Updated exception handling so that issue #215 can be resolved

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

@@ -30,6 +30,8 @@ import org.owasp.dependencycheck.data.update.UpdateService;
 import org.owasp.dependencycheck.data.update.exception.UpdateException;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.exception.NoDataException;
+import org.owasp.dependencycheck.exception.ExceptionCollection;
+import org.owasp.dependencycheck.exception.InitializationException;
 import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
@@ -47,8 +49,10 @@ import java.util.Map;
 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
+ * Scans files, directories, etc. for Dependencies. Analyzers are loaded and
- * file is encountered and an Analyzer is associated with the file type then the file is turned into a dependency.
+ * 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.
  *
  * @author Jeremy Long
  */
@@ -69,7 +73,8 @@ public class Engine implements FileFilter {
     private final Set<FileTypeAnalyzer> fileTypeAnalyzers = new HashSet<FileTypeAnalyzer>();
 
     /**
-     * The ClassLoader to use when dynamically loading Analyzer and Update services.
+     * The ClassLoader to use when dynamically loading Analyzer and Update
+     * services.
      */
     private ClassLoader serviceClassLoader = Thread.currentThread().getContextClassLoader();
     /**
@@ -80,7 +85,8 @@ public class Engine implements FileFilter {
     /**
      * Creates a new Engine.
      *
-     * @throws DatabaseException thrown if there is an error connecting to the database
+     * @throws DatabaseException thrown if there is an error connecting to the
+     * database
      */
     public Engine() throws DatabaseException {
         initializeEngine();
@@ -90,7 +96,8 @@ public class Engine implements FileFilter {
      * Creates a new Engine.
      *
      * @param serviceClassLoader a reference the class loader being used
-     * @throws DatabaseException thrown if there is an error connecting to the database
+     * @throws DatabaseException thrown if there is an error connecting to the
+     * database
      */
     public Engine(ClassLoader serviceClassLoader) throws DatabaseException {
         this.serviceClassLoader = serviceClassLoader;
@@ -98,9 +105,11 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Creates a new Engine using the specified classloader to dynamically load Analyzer and Update services.
+     * Creates a new Engine using the specified classloader to dynamically load
+     * Analyzer and Update services.
      *
-     * @throws DatabaseException thrown if there is an error connecting to the database
+     * @throws DatabaseException thrown if there is an error connecting to the
+     * database
      */
     protected final void initializeEngine() throws DatabaseException {
         ConnectionFactory.initialize();
@@ -115,7 +124,8 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Loads the analyzers specified in the configuration file (or system properties).
+     * Loads the analyzers specified in the configuration file (or system
+     * properties).
      */
     private void loadAnalyzers() {
         if (!analyzers.isEmpty()) {
@@ -164,8 +174,9 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Scans an array of files or directories. If a directory is specified, it will be scanned recursively. Any dependencies
+     * Scans an array of files or directories. If a directory is specified, it
-     * identified are added to the dependency collection.
+     * will be scanned recursively. Any dependencies identified are added to the
+     * dependency collection.
      *
      * @param paths an array of paths to files or directories to be analyzed
      * @return the list of dependencies scanned
@@ -183,8 +194,9 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Scans a given file or directory. If a directory is specified, it will be scanned recursively. Any dependencies identified
+     * Scans a given file or directory. If a directory is specified, it will be
-     * are added to the dependency collection.
+     * scanned recursively. Any dependencies identified are added to the
+     * dependency collection.
      *
      * @param path the path to a file or directory to be analyzed
      * @return the list of dependencies scanned
@@ -195,8 +207,9 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Scans an array of files or directories. If a directory is specified, it will be scanned recursively. Any dependencies
+     * Scans an array of files or directories. If a directory is specified, it
-     * identified are added to the dependency collection.
+     * will be scanned recursively. Any dependencies identified are added to the
+     * dependency collection.
      *
      * @param files an array of paths to files or directories to be analyzed.
      * @return the list of dependencies
@@ -214,8 +227,9 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Scans a collection of files or directories. If a directory is specified, it will be scanned recursively. Any dependencies
+     * Scans a collection of files or directories. If a directory is specified,
-     * identified are added to the dependency collection.
+     * it will be scanned recursively. Any dependencies identified are added to
+     * the dependency collection.
      *
      * @param files a set of paths to files or directories to be analyzed
      * @return the list of dependencies scanned
@@ -233,8 +247,9 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Scans a given file or directory. If a directory is specified, it will be scanned recursively. Any dependencies identified
+     * Scans a given file or directory. If a directory is specified, it will be
-     * are added to the dependency collection.
+     * scanned recursively. Any dependencies identified are added to the
+     * dependency collection.
      *
      * @param file the path to a file or directory to be analyzed
      * @return the list of dependencies scanned
@@ -257,7 +272,8 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Recursively scans files and directories. Any dependencies identified are added to the dependency collection.
+     * Recursively scans files and directories. Any dependencies identified are
+     * added to the dependency collection.
      *
      * @param dir the directory to scan
      * @return the list of Dependency objects scanned
@@ -282,7 +298,8 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Scans a specified file. If a dependency is identified it is added to the dependency collection.
+     * Scans a specified file. If a dependency is identified it is added to the
+     * dependency collection.
      *
      * @param file The file to scan
      * @return the scanned dependency
@@ -301,20 +318,38 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Runs the analyzers against all of the dependencies. Since the mutable dependencies list is exposed via
+     * Runs the analyzers against all of the dependencies. Since the mutable
-     * {@link #getDependencies()}, this method iterates over a copy of the dependencies list. Thus, the potential for
+     * dependencies list is exposed via {@link #getDependencies()}, this method
-     * {@link java.util.ConcurrentModificationException}s is avoided, and analyzers may safely add or remove entries from the
+     * iterates over a copy of the dependencies list. Thus, the potential for
-     * dependencies list.
+     * {@link java.util.ConcurrentModificationException}s is avoided, and
+     * analyzers may safely add or remove entries from the dependencies list.
+     *
+     * Every effort is made to complete analysis on the dependencies. In some
+     * cases an exception will occur with part of the analysis being performed
+     * which may not affect the entire analysis. If an exception occurs it will
+     * be included in the thrown exception collection.
+     *
+     * @throws ExceptionCollection a collections of any exceptions that occurred
+     * during analysis
      */
-    public void analyzeDependencies() {
+    public void analyzeDependencies() throws ExceptionCollection {
+        List<Throwable> exceptions = new ArrayList<Throwable>();
         boolean autoUpdate = true;
         try {
             autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
         } catch (InvalidSettingException ex) {
             LOGGER.debug("Invalid setting for auto-update; using true.");
+            exceptions.add(ex);
         }
         if (autoUpdate) {
+            try {
                 doUpdates();
+            } catch (UpdateException ex) {
+                exceptions.add(ex);
+                LOGGER.warn("Unable to update Cached Web DataSource, using local "
+                        + "data instead. Results may not include recent vulnerabilities.");
+                LOGGER.debug("Update Error", ex);
+            }
         }
 
