Merge branch 'master' into reporting

Conflicts:
	dependency-check-cli/pom.xml

Former-commit-id: f381a7191effbe65f852c76e5e19033e4a264171

.gitignore

@@ -1,4 +1,6 @@
 */target/**
+# IntelliJ test run side-effects
+dependency-check-core/data/
 # Intellij project files
 *.iml
 *.ipr

dependency-check-cli/pom.xml

@@ -198,7 +198,7 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
                 <version>${reporting.javadoc-plugin.version}</version>
                 <configuration>
                     <failOnError>false</failOnError>
-                    <bottom>Copyright© 2012-15 Jeremy Long. All Rights Reserved.</bottom>
+                    <bottom>Copyright<EFBFBD> 2012-15 Jeremy Long. All Rights Reserved.</bottom>
                 </configuration>
                 <reportSets>
                     <reportSet>
@@ -333,7 +333,6 @@ Copyright (c) 2012 - Jeremy Long. All Rights Reserved.
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
-            <version>${logback.version}</version>
         </dependency>
     </dependencies>
 </project>

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

@@ -351,22 +351,27 @@ public class App {
         }
     }
 
+    /**
+     * Creates a file appender and adds it to logback.
+     *
+     * @param verboseLog the path to the verbose log file
+     */
     private void prepareLogger(String verboseLog) {
-        StaticLoggerBinder loggerBinder = StaticLoggerBinder.getSingleton();
+        final StaticLoggerBinder loggerBinder = StaticLoggerBinder.getSingleton();
-        LoggerContext context = (LoggerContext) loggerBinder.getLoggerFactory();
+        final LoggerContext context = (LoggerContext) loggerBinder.getLoggerFactory();
 
         final PatternLayoutEncoder encoder = new PatternLayoutEncoder();
         encoder.setPattern("%d %C:%L%n%-5level - %msg%n");
         encoder.setContext(context);
         encoder.start();
-        FileAppender fa = new FileAppender();
+        final FileAppender fa = new FileAppender();
         fa.setAppend(true);
         fa.setEncoder(encoder);
         fa.setContext(context);
         fa.setFile(verboseLog);
         final File f = new File(verboseLog);
         String name = f.getName();
-        int i = name.lastIndexOf('.');
+        final int i = name.lastIndexOf('.');
         if (i > 1) {
             name = name.substring(0, i);
         }

dependency-check-core/pom.xml

@@ -372,8 +372,13 @@ Copyright (c) 2012 Jeremy Long. All Rights Reserved.
         </dependency>
         <!-- Set this to test so that each project that uses this has to have its own implementation of SLF4J -->
         <dependency>
-            <groupId>org.slf4j</groupId>
+            <groupId>ch.qos.logback</groupId>
-            <artifactId>slf4j-simple</artifactId>
+            <artifactId>logback-core</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
             <scope>test</scope>
         </dependency>
         <!-- For the CAL10N support -->

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

@@ -17,13 +17,6 @@
  */
 package org.owasp.dependencycheck;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.EnumMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
 import org.owasp.dependencycheck.analyzer.AnalysisPhase;
 import org.owasp.dependencycheck.analyzer.Analyzer;
 import org.owasp.dependencycheck.analyzer.AnalyzerService;
@@ -43,6 +36,14 @@ import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.io.File;
+import java.util.ArrayList;
+import java.util.EnumMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+
 /**
  * Scans files, directories, etc. for Dependencies. Analyzers are loaded and used to process the files found by the scan, if a
  * file is encountered and an Analyzer is associated with the file type then the file is turned into a dependency.
@@ -167,7 +168,6 @@ public class Engine {
      *
      * @param paths an array of paths to files or directories to be analyzed
      * @return the list of dependencies scanned
-     *
      * @since v0.3.2.5
      */
     public List<Dependency> scan(String[] paths) {
@@ -200,7 +200,6 @@ public class Engine {
      *
      * @param files an array of paths to files or directories to be analyzed.
      * @return the list of dependencies
-     *
      * @since v0.3.2.5
      */
     public List<Dependency> scan(File[] files) {
@@ -220,7 +219,6 @@ public class Engine {
      *
      * @param files a set of paths to files or directories to be analyzed
      * @return the list of dependencies scanned
-     *
      * @since v0.3.2.5
      */
     public List<Dependency> scan(Set<File> files) {
@@ -240,7 +238,6 @@ public class Engine {
      *
      * @param files a set of paths to files or directories to be analyzed
      * @return the list of dependencies scanned
-     *
      * @since v0.3.2.5
      */
     public List<Dependency> scan(List<File> files) {
@@ -260,9 +257,7 @@ public class Engine {
      *
      * @param file the path to a file or directory to be analyzed
      * @return the list of dependencies scanned
-     *
      * @since v0.3.2.4
-     *
      */
     public List<Dependency> scan(File file) {
         if (file.exists()) {
@@ -324,7 +319,7 @@ public class Engine {
         Dependency dependency = null;
         if (supportsExtension(extension)) {
             dependency = new Dependency(file);
-            if (extension == null ? fileName == null : extension.equals(fileName)) {
+            if (extension.equals(fileName)) {
                 dependency.setFileExtension(extension);
             }
             dependencies.add(dependency);
@@ -333,7 +328,10 @@ public class Engine {
     }
 
