added comments, minor refactoring as part of reviewing hash db code for memory leaks. No logic changes

Core/src/org/sleuthkit/autopsy/ingest/FileIngestPipeline.java

@@ -68,6 +68,10 @@ final class FileIngestPipeline {
         return modules.isEmpty();
     }
 
+    /**
+     * Start up all of the modules in the pipeline. 
+     * @return List of errors or empty list if no errors
+     */
     List<IngestModuleError> startUp() {
         List<IngestModuleError> errors = new ArrayList<>();
         for (FileIngestModuleDecorator module : modules) {
@@ -80,6 +84,13 @@ final class FileIngestPipeline {
         return errors;
     }
 
+    /**
+     * Process the file down the pipeline of modules.
+     * Startup must have been called before this is called.
+     * 
+     * @param file File to analyze
+     * @return List of errors or empty list if no errors
+     */
     List<IngestModuleError> process(AbstractFile file) {
         List<IngestModuleError> errors = new ArrayList<>();
         for (FileIngestModuleDecorator module : modules) {

Core/src/org/sleuthkit/autopsy/ingest/FileIngestTask.java

@@ -21,6 +21,10 @@ package org.sleuthkit.autopsy.ingest;
 import java.util.Objects;
 import org.sleuthkit.datamodel.AbstractFile;
 
+/**
+ * Represents a single file analysis task, which is defined
+ * by a file to analyze and the InjestJob/Pipeline to run it on.
+ */
 final class FileIngestTask extends IngestTask {
 
     private final AbstractFile file;

Core/src/org/sleuthkit/autopsy/ingest/IngestJob.java

@@ -32,6 +32,10 @@ import org.sleuthkit.autopsy.coreutils.Logger;
 import org.sleuthkit.datamodel.AbstractFile;
 import org.sleuthkit.datamodel.Content;
 
+/**
+ * InjestJobs store all settings and data associated with the user selecting a
+ * datasource and running a set of ingest modules on it. 
+ */
 final class IngestJob {
 
     private static final Logger logger = Logger.getLogger(IngestManager.class.getName());
@@ -102,6 +106,11 @@ final class IngestJob {
         return processUnallocatedSpace;
     }
 
+    /**
+     * Create the file and data source pipelines.
+     * @param ingestModuleTemplates
+     * @throws InterruptedException 
+     */
     private void createIngestPipelines(List<IngestModuleTemplate> ingestModuleTemplates) throws InterruptedException {
         IngestJobContext context = new IngestJobContext(this);
         dataSourceIngestPipeline = new DataSourceIngestPipeline(context, ingestModuleTemplates);
@@ -118,6 +127,11 @@ final class IngestJob {
         return true;
     }
 
+    /**
+     * Start both the data source and file ingest pipelines
+     * @return
+     * @throws InterruptedException 
+     */
     private List<IngestModuleError> start() throws InterruptedException {
         List<IngestModuleError> errors = startUpIngestPipelines();
         if (errors.isEmpty()) {
@@ -142,6 +156,14 @@ final class IngestJob {
         return errors;
     }
 
+    
+    /**
+     * Startup each of the file and data source ingest modules to collect
+     * possible errors.
+     * 
+     * @return
+     * @throws InterruptedException 
+     */
     private List<IngestModuleError> startUpIngestPipelines() throws InterruptedException {
         List<IngestModuleError> errors = new ArrayList<>();
         errors.addAll(dataSourceIngestPipeline.startUp());

HashDatabase/src/org/sleuthkit/autopsy/hashdatabase/HashDbIngestModule.java

@@ -44,7 +44,7 @@ import org.sleuthkit.datamodel.TskException;
 import org.sleuthkit.autopsy.hashdatabase.HashDbManager.HashDb;
 import org.sleuthkit.autopsy.ingest.FileIngestModule;
 import org.sleuthkit.autopsy.ingest.IngestModuleReferenceCounter;
-import org.sleuthkit.datamodel.HashInfo;
+import org.sleuthkit.datamodel.HashHitInfo;
 
 public class HashDbIngestModule implements FileIngestModule {
     private static final Logger logger = Logger.getLogger(HashDbIngestModule.class.getName());
@@ -82,8 +82,8 @@ public class HashDbIngestModule implements FileIngestModule {
     @Override
     public void startUp(org.sleuthkit.autopsy.ingest.IngestJobContext context) throws IngestModuleException {
         jobId = context.getJobId();  
-        getEnabledHashSets(hashDbManager.getKnownBadFileHashSets(), knownBadHashSets);
+        updateEnabledHashSets(hashDbManager.getKnownBadFileHashSets(), knownBadHashSets);
-        getEnabledHashSets(hashDbManager.getKnownFileHashSets(), knownHashSets);        
+        updateEnabledHashSets(hashDbManager.getKnownFileHashSets(), knownHashSets);        
         
         if (refCounter.incrementAndGet(jobId) == 1) {                  
             // if first module for this job then post error msgs if needed
@@ -108,9 +108,14 @@ public class HashDbIngestModule implements FileIngestModule {
         }
     }
     