         //need to ensure that data exists
@@ -323,12 +358,13 @@ public class Engine implements FileFilter {
         } catch (NoDataException ex) {
             LOGGER.error("{}\n\nUnable to continue dependency-check analysis.", ex.getMessage());
             LOGGER.debug("", ex);
-            return;
+            exceptions.add(ex);
+            throw new ExceptionCollection(exceptions, true);
         } catch (DatabaseException ex) {
             LOGGER.error("{}\n\nUnable to continue dependency-check analysis.", ex.getMessage());
             LOGGER.debug("", ex);
-            return;
+            exceptions.add(ex);
-
+            throw new ExceptionCollection(exceptions, true);
         }
 
         LOGGER.debug("\n----------------------------------------------------\nBEGIN ANALYSIS\n----------------------------------------------------");
@@ -340,7 +376,12 @@ public class Engine implements FileFilter {
             final List<Analyzer> analyzerList = analyzers.get(phase);
 
             for (Analyzer a : analyzerList) {
+                try {
                     a = initializeAnalyzer(a);
+                } catch (InitializationException ex) {
+                    exceptions.add(ex);
+                    continue;
+                }
 
                 /* need to create a copy of the collection because some of the
                  * analyzers may modify it. This prevents ConcurrentModificationExceptions.
@@ -361,10 +402,12 @@ public class Engine implements FileFilter {
                         } catch (AnalysisException ex) {
                             LOGGER.warn("An error occurred while analyzing '{}'.", d.getActualFilePath());
                             LOGGER.debug("", ex);
+                            exceptions.add(ex);
                         } catch (Throwable ex) {
                             //final AnalysisException ax = new AnalysisException(axMsg, ex);
                             LOGGER.warn("An unexpected error occurred during analysis of '{}'", d.getActualFilePath());
                             LOGGER.debug("", ex);
+                            exceptions.add(ex);
                         }
                     }
                 }
@@ -380,6 +423,9 @@ public class Engine implements FileFilter {
 
         LOGGER.debug("\n----------------------------------------------------\nEND ANALYSIS\n----------------------------------------------------");
         LOGGER.info("Analysis Complete ({} ms)", System.currentTimeMillis() - analysisStart);
+        if (exceptions.size() > 0) {
+            throw new ExceptionCollection(exceptions);
+        }
     }
 
     /**
@@ -387,12 +433,14 @@ public class Engine implements FileFilter {
      *
      * @param analyzer the analyzer to initialize
      * @return the initialized analyzer
+     * @throws InitializationException thrown when there is a problem
+     * initializing the analyzer
      */
-    protected Analyzer initializeAnalyzer(Analyzer analyzer) {
+    protected Analyzer initializeAnalyzer(Analyzer analyzer) throws InitializationException {
         try {
             LOGGER.debug("Initializing {}", analyzer.getName());
             analyzer.initialize();
-        } catch (Throwable ex) {
+        } catch (InitializationException ex) {
             LOGGER.error("Exception occurred initializing {}.", analyzer.getName());
             LOGGER.debug("", ex);
             try {
@@ -400,6 +448,16 @@ public class Engine implements FileFilter {
             } catch (Throwable ex1) {
                 LOGGER.trace("", ex1);
             }
+            throw ex;
+        } catch (Throwable ex) {
+            LOGGER.error("Unexpected exception occurred initializing {}.", analyzer.getName());
+            LOGGER.debug("", ex);
+            try {
+                analyzer.close();
+            } catch (Throwable ex1) {
+                LOGGER.trace("", ex1);
+            }
+            throw new InitializationException("Unexpected Exception", ex);
         }
         return analyzer;
     }
@@ -419,28 +477,26 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Cycles through the cached web data sources and calls update on all of them.
+     * Cycles through the cached web data sources and calls update on all of
+     * them.
+     *
+     * @throws UpdateException
      */
-    public void doUpdates() {
+    public void doUpdates() throws UpdateException {
         LOGGER.info("Checking for updates");
         final long updateStart = System.currentTimeMillis();
         final UpdateService service = new UpdateService(serviceClassLoader);
         final Iterator<CachedWebDataSource> iterator = service.getDataSources();
         while (iterator.hasNext()) {
             final CachedWebDataSource source = iterator.next();
-            try {
             source.update();
-            } catch (UpdateException ex) {
-                LOGGER.warn(
-                        "Unable to update Cached Web DataSource, using local data instead. Results may not include recent vulnerabilities.");
-                LOGGER.debug("Unable to update details for {}", source.getClass().getName(), ex);
-            }
         }
         LOGGER.info("Check for updates complete ({} ms)", System.currentTimeMillis() - updateStart);
     }
 
