cleanup and rebuild javadocs

Java/src/main/java/com/nuix/superutilities/annotations/AnnotationRepository.java

@@ -346,7 +346,6 @@ public void storeAllTags(Case nuixCase) throws IOException, SQLException {
 	 * @param nuixCase The case in which items will be tagged.
 	 * @param matchingMethod Determines how a record in the DB file is associated to an item in the case to apply tags to it.
 	 * @throws SQLException Thrown if there are errors while interacting with the SQLite DB file.
-	 * @throws  Thrown by Nuix if there is something 
 	 */
 	public void applyTagsFromDatabaseToCase(Case nuixCase, AnnotationMatchingMethod matchingMethod) throws SQLException {
 		// Will reuse this multiple times to provide values to be bound to prepared SQL statements later

Java/src/main/java/com/nuix/superutilities/annotations/BulkRedactorSettings.java

@@ -14,7 +14,7 @@
 import nuix.MarkupSet;
 
 /***
- * Provides settings regarding bulk redaction performed by {@link BulkRedactor#findAndMarkup(Case, BulkRedactorSettings, Collection)}.
+ * Provides settings regarding bulk redaction performed by {@link BulkRedactor#findAndMarkup(Case, BulkRedactorSettings, Collection, int)}.
  * @author Jason Wells
  *
  */

Java/src/main/java/com/nuix/superutilities/export/TemplateExporter.java

@@ -63,7 +63,7 @@ public String render(Item item, Map<String,Object> data){
 		return (String) container.callMethod("", "render", new Object[]{item,toSend});
 	}
 
-	public void renderToFile(Item item, File outputFile, Map<String,Object> data) throws Exception{
+	public void renderToFile(Item item, File outputFile, Map<String,Object> data) throws Exception {
 		FileOutputStream fos = null;
 		BufferedWriter bw = null;
 

Java/src/main/java/com/nuix/superutilities/items/SuperItemUtility.java

@@ -5,6 +5,7 @@
 import java.net.URLDecoder;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -267,4 +268,36 @@ public boolean itemsAreSiblings(Item a, Item b){
 
 		return true;
 	}
+
+	/***
+	 * Gets items and sibling items within a certain ordinal distance.
+	 * @param items The items to obtain the neighboring siblings of
+	 * @param itemsBefore How many siblings before each item to include
+	 * @param itemsAfter How many siblings after each item to include
+	 * @return A new list of items which includes both input items and neighboring siblings, sorted by position
+	 */
+	public List<Item> getItemsAndNeighboringSiblings(List<Item> items, int itemsBefore, int itemsAfter){
+		if(itemsBefore < 0) { itemsBefore = 0; }
+		if(itemsAfter < 0) { itemsAfter = 0; }
+
+		if(items.size() < 1) { return Collections.emptyList(); }
+		else {
+			Set<Item> tempSet = new HashSet<Item>();
+			for(Item item : items) {
+				Item parent = item.getParent();
+				List<Item> siblings = parent.getChildren();
+				int itemIndex = siblings.indexOf(item);
+				int first = itemIndex - itemsBefore;
+				int last = itemIndex + itemsAfter;
+				if(first < 0) { first = 0; }
+				if(last > items.size() - 1) { last = items.size() - 1; }
+				for (int i = first; i <= last; i++) {
+					tempSet.add(items.get(i));
+				}
+			}
+			List<Item> result = new ArrayList<Item>();
+			result.addAll(tempSet);
+			return SuperUtilities.getItemUtility().sortItemsByPosition(result);
+		}
+	}
 }

Java/src/main/java/com/nuix/superutilities/misc/ProfileDigester.java

@@ -329,7 +329,7 @@ public void setDigestCustomField(String digestCustomField) {
 
 	/***
 	 * Gets whether an existing value in the specified custom metadata field should be used if present.  When true,
-	 * if an item has the custom field specified by callin {@link #setDigestCustomField(String)) and it has a value, that value will
+	 * if an item has the custom field specified by calling {@link #setDigestCustomField(String)} and it has a value, that value will
 	 * be used rather than calculating a value.  If false the value will always be calculated fresh.
 	 * @return Whether an existing value in the specified custom metadata field should be used when present
 	 */
@@ -339,9 +339,9 @@ public boolean getUseExistingValueWhenPresent() {
 
