coverity, checkstyle, pmd, and findbugs suggested corrections

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

@@ -17,7 +17,6 @@
  */
 package org.owasp.dependencycheck.analyzer;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileFilter;
 import java.io.FileOutputStream;
@@ -36,9 +35,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
 import org.xml.sax.SAXException;
-import java.io.InputStreamReader;
-import java.nio.file.Path;
-import java.nio.file.Paths;
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -122,6 +118,10 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
         }
 
         final List<String> args = buildArgumentList();
+        if (args == null) {
+            LOGGER.warn("Assembly Analyzer was unable to execute");
+            return;
+        }
         args.add(dependency.getActualFilePath());
         final ProcessBuilder pb = new ProcessBuilder(args);
         Document doc = null;
@@ -249,6 +249,7 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
                     + "'exe' or 'dll' was scanned. The 'mono' executale could not be found on "
                     + "the path; either disable the Assembly Analyzer or configure the path mono.");
             LOGGER.error("----------------------------------------------------");
+            return;
         }
         try {
             final ProcessBuilder pb = new ProcessBuilder(args);
@@ -353,10 +354,10 @@ public class AssemblyAnalyzer extends AbstractFileTypeAnalyzer {
      * <code>false</code>
      */
     private boolean isInPath(String file) {
-        ProcessBuilder pb = new ProcessBuilder("which", file);
+        final ProcessBuilder pb = new ProcessBuilder("which", file);
         try {
-            Process proc = pb.start();
+            final Process proc = pb.start();
-            int retCode = proc.waitFor();
+            final int retCode = proc.waitFor();
             if (retCode == 0) {
                 return true;
             }

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

@@ -196,6 +196,9 @@ public class CMakeAnalyzer extends AbstractFileTypeAnalyzer {
      * @param engine the dependency-check engine
      * @param contents the version information
      */
+    @edu.umd.cs.findbugs.annotations.SuppressFBWarnings(
+            value = "DM_DEFAULT_ENCODING",
+            justification = "Default encoding is only used if UTF-8 is not available")
     private void analyzeSetVersionCommand(Dependency dependency, Engine engine, String contents) {
         Dependency currentDep = dependency;
 

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

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *
- * © Copyright IBM Corporation 2016.
+ * Copyright (c) 2016 IBM Corporation. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
@@ -154,19 +154,32 @@ public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
         setPackagePath(dependency);
     }
 
+    /**
+     * Extracts evidence from the contents and adds it to the given evidence
+     * collection.
+     *
+     * @param evidences the evidence collection to update
+     * @param contents the text to extract evidence from
+     * @param blockVariable the block variable within the content to search for
+     * @param field the name of the field being searched for
+     * @param fieldPattern the field pattern within the contents to search for
+     * @param confidence the confidence level of the evidence if found
+     * @return the string that was added as evidence
+     */
     private String addStringEvidence(EvidenceCollection evidences, String contents,
             String blockVariable, String field, String fieldPattern, Confidence confidence) {
         String value = "";
 
         //capture array value between [ ]
         final Matcher arrayMatcher = Pattern.compile(
-                String.format("\\s*?%s\\.%s\\s*?=\\s*?\\{\\s*?(.*?)\\s*?\\}", blockVariable, fieldPattern), Pattern.CASE_INSENSITIVE).matcher(contents);
+                String.format("\\s*?%s\\.%s\\s*?=\\s*?\\{\\s*?(.*?)\\s*?\\}", blockVariable, fieldPattern),
+                Pattern.CASE_INSENSITIVE).matcher(contents);
         if (arrayMatcher.find()) {
             value = arrayMatcher.group(1);
-        } //capture single value between quotes
+        } else { //capture single value between quotes
-        else {
             final Matcher matcher = Pattern.compile(
-                    String.format("\\s*?%s\\.%s\\s*?=\\s*?(['\"])(.*?)\\1", blockVariable, fieldPattern), Pattern.CASE_INSENSITIVE).matcher(contents);
+                    String.format("\\s*?%s\\.%s\\s*?=\\s*?(['\"])(.*?)\\1", blockVariable, fieldPattern),
+                    Pattern.CASE_INSENSITIVE).matcher(contents);
             if (matcher.find()) {
                 value = matcher.group(2);
             }
@@ -177,9 +190,14 @@ public class CocoaPodsAnalyzer extends AbstractFileTypeAnalyzer {
         return value;
     }
 