     /**
-     * Returns a full list of all of the analyzers. This is useful for reporting which analyzers where used.
+     * Returns a full list of all of the analyzers. This is useful for reporting
+     * which analyzers where used.
      *
      * @return a list of Analyzers
      */
@@ -457,7 +513,8 @@ public class Engine implements FileFilter {
      * Checks all analyzers to see if an extension is supported.
      *
      * @param file a file extension
-     * @return true or false depending on whether or not the file extension is supported
+     * @return true or false depending on whether or not the file extension is
+     * supported
      */
     @Override
     public boolean accept(File file) {
@@ -483,10 +540,12 @@ public class Engine implements FileFilter {
     }
 
     /**
-     * Checks the CPE Index to ensure documents exists. If none exist a NoDataException is thrown.
+     * Checks the CPE Index to ensure documents exists. If none exist a
+     * NoDataException is thrown.
      *
      * @throws NoDataException thrown if no data exists in the CPE Index
-     * @throws DatabaseException thrown if there is an exception opening the database
+     * @throws DatabaseException thrown if there is an exception opening the
+     * database
      */
     private void ensureDataExists() throws NoDataException, DatabaseException {
         final CveDB cve = new CveDB();

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

@@ -27,6 +27,7 @@ import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Identifier;
 import org.owasp.dependencycheck.dependency.Vulnerability;
+import org.owasp.dependencycheck.exception.ExceptionCollection;
 import org.owasp.dependencycheck.exception.ScanAgentException;
 import org.owasp.dependencycheck.reporting.ReportGenerator;
 import org.owasp.dependencycheck.utils.Settings;
@@ -34,10 +35,12 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * This class provides a way to easily conduct a scan solely based on existing evidence metadata rather than collecting evidence
+ * This class provides a way to easily conduct a scan solely based on existing
- * from the files themselves. This class is based on the Ant task and Maven plugin with the exception that it takes a list of
+ * evidence metadata rather than collecting evidence from the files themselves.
- * dependencies that can be programmatically added from data in a spreadsheet, database or some other datasource and conduct a
+ * This class is based on the Ant task and Maven plugin with the exception that
- * scan based on this pre-defined evidence.
+ * it takes a list of dependencies that can be programmatically added from data
+ * in a spreadsheet, database or some other datasource and conduct a scan based
+ * on this pre-defined evidence.
  *
  * <h2>Example:</h2>
  * <pre>
@@ -138,7 +141,8 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Specifies the destination directory for the generated Dependency-Check report.
+     * Specifies the destination directory for the generated Dependency-Check
+     * report.
      */
     private String reportOutputDirectory;
 
@@ -161,9 +165,11 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Specifies if the build should be failed if a CVSS score above a specified level is identified. The default is 11 which
+     * Specifies if the build should be failed if a CVSS score above a specified
-     * means since the CVSS scores are 0-10, by default the build will never fail and the CVSS score is set to 11. The valid range
+     * level is identified. The default is 11 which means since the CVSS scores
-     * for the fail build on CVSS is 0 to 11, where anything above 10 will not cause the build to fail.
+     * are 0-10, by default the build will never fail and the CVSS score is set
+     * to 11. The valid range for the fail build on CVSS is 0 to 11, where
+     * anything above 10 will not cause the build to fail.
      */
     private float failBuildOnCVSS = 11;
 
@@ -186,8 +192,8 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not recommended that this be turned to false. Default
+     * Sets whether auto-updating of the NVD CVE/CPE data is enabled. It is not
-     * is true.
+     * recommended that this be turned to false. Default is true.
      */
     private boolean autoUpdate = true;
 
@@ -233,8 +239,9 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * The report format to be generated (HTML, XML, VULN, ALL). This configuration option has no affect if using this within the
+     * The report format to be generated (HTML, XML, VULN, ALL). This
-     * Site plugin unless the externalReport is set to true. Default is HTML.
+     * configuration option has no affect if using this within the Site plugin
+     * unless the externalReport is set to true. Default is HTML.
      */
     private ReportGenerator.Format reportFormat = ReportGenerator.Format.HTML;
 
