From e00fe4140cd08c56637dfbc17dfb6b650a155e8f Mon Sep 17 00:00:00 2001
From: bobhanson <hansonr@stolaf.edu>
Date: Thu, 5 Dec 2024 13:08:58 -0600
Subject: [PATCH] FAIRSpec-gui fixes for substructure search

---
 docs/examples/assets/FAIRSpec-config.js       |  8 ++
 docs/examples/assets/FAIRSpec-get.js          | 49 +++++++---
 docs/examples/assets/FAIRSpec-gui.js          | 89 +++++++++----------
 .../html/site/assets/FAIRSpec-config.js       |  8 ++
 .../html/site/assets/FAIRSpec-get.js          | 45 ++++++++--
 .../html/site/assets/FAIRSpec-gui.js          | 77 ++++++++--------
 6 files changed, 174 insertions(+), 102 deletions(-)

diff --git a/docs/examples/assets/FAIRSpec-config.js b/docs/examples/assets/FAIRSpec-config.js
index b579a65..5d6083a 100644
--- a/docs/examples/assets/FAIRSpec-config.js
+++ b/docs/examples/assets/FAIRSpec-config.js
@@ -29,3 +29,11 @@ IFD = {
 	contentHeader: null,
 	cache: {}
 }
+
+IFD.MODE_NONE       = "none";
+IFD.MODE_COMPOUNDS  = "compounds";
+IFD.MODE_STRUCTURES = "structures";
+IFD.MODE_SPECTRA    = "spectra";
+IFD.MODE_SAMPLES  = "samples";
+IFD.MODE_SAMPLESPECTRA = "samplespectra";
+
diff --git a/docs/examples/assets/FAIRSpec-get.js b/docs/examples/assets/FAIRSpec-get.js
index bc996e5..3ae9d9d 100644
--- a/docs/examples/assets/FAIRSpec-get.js
+++ b/docs/examples/assets/FAIRSpec-get.js
@@ -46,8 +46,12 @@
 
 ;(function() {
 
+IFD.getCollection = function(aidID) {
+	return IFD.collections[aidID];
+} 
+
 IFD.getSmilesForStructureID = function(aidID, id) {
-	var struc = IFD.collections[aidID].structures[id];
+	var struc = IFD.getCollection(aidID).structures[id];
 	if (!struc) return "";
 	var reps = struc.representations;
 	var types = IFD.getRepTypes(reps);
@@ -55,7 +59,7 @@ IFD.getSmilesForStructureID = function(aidID, id) {
 }
 
 IFD.getSpectrumIDsForSample = function(aidID,id) {
-	var samplespecs = IFD.collections[aidID]["sample-spectra associations"];
+	var samplespecs = IFD.getCollection(aidID)["sample-spectra associations"];
 	var items = IFD.items[aidID].samplespectra;
 	for (var i = 0; i < items.length; i++) {
 		var assoc = samplespecs[items[i]];
@@ -67,11 +71,11 @@ IFD.getSpectrumIDsForSample = function(aidID,id) {
 }
 
 IFD.getCompoundIndexesForText = function(aidID, text) {
-	var compounds = IFD.collections[aidID].compounds;	
+	var compounds = IFD.getCollection(aidID).compounds;
 	var keys = IFD.getCompoundCollectionKeys();
 	var ids = [];
-	var citems = IFD.items[aidID].compounds;
 	text = text.toLowerCase();
+	var citems = IFD.items[aidID].compounds;
 	for (var i = 0; i < citems.length; i++) {
 		var assoc = compounds[citems[i]];
 		var found = false;
@@ -90,8 +94,8 @@ var testText = function(s, text) {
 }
 
 IFD.getCompoundIndexesForStructures = function(aidID, strucIDs) {
-	var compounds = IFD.collections[aidID].compounds;
-	var structures = IFD.collections[aidID].structures;
+	var compounds = IFD.getCollection(aidID).compounds;
+	var structures = IFD.getCollection(aidID).structures;
 	var keys = IFD.getCompoundCollectionKeys();
 	var ids = [];
 	var citems = IFD.items[aidID].compounds;
@@ -112,7 +116,7 @@ IFD.getCompoundIndexesForStructures = function(aidID, strucIDs) {
 }
 