-    private void getEnabledHashSets(List<HashDb> hashSets, List<HashDb> enabledHashSets) {
+    /**
+     * Cycle through list of hashsets and return the subset that is enabled.
+     * @param allHashSets List of all hashsets from DB manager
+     * @param enabledHashSets List of enabled ones to return.  
+     */
+    private void updateEnabledHashSets(List<HashDb> allHashSets, List<HashDb> enabledHashSets) {
         enabledHashSets.clear();
-        for (HashDb db : hashSets) {
+        for (HashDb db : allHashSets) {
             if (settings.isHashSetEnabled(db.getHashSetName())) {
                 try {
                     if (db.hasIndex()) {
@@ -178,7 +183,7 @@ public class HashDbIngestModule implements FileIngestModule {
         for (HashDb db : knownBadHashSets) {
             try {
                 long lookupstart = System.currentTimeMillis();
-                HashInfo hashInfo = db.lookUp(file);
+                HashHitInfo hashInfo = db.lookupMD5(file);
                 if (null != hashInfo) {
                     foundBad = true;
                     totals.totalKnownBadCount.incrementAndGet();
@@ -239,7 +244,7 @@ public class HashDbIngestModule implements FileIngestModule {
             for (HashDb db : knownHashSets) {
                 try {
                     long lookupstart = System.currentTimeMillis();
-                    if (db.hasMd5HashOf(file)) {
+                    if (db.lookupMD5Quick(file)) {
                         try {
                             skCase.setKnown(file, TskData.FileKnown.KNOWN);
                             break;

HashDatabase/src/org/sleuthkit/autopsy/hashdatabase/HashDbManager.java

@@ -49,7 +49,7 @@ import org.netbeans.api.progress.ProgressHandleFactory;
 import org.sleuthkit.autopsy.coreutils.Logger;
 import org.sleuthkit.datamodel.AbstractFile;
 import org.sleuthkit.datamodel.Content;
-import org.sleuthkit.datamodel.HashInfo;
+import org.sleuthkit.datamodel.HashHitInfo;
 import org.sleuthkit.datamodel.HashEntry;
 import org.sleuthkit.datamodel.SleuthkitJNI;
 import org.sleuthkit.datamodel.TskCoreException;
@@ -883,7 +883,13 @@ public class HashDbManager implements PropertyChangeListener {
             SleuthkitJNI.addToHashDatabase(hashes, handle);
         }
 
-        public boolean hasMd5HashOf(Content content) throws TskCoreException {
+        /**
+         * Perform a basic boolean lookup of the file's hash. 
+         * @param content
+         * @return True if file's MD5 is in the hash database
+         * @throws TskCoreException 
+         */
+        public boolean lookupMD5Quick(Content content) throws TskCoreException {
             boolean result = false;
             assert content instanceof AbstractFile;
             if (content instanceof AbstractFile) {
@@ -895,8 +901,14 @@ public class HashDbManager implements PropertyChangeListener {
             return result;
         }
 
-        public HashInfo lookUp(Content content) throws TskCoreException {
+        /**
-            HashInfo result = null;
+         * Lookup hash value in DB and provide details on file. 
+         * @param content
+         * @return null if file is not in database.
+         * @throws TskCoreException 
+         */
+        public HashHitInfo lookupMD5(Content content) throws TskCoreException {
+            HashHitInfo result = null;
             // This only works for AbstractFiles and MD5 hashes at present. 
             assert content instanceof AbstractFile;
             if (content instanceof AbstractFile) {
@@ -907,6 +919,7 @@ public class HashDbManager implements PropertyChangeListener {
             }
             return result;
         }
+        
 
         boolean hasIndex() throws TskCoreException {
             return SleuthkitJNI.hashDatabaseHasLookupIndex(handle);