Fixes for gui and more

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

@@ -171,6 +171,7 @@ protected void setDerivedFlags() {
 		// _IFD_collection.zip file
 		createZippedCollection = createZippedCollection && !insitu && !debugReadOnly;
 
+		cleanCollectionDir &= !insitu;
 		readOnly |= debugReadOnly; // for testing; when true, no output other than a log file is produced
 		noOutput = (createFindingAidOnly || readOnly);
 		skipPubInfo = !dataciteUp || debugReadOnly; // true to allow no internet connection and so no pub calls

src/main/java/com/integratedgraphics/extractor/IFDExtractorLayer2.java

@@ -76,12 +76,23 @@ abstract class IFDExtractorLayer2 extends IFDExtractorLayer1 {
 	 */
 	private Map<String, IFDRepresentableObject<?>> htLocalizedNameToObject = new LinkedHashMap<>();
 
+	/**
+	 * retrieves a clone data source or a cloned object from an id 
+	 */
+	private Map<String, IFDRepresentableObject<?>> htCloneMap = new HashMap<>();
+
 	/**
 	 * a list of properties that vendors have indicated need addition, keyed by the
 	 * zip path for the resource
 	 */
 	private List<Object[]> deferredPropertyList;
 
+	/**
+	 * an insertion pointer into the deferredPropertyList;
+	 * reset to 0 after Phase 2b.
+	 */
+	private int deferredPropertyPointer;
+
 	/**
 	 * a key for the deferredObjectList that indicates we have a new resource
 	 * setting
@@ -316,6 +327,7 @@ protected void processPhase2(File targetDir) throws IFDException, IOException {
 		// removing resources that are totally unnecessary and extracting properties
 		// and representations using IFDVendorPluginI services.
 
+		deferredPropertyPointer = 0;
 		if (rezipCache != null && rezipCache.size() > 0) {
 			phase2cGetNextRezipName();
 			lastRezipPath = null;
@@ -506,6 +518,8 @@ private Map<String, ArchiveEntry> phase2ReadZipContentsIteratively(InputStream i
 						phase2aProcessEntry(baseOriginPath, oPath, ais, zipEntry, accepted);
 					break;
 				case PHASE_2C:
+
+
 					// rezipping
 					if (oPath.equals(currentRezipPath)) {
 						// nextRealEntry here may be the first
@@ -1049,7 +1063,7 @@ private ArchiveEntry phase2cRezipEntry(String baseName, String oPath, ArchiveInp
 		IFDRepresentation r = faHelper.getSpecDataRepresentation(localizedName);
 		if (r == null) {
 			// probably the case, as this renamed representation has not been added yet.
-		} else {
+		} else if (!insitu){
 			r.setLength(len);
 		}
 		if (oPath.endsWith(".zip"))
@@ -1433,7 +1447,14 @@ private static String phase2dGetStructureNameFromPath(String originPath) {
 		return name;
 	}
 
+	/**
+	 * Get the clone source
+	 * @param spec
+	 * @return
+	 */
 	private IFDRepresentableObject<?> phase2dGetClonedData(IFDRepresentableObject<?> spec) {
+		if (htCloneMap.isEmpty())
+			return spec;
 		IFDRepresentableObject<?> d = (spec.isValid() ? null : htCloneMap.get(spec.getID()));
 		return (d == null ? spec : d);
 	}
@@ -1507,13 +1528,13 @@ public void addProperty(String key, Object val) {
 	public void addDeferredPropertyOrRepresentation(String key, Object val, boolean isInline, String mediaType,
 			String note, String method) {
 
-		// System.out.println("L2 adddef >>>" +key + " src=" + method + " " + val);
+		//System.out.println("L2 adddef >>>" +key + " src=" + method + " " + val);
 		if (key == null) {
-			deferredPropertyList.add(null);
+			deferredPropertyList.add(deferredPropertyPointer++, null);
 			return;
 		}
 		deferredPropertyList
-				.add(new Object[] { originPath, localizedName, key, val, Boolean.valueOf(isInline), mediaType, note, method });
+				.add(deferredPropertyPointer++, new Object[] { originPath, localizedName, key, val, Boolean.valueOf(isInline), mediaType, note, method });
 		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.
@@ -1533,7 +1554,6 @@ public void addDeferredPropertyOrRepresentation(String key, Object val, boolean
 		}
 	}
 
-	private Map<String, IFDRepresentableObject<?>> htCloneMap = new HashMap<>();
 
 	/**
 	 * Register a digital item as significant and to be included in the collection.

src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-gui.js

@@ -1,8 +1,6 @@
 // ${IUPAC FAIRSpec}/src/html/site/assets/FAIRSpec-gui.js
 // 
-// Bob Hanson hansonr@stolaf.edu 2024.12.12
-
-// anonymous function for local functions
+// Bob Hanson hansonr@stolaf.edu 2024.12.13
 