 	/***
 	 * Sets whether an existing value in the specified custom metadata field should be used if present.  When true,
-	 * if an item has the custom field specified by calling {@link #setDigestCustomField(String)) and it has a value, that value will
+	 * if an item has the custom field specified by calling {@link #setDigestCustomField(String)} and it has a value, that value will
 	 * be used rather than calculating a value.  If false the value will always be calculated fresh.
-	 * @param useExistingValueWhenPresent
+	 * @param useExistingValueWhenPresent whether an existing value in the specified custom metadata field should be used if present
 	 */
 	public void setUseExistingValueWhenPresent(boolean useExistingValueWhenPresent) {
 		this.useExistingValueWhenPresent = useExistingValueWhenPresent;

Java/src/main/java/com/nuix/superutilities/misc/ZipHelper.java

@@ -1,5 +1,7 @@
 package com.nuix.superutilities.misc;
 
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -8,10 +10,45 @@
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
+import org.apache.commons.compress.archivers.sevenz.SevenZArchiveEntry;
+import org.apache.commons.compress.archivers.sevenz.SevenZMethod;
+import org.apache.commons.compress.archivers.sevenz.SevenZOutputFile;
 import org.apache.commons.io.IOUtils;
 import org.apache.jena.ext.com.google.common.primitives.Ints;
 
 public class ZipHelper {
+
+	public static void compressDirectoryToSevenZipFile(String directory, String sevenZipFile) throws IOException {
+		SevenZOutputFile sevenZipOutput = new SevenZOutputFile(new File(sevenZipFile));
+		sevenZipOutput.setContentCompression(SevenZMethod.DEFLATE);
+		compressDirectoryToSevenZipFile(directory, directory, sevenZipOutput);
+		sevenZipOutput.finish();
+		sevenZipOutput.close();
+	}
+
+	private static void compressDirectoryToSevenZipFile(String rootDir, String sourceDir, SevenZOutputFile sevenZipOutput) throws IOException {
+		for (File file : new File(sourceDir).listFiles()) {
+	        if (file.isDirectory()) {
+	        	compressDirectoryToSevenZipFile(rootDir, sourceDir + File.separator + file.getName(), sevenZipOutput);
+	        } else {
+	        	String dir = sourceDir.replace(rootDir, "");
+	        	SevenZArchiveEntry entry = null;
+	        	if (!dir.trim().isEmpty()) {
+	        		entry = sevenZipOutput.createArchiveEntry(file,dir + File.separator + file.getName());	
+	        	} else {
+	        		entry = sevenZipOutput.createArchiveEntry(file,file.getName());
+	        	}
+	        	sevenZipOutput.putArchiveEntry(entry);
+	        	FileInputStream in = new FileInputStream(sourceDir + File.separator + file.getName());
+	            BufferedInputStream bufferedIn = new BufferedInputStream(in);
+	        	sevenZipOutput.write(bufferedIn);
+	        	bufferedIn.close();
+	        	in.close();
+	        	sevenZipOutput.closeArchiveEntry();
+	        }
+		}
+	}
+
 	/***
 	 * Compresses the contents of the given directory (files and sub-directories) in to a Zip file.
 	 * @param directory The directory to archive into the Zip file.
@@ -23,8 +60,12 @@ public class ZipHelper {
 	@SuppressWarnings("deprecation")
 	public static void compressDirectoryToZipFile(String directory, String zipFile, int compressionLevel) throws IOException, FileNotFoundException {
 		ZipOutputStream zipStream = null;
+		FileOutputStream fileOutStream = null;
+		BufferedOutputStream bufferedOutStream = null;
 		try{
-			zipStream = new ZipOutputStream(new FileOutputStream(zipFile));
+			fileOutStream = new FileOutputStream(zipFile);
+			bufferedOutStream = new BufferedOutputStream(fileOutStream);
+			zipStream = new ZipOutputStream(bufferedOutStream);
 			zipStream.setLevel(Ints.constrainToRange(compressionLevel, 0, 9));
 			compressDirectoryToZipfile(directory,directory,zipStream);	
 		} finally {
@@ -57,7 +98,8 @@ private static void compressDirectoryToZipfile(String rootDir, String sourceDir,
 
 	            out.putNextEntry(entry);
 	            FileInputStream in = new FileInputStream(sourceDir + File.separator + file.getName());
-	            IOUtils.copy(in, out);
+	            BufferedInputStream bufferedIn = new BufferedInputStream(in);
+	            IOUtils.copy(bufferedIn, out);
 	            IOUtils.closeQuietly(in);
 	        }
 	    }