     /**
-     * Runs the analyzers against all of the dependencies.
+     * Runs the analyzers against all of the dependencies. Since the mutable dependencies list is exposed via
+     * {@link #getDependencies()}, this method iterates over a copy of the dependencies list. Thus, the potential for
+     * {@link java.util.ConcurrentModificationException}s is avoided, and analyzers may safely add or remove entries
+     * from the dependencies list.
      */
     public void analyzeDependencies() {
         boolean autoUpdate = true;

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

@@ -42,7 +42,6 @@ import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Evidence;
 import org.owasp.dependencycheck.utils.DCResources;
 import org.owasp.dependencycheck.utils.Settings;
-import org.slf4j.Logger;
 import org.slf4j.cal10n.LocLogger;
 import org.slf4j.cal10n.LocLoggerFactory;
 import org.w3c.dom.Document;
@@ -79,15 +78,15 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Message Conveyer
      */
-    private IMessageConveyor messageConveyer = new MessageConveyor(Locale.getDefault());
+    private final IMessageConveyor MESSAGE_CONVERYOR = new MessageConveyor(Locale.getDefault());
     /**
      * LocLoggerFactory for localized logger
      */
-    private LocLoggerFactory llFactory = new LocLoggerFactory(messageConveyer);
+    private final LocLoggerFactory LLFACTORY = new LocLoggerFactory(MESSAGE_CONVERYOR);
     /**
      * Logger
      */
-    private LocLogger LOGGER = llFactory.getLocLogger(AssemblyAnalyzer.class);
+    private final LocLogger LOGGER = LLFACTORY.getLocLogger(AssemblyAnalyzer.class);
 
     /**
      * Builds the beginnings of a List for ProcessBuilder

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

@@ -35,9 +35,8 @@ import org.owasp.dependencycheck.utils.Settings;
 import org.owasp.dependencycheck.utils.UrlStringUtils;
 
 /**
- * Used to analyze Autoconf input files named configure.ac or configure.in.
+ * Used to analyze Autoconf input files named configure.ac or configure.in. Files simply named "configure" are also analyzed,
- * Files simply named "configure" are also analyzed, assuming they are generated
+ * assuming they are generated by Autoconf, and contain certain special package descriptor variables.
- * by Autoconf, and contain certain special package descriptor variables.
  *
  * @author Dale Visser <dvisser@ida.org>
  * @see <a href="https://www.gnu.org/software/autoconf/">Autoconf - GNU Project - Free Software Foundation (FSF)</a>
@@ -85,10 +84,11 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
      * Matches AC_INIT statement in configure.ac file.
      */
     private static final Pattern AC_INIT_PATTERN;
+
     static {
         // each instance of param or sep_param has a capture group
         final String param = "\\[{0,2}(.+?)\\]{0,2}";
-		final String sep_param = "\\s*,\\s*" + param;
+        final String sepParam = "\\s*,\\s*" + param;
         // Group 1: Package
         // Group 2: Version
         // Group 3: optional
@@ -98,8 +98,8 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
         // Group 7: optional
         // Group 8: URL (if it exists)
         AC_INIT_PATTERN = Pattern.compile(String.format(
-				"AC_INIT\\(%s%s(%s)?(%s)?(%s)?\\s*\\)", param, sep_param,
+                "AC_INIT\\(%s%s(%s)?(%s)?(%s)?\\s*\\)", param, sepParam,
-				sep_param, sep_param, sep_param), Pattern.DOTALL
+                sepParam, sepParam, sepParam), Pattern.DOTALL
                 | Pattern.CASE_INSENSITIVE);
     }
 
@@ -133,8 +133,7 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
     }
 
     /**
-	 * Returns the key used in the properties file to reference the analyzer's
+     * Returns the key used in the properties file to reference the analyzer's enabled property.
-	 * enabled property.
      *
      * @return the analyzer's enabled property setting key
      */
@@ -174,6 +173,13 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
         }
     }
 