 IFD.getStructureIDsForSpectra = function(aidID, specIDs) {
-	var compounds = IFD.collections[aidID].compounds;
+	var compounds = IFD.getCollection(aidID).compounds;
 	var keys = IFD.getCompoundCollectionKeys();
 	var ids = [];
 	var items = IFD.items[aidID].compounds;
@@ -233,12 +237,14 @@ IFD.shortType = function(type) {
 IFD.getCollectionSetById = function(aid) {
 	IFD.byID = !!aid.collectionSet.itemsByID;
 	IFD.itemsKey = (IFD.byID ? "itemsByID" : "items");
-	IFD.collectionKeys = (IFD.byID ? null : {});
+	IFD.collectionKeys = {};
 	var collections = aid.collectionSet.itemsByID || aid.collectionSet.items;
 	var dc = IFD.collections[aid.id] = {};
+	if (IFD.findingAidID == '.')
+		IFD.collections['.'] = dc;
 	for (var i in collections) {
 		c = collections[i];
-		dc[c.id] = c.items || c.itemsById;
+		dc[c.id] = c.items || c.itemsByID;
 		if (!IFD.byID) {
 			IFD.collectionKeys[c.id] = c.collections; // compounds only
 		}
@@ -246,6 +252,29 @@ IFD.getCollectionSetById = function(aid) {
 	return dc;
 }
 
+IFD.getCollectionSetItems = function(aid) {
+	var dc = IFD.getCollectionSetById(aid);
+	var dItems = IFD.items[aid.id] = {};
+	if (IFD.findingAidID == '.')
+		IFD.items['.'] = dItems;
+	if (dc[IFD.MODE_SAMPLES]) {
+		dItems[IFD.MODE_SAMPLES] = IFD.getIDs(dc[IFD.MODE_SAMPLES]);
+	}
+	if (dc[IFD.MODE_COMPOUNDS]) {
+		dItems[IFD.MODE_COMPOUNDS] = IFD.getIDs(dc[IFD.MODE_COMPOUNDS]);
+	}
+	if (dc[IFD.MODE_STRUCTURES]) {
+		dItems[IFD.MODE_STRUCTURES] = IFD.getIDs(dc[IFD.MODE_STRUCTURES]);
+	}
+	if (dc[IFD.MODE_SPECTRA]) {
+		dItems[IFD.MODE_SPECTRA] = IFD.getIDs(dc[IFD.MODE_SPECTRA]);
+	}
+	if (dc["sample-spectra associations"]) {
+		dItems[IFD.MODE_SAMPLESPECTRA] = IFD.getIDs(dc["sample-spectra associations"]);
+	}
+	return dItems;
+}
+
 IFD.getCompoundCollectionKeys = function() {
 	var ckeys = IFD.collectionKeys.compounds;
 	if (ckeys && !ckeys[0]) {
@@ -272,7 +301,7 @@ IFD.getSMILES = function(aidID, retIDs, retSMILES, allowReactions, withAidID) {
 	var structureIDs = IFD.items[aidID]["structures"];
 	for (var i = 0; i < structureIDs.length; i++) {
 		var id = structureIDs[i];
-		var struc = IFD.collections[aidID].structures[id];
+		var struc = IFD.getCollection(aidID).structures[id];
 		var reps = struc.representations;
 		var types = IFD.getRepTypes(reps, "smiles");
 		if (types.smiles) {
diff --git a/docs/examples/assets/FAIRSpec-gui.js b/docs/examples/assets/FAIRSpec-gui.js
index 16685d5..87fa4f3 100644
--- a/docs/examples/assets/FAIRSpec-gui.js
+++ b/docs/examples/assets/FAIRSpec-gui.js
@@ -19,11 +19,7 @@
 	var MAIN_SEARCH_PROP = "main_search_prop";
 	var MAIN_SEARCH     = "main_search";
 	var MAIN_SUMMARY    = "main_summary";
-	var MODE_NONE       = "none";
-	var MODE_COMPOUNDS  = "compounds";
-	var MODE_STRUCTURES = "structures";
-	var MODE_SPECTRA    = "spectra";
-	var MODE_SAMPLES  = "samples";
+	
 	var NMRDB_PREDICT_SMILES = "https://www.nmrdb.org/service.php?name=%TYPE%-prediction&smiles=%SMILES%";
 	// where type = 1h, 13c, cosy, hmbc, hsqc
 	