+    /**
+     * Sets the package path on the given dependency.
+     *
+     * @param dep the dependency to update
+     */
     private void setPackagePath(Dependency dep) {
-        File file = new File(dep.getFilePath());
+        final File file = new File(dep.getFilePath());
-        String parent = file.getParent();
+        final String parent = file.getParent();
         if (parent != null) {
             dep.setPackagePath(parent);
         }

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

@@ -411,6 +411,14 @@ public class DependencyBundlingAnalyzer extends AbstractAnalyzer implements Anal
         return false;
     }
 
+    /**
+     * Determines which of the swift dependencies should be considered the
+     * primary.
+     *
+     * @param dependency1 the first swift dependency to compare
+     * @param dependency2 the second swift dependency to compare
+     * @return the primary swift dependency
+     */
     private Dependency getMainSwiftDependency(Dependency dependency1, Dependency dependency2) {
         if (isSameSwiftPackage(dependency1, dependency2)) {
             if (dependency1.getFileName().endsWith(".podspec")) {

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

@@ -70,10 +70,12 @@ public class FileNameAnalyzer extends AbstractAnalyzer implements Analyzer {
     /**
      * Python init files
      */
+    //CSOFF: WhitespaceAfter
     private static final NameFileFilter IGNORED_FILES = new NameFileFilter(new String[]{
         "__init__.py",
         "__init__.pyc",
         "__init__.pyo",});
+    //CSON: WhitespaceAfter
 
     /**
      * Collects information about the file name.

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

@@ -228,10 +228,13 @@ public class PythonDistributionAnalyzer extends AbstractFileTypeAnalyzer {
             throw new AnalysisException(ex);
         }
 
-        collectWheelMetadata(
+        File matchingFile = getMatchingFile(temp, folderFilter);
-                dependency,
+        if (matchingFile != null) {
-                getMatchingFile(getMatchingFile(temp, folderFilter),
+            matchingFile = getMatchingFile(matchingFile, metadataFilter);
-                        metadataFilter));
+            if (matchingFile != null) {
+                collectWheelMetadata(dependency, matchingFile);
+            }
+        }
     }
 
     /**

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

@@ -280,11 +280,16 @@ public class RubyBundleAuditAnalyzer extends AbstractFileTypeAnalyzer {
         }
         final File parentFile = dependency.getActualFile().getParentFile();
         final Process process = launchBundleAudit(parentFile);
+        final int exitValue;
         try {
-            process.waitFor();
+            exitValue = process.waitFor();
         } catch (InterruptedException ie) {
             throw new AnalysisException("bundle-audit process interrupted", ie);
         }
+        if (exitValue != 0) {
+            final String msg = String.format("Unexpected exit code from bundle-audit process; exit code: %s", exitValue);
+            throw new AnalysisException(msg);
+        }
         BufferedReader rdr = null;
         BufferedReader errReader = null;
         try {

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

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *
- * © Copyright IBM Corporation 2016.
+ * Copyright (c) 2016 IBM Corporation. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 

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

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  *
- * © Copyright IBM Corporation 2016.
+ * Copyright (c) 2016 IBM Corporation. All Rights Reserved.
  */
 package org.owasp.dependencycheck.analyzer;
 
@@ -146,6 +146,17 @@ public class SwiftPackageManagerAnalyzer extends AbstractFileTypeAnalyzer {
         setPackagePath(dependency);
     }
 
+    /**
+     * Extracts evidence from the package description and adds it to the given
+     * evidence collection.
+     *
+     * @param evidences the evidence collection to update
+     * @param packageDescription the text to extract evidence from
+     * @param field the name of the field being searched for
+     * @param fieldPattern the field pattern within the contents to search for
+     * @param confidence the confidence level of the evidence if found
+     * @return the string that was added as evidence
+     */
     private String addStringEvidence(EvidenceCollection evidences,
             String packageDescription, String field, String fieldPattern, Confidence confidence) {
         String value = "";
@@ -166,6 +177,11 @@ public class SwiftPackageManagerAnalyzer extends AbstractFileTypeAnalyzer {
         return value;
     }
 
+    /**
+     * Sets the package path on the given dependency.
+     *
+     * @param dep the dependency to update
+     */
     private void setPackagePath(Dependency dep) {
         final File file = new File(dep.getFilePath());
         final String parent = file.getParent();

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

@@ -212,7 +212,7 @@ public class ExceptionCollection extends Exception {
      */
     @Override
     public String getMessage() {
-        StringBuilder sb = new StringBuilder();
+        final StringBuilder sb = new StringBuilder();
         final String msg = super.getMessage();
         if (msg == null || msg.isEmpty()) {
             sb.append("One or more exceptions occured during analysis:");

dependency-check-core/src/main/java/org/owasp/dependencycheck/xml/suppression/SuppressionErrorHandler.java