+    /**
+     * Extracts evidence from the configuration.
+     *
+     * @param dependency the dependency being analyzed
+     * @param name the name of the source of evidence
+     * @param contents the contents to analyze for evidence
+     */
     private void extractConfigureScriptEvidence(Dependency dependency,
             final String name, final String contents) {
         final Matcher matcher = PACKAGE_VAR.matcher(contents);
@@ -198,6 +204,13 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
         }
     }
 
+    /**
+     * Retrieves the contents of a given file.
+     *
+     * @param actualFile the file to read
+     * @return the contents of the file
+     * @throws AnalysisException thrown if there is an IO Exception
+     */
     private String getFileContents(final File actualFile)
             throws AnalysisException {
         String contents = "";
@@ -210,6 +223,13 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
         return contents;
     }
 
+    /**
+     * Gathers evidence from a given file
+     *
+     * @param dependency the dependency to add evidence to
+     * @param name the source of the evidence
+     * @param contents the evidence to analyze
+     */
     private void gatherEvidence(Dependency dependency, final String name,
             String contents) {
         final Matcher matcher = AC_INIT_PATTERN.matcher(contents);
@@ -243,8 +263,7 @@ public class AutoconfAnalyzer extends AbstractFileTypeAnalyzer {
     /**
      * Initializes the file type analyzer.
      *
-	 * @throws Exception
+     * @throws Exception thrown if there is an exception during initialization
-	 *             thrown if there is an exception during initialization
      */
     @Override
     protected void initializeFileTypeAnalyzer() throws Exception {

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

@@ -657,6 +657,9 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
 
             final String source = "Manifest";
 
+            String specificationVersion = null;
+            boolean hasImplementationVersion = false;
+
             for (Entry<Object, Object> entry : atts.entrySet()) {
                 String key = entry.getKey().toString();
                 String value = atts.getValue(key);
@@ -670,8 +673,11 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                     productEvidence.addEvidence(source, key, value, Confidence.HIGH);
                     addMatchingValues(classInformation, value, productEvidence);
                 } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VERSION.toString())) {
+                    hasImplementationVersion = true;
                     foundSomething = true;
                     versionEvidence.addEvidence(source, key, value, Confidence.HIGH);
+                } else if ("specification-version".equalsIgnoreCase(key)) {
+                    specificationVersion = key;
                 } else if (key.equalsIgnoreCase(Attributes.Name.IMPLEMENTATION_VENDOR.toString())) {
                     foundSomething = true;
                     vendorEvidence.addEvidence(source, key, value, Confidence.HIGH);
@@ -724,9 +730,9 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
 
                         foundSomething = true;
                         if (key.contains("version")) {
-                            if (key.contains("specification")) {
+                            if (!key.contains("specification")) {
-                                versionEvidence.addEvidence(source, key, value, Confidence.LOW);
+                                //versionEvidence.addEvidence(source, key, value, Confidence.LOW);
-                            } else {
+                                //} else {
                                 versionEvidence.addEvidence(source, key, value, Confidence.MEDIUM);
                             }
                         } else if ("build-id".equals(key)) {
@@ -778,6 +784,10 @@ public class JarAnalyzer extends AbstractFileTypeAnalyzer {
                     }
                 }
             }
+            if (specificationVersion != null && !hasImplementationVersion) {
+                foundSomething = true;
+                versionEvidence.addEvidence(source, "specificationn-version", specificationVersion, Confidence.HIGH);
+            }
         } finally {
             if (jar != null) {
                 jar.close();

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

@@ -48,14 +48,6 @@ public class NexusSearch {
      * Whether to use the Proxy when making requests.
      */
     private boolean useProxy;
-    /**
-     * The username to use if the Nexus requires authentication.
-     */
-    private String userName = null;
-    /**
-     * The password to use if the Nexus requires authentication.
-     */
-    private char[] password;
     /**
      * Used for logging.
      */

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

@@ -73,7 +73,7 @@ public class CveDB {
      */
     public CveDB() throws DatabaseException {
         super();
-        statementBundle = java.util.ResourceBundle.getBundle("data/dbStatements");
+        statementBundle = ResourceBundle.getBundle("data/dbStatements");
         try {
             open();
             databaseProperties = new DatabaseProperties(this);