@@ -31,7 +27,7 @@
 	var divId = 0;
 	
 	var dirFor = function(aidID) {
-		return IFD.properties.baseDir + "/" + aidID;
+		return IFD.properties.baseDir + (IFD.findingAidID == '.' ? "" : "/" + aidID);
 	}
 	
 	var fileFor = function(aidID, fname) {
@@ -68,7 +64,7 @@
 
 	// external
 	IFD.loadFindingAids = function() {
-		var aids = IFD.findingAids || [];
+		var aids = IFD.findingAids || ["."];
 		IFD.aidIDs = [];
 		var s = (aids.length == 1 ? null : '<select id=articles onchange="IFD.loadSelected(this.selectedOptions[0].value)"><option value="">Select a Finding Aid</option>')
 		// set up for ./name/IFD.findingAid.json
@@ -126,7 +122,7 @@
 		aidID || (aidID = "");
 		setResults("");
 		var dir = dirFor(aidID);
-		if (IFD.findingAidID == aidID) return;
+		if (IFD.findingAidID == '.' || IFD.findingAidID == aidID) return;
 		IFD.findingAidID = aidID;
 		if (IFD.findingAidDir == dir) return;
 		IFD.findingAidDir = dir;
@@ -137,7 +133,7 @@
 		IFD.findingAidFile = fileFor(aidID, IFD.properties.findingAidFileName);
 		var aid = IFD.cacheGet(aidID);
 		if (aid == null) {
-			$.ajax({url:IFD.findingAidFile, dataType:"json", success:callbackLoaded, error:callbackLoadFailed});
+			$.ajax({url:IFD.findingAidFile, dataType:"json", success:callbackLoaded, error:function(){callbackLoadFailed()}});
 		} else {
 			loadAid(aid, collection);
 		}
@@ -146,8 +142,8 @@
 	//external
 	IFD.showSamples = function(aidID, ids) {
 		IFD.select(aidID);
-		setMode(MODE_SAMPLES);
-		ids || (ids = IFD.items[aidID][MODE_SAMPLES]);
+		setMode(IFD.MODE_SAMPLES);
+		ids || (ids = IFD.items[aidID][IFD.MODE_SAMPLES]);
 		var s = "<table>";
 		for (var i = 0; i < ids.length; i++) {
 			s += "<tr class=\"tableRow" + (i%2) + "\">" + showSample(aidID,ids[i]) + "</tr>";
@@ -160,13 +156,18 @@
 	IFD.showCompounds = function(aidID, ids) {
 		loadMainSummary(IFD.aid, false);
 		IFD.select(aidID);
-		setMode(MODE_COMPOUNDS);
-		ids || (ids = IFD.items[aidID][MODE_COMPOUNDS]);
-		var s = "<table>";
-		for (var i = 0; i < ids.length; i++) {
-			s += "<tr class=\"tablerow" + (i%2) + "\">" + showCompound(aidID,ids[i]) + "</tr>";
+		setMode(IFD.MODE_COMPOUNDS);
+		ids || (ids = IFD.items[aidID][IFD.MODE_COMPOUNDS]);
+		var s;
+		if (ids.length == 0) {
+			s = "no compounds found";
+		} else {
+			s = "<table>";
+			for (var i = 0; i < ids.length; i++) {
+				s += "<tr class=\"tablerow" + (i%2) + "\">" + showCompound(aidID,ids[i]) + "</tr>";
+			}
+			s += "</table>";
 		}
-		s += "</table>";
 		setResults(s);
 	} 
 	
@@ -174,8 +175,8 @@
 	IFD.showSpectra = function(aidID, ids) {
 		loadMainSummary(IFD.aid, false);
 		IFD.select(aidID);
-		setMode(MODE_SPECTRA);
-		ids || (ids = IFD.items[aidID][MODE_SPECTRA]);
+		setMode(IFD.MODE_SPECTRA);
+		ids || (ids = IFD.items[aidID][IFD.MODE_SPECTRA]);
 		var s = "<table>";
 		for (var i = 0; i < ids.length; i++) {
 			s += "<tr class=\"tableRow" + (i%2) + "\">" + showSpectrum(aidID,ids[i]) + "</tr>";
@@ -188,8 +189,8 @@
 	IFD.showStructures = function(aidID, ids) {
 		loadMainSummary(IFD.aid, false);
 		IFD.select(aidID);
-		setMode(MODE_STRUCTURES);
-		ids || ids === false || (ids = IFD.getItems(aidID, MODE_STRUCTURES));
+		setMode(IFD.MODE_STRUCTURES);
+		ids || ids === false || (ids = IFD.getItems(aidID, IFD.MODE_STRUCTURES));
 		var s = showCompoundStructures(aidID,ids, false, true);
 		setResults(s);
 	} 	
@@ -204,7 +205,7 @@
 	}
 