@@ -283,7 +290,9 @@ public class DependencyCheckScanAgent {
      * Get the value of proxyServer.
      *
      * @return the value of proxyServer
-     * @deprecated use {@link org.owasp.dependencycheck.agent.DependencyCheckScanAgent#getProxyServer()} instead
+     * @deprecated use
+     * {@link org.owasp.dependencycheck.agent.DependencyCheckScanAgent#getProxyServer()}
+     * instead
      */
     @Deprecated
     public String getProxyUrl() {
@@ -694,8 +703,8 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Additional ZIP File extensions to add analyze. This should be a comma-separated list of file extensions to treat like ZIP
+     * Additional ZIP File extensions to add analyze. This should be a
-     * files.
+     * comma-separated list of file extensions to treat like ZIP files.
      */
     private String zipExtensions;
 
@@ -836,11 +845,17 @@ public class DependencyCheckScanAgent {
      * Executes the Dependency-Check on the dependent libraries.
      *
      * @return the Engine used to scan the dependencies.
-     * @throws org.owasp.dependencycheck.data.nvdcve.DatabaseException thrown if there is an exception connecting to the database
+     * @throws org.owasp.dependencycheck.data.nvdcve.DatabaseException thrown if
+     * there is an exception connecting to the database
      */
-    private Engine executeDependencyCheck() throws DatabaseException {
+    private Engine executeDependencyCheck() throws ExceptionCollection {
         populateSettings();
-        final Engine engine = new Engine();
+        final Engine engine;
+        try {
+            engine = new Engine();
+        } catch (DatabaseException ex) {
+            throw new ExceptionCollection(ex, true);
+        }
         engine.setDependencies(this.dependencies);
         engine.analyzeDependencies();
         return engine;
@@ -881,8 +896,9 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Takes the properties supplied and updates the dependency-check settings. Additionally, this sets the system properties
+     * Takes the properties supplied and updates the dependency-check settings.
-     * required to change the proxy server, port, and connection timeout.
+     * Additionally, this sets the system properties required to change the
+     * proxy server, port, and connection timeout.
      */
     private void populateSettings() {
         Settings.initialize();
@@ -925,7 +941,8 @@ public class DependencyCheckScanAgent {
      * Executes the dependency-check and generates the report.
      *
      * @return a reference to the engine used to perform the scan.
-     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if there is an exception executing the scan.
+     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if
+     * there is an exception executing the scan.
      */
     public Engine execute() throws ScanAgentException {
         Engine engine = null;
@@ -940,10 +957,12 @@ public class DependencyCheckScanAgent {
             if (this.failBuildOnCVSS <= 10) {
                 checkForFailure(engine.getDependencies());
             }
-        } catch (DatabaseException ex) {
+        } catch (ExceptionCollection ex) {
-            LOGGER.error(
+            if (ex.isFatal()) {
-                    "Unable to connect to the dependency-check database; analysis has stopped");
+                LOGGER.error("A fatal exception occurred during analysis; analysis has stopped. Please see the debug log for more details.");
                 LOGGER.debug("", ex);
+            }
+            throw new ScanAgentException("One or more exceptions occurred during analysis; please see the debug log for more details.", ex);
         } finally {
             Settings.cleanup(true);
             if (engine != null) {
@@ -954,11 +973,12 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Checks to see if a vulnerability has been identified with a CVSS score that is above the threshold set in the
+     * Checks to see if a vulnerability has been identified with a CVSS score
-     * configuration.
+     * that is above the threshold set in the configuration.
      *
      * @param dependencies the list of dependency objects
-     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if there is an exception executing the scan.
+     * @throws org.owasp.dependencycheck.exception.ScanAgentException thrown if
+     * there is an exception executing the scan.
      */
     private void checkForFailure(List<Dependency> dependencies) throws ScanAgentException {
         final StringBuilder ids = new StringBuilder();
@@ -986,7 +1006,8 @@ public class DependencyCheckScanAgent {
     }
 
     /**
-     * Generates a warning message listing a summary of dependencies and their associated CPE and CVE entries.
+     * Generates a warning message listing a summary of dependencies and their
+     * associated CPE and CVE entries.
      *
      * @param dependencies a list of dependency objects
      */