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

@@ -189,9 +189,8 @@ public class StandardUpdate {
     }
 
     /**
-     * Determines if the index needs to be updated. This is done by fetching the NVD CVE meta data and checking the last
+     * Determines if the index needs to be updated. This is done by fetching the NVD CVE meta data and checking the last update
-     * update date. If the data needs to be refreshed this method will return the NvdCveUrl for the files that need to
+     * date. If the data needs to be refreshed this method will return the NvdCveUrl for the files that need to be updated.
-     * be updated.
      *
      * @return the collection of files that need to be updated
      * @throws MalformedURLException is thrown if the URL for the NVD CVE Meta data is incorrect

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

@@ -599,8 +599,8 @@ public class Dependency implements Serializable, Comparable<Dependency> {
     private Set<Dependency> relatedDependencies = new TreeSet<Dependency>();
 
     /**
-     * Get the value of {@link #relatedDependencies}. This field is used to collect other dependencies which really
+     * Get the value of {@link #relatedDependencies}. This field is used to collect other dependencies which really represent the
-     * represent the same dependency, and may be presented as one item in reports.
+     * same dependency, and may be presented as one item in reports.
      *
      * @return the value of relatedDependencies
      */
@@ -660,22 +660,19 @@ public class Dependency implements Serializable, Comparable<Dependency> {
 
     /**
      * Adds a related dependency. The internal collection is normally a {@link java.util.TreeSet}, which relies on
-     * {@link #compareTo(Dependency)}. A consequence of this is that if you attempt to add a dependency with the
+     * {@link #compareTo(Dependency)}. A consequence of this is that if you attempt to add a dependency with the same file path
-     * same file path (modulo character case) as one that is already in the collection, it won't get added.
+     * (modulo character case) as one that is already in the collection, it won't get added.
      *
      * @param dependency a reference to the related dependency
      */
     public void addRelatedDependency(Dependency dependency) {
-        boolean debug = false;
         if (this == dependency) {
             LOGGER.warn("Attempted to add a circular reference - please post the log file to issue #172 here "
                     + "https://github.com/jeremylong/DependencyCheck/issues/172");
-            debug = true;
+            LOGGER.debug("this: {}", this);
+            LOGGER.debug("dependency: {}", dependency);
         } else if (!relatedDependencies.add(dependency)) {
-            LOGGER.warn("Failed to add dependency, likely due to referencing the same file as another dependency in the set.");
+            LOGGER.debug("Failed to add dependency, likely due to referencing the same file as another dependency in the set.");
-            debug = true;
-        }
-        if (debug) {
             LOGGER.debug("this: {}", this);
             LOGGER.debug("dependency: {}", dependency);
         }
@@ -735,22 +732,22 @@ public class Dependency implements Serializable, Comparable<Dependency> {
             return false;
         }
         final Dependency other = (Dependency) obj;
-        return ObjectUtils.equals(this.actualFilePath, other.actualFilePath) &&
+        return ObjectUtils.equals(this.actualFilePath, other.actualFilePath)
-                ObjectUtils.equals(this.filePath, other.filePath) &&
+                && ObjectUtils.equals(this.filePath, other.filePath)
-                ObjectUtils.equals(this.fileName, other.fileName) &&
+                && ObjectUtils.equals(this.fileName, other.fileName)
-                ObjectUtils.equals(this.fileExtension, other.fileExtension) &&
+                && ObjectUtils.equals(this.fileExtension, other.fileExtension)
-                ObjectUtils.equals(this.md5sum, other.md5sum) &&
+                && ObjectUtils.equals(this.md5sum, other.md5sum)
-                ObjectUtils.equals(this.sha1sum, other.sha1sum) &&
+                && ObjectUtils.equals(this.sha1sum, other.sha1sum)
-                ObjectUtils.equals(this.identifiers, other.identifiers) &&
+                && ObjectUtils.equals(this.identifiers, other.identifiers)
-                ObjectUtils.equals(this.vendorEvidence, other.vendorEvidence) &&
+                && ObjectUtils.equals(this.vendorEvidence, other.vendorEvidence)
-                ObjectUtils.equals(this.productEvidence, other.productEvidence) &&
+                && ObjectUtils.equals(this.productEvidence, other.productEvidence)
-                ObjectUtils.equals(this.versionEvidence, other.versionEvidence) &&
+                && ObjectUtils.equals(this.versionEvidence, other.versionEvidence)
-                ObjectUtils.equals(this.description, other.description) &&
+                && ObjectUtils.equals(this.description, other.description)
-                ObjectUtils.equals(this.license, other.license) &&
+                && ObjectUtils.equals(this.license, other.license)
-                ObjectUtils.equals(this.vulnerabilities, other.vulnerabilities) &&
+                && ObjectUtils.equals(this.vulnerabilities, other.vulnerabilities)
-                ObjectUtils.equals(this.relatedDependencies, other.relatedDependencies) &&
+                && ObjectUtils.equals(this.relatedDependencies, other.relatedDependencies)
-                ObjectUtils.equals(this.projectReferences, other.projectReferences) &&
+                && ObjectUtils.equals(this.projectReferences, other.projectReferences)
-                ObjectUtils.equals(this.availableVersions, other.availableVersions);
+                && ObjectUtils.equals(this.availableVersions, other.availableVersions);
     }
 