 	IFD.showAid = function(aidID) {
-		window.open(fileFor(aidID, IFD.properties.findingAidFileName), "_blank");
+		window.open(fileFor(IFD.findingAidID, IFD.properties.findingAidFileName), "_blank");
 	}
 
 	IFD.showVersion = function(aid) {
@@ -234,7 +235,7 @@
 		loadAid(aid);
 	}
 
-	var callbackLoadFailed = function(x,y,z) {
+	var callbackLoadFailed = function(x) {
 		alert([x,y,z]);
 		return;
 	}
@@ -413,41 +414,39 @@
 	}
 
 	var addTopRow = function(aid) {
-		var dc = IFD.getCollectionSetById(aid);
+		var dItems = IFD.getCollectionSetItems(aid);
 		var id = aid.id;
-		var dItems = IFD.items[id] = {};
 		var sep = "&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;" 
-			//+ ==&gt;
 			+ "&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;";
 		var s = "";
-		if (dc.samples) {
+		var items = dItems[IFD.MODE_SAMPLES];
+		if (items) {
 			if (s)
 				s += sep;
-			var items = dItems[MODE_SAMPLES] = IFD.getIDs(dc.samples);
 			s += "<a href=\"javascript:IFD.showSamples('"+aid.id+"')\">Samples(" + items.length + ")</a>";
 		}
-		if (dc.compounds) {
-			var items = dItems[MODE_COMPOUNDS] = IFD.getIDs(dc.compounds);
+		items = dItems[IFD.MODE_COMPOUNDS];
+		if (items) {
 			if (s)
 				s += sep;
 			s += "<a href=\"javascript:IFD.showCompounds('"+id+"')\">Compounds(" + items.length + ")</a>";
 		}
-		if (dc.structures) {
-			var items = dItems[MODE_STRUCTURES] = IFD.getIDs(dc.structures);
+		items = dItems[IFD.MODE_STRUCTURES];
+		if (items) {
 			if (s)
 				s += sep;
 			s += "<a href=\"javascript:IFD.showStructures('"+aid.id+"')\">Structures(" + items.length + ")</a>";
 		}
-		if (dc.spectra) {
-			var items = dItems[MODE_SPECTRA] = IFD.getIDs(dc.spectra);
+		items = dItems[IFD.MODE_SPECTRA];
+		if (items) {
 			if (s)
 				s += sep;
 			s += "<a href=\"javascript:IFD.showSpectra('"+id+"')\">Spectra(" + items.length + ")</a>";
 		}
 
-	// TODO fold this information into "samples"
-		if (dc["sample-spectra associations"]) {
-			var items = dItems["samplespectra"] = IFD.getIDs(dc["sample-spectra associations"]);
+		items = dItems[IFD.MODE_SAMPLESPECTRA];
+		if (items) {
+			// TODO fold this information into "samples"
 //			s += "<a href=\"javascript:IFD.showSampleSpectraAssociations('"+aid.id+"')\">Sample-Spectra Associations(" + items.length + ")</a>";
 		}
 		return "<tr><td><b>Collections:</b>&nbsp;&nbsp;</td><td>"
@@ -455,7 +454,7 @@
 	}
 
 	var showSample = function(aidID,id) {
-		var sample = IFD.collections[aidID].samples[id];
+		var sample = IFD.getCollection(aidID).samples[id];
 		var specids = IFD.getSpectrumIDsForSample(aidID, id);
 		var structureIDs = IFD.getStructureIDsForSpectra(aidID,specids);
 		var s = getHeader("Sample/s", "Sample " + id); 
@@ -496,7 +495,7 @@
 	}
 
 	var showSpectrum = function(aidID,id) {
-		var spec = IFD.collections[aidID].spectra[id];
+		var spec = IFD.getCollection(aidID).spectra[id];
 		var structureIDs = IFD.getStructureIDsForSpectra(aidID, [id]);
 		var sampleID = spec.properties && spec.properties.originating_sample_id;
 		var sid = (IFD.byID ? id : spec.id); 
@@ -524,7 +523,7 @@
 	}
 