Java/src/main/java/com/nuix/superutilities/regex/PatternInfo.java

@@ -25,6 +25,8 @@ public PatternInfo(String title, String expression){
 	/***
 	 * Compiles the regular expression String provided into a Java Pattern object
 	 * @param caseSensitive Whether it should be case sensitive
+	 * @param multiline Whether the multi-line matching flag should be set
+	 * @param dotAll Whether the dot matches all flag should be set
 	 */
 	public void compile(boolean caseSensitive, boolean multiline, boolean dotAll){
 		if(pattern == null){
@@ -53,8 +55,8 @@ public String getExpression() {
 	}
 
 	/***
-	 * Gets the compiled Pattern object.  Note this will return null until {@link #compile(boolean)} is called.
-	 * @return The compiled Pattern object or null if {@link #compile(boolean)} has not yet been called.
+	 * Gets the compiled Pattern object.  Note this will return null until {@link #compile(boolean, boolean, boolean)} is called.
+	 * @return The compiled Pattern object or null if {@link #compile(boolean, boolean, boolean)} has not yet been called.
 	 */
 	public Pattern getPattern() {
 		return pattern;

Java/src/main/java/com/nuix/superutilities/reporting/IntersectionReport.java

@@ -7,6 +7,7 @@
 import java.util.stream.Collectors;
 
 import org.apache.log4j.Logger;
+import org.joda.time.DateTime;
 
 import com.aspose.cells.BackgroundType;
 import com.aspose.cells.Color;
@@ -32,6 +33,40 @@ public class IntersectionReport {
 
 	private static Logger logger = Logger.getLogger(IntersectionReport.class);
 
+	/***
+	 * Analyzes batch loads in the given case, determining which have a loaded datetime that falls
+	 * within the specified range, returning the GUIDs of the batch loads which qualify.
+	 * @param nuixCase The case to analyze
+	 * @param min The minimum date time, can be null
+	 * @param max The maximum date time, can be null
+	 * @return Returns a list of zero or more GUIDs for the batch loads loaded within the given date range
+	 */
+	public static List<String> findBatchLoadsInDateRange(Case nuixCase, DateTime min, DateTime max) {
+		List<String> inRangeBatchLoadGuids = new ArrayList<String>();
+		List<BatchLoadDetails> allBatchLoads = nuixCase.getBatchLoads();
+
+		// Filter all batch loads by whether their loaded date falls within
+		// the range specifies by the min/max values
+		for(BatchLoadDetails bld : allBatchLoads) {
+			boolean satisfiesMin = true;
+			boolean satisfiesMax = true;
+
+			if(min != null) {
+				satisfiesMin = bld.getLoaded().isAfter(min);
+			}
+
+			if(max != null) {
+				satisfiesMax = bld.getLoaded().isBefore(max);
+			}
+
+			if(satisfiesMin && satisfiesMax) {
+				inRangeBatchLoadGuids.add(bld.getBatchId());
+			}
+		}
+
+		return inRangeBatchLoadGuids;
+	}
+
 	private SimpleXlsx xlsx = null;
 
 	private Style rowCategoryLabelStyle = null;
@@ -163,27 +198,8 @@ public void generate(Case nuixCase, String sheetName, IntersectionReportSheetCon
 		// in the case and filter to those within our date range.  Using that filtered set we then get their batch
 		// load GUIDs and use that to attach additional scope query for those batch loads.
 		if(sheetConfig.hasBatchLoadDateCriteria()) {
-			List<String> inRangeBatchLoadGuids = new ArrayList<String>();
-			List<BatchLoadDetails> allBatchLoads = nuixCase.getBatchLoads();
-
-			// Filter all batch loads by whether their loaded date falls within
-			// the range specifies by the min/max values
-			for(BatchLoadDetails bld : allBatchLoads) {
-				boolean satisfiesMin = true;
-				boolean satisfiesMax = true;
-
-				if(sheetConfig.getBatchLoadMinDate() != null) {
-					satisfiesMin = bld.getLoaded().isAfter(sheetConfig.getBatchLoadMinDate());
-				}
-
-				if(sheetConfig.getBatchLoadMaxDate() != null) {
-					satisfiesMax = bld.getLoaded().isBefore(sheetConfig.getBatchLoadMaxDate());
-				}
-
-				if(satisfiesMin && satisfiesMax) {
-					inRangeBatchLoadGuids.add(bld.getBatchId());
-				}
-			}
+			List<String> inRangeBatchLoadGuids = findBatchLoadsInDateRange(nuixCase,
+					sheetConfig.getBatchLoadMinDate(),sheetConfig.getBatchLoadMaxDate());
 
 			String batchLoadGuidQuery = "";
 			if(inRangeBatchLoadGuids.size() > 0) {