     /**

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

@@ -17,6 +17,9 @@
  */
 package org.owasp.dependencycheck.dependency;
 
+import org.apache.commons.lang.ObjectUtils;
+import org.apache.commons.lang.StringUtils;
+
 import java.io.Serializable;
 
 /**
@@ -26,6 +29,16 @@ import java.io.Serializable;
  */
 public class Evidence implements Serializable, Comparable<Evidence> {
 
+    /**
+     * Used as starting point for generating the value in {@link #hashCode()}.
+     */
+    private static final int MAGIC_HASH_INIT_VALUE = 3;
+
+    /**
+     * Used as a multiplier for generating the value in {@link #hashCode()}.
+     */
+    private static final int MAGIC_HASH_MULTIPLIER = 67;
+
     /**
      * Creates a new Evidence object.
      */
@@ -46,6 +59,7 @@ public class Evidence implements Serializable, Comparable<Evidence> {
         this.value = value;
         this.confidence = confidence;
     }
+
     /**
      * The name of the evidence.
      */
@@ -68,6 +82,7 @@ public class Evidence implements Serializable, Comparable<Evidence> {
     public void setName(String name) {
         this.name = name;
     }
+
     /**
      * The source of the evidence.
      */
@@ -90,6 +105,7 @@ public class Evidence implements Serializable, Comparable<Evidence> {
     public void setSource(String source) {
         this.source = source;
     }
+
     /**
      * The value of the evidence.
      */
@@ -124,6 +140,7 @@ public class Evidence implements Serializable, Comparable<Evidence> {
     public void setValue(String value) {
         this.value = value;
     }
+
     /**
      * A value indicating if the Evidence has been "used" (aka read).
      */
@@ -146,6 +163,7 @@ public class Evidence implements Serializable, Comparable<Evidence> {
     public void setUsed(boolean used) {
         this.used = used;
     }
+
     /**
      * The confidence level for the evidence.
      */
@@ -176,11 +194,11 @@ public class Evidence implements Serializable, Comparable<Evidence> {
      */
     @Override
     public int hashCode() {
-        int hash = 3;
+        int hash = MAGIC_HASH_INIT_VALUE;
-        hash = 67 * hash + (this.name != null ? this.name.hashCode() : 0);
+        hash = MAGIC_HASH_MULTIPLIER * hash + ObjectUtils.hashCode(StringUtils.lowerCase(this.name));
-        hash = 67 * hash + (this.source != null ? this.source.hashCode() : 0);
+        hash = MAGIC_HASH_MULTIPLIER * hash + ObjectUtils.hashCode(StringUtils.lowerCase(this.source));
-        hash = 67 * hash + (this.value != null ? this.value.hashCode() : 0);
+        hash = MAGIC_HASH_MULTIPLIER * hash + ObjectUtils.hashCode(StringUtils.lowerCase(this.value));
-        hash = 67 * hash + (this.confidence != null ? this.confidence.hashCode() : 0);
+        hash = MAGIC_HASH_MULTIPLIER * hash + ObjectUtils.hashCode(this.confidence);
         return hash;
     }
 
@@ -200,19 +218,10 @@ public class Evidence implements Serializable, Comparable<Evidence> {
         }
         final Evidence e = (Evidence) that;
 
-        return testEquality(name, e.name) && testEquality(source, e.source) && testEquality(value, e.value)
+        return StringUtils.equalsIgnoreCase(name, e.name)
-                && (confidence == null ? e.confidence == null : confidence == e.confidence);
+                && StringUtils.equalsIgnoreCase(source, e.source)
-    }
+                && StringUtils.equalsIgnoreCase(value, e.value)
-
+                && ObjectUtils.equals(confidence, e.confidence);
-    /**
-     * Simple equality test for use within the equals method. This does a case insensitive compare.
-     *
-     * @param l a string to compare.
-     * @param r another string to compare.
-     * @return whether the two strings are the same.
-     */
-    private boolean testEquality(String l, String r) {
-        return l == null ? r == null : l.equalsIgnoreCase(r);
     }
 