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

@@ -0,0 +1,131 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2016 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.exception;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * A collection of several exceptions.
+ *
+ * @author Jeremy Lomg
+ */
+public class ExceptionCollection extends Exception {
+
+    /**
+     * Instantiates a new exception collection.
+     *
+     * @param exceptions a list of exceptions
+     */
+    public ExceptionCollection(List<Throwable> exceptions) {
+        super();
+        this.exceptions = exceptions;
+    }
+    /**
+     * Instantiates a new exception collection.
+     *
+     * @param exceptions a list of exceptions
+     * @param fatal indicates if the exception that occurred is fatal - meaning
+     * that no analysis was performed.
+     */
+    public ExceptionCollection(List<Throwable> exceptions, boolean fatal) {
+        super();
+        this.exceptions = exceptions;
+        this.fatal = fatal;
+    }
+        /**
+     * Instantiates a new exception collection.
+     *
+     * @param exceptions a list of exceptions
+     * @param fatal indicates if the exception that occurred is fatal - meaning
+     * that no analysis was performed.
+     */
+    public ExceptionCollection(Throwable exceptions, boolean fatal) {
+        super();
+        this.exceptions.add(exceptions);
+        this.fatal = fatal;
+    }
+    /**
+     * Instantiates a new exception collection.
+     */
+    public ExceptionCollection() {
+        super();
+        this.exceptions = new ArrayList<Throwable>();
+    }
+    /**
+     * The serial version uid.
+     */
+    private static final long serialVersionUID = 1L;
+
+    /**
+     * A collection of exceptions.
+     */
+    private List<Throwable> exceptions;
+
+    /**
+     * Get the value of exceptions.
+     *
+     * @return the value of exceptions
+     */
+    public List<Throwable> getExceptions() {
+        return exceptions;
+    }
+
+    /**
+     * Adds an exception to the collection.
+     *
+     * @param ex the exception to add
+     */
+    public void addException(Throwable ex) {
+        this.exceptions.add(ex);
+    }
+        /**
+     * Adds an exception to the collection.
+     *
+     * @param ex the exception to add
+     */
+    public void addException(Throwable ex, boolean fatal) {
+        addException(ex);
+        this.fatal = fatal;
+    }
+
+    /**
+     * Flag indicating if a fatal exception occurred that would prevent the attempt
+     * at completing the analysis even if exceptions occurred.
+     */
+    private boolean fatal = false;
+
+    /**
+     * Get the value of fatal
+     *
+     * @return the value of fatal
+     */
+    public boolean isFatal() {
+        return fatal;
+    }
+
+    /**
+     * Set the value of fatal
+     *
+     * @param fatal new value of fatal
+     */
+    public void setFatal(boolean fatal) {
+        this.fatal = fatal;
+    }
+
+}

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

@@ -0,0 +1,66 @@
+/*
+ * This file is part of dependency-check-core.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ * Copyright (c) 2016 Jeremy Long. All Rights Reserved.
+ */
+package org.owasp.dependencycheck.exception;
+
+/**
+ * An exception used when generating reports.
+ *
+ * @author Jeremy Long
+ */
+public class ReportException extends Exception {
+
+    /**
+     * The serial version uid.
+     */
+    private static final long serialVersionUID = 1L;
+
+    /**
+     * Creates a new ReportException.
+     */
+    public ReportException() {
+        super();
+    }
+
+    /**
+     * Creates a new ReportException.
+     *
+     * @param msg a message for the exception.
+     */
+    public ReportException(String msg) {
+        super(msg);
+    }
+
+    /**
+     * Creates a new ReportException.
+     *
+     * @param ex the cause of the exception.
+     */
+    public ReportException(Throwable ex) {
+        super(ex);
+    }
+
+    /**
+     * Creates a new ReportException.
+     *
+     * @param msg a message for the exception.
+     * @param ex the cause of the exception.
+     */
+    public ReportException(String msg, Throwable ex) {
+        super(msg, ex);
+    }
+}

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

@@ -26,6 +26,7 @@ import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
+import java.io.UnsupportedEncodingException;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Date;
@@ -37,13 +38,16 @@ import org.apache.velocity.runtime.RuntimeConstants;
 import org.owasp.dependencycheck.analyzer.Analyzer;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
 import org.owasp.dependencycheck.dependency.Dependency;
+import org.owasp.dependencycheck.exception.ReportException;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * The ReportGenerator is used to, as the name implies, generate reports. Internally the generator uses the Velocity
+ * The ReportGenerator is used to, as the name implies, generate reports.
- * Templating Engine. The ReportGenerator exposes a list of Dependencies to the template when generating the report.
+ * 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
  */
@@ -79,7 +83,7 @@ public class ReportGenerator {
     /**
      * The Velocity Engine.
      */
-    private final VelocityEngine engine;
+    private final VelocityEngine velocityEngine;
     /**
      * The Velocity Engine Context.
      */
@@ -91,13 +95,14 @@ public class ReportGenerator {
      * @param applicationName the application name being analyzed
      * @param dependencies the list of dependencies
      * @param analyzers the list of analyzers used
-     * @param properties the database properties (containing timestamps of the NVD CVE data)
+     * @param properties the database properties (containing timestamps of the
+     * NVD CVE data)
      */
     public ReportGenerator(String applicationName, List<Dependency> dependencies, List<Analyzer> analyzers, DatabaseProperties properties) {
-        engine = createVelocityEngine();
+        velocityEngine = createVelocityEngine();
         context = createContext();
 
-        engine.init();
+        velocityEngine.init();
 
         final DateFormat dateFormat = new SimpleDateFormat("MMM d, yyyy 'at' HH:mm:ss z");
         final DateFormat dateFormatXML = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSZ");
@@ -119,19 +124,19 @@ public class ReportGenerator {
     /**
      * Creates a new Velocity Engine.
      *
-     * @return a velocity engine.
+     * @return a velocity engine
      */
     private VelocityEngine createVelocityEngine() {
-        final VelocityEngine engine = new VelocityEngine();
+        final VelocityEngine velocity = new VelocityEngine();
         // Logging redirection for Velocity - Required by Jenkins and other server applications
-        engine.setProperty(RuntimeConstants.RUNTIME_LOG_LOGSYSTEM_CLASS, VelocityLoggerRedirect.class.getName());
+        velocity.setProperty(RuntimeConstants.RUNTIME_LOG_LOGSYSTEM_CLASS, VelocityLoggerRedirect.class.getName());
-        return engine;
+        return velocity;
     }
 