 	var showCompound = function(aidID,id) {
-		var cmpd = IFD.collections[aidID].compounds[id];
+		var cmpd = IFD.getCollection(aidID).compounds[id];
 		var keys = IFD.getCompoundCollectionKeys();
 		var structureIDs = cmpd[IFD.itemsKey][keys.structures];
 		var spectraIDs = cmpd[IFD.itemsKey][keys.spectra];
@@ -577,7 +576,7 @@
 	var showCompoundStructure = function(aidID, id, showID, tableRow) {
 		var cl = (tableRow > 0 ? " class=tablerow" + (tableRow%2) : "");
 		var s = "<td" + cl + "><table cellpadding=10><tr>";
-		var struc = IFD.collections[aidID].structures[id];
+		var struc = IFD.getCollection(aidID).structures[id];
 		var sid = struc.id;
 		var props = struc.properties;
 		var reps = struc.representations;
@@ -585,7 +584,7 @@
 		s += "<td rowspan=2 valign=\"top\">";
 		if (showID) {
 			var h = (id.indexOf("Structure") == 0 ? removeUnderline(sid) : "Structure " + sid);
-			s += "<span class=structurehead>"+ (IFD.resultsMode == MODE_STRUCTURES ? getHeader("Structure/s", h) : h) + "</span><br>";
+			s += "<span class=structurehead>"+ (IFD.resultsMode == IFD.MODE_STRUCTURES ? getHeader("Structure/s", h) : h) + "</span><br>";
 		}
 		v = IFD.getStructureVisual(reps);
 		if (v){
@@ -606,7 +605,7 @@
 	}
 
 	var showCompoundSpectra = function(aidID,ids,smiles,withTitle) {
-		ids || (ids = IFD.items[aidID][MODE_SPECTRA]);
+		ids || (ids = IFD.items[aidID][IFD.MODE_SPECTRA]);
 		var s = "<table>"
 			if (withTitle)
 				s += "<tr><td style=\"width:100px\" valign=top><span class=spectitle>Spectra</span></td></tr>";
@@ -632,7 +631,7 @@
 
 	var setResults = function(s) {
 		addOrAppendJQ("#results",s, true);
-		loadContents(!!s);
+		loadContents(s && !s.startsWith("no "));
 	}
 
 	var loadContents = function(hasContent) {
@@ -754,7 +753,7 @@
 	}
 
 	var addCompoundSpectrumRow = function(aidID, id, smiles, tableRow) {
-		var spec = IFD.collections[aidID].spectra[id];
+		var spec = IFD.getCollection(aidID).spectra[id];
 		var cl = (tableRow > 0 ? " class=tablerow" + (tableRow%2) : "");
 		var s = "<tr><td"+ cl + " id='q1' rowspan=2 style=\"width:100px\" valign=top>" 
 			+ (IFD.byID ? id : "") 
diff --git a/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-config.js b/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-config.js
index b579a65..5d6083a 100644
--- a/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-config.js
+++ b/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-config.js
@@ -29,3 +29,11 @@ IFD = {
 	contentHeader: null,
 	cache: {}
 }
+
+IFD.MODE_NONE       = "none";
+IFD.MODE_COMPOUNDS  = "compounds";
+IFD.MODE_STRUCTURES = "structures";
+IFD.MODE_SPECTRA    = "spectra";
+IFD.MODE_SAMPLES  = "samples";
+IFD.MODE_SAMPLESPECTRA = "samplespectra";
+
diff --git a/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-get.js b/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-get.js
index ec0ebfb..3ae9d9d 100644
--- a/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-get.js
+++ b/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-get.js
@@ -46,8 +46,12 @@
 
 ;(function() {
 
+IFD.getCollection = function(aidID) {
+	return IFD.collections[aidID];
+} 
+
 IFD.getSmilesForStructureID = function(aidID, id) {
-	var struc = IFD.collections[aidID].structures[id];
+	var struc = IFD.getCollection(aidID).structures[id];
 	if (!struc) return "";
 	var reps = struc.representations;
 	var types = IFD.getRepTypes(reps);
@@ -55,7 +59,7 @@ IFD.getSmilesForStructureID = function(aidID, id) {
 }
 
 IFD.getSpectrumIDsForSample = function(aidID,id) {
-	var samplespecs = IFD