLogger(DependencyCheckMojo.class.getName()).log(Level.FINE, null, ex);

pom.xml

@@ -73,7 +73,7 @@ Copyright (c) 2012 - Jeremy Long
                 <role>developer</role>
             </roles>
             <properties>
-              <twitter>@willathome</twitter>
+                <twitter>@willathome</twitter>
             </properties>
         </developer>
     </developers>

src/site/site.xml

@@ -20,7 +20,7 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
     <skin>
         <groupId>org.apache.maven.skins</groupId>
         <artifactId>maven-fluido-skin</artifactId>
-        <version>1.3.0</version>
+        <version>1.3.1</version>
     </skin>
     <custom>
         <fluidoSkin>
@@ -37,6 +37,7 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
                 <showUser>true</showUser>
                 <showFollowers>true</showFollowers>
             </twitter>
+            <googlePlusOne />
         </fluidoSkin>
     </custom>
     <bannerLeft>
@@ -44,6 +45,21 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
     </bannerLeft>
     <publishDate position="right" />
     <version position="right" />
+    <poweredBy>
+        <logo name="Maven" href="http://maven.apache.org/"
+              title="built with maven"
+              alt="built with maven"
+              img="http://jeremylong.github.io/DependencyCheck/images/logos/maven-feather.png"/>
+        <logo name="IntelliJ" href="http://maven.apache.org/"
+              title="developed using" width="170px"
+              alt="developed using"
+              img="http://jeremylong.github.io/DependencyCheck/images/logos/logo_intellij_idea.png"/>
+        <logo name="Cloudbees" href="http://www.cloudbees.com/"
+              title="built on cloudbees"
+              alt="built on cloudbees"
+              img="http://jeremylong.github.io/DependencyCheck/images/logos/Button-Built-on-CB-1.png"/>
+    </poweredBy>
+
     <body>
         <head>
             <style type="text/css">
@@ -59,13 +75,13 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
             <item name="False Positives" href="./suppression.html">
                 <description>Suppressing False Positives</description>
             </item>
-			<item name="Project Presentation (pptx)" href="./dependency-check.pptx">
+            <item name="Project Presentation (pptx)" href="./dependency-check.pptx">
                 <description>PowerPoint Deck</description>
             </item>
-			<item name="Project Presentation (pdf)" href="./dependency-check.pdf">
+            <item name="Project Presentation (pdf)" href="./dependency-check.pdf">
                 <description>PowerPoint Deck</description>
             </item>
-			<item name="Sample Report" href="./SampleReport.html">
+            <item name="Sample Report" href="./SampleReport.html">
                 <description>Sample Report</description>
             </item>
         </menu>
@@ -86,6 +102,6 @@ Copyright (c) 2013 Jeremy Long. All Rights Reserved.
                 <description>A Jenkins plugin for dependency-check.</description>
             </item>
         </menu>
-        <footer/>
+        <footer>Copyright © 2012-2014 Jeremy Long. All Rights Reserved.</footer>
     </body>
 </project>