     /**
      * Creates a new Velocity Context.
      *
-     * @return a Velocity Context.
+     * @return a Velocity Context
      */
     private Context createContext() {
         return new VelocityContext();
@@ -143,7 +148,7 @@ public class ReportGenerator {
      * @param outputStream the OutputStream to send the generated report to
      * @param format the format the report should be written in
      * @throws IOException is thrown when the template file does not exist
-     * @throws Exception is thrown if there is an error writing out the reports.
+     * @throws Exception is thrown if there is an error writing out the reports
      */
     public void generateReports(OutputStream outputStream, Format format) throws IOException, Exception {
         if (format == Format.XML || format == Format.ALL) {
@@ -162,10 +167,9 @@ public class ReportGenerator {
      *
      * @param outputDir the path where the reports should be written
      * @param format the format the report should be written in
-     * @throws IOException is thrown when the template file does not exist
+     * @throws ReportException is thrown if there is an error writing out the reports
-     * @throws Exception is thrown if there is an error writing out the reports.
      */
-    public void generateReports(String outputDir, Format format) throws IOException, Exception {
+    public void generateReports(String outputDir, Format format) throws ReportException {
         if (format == Format.XML || format == Format.ALL) {
             generateReport("XmlReport", outputDir + File.separator + "dependency-check-report.xml");
         }
@@ -181,11 +185,12 @@ public class ReportGenerator {
      * Generates the Dependency Reports for the identified dependencies.
      *
      * @param outputDir the path where the reports should be written
-     * @param outputFormat the format the report should be written in (XML, HTML, ALL)
+     * @param outputFormat the format the report should be written in (XML,
-     * @throws IOException is thrown when the template file does not exist
+     * HTML, ALL)
-     * @throws Exception is thrown if there is an error writing out the reports.
+     * @throws ReportException is thrown if there is an error creating out the
+     * reports
      */
-    public void generateReports(String outputDir, String outputFormat) throws IOException, Exception {
+    public void generateReports(String outputDir, String outputFormat) throws ReportException {
         final String format = outputFormat.toUpperCase();
         final String pathToCheck = outputDir.toLowerCase();
         if (format.matches("^(XML|HTML|VULN|ALL)$")) {
@@ -217,16 +222,16 @@ public class ReportGenerator {
     }
 
     /**
-     * Generates a report from a given Velocity Template. The template name provided can be the name of a template
+     * Generates a report from a given Velocity Template. The template name
-     * contained in the jar file, such as 'XmlReport' or 'HtmlReport', or the template name can be the path to a
+     * 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 templateName the name of the template to load
-     * @param outputStream the OutputStream to write the report to.
+     * @param outputStream the OutputStream to write the report to
-     * @throws IOException is thrown when the template file does not exist.
+     * @throws ReportException is thrown when an exception occurs
-     * @throws Exception is thrown when an exception occurs.
      */
-    protected void generateReport(String templateName, OutputStream outputStream) throws IOException, Exception {
+    protected void generateReport(String templateName, OutputStream outputStream) throws ReportException {
         InputStream input = null;
         String templatePath = null;
         final File f = new File(templateName);
@@ -235,27 +240,30 @@ public class ReportGenerator {
                 templatePath = templateName;
                 input = new FileInputStream(f);
             } catch (FileNotFoundException ex) {
-                LOGGER.error("Unable to generate the report, the report template file could not be found.");
+                throw new ReportException("Unable to locate template file: " + templateName, ex);
-                LOGGER.debug("", ex);
             }
         } else {
             templatePath = "templates/" + templateName + ".vsl";
             input = this.getClass().getClassLoader().getResourceAsStream(templatePath);
         }
         if (input == null) {
-            throw new IOException("Template file doesn't exist");
+            throw new ReportException("Template file doesn't exist: " + templatePath);
         }
 
-        final InputStreamReader reader = new InputStreamReader(input, "UTF-8");
+        InputStreamReader reader = null;
         OutputStreamWriter writer = null;
 
         try {
+            reader = new InputStreamReader(input, "UTF-8");
             writer = new OutputStreamWriter(outputStream, "UTF-8");
-
+            if (!velocityEngine.evaluate(context, writer, templatePath, reader)) {
-            if (!engine.evaluate(context, writer, templatePath, reader)) {
+                throw new ReportException("Failed to convert the template into html.");
-                throw new Exception("Failed to convert the template into html.");
             }
             writer.flush();
+        } catch (UnsupportedEncodingException ex) {
+            throw new ReportException("Unable to generate the report using UTF-8", ex);
+        } catch (IOException ex) {
+            throw new ReportException("Unable to write the report", ex);
         } finally {
             if (writer != null) {
                 try {
@@ -271,6 +279,7 @@ public class ReportGenerator {
                     LOGGER.trace("", ex);
                 }
             }
+            if (reader != null) {
                 try {
                     reader.close();
                 } catch (IOException ex) {
@@ -278,18 +287,19 @@ public class ReportGenerator {
                 }
             }
         }
+    }
 
