Adds the -insitu flag

generates a finding aid but no IUPAC FAIRSpec Collection
within the *originating* directory source.

Safeguards need to be put in place, but it does work, and the Finding
Aid maintains a significant number of representations in byte[] form.

src/main/java/com/integratedgraphics/extractor/DOICrawler.java

@@ -534,7 +534,7 @@ public DOICrawler(String... args) {
 	 */
 	@Override
 	public void addDeferredPropertyOrRepresentation(String key, Object val, 
-			boolean isInLine, String mediaType, String note) {
+			boolean isInLine, String mediaType, String note, String src) {
 		// TODO Auto-generated method stub
 
 	}
@@ -698,7 +698,7 @@ protected void createFindingAid() {
 			processRecords(null, doiList);
 			String aid = faHelper.generateFindingAid(targetPath);
 			if (aid != null && createLandingPage) {
-				buildSite();
+				buildSite(targetPath);
 			}
 
 		} catch (Exception e) {

src/main/java/com/integratedgraphics/extractor/ExtractorUtils.java

@@ -892,9 +892,9 @@ public void setLocalSourceFileName(String name) {
 		public void setLists(String rootPath, String ignore, String accept) {
 			if (lstManifest != null)
 				return;
-			lstManifest = new FileList(rootPath, "manifest");
-			lstIgnored = new FileList(rootPath, "ignored");
-			lstAccepted = new FileList(rootPath, "accepted");
+			lstManifest = new FileList(rootPath, "manifest", null);
+			lstIgnored = new FileList(rootPath, "ignored", null);
+			lstAccepted = new FileList(rootPath, "accepted", null);
 			if (ignore != null)
 				lstIgnored.setAcceptPattern(ignore);
 			if (accept != null)

src/main/java/com/integratedgraphics/extractor/FindingAidCreator.java

@@ -68,6 +68,13 @@ public abstract class FindingAidCreator implements MetadataReceiverI {
 	 */
 	protected boolean addPublicationMetadata = false;
 
+	/**
+	 * setting insitu true generates an entirely self-contained finding aid, with
+	 * no local files at all, only origin files, without any rezipping, 
+	 * in the origin directory. The target directory only contains ancillary files.
+	 */
+	protected boolean insitu = false;
+
 	/**
 	 * set true to zip up the extracted collection, placing that in the target
 	 * directory
@@ -159,7 +166,7 @@ protected void setDerivedFlags() {
 		// this next is independent of readOnly
 		// false to bypass final creation of an
 		// _IFD_collection.zip file
-		createZippedCollection = createZippedCollection && !debugReadOnly;
+		createZippedCollection = createZippedCollection && !insitu && !debugReadOnly;
 
 		readOnly |= debugReadOnly; // for testing; when true, no output other than a log file is produced
 		noOutput = (createFindingAidOnly || readOnly);
@@ -248,6 +255,10 @@ protected String checkFlags(String flags) {
 			createZippedCollection = false;
 		}
 
+		if (flags.indexOf("-insitu;") >= 0) {
+			insitu = true;
+		}
+
 		if (flags.indexOf("-readonly;") >= 0) {
 			readOnly = true;
 		}
@@ -417,9 +428,9 @@ public IFDFindingAid getFindingAid() {
 		return getHelper().getFindingAid();
 	}
 
-	protected void buildSite() {
+	protected void buildSite(File htmlPath) {
 		try {
-			PageCreator.buildSite(targetPath, true, launchLandingPage);
+			PageCreator.buildSite(htmlPath, true, launchLandingPage);
 		} catch (Exception e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();

src/main/java/com/integratedgraphics/extractor/IFDExtractor.java

@@ -135,8 +135,12 @@ protected static String getCommandLineHelp() {
 				+ "\n-requirePubInfo (throw an error is datacite cannot be reached; post-publication-related collections only)";
 	}
 
-	public void runExtraction(String ifdExtractFile, String localSourceArchive, String targetDir) {
-		runExtraction(new String[] { ifdExtractFile, localSourceArchive, targetDir });
+	public IFDExtractor() {
+		initializeExtractor();
+	}
+
+	public void runExtraction(String ifdExtractFile, String localSourceArchive, String targetDir, String flags) {
+		runExtraction(new String[] { ifdExtractFile, localSourceArchive, targetDir, flags });
 	}
 
 	public void runExtraction(String[] args) {
@@ -166,7 +170,6 @@ public void runExtraction(String[] args) {
 			throw new NullPointerException("No IFD-extract.json or test set?");
 		if (targetDir == null)
 			targetDir = "site";
-		new File(targetDir).mkdirs();
 		FAIRSpecUtilities.setLogging(targetDir + "/extractor.log");
 		int failed = 0;
 		logToSys("Extractor.runExtraction output to " + new File(targetDir).getAbsolutePath());
@@ -212,10 +215,6 @@ public String processFlags(String[] args, String moreFlags) {
 		return flags;
 	}
 