@@ -17,8 +17,6 @@
  */
 package org.owasp.dependencycheck.xml.suppression;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.xml.sax.ErrorHandler;
 import org.xml.sax.SAXException;
 import org.xml.sax.SAXParseException;
@@ -33,7 +31,7 @@ public class SuppressionErrorHandler implements ErrorHandler {
     /**
      * The logger.
      */
-    private static final Logger LOGGER = LoggerFactory.getLogger(SuppressionErrorHandler.class);
+    //private static final Logger LOGGER = LoggerFactory.getLogger(SuppressionErrorHandler.class);
 
     /**
      * Builds a prettier exception message.

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

@@ -58,11 +58,11 @@ public final class Checksum {
      * @throws NoSuchAlgorithmException when an algorithm is specified that does not exist
      */
     public static byte[] getChecksum(String algorithm, File file) throws NoSuchAlgorithmException, IOException {
-        MessageDigest digest = MessageDigest.getInstance(algorithm);
+        final MessageDigest digest = MessageDigest.getInstance(algorithm);
         FileInputStream fis = null;
         try {
             fis = new FileInputStream(file);
-            FileChannel ch = fis.getChannel();
+            final FileChannel ch = fis.getChannel();
             long remainingToRead = file.length();
             long start = 0;
             while (remainingToRead > 0) {
@@ -74,7 +74,7 @@ public final class Checksum {
                     amountToRead = remainingToRead;
                     remainingToRead = 0;
                 }
-                MappedByteBuffer byteBuffer = ch.map(FileChannel.MapMode.READ_ONLY, start, amountToRead);
+                final MappedByteBuffer byteBuffer = ch.map(FileChannel.MapMode.READ_ONLY, start, amountToRead);
                 digest.update(byteBuffer);
                 start += amountToRead;
             }
@@ -99,7 +99,7 @@ public final class Checksum {
      * @throws NoSuchAlgorithmException when the MD5 algorithm is not available
      */
     public static String getMD5Checksum(File file) throws IOException, NoSuchAlgorithmException {
-        byte[] b = getChecksum("MD5", file);
+        final byte[] b = getChecksum("MD5", file);
         return getHex(b);
     }
 
@@ -112,7 +112,7 @@ public final class Checksum {
      * @throws NoSuchAlgorithmException when the SHA1 algorithm is not available
      */
     public static String getSHA1Checksum(File file) throws IOException, NoSuchAlgorithmException {
-        byte[] b = getChecksum("SHA1", file);
+        final byte[] b = getChecksum("SHA1", file);
         return getHex(b);
     }
     /**

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

@@ -304,7 +304,7 @@ public final class Downloader {
         Throwable cause = ex;
         while (cause != null) {
             if (cause instanceof java.net.UnknownHostException) {
-                final String msg = String.format("Unable to resolve domain '%s'", cause.getMessage());
+                final String msg = format("Unable to resolve domain '%s'", cause.getMessage());
                 LOGGER.error(msg);
                 throw new DownloadFailedException(msg);
             }

src/main/config/checkstyle-suppressions.xml

@@ -7,8 +7,9 @@
 <suppressions>
     <suppress checks=".*" files=".*[\\/]package-info\.java" />
     <suppress checks=".*" files=".*[\\/]org[\\/]owasp[\\/]dependencycheck[\\/]utils[\\/]Filter.java" />
-    <suppress checks=".*" files=".*[\\/]org[\\/]owasp[\\/]dependencycheck[\\/]utils[\\/]Checksum.java" />
+    <!--suppress checks=".*" files=".*[\\/]org[\\/]owasp[\\/]dependencycheck[\\/]utils[\\/]Checksum.java" /-->
     <suppress checks=".*" files=".*[\\/]generated[\\/].*.java" />
     <suppress checks=".*" files=".*[\\/]maven-plugin-plugin-sources[\\/].*.properties" />
-    <suppress checks=".*" files=".*[\\/]org[\\/]owasp[\\/]dependencycheck[\\/]org[\\/]apache[\\/].*.java" />
+    <!--suppress checks=".*" files=".*[\\/]org[\\/]owasp[\\/]dependencycheck[\\/]org[\\/]apache[\\/].*.java" /-->
+    <suppress checks="RegexpHeader" files=".*[\\/]org[\\/]owasp[\\/]dependencycheck[\\/]utils[\\/]SSLSocketFactoryEx.java" />
 </suppressions>