     /**
-     * Generates a report from a given Velocity Template. The template name provided can be the name of a template
+     * Generates a report from a given Velocity Template. The template name
-     * contained in the jar file, such as 'XmlReport' or 'HtmlReport', or the template name can be the path to a
+     * 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 templateName the name of the template to load
-     * @param outFileName the filename and path to write the report to.
+     * @param outFileName the filename and path to write the report to
-     * @throws IOException is thrown when the template file does not exist.
+     * @throws ReportException is thrown when the report cannot be generated
-     * @throws Exception is thrown when an exception occurs.
      */
-    protected void generateReport(String templateName, String outFileName) throws Exception {
+    protected void generateReport(String templateName, String outFileName) throws ReportException {
         File outFile = new File(outFileName);
         if (outFile.getParentFile() == null) {
             outFile = new File(".", outFileName);
@@ -297,7 +307,7 @@ public class ReportGenerator {
         if (!outFile.getParentFile().exists()) {
             final boolean created = outFile.getParentFile().mkdirs();
             if (!created) {
-                throw new Exception("Unable to create directory '" + outFile.getParentFile().getAbsolutePath() + "'.");
+                throw new ReportException("Unable to create directory '" + outFile.getParentFile().getAbsolutePath() + "'.");
             }
         }
 
@@ -305,6 +315,8 @@ public class ReportGenerator {
         try {
             outputSteam = new FileOutputStream(outFile);
             generateReport(templateName, outputSteam);
+        } catch (FileNotFoundException ex) {
+            throw new ReportException("Unable to write to file: " + outFile, ex);
         } finally {
             if (outputSteam != null) {
                 try {

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

@@ -17,12 +17,19 @@
  */
 package org.owasp.dependencycheck;
 
+import java.io.IOException;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 import static org.junit.Assert.assertTrue;
 
 import org.junit.Test;
 import org.owasp.dependencycheck.data.nvdcve.CveDB;
+import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseProperties;
+import org.owasp.dependencycheck.exception.ExceptionCollection;
+import org.owasp.dependencycheck.exception.ReportException;
 import org.owasp.dependencycheck.reporting.ReportGenerator;
+import org.owasp.dependencycheck.utils.InvalidSettingException;
 import org.owasp.dependencycheck.utils.Settings;
 
 /**
@@ -34,10 +41,14 @@ public class EngineIntegrationTest extends BaseDBTestCase {
     /**
      * Test running the entire engine.
      *
-     * @throws Exception is thrown when an exception occurs.
+     * @throws java.io.IOException
+     * @throws org.owasp.dependencycheck.utils.InvalidSettingException
+     * @throws org.owasp.dependencycheck.data.nvdcve.DatabaseException
+     * @throws org.owasp.dependencycheck.exception.ReportException
+     * @throws org.owasp.dependencycheck.exception.ExceptionCollection
      */
     @Test
-    public void testEngine() throws Exception {
+    public void testEngine() throws IOException, InvalidSettingException, DatabaseException, ReportException, ExceptionCollection {
         String testClasses = "target/test-classes";
         boolean autoUpdate = Settings.getBoolean(Settings.KEYS.AUTO_UPDATE);
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, false);
@@ -45,7 +56,23 @@ public class EngineIntegrationTest extends BaseDBTestCase {
         Settings.setBoolean(Settings.KEYS.AUTO_UPDATE, autoUpdate);
         instance.scan(testClasses);
         assertTrue(instance.getDependencies().size() > 0);
+        try {
             instance.analyzeDependencies();
+        } catch (ExceptionCollection ex) {
+            if (ex.getExceptions().size()==1 &&
+                    (ex.getExceptions().get(0).getMessage().contains("bundle-audit") ||
+                    ex.getExceptions().get(0).getMessage().contains("AssemblyAnalyzer"))) {
+                //this is fine to ignore
+            } else if (ex.getExceptions().size()==2 &&
+                    ((ex.getExceptions().get(0).getMessage().contains("bundle-audit") &&
+                    ex.getExceptions().get(1).getMessage().contains("AssemblyAnalyzer")) ||
+                    (ex.getExceptions().get(1).getMessage().contains("bundle-audit") &&
+                    ex.getExceptions().get(0).getMessage().contains("AssemblyAnalyzer")))) {
+                //this is fine to ignore
+            } else {
+                throw ex;
+            }
+        }
         CveDB cveDB = new CveDB();
         cveDB.open();
         DatabaseProperties dbProp = cveDB.getDatabaseProperties();

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

@@ -26,6 +26,7 @@ import java.io.File;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
+import java.util.logging.Level;
 
 import org.junit.After;
 import org.junit.Assume;
@@ -40,6 +41,7 @@ import org.owasp.dependencycheck.dependency.Dependency;
 import org.owasp.dependencycheck.dependency.Evidence;
 import org.owasp.dependencycheck.dependency.Identifier;
 import org.owasp.dependencycheck.dependency.Vulnerability;
+import org.owasp.dependencycheck.exception.ExceptionCollection;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -176,6 +178,7 @@ public class RubyBundleAuditAnalyzerTest extends BaseDBTestCase {
      * Test Ruby dependencies and their paths.
      *
      * @throws AnalysisException is thrown when an exception occurs.
+     * @throws DatabaseException thrown when an exception occurs
      */
     @Test
     public void testDependenciesPath() throws AnalysisException, DatabaseException {
@@ -187,6 +190,8 @@ public class RubyBundleAuditAnalyzerTest extends BaseDBTestCase {
         } catch (NullPointerException ex) {
             LOGGER.error("NPE", ex);
             throw ex;
+        } catch (ExceptionCollection ex) {
+            Assume.assumeNoException("Exception setting up RubyBundleAuditAnalyzer; bundle audit may not be installed, or property \"analyzer.bundle.audit.path\" may not be set.", ex);
         }
         List<Dependency> dependencies = engine.getDependencies();
         LOGGER.info(dependencies.size() + " dependencies found.");