     /**
@@ -225,13 +234,13 @@ public class Evidence implements Serializable, Comparable<Evidence> {
         if (o == null) {
             return 1;
         }
-        if (equalsWithNullCheck(source, o.source)) {
+        if (StringUtils.equalsIgnoreCase(source, o.source)) {
-            if (equalsWithNullCheck(name, o.name)) {
+            if (StringUtils.equalsIgnoreCase(name, o.name)) {
-                if (equalsWithNullCheck(value, o.value)) {
+                if (StringUtils.equalsIgnoreCase(value, o.value)) {
-                    if (equalsWithNullCheck(confidence, o.confidence)) {
+                    if (ObjectUtils.equals(confidence, o.confidence)) {
                         return 0; //they are equal
                     } else {
-                        return compareToWithNullCheck(confidence, o.confidence);
+                        return ObjectUtils.compare(confidence, o.confidence);
                     }
                 } else {
                     return compareToIgnoreCaseWithNullCheck(value, o.value);
@@ -244,38 +253,6 @@ public class Evidence implements Serializable, Comparable<Evidence> {
         }
     }
 
-    /**
-     * Equality check with an exhaustive, possibly duplicative, check against nulls.
-     *
-     * @param me the value to be compared
-     * @param other the other value to be compared
-     * @return true if the values are equal; otherwise false
-     */
-    private boolean equalsWithNullCheck(String me, String other) {
-        if (me == null && other == null) {
-            return true;
-        } else if (me == null || other == null) {
-            return false;
-        }
-        return me.equalsIgnoreCase(other);
-    }
-
-    /**
-     * Equality check with an exhaustive, possibly duplicative, check against nulls.
-     *
-     * @param me the value to be compared
-     * @param other the other value to be compared
-     * @return true if the values are equal; otherwise false
-     */
-    private boolean equalsWithNullCheck(Confidence me, Confidence other) {
-        if (me == null && other == null) {
-            return true;
-        } else if (me == null || other == null) {
-            return false;
-        }
-        return me.equals(other);
-    }
-
     /**
      * Wrapper around {@link java.lang.String#compareToIgnoreCase(java.lang.String) String.compareToIgnoreCase} with an
      * exhaustive, possibly duplicative, check against nulls.
@@ -295,25 +272,6 @@ public class Evidence implements Serializable, Comparable<Evidence> {
         return me.compareToIgnoreCase(other);
     }
 
-    /**
-     * Wrapper around {@link java.lang.Enum#compareTo(java.lang.Enum) Enum.compareTo} with an exhaustive, possibly duplicative,
-     * check against nulls.
-     *
-     * @param me the value to be compared
-     * @param other the other value to be compared
-     * @return true if the values are equal; otherwise false
-     */
-    private int compareToWithNullCheck(Confidence me, Confidence other) {
-        if (me == null && other == null) {
-            return 0;
-        } else if (me == null) {
-            return -1; //the other string is greater then me
-        } else if (other == null) {
-            return 1; //me is greater then the other string
-        }
-        return me.compareTo(other);
-    }
-
     /**
      * Standard toString() implementation.
      *

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

@@ -32,13 +32,40 @@ import ch.qos.cal10n.LocaleData;
 )
 public enum DCResources {
 
+    /**
+     * Not deployed.
+     */
     NOTDEPLOYED,
+    /**
+     * grok error.
+     */
     GROKERROR,
+    /**
+     * The dependency is not an assembly.
+     */
     NOTASSEMBLY,
+    /**
+     * GROK Return Code.
+     */
     GROKRC,
+    /**
+     * Grok assembly was extracted.
+     */
     GROKDEPLOYED,
+    /**
+     * Grok assembly was not extracted.
+     */
     GROKNOTDEPLOYED,
+    /**
+     * Grok failed to initialize.
+     */
     GROKINITFAIL,
+    /**
+     * Grok initialized.
+     */
     GROKINITMSG,
+    /**
+     * Grok assembly was not deleted.
+     */
     GROKNOTDELETED
 }

dependency-check-core/src/main/resources/dependencycheck.properties

@@ -70,3 +70,6 @@ analyzer.nexus.proxy=true
 # the URL for searching search.maven.org for SHA-1 and whether it's enabled
 analyzer.central.enabled=true
 analyzer.central.url=http://search.maven.org/solrsearch/select
+
+# the number of nested archives that will be searched.
+archive.scan.depth=3

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

@@ -34,8 +34,6 @@ import org.owasp.dependencycheck.dependency.Evidence;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.slf4j.impl.SimpleLogger;
-import org.slf4j.impl.SimpleLoggerFactory;
 
 /**
  * Tests for the AssemblyAnalyzer.