-	public IFDExtractor() {
-		initializeExtractor();
-	}
-
 	public String dumpFlags() {
 		String s = " stopOnAnyFailure = " + stopOnAnyFailure //
 				+ "\n debugging = " + debugging //
@@ -311,12 +310,18 @@ public void run(File ifdExtractScriptFile, File targetPath, String localsourceAr
 			throws IOException, IFDException {
 		log("!Extractor\n ifdExtractScriptFile= " + ifdExtractScriptFile + "\n localsourceArchive = "
 				+ localsourceArchive + "\n targetDir = " + targetPath.getAbsolutePath());
-		if (extractAndCreateFindingAid(ifdExtractScriptFile, localsourceArchive, targetPath) == null) {
+
+		File htmlPath = (insitu ? new File(localsourceArchive) : targetPath);
+
+		String serializedFA = extractAndCreateFindingAid(ifdExtractScriptFile, localsourceArchive, targetPath);
+		if (serializedFA == null) {
 			if (!allowNoPubInfo) {
 				throw new IFDException("Extractor failed");
 			}
 		} else if (createLandingPage) {
-			buildSite();
+			if (insitu)
+				FAIRSpecUtilities.writeBytesToFile(serializedFA.getBytes(), new File(htmlPath, "IFD.findingaid.json"));
+			buildSite(htmlPath);
 		}
 
 		log("!Extractor extracted " + lstManifest.size() + " files (" + lstManifest.getByteCount() + " bytes)"

src/main/java/com/integratedgraphics/extractor/IFDExtractorLayer0.java

@@ -64,6 +64,11 @@ abstract class IFDExtractorLayer0 extends FindingAidCreator implements FAIRSpecE
 	protected String stopAfter;
 
 	protected void checkStopAfter(String what) {
+		System.out.println(what 
+				+ " " + helper.getCompoundCollection().size()
+				+ " " + helper.getStructureCollection().size()
+				+ " " + helper.getSpecCollection().size()
+				);
 		boolean stopping = what.equals(stopAfter);
 		if (stopping) {
 			System.out.println("stopping after " + what);
@@ -143,7 +148,7 @@ protected void checkStopAfter(String what) {
 	/**
 	 * list of files to always accept, specified an extractor JSON template
 	 */
-	protected FileList lstAccepted = new FileList(null, "accepted");
+	protected FileList lstAccepted = new FileList(null, "accepted", null);
 
 	/**
 	 * list of files ignored -- probably MACOSX trash or Google desktop.ini trash
@@ -158,14 +163,14 @@ protected void checkStopAfter(String what) {
 	/**
 	 * list of files rejected -- probably MACOSX trash or Google desktop.ini trash
 	 */
-	protected final FileList lstRejected = new FileList(null, "rejected");
+	protected final FileList lstRejected = new FileList(null, "rejected", ".");
 
 	/**
 	 * Track the files written to the collection, even if there is no output. This
 	 * allows for removing ZIP files from the finding aid and manifest if they are
 	 * not actually written.
 	 */
-	protected FileList lstWritten = new FileList(null, "written");
+	protected FileList lstWritten = new FileList(null, "written", null);
 
 	/**
 	 * objects found in IFD-extract.json
@@ -214,7 +219,7 @@ protected void checkStopAfter(String what) {
 	public void addProperty(String key, Object val) {
 		if (val != IFDProperty.NULL)
 			log(this.localizedName + " addProperty " + key + "=" + val);
-		addDeferredPropertyOrRepresentation(key, val, false, null, null);
+		addDeferredPropertyOrRepresentation(key, val, false, null, null, "L0 vndaddprop");
 	}
 
 	/**
@@ -230,21 +235,21 @@ public void addProperty(String key, Object val) {
 	 *                  extraction
 	 * @param val       either a String value or an Object[] with elements byte[]
 	 *                  and String name
+	 * @param mediaType a media type for a representation, or null
 	 * @param isInline  representation data is being provided as inline-data, to be
 	 *                  saved only in the finding aid (InChI, SMILES, InChIKey)
-	 * @param mediaType a media type for a representation, or null
 	 */
 	@Override
 	public void addDeferredPropertyOrRepresentation(String key, Object val, boolean isInline, String mediaType,
-			String note) {
+			String note, String src) {
 		// System.out.println("!!!" + key + " ln=" + localizedName + " op=" +
 		// originPath);
 		if (key == null) {
 			deferredPropertyList.add(null);
 			return;
 		}
 		deferredPropertyList
-				.add(new Object[] { originPath, localizedName, key, val, Boolean.valueOf(isInline), mediaType, note });
+				.add(new Object[] { originPath, localizedName, key, val, Boolean.valueOf(isInline), mediaType, note, src });
 		if (key.startsWith(DefaultStructureHelper.STRUC_FILE_DATA_KEY)) {
 			// Phase 2a has identified a structure before a compound has been established in Phase 2b.
 			// Mestrelab vendor plug-in has found a MOL or SDF file in Phase 2b.
@@ -461,6 +466,8 @@ private void writeDigitalItem(String originPath, ArchiveInputStream ais, long le
 			lstManifest.add(localizedName, len);
 			break;
 		}
+		if (insitu)
+			return;
 		File f = getAbsoluteFileTarget(localizedName);
 		FAIRSpecUtilities.getLimitedStreamBytes(ais, len, new FileOutputStream(f), false, true);
 	}