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

@@ -23,13 +23,16 @@ import org.owasp.dependencycheck.analyzer.Analyzer;
 import org.owasp.dependencycheck.analyzer.CPEAnalyzer;
 import org.owasp.dependencycheck.analyzer.FileTypeAnalyzer;
 import org.owasp.dependencycheck.data.nvdcve.DatabaseException;
+import org.owasp.dependencycheck.data.update.exception.UpdateException;
+import org.owasp.dependencycheck.exception.ExceptionCollection;
+import org.owasp.dependencycheck.exception.InitializationException;
 import org.owasp.dependencycheck.utils.Settings;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * A modified version of the core engine specifically designed to persist some data between multiple executions of a multi-module
+ * A modified version of the core engine specifically designed to persist some
- * Maven project.
+ * data between multiple executions of a multi-module Maven project.
  *
  * @author Jeremy Long
  */
@@ -52,16 +55,19 @@ public class Engine extends org.owasp.dependencycheck.Engine {
      */
     private List<MavenProject> reactorProjects;
     /**
-     * Key used in the MavenProject context values to note whether or not an update has been executed.
+     * Key used in the MavenProject context values to note whether or not an
+     * update has been executed.
      */
     public static final String UPDATE_EXECUTED_FLAG = "dependency-check-update-executed";
 
     /**
-     * Creates a new Engine to perform anyalsis on dependencies.
+     * Creates a new Engine to perform analysis on dependencies.
      *
      * @param project the current Maven project
-     * @param reactorProjects the reactor projects for the current Maven execution
+     * @param reactorProjects the reactor projects for the current Maven
-     * @throws DatabaseException thrown if there is an issue connecting to the database
+     * execution
+     * @throws DatabaseException thrown if there is an issue connecting to the
+     * database
      */
     public Engine(MavenProject project, List<MavenProject> reactorProjects) throws DatabaseException {
         this.currentProject = project;
@@ -71,9 +77,12 @@ public class Engine extends org.owasp.dependencycheck.Engine {
 
     /**
      * Runs the analyzers against all of the dependencies.
+     *
+     * @throws ExceptionCollection thrown if an exception occurred; contains a
+     * collection of exceptions that occurred during analysis.
      */
     @Override
-    public void analyzeDependencies() {
+    public void analyzeDependencies() throws ExceptionCollection {
         final MavenProject root = getExecutionRoot();
         if (root != null) {
             LOGGER.debug("Checking root project, {}, if updates have already been completed", root.getArtifactId());
@@ -91,8 +100,10 @@ public class Engine extends org.owasp.dependencycheck.Engine {
 
     /**
      * Runs the update steps of dependency-check.
+     *
+     * @throws UpdateException thrown if there is an exception
      */
-    public void update() {
+    public void update() throws UpdateException {
         final MavenProject root = getExecutionRoot();
         if (root != null && root.getContextValue(UPDATE_EXECUTED_FLAG) != null) {
             System.setProperty(Settings.KEYS.AUTO_UPDATE, Boolean.FALSE.toString());
@@ -103,20 +114,21 @@ public class Engine extends org.owasp.dependencycheck.Engine {
     /**
      * This constructor should not be called. Use Engine(MavenProject) instead.
      *
-     * @throws DatabaseException thrown if there is an issue connecting to the database
+     * @throws DatabaseException thrown if there is an issue connecting to the
+     * database
      */
     private Engine() throws DatabaseException {
     }
 
     /**
-     * Initializes the given analyzer. This skips the initialization of the CPEAnalyzer if it has been initialized by a previous
+     * Initializes the given analyzer. This skips the initialization of the
-     * execution.
+     * CPEAnalyzer if it has been initialized by a previous execution.
      *
      * @param analyzer the analyzer to initialize
      * @return the initialized analyzer
      */
     @Override
-    protected Analyzer initializeAnalyzer(Analyzer analyzer) {
+    protected Analyzer initializeAnalyzer(Analyzer analyzer) throws InitializationException {
         if (analyzer instanceof CPEAnalyzer) {
             CPEAnalyzer cpe = getPreviouslyLoadedCPEAnalyzer();
             if (cpe != null && cpe.isOpen()) {
@@ -129,7 +141,8 @@ public class Engine extends org.owasp.dependencycheck.Engine {
     }
 
     /**
-     * Releases resources used by the analyzers by calling close() on each analyzer.
+     * Releases resources used by the analyzers by calling close() on each
+     * analyzer.
      */
     @Override
     public void cleanup() {
@@ -216,8 +229,10 @@ public class Engine extends org.owasp.dependencycheck.Engine {
     }
 
     /**
-     * Resets the file type analyzers so that they can be re-used to scan additional directories. Without the reset the analyzer
+     * Resets the file type analyzers so that they can be re-used to scan
-     * might be disabled because the first scan/analyze did not identify any files that could be processed by the analyzer.
+     * additional directories. Without the reset the analyzer might be disabled
+     * because the first scan/analyze did not identify any files that could be
+     * processed by the analyzer.
      */
     public void resetFileTypeAnalyzers() {
         for (FileTypeAnalyzer a : getFileTypeAnalyzers()) {