 ;(function() {
 
@@ -300,6 +298,7 @@
 	}
 
 	var loadMainSummary = function(aid, isAll) {
+		clearPDFCache();
 		var s;
 		if (isAll && IFD.mainText) {
 			s = IFD.mainText;
@@ -520,8 +519,8 @@
 			s += "<td>&nbsp;&nbsp;</td><td><b>" + title + "</b></td>"
 		s += "</tr></table>";
 		var smiles = IFD.getSmilesForStructureID(aidID, structureIDs[0]);
-		s += showCompoundSpectra(aidID,[id],smiles,false, isAll);
 		s += showCompoundStructures(aidID,structureIDs, false);
+		s += showCompoundSpectra(aidID,[id],smiles,false, isAll);
 		s += "<hr style='color:blue'>";
 		return s;
 	}
@@ -706,12 +705,13 @@
 	}
 
 	var addRepresentationTable = function(isData, aidID, reps, specialItem, isAll) {
+		var justImage = (!isData && IFD.resultsMode == IFD.MODE_SPECTRA);
 		var s = ""
 		for (var i = 0; i < reps.length; i++) {
 			var type = IFD.shortType(reps[i].representationType);
 			if (type == specialItem) {
 				s = addRepresentationRow(isData, aidID, reps[i], type) + s;
-			} else if ("!" + type != specialItem) {
+			} else if (!justImage && "!" + type != specialItem) {
 				s += addRepresentationRow(isData, aidID, reps[i], type);
 			}
 		}
@@ -755,12 +755,30 @@
 
 	IFD.showHead = function(i) {alert(heads[i])}
 
+	var clearPDFCache = function() {
+		IFD.pdfData = [];
+		IFD.pdfDataPt = 0;		
+	}
+
+	clearPDFCache();
+
 	var anchorBase64 = function(label, sdata, mediaType) {
 		mediaType || (mediaType = "application/octet-stream");
 		var s = "<a href=\"data:" + mediaType + sdata + "\")>" + label + "</a>";
-		if (mediaType.indexOf("/pdf") < 0) 
-			return s;
-		return "<object data=\"data:application/pdf" + sdata + "\" type=\"application/pdf\" width=\"800\" height=\"600\">" + s +"</object>";
+		if (mediaType.indexOf("/pdf") >= 0) {
+			s += getPDFLink("data:application/pdf" + sdata);
+		}
+		return s;
+	}
+
+	var getPDFLink = function(uri) {
+		var s = "&nbsp;&nbsp;<span id=pdf" + IFD.pdfDataPt + "><a href=\"javascript:IFD.viewPDF("+IFD.pdfDataPt+")\">VIEW</a></div>";
+		IFD.pdfData[IFD.pdfDataPt++] = "<object data=\"" + uri + "\" type=\"application/pdf\" width=\"800\" height=\"600\"></object>";
+		return s;
+	}
+
+	IFD.viewPDF = function(i) {
+		$("#pdf" + i).html(IFD.pdfData[i]);
 	}
 
 	var getSpectrumPrediction = function(props, smiles) {
@@ -871,7 +889,7 @@
 				url = "data:application/octet-stream" + url;
 			s = "<a target=_blank href=\"" + url + "\">" + shortName + "</a>" + " (" + getSizeString(len) + (mediaType ? " " + mediaType : "") + ")";				
 			if (IFD.resultsMode == IFD.MODE_SPECTRA && shortName.endsWith(".pdf")) {
-				s = "<object data=\"" + url + "\" type=\"application/pdf\" width=\"800\" height=\"600\">" + s +"</object>";
+				s +=  getPDFLink(url);
 			}
 		}
 		note = (note && note.startsWith("Warning") ? note : null);

src/main/java/com/integratedgraphics/ifd/vendor/mestrelab/MestrelabIFDVendorPlugin.java