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

@@ -96,7 +96,7 @@ public class CPEAnalyzerIntegrationTest extends AbstractDatabaseTestCase {
             callDetermineCPE_full("hazelcast-2.5.jar", null, instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
             callDetermineCPE_full("spring-context-support-2.5.5.jar", "cpe:/a:vmware:springsource_spring_framework:2.5.5", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
             callDetermineCPE_full("spring-core-3.0.0.RELEASE.jar", "cpe:/a:vmware:springsource_spring_framework:3.0.0", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
-            callDetermineCPE_full("org.mortbay.jetty.jar", "cpe:/a:mortbay_jetty:jetty:4.2", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
+            callDetermineCPE_full("org.mortbay.jetty.jar", "cpe:/a:mortbay_jetty:jetty:4.2.27", instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
             callDetermineCPE_full("jaxb-xercesImpl-1.5.jar", null, instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
             callDetermineCPE_full("ehcache-core-2.2.0.jar", null, instance, fnAnalyzer, jarAnalyzer, hAnalyzer, fp);
         } finally {

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

@@ -19,6 +19,7 @@ package org.owasp.dependencycheck.dependency;
 
 import org.junit.Test;
 import static org.junit.Assert.*;
+import static org.hamcrest.CoreMatchers.*;
 
 /**
  *
@@ -53,6 +54,14 @@ public class EvidenceTest {
         assertTrue(instance.equals(that8));
     }
 
+    @Test
+    public void testHashcodeContract() throws Exception {
+        final Evidence titleCase = new Evidence("Manifest", "Implementation-Title", "Spring Framework", Confidence.HIGH);
+        final Evidence lowerCase = new Evidence("manifest", "implementation-title", "spring framework", Confidence.HIGH);
+        assertThat(titleCase, is(equalTo(lowerCase)));
+        assertThat(titleCase.hashCode(), is(equalTo(lowerCase.hashCode())));
+    }
+
     /**
      * Test of compareTo method, of class Evidence.
      */

dependency-check-core/src/test/resources/log.properties

@@ -1,21 +0,0 @@
-handlers=java.util.logging.ConsoleHandler, java.util.logging.FileHandler
-
-# logging levels
-# FINEST, FINER, FINE, CONFIG, INFO, WARNING and SEVERE.
-
-# Configure the ConsoleHandler.
-java.util.logging.ConsoleHandler.level=SEVERE
-
-# Configure the FileHandler.
-java.util.logging.FileHandler.formatter=java.util.logging.SimpleFormatter
-java.util.logging.FileHandler.level=FINEST
-
-# The following special tokens can be used in the pattern property
-# which specifies the location and name of the log file.
-#   / - standard path separator
-#   %t - system temporary directory
-#   %h - value of the user.home system property
-#   %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

dependency-check-core/src/test/resources/logback-test.xml

@@ -0,0 +1,23 @@
+<configuration>
+    <contextName>dependency-check</contextName>
+    <!-- Logging configuration -->
+    <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
+        <Target>System.out</Target>
+        <encoder>
+            <pattern>[%level] %msg%n</pattern>
+        </encoder>
+    </appender>
+    <root level="INFO">
+        <appender-ref ref="console"/>
+    </root>
+
+    <logger name="org.owasp.dependencycheck.analyzer.AssemblyAnalyzerTest" additivity="false" level="WARN">
+        <appender-ref ref="console"/>
+    </logger>
+    <logger name="org.owasp.dependencycheck.data.central.CentralSearchTest" additivity="false" level="WARN">
+        <appender-ref ref="console"/>
+    </logger>
+    <logger name="org.owasp.dependencycheck.data.nexus.NexusSearchTest" additivity="false" level="WARN">
+        <appender-ref ref="console"/>
+    </logger>
+</configuration>

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

@@ -149,7 +149,7 @@ public class AggregateMojo extends BaseDependencyCheckMojo {
                     if (mpp.compareTo(mod.getBasedir()) == 0 && descendants.add(mod)) {
                         if (getLog().isDebugEnabled()) {
                             getLog().debug(String.format("Decendent module %s added", mod.getName()));
-                        };
+                        }
                     }
                 } catch (IOException ex) {
                     if (getLog().isDebugEnabled()) {