@@ -69,12 +69,12 @@ private String setOrigin(String val) {
 				"Temperature", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_ABSOLUTE_TEMPERATURE"), //prop
 				"DIM", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_DIMENSION"), //prop
 				"TITLE", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_TITLE"), //prop
-				"F1", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_FREQ_1"), //prop
-				"F2", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_FREQ_2"), //prop
-				"F3", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_FREQ_3"), //prop
-				"N1", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_NUCL_1"), //prop
-				"N2", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_NUCL_2"), //prop
-				"N3", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_NUCL_3"), //prop
+				"Spectrometer Frequency", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_FREQ_1"), //prop
+				"Spectrometer Frequency2", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_FREQ_2"), //prop
+				"Spectrometer Frequency3", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_FREQ_3"), //prop
+				"Nucleus", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_NUCL_1"), //prop
+				"Nucleus2", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_NUCL_2"), //prop
+				"Nucleus3", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.EXPT_NUCL_3"), //prop
 				"SF", getProp("IFD_PROPERTY_DATAOBJECT_FAIRSPEC_NMR.INSTR_NOMINAL_FREQ"), //prop
 				"TIMESTAMP", IFDConst.IFD_PROPERTY_DATAOBJECT_TIMESTAMP, //prop
 		};
@@ -190,15 +190,16 @@ void addParam(String key, Object oval, Param param1, Param param2) {
 				case "Site":
 				case "Solvent":
 				case "Title":
+				case "Instrument":
+				case "Spectrometer":
 				default:
 					oval = FAIRSpecUtilities.rep(val, "\n", " ").trim();
 					break;
+				case "Purity":
+					break;
 				case "Data File Name":
 					pageGlobals.isJDF = (val.endsWith(".jdf"));
 					return;
-				case "Instrument":
-				case "Spectrometer":
-					break;
 				case "Temperature":
 					double d = Double.parseDouble(val);
 					if (pageGlobals.isJDF) {
@@ -208,19 +209,16 @@ void addParam(String key, Object oval, Param param1, Param param2) {
 					oval = Double.valueOf(d);
 					break;
 				case "Nucleus":
-					key = "N1";
 					pageGlobals.nuc1 = val;
 					if (param2 != null) {
-						params.put("N2", param2.value);
+						params.put("Nucleus2", param2.value);
 					}
 					break;
-				case "Purity":
 				case "Spectrometer Frequency":
-					key = "F1";
 					pageGlobals.freq = Double.parseDouble(val);
 					oval = Double.valueOf(pageGlobals.freq);
 					if (param2 != null) {
-						params.put("F2", Double.valueOf(param2.value));
+						params.put("Spectrometer Frequency2", Double.valueOf(param2.value));
 					}
 					break;
 				case "Spectrum Quality":
@@ -311,7 +309,11 @@ protected void report(String key, Object val) {
 			addProperty(IFDConst.IFD_PROPERTY_DESCRIPTION, val);
 			addProperty(IFDExtractor.PAGE_ID_PROPERTY_SOURCE, val);
 		}
-		addProperty(k == null ? key : k, val);
+		// SM and DIM are derived
+		if (!key.startsWith("!"))
+			addProperty(key, val);
+		if (k != null)
+			addProperty(k, val);
 	}
 
 	private void close() {
@@ -324,8 +326,8 @@ private void close() {
 	private void finalizeParams() {
 		if (params != null && pageGlobals.freq != 0) {
 			int f = getNominalFrequency(pageGlobals.freq, pageGlobals.nuc1);
-			params.put("SF", Double.valueOf(f));
-			params.put("DIM", Integer.valueOf(pageGlobals.dim) + "D");
+			params.put("!SF", Integer.valueOf(f));
+			params.put("!DIM", Integer.valueOf(pageGlobals.dim) + "D");
 			params.put("mnovaVersion", mnovaVersion);
 		} 
 		params = null;

src/main/java/org/iupac/fairdata/core/IFDRepresentableObject.java

@@ -67,10 +67,10 @@ public IFDRepresentableObject(String label, String type) {
 	 */
 	@SuppressWarnings("unchecked")
 	public IFDRepresentation findOrAddRepresentation(String resourceID,	String originPath, String rootPath, String localName, Object data, String type, String mediaType) {		
-		String key = (data == null ? localName : data instanceof byte[] ? new String((byte[]) data) : data.toString());
+		String key = (localName != null ? localName : data instanceof byte[] ? new String((byte[]) data) : data.toString());
 		IFDRepresentation rep = getRepresentation(resourceID, key);
 		if (rep == null) {
-			rep = newRepresentation((localName == null ? null : new IFDReference(resourceID, originPath, rootPath, localName)), data, 0, type, mediaType);
+			rep = newRepresentation((localName == null ? null : new IFDReference(resourceID, originPath, rootPath, localName)), data, 0, type, mediaType);			
 			add((T) rep);
 			map.put(resourceID + "::" + key, rep);
 			if (localName != null && data != null)

src/main/java/org/iupac/fairdata/core/IFDRepresentation.java

@@ -37,9 +37,6 @@ public IFDRepresentation(IFDReference ref, Object data, long len, String type, S
 		//this.test = staticTest++;
 		this.ref = ref;
 		this.data = data;
-//			System.out.println(this.test + " " + subtype + " " + len + " " + ref);
-//			if (this.test == 44)
-//				System.out.println("IDFReptest");
 		this.len = (data instanceof String ? ((String) data).length()
 				: data instanceof byte[] ? ((byte[]) data).length 
 				: ref != null || len != 0 ? len 
@@ -61,7 +58,6 @@ public void setType(String type) {
 	}
 
 	public void setRef(IFDReference ref) {
-		System.out.println("IFDRep ref=" + ref);
 		this.ref = ref;
 	}