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

@@ -67,10 +67,6 @@ public abstract class BaseDependencyCheckMojo extends AbstractMojo implements Ma
      * The properties file location.
      */
     private static final String PROPERTIES_FILE = "mojo.properties";
-    /**
-     * Name of the logging properties file.
-     */
-    private static final String LOG_PROPERTIES_FILE = "log.properties";
     /**
      * System specific new line character.
      */
@@ -949,10 +945,11 @@ public abstract class BaseDependencyCheckMojo extends AbstractMojo implements Ma
             } else {
                 file = new File(writeTo, dataFileName);
             }
-            File parent = file.getParentFile();
+            final File parent = file.getParentFile();
             if (!parent.isDirectory()) {
                 if (parent.mkdirs()) {
-                    getLog().error(String.format("Directory '%s' does not exist and cannot be created; unable to write data file.", parent.getAbsolutePath()));
+                    getLog().error(String.format("Directory '%s' does not exist and cannot be created; unable to write data file.",
+                            parent.getAbsolutePath()));
                 }
             }
 

dependency-check-maven/src/main/java/org/owasp/dependencycheck/maven/slf4j/MavenLoggerAdapter.java

@@ -18,22 +18,32 @@
 package org.owasp.dependencycheck.maven.slf4j;
 
 import org.apache.maven.plugin.logging.Log;
-import org.slf4j.helpers.FormattingTuple;
 import org.slf4j.helpers.MarkerIgnoringBase;
 import org.slf4j.helpers.MessageFormatter;
 
 /**
- * Created by colezlaw on 6/14/15.
+ * Created on 6/14/15.
+ *
+ * @author colezlaw
  */
 public class MavenLoggerAdapter extends MarkerIgnoringBase {
 
     private Log log;
 
+    /**
+     * Creates a new Maven Logger Adapter.
+     *
+     * @param log the maven log
+     */
     public MavenLoggerAdapter(Log log) {
         super();
         this.log = log;
     }
 
+    /**
+     *
+     * @return
+     */
     @Override
     public boolean isTraceEnabled() {
         if (log != null) {

dependency-check-maven/src/main/java/org/owasp/dependencycheck/maven/slf4j/MavenLoggerFactory.java

@@ -22,7 +22,9 @@ import org.slf4j.ILoggerFactory;
 import org.slf4j.Logger;
 
 /**
- * Created by colezlaw on 6/14/15.
+ * Created on 6/14/15.
+ *
+ * @author colezlaw
  */
 public class MavenLoggerFactory implements ILoggerFactory {
 

dependency-check-maven/src/main/java/org/slf4j/impl/StaticLoggerBinder.java

@@ -48,7 +48,7 @@ public class StaticLoggerBinder implements LoggerFactoryBinder {
     /**
      * Maven mojos have their own logger, so we'll use one of those
      */
-    private Log log;
+    private Log log = null;
 
     /**
      * Set the Task which will this is to log through.
@@ -70,7 +70,7 @@ public class StaticLoggerBinder implements LoggerFactoryBinder {
     private static final String loggerFactoryClassStr = MavenLoggerFactory.class.getName();
 
     /**
-     * The ILoggerFactory instance returned by the {@link #getLoggerFactory} method should always be the smae object
+     * The ILoggerFactory instance returned by the {@link #getLoggerFactory} method should always be the same object
      */
     private ILoggerFactory loggerFactory;
 
@@ -83,6 +83,7 @@ public class StaticLoggerBinder implements LoggerFactoryBinder {
      *
      * @return the logger factory
      */
+    @Override
     public ILoggerFactory getLoggerFactory() {
         return loggerFactory;
     }
@@ -92,6 +93,7 @@ public class StaticLoggerBinder implements LoggerFactoryBinder {
      *
      * @return the logger factory class string
      */
+    @Override
     public String getLoggerFactoryClassStr() {
         return loggerFactoryClassStr;
     }

dependency-check-utils/pom.xml

@@ -230,8 +230,13 @@ Copyright (c) 2014 - Jeremy Long. All Rights Reserved.
             <scope>compile</scope>
         </dependency>
         <dependency>
-            <groupId>org.slf4j</groupId>
+            <groupId>ch.qos.logback</groupId>
-            <artifactId>slf4j-simple</artifactId>
+            <artifactId>logback-core</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
             <scope>test</scope>
         </dependency>
     </dependencies>

dependency-check-utils/src/test/resources/logback-test.xml

@@ -0,0 +1,13 @@
+<configuration>
+    <contextName>dependency-check</contextName>
+    <!-- Logging configuration -->
+    <appender name="console" class="ch.qos.logback.core.ConsoleAppender">
+        <Target>System.out</Target>
+        <encoder>
+            <pattern>[%level] %msg%n</pattern>
+        </encoder>
+    </appender>
+    <root level="INFO">
+        <appender-ref ref="console"/>
+    </root>
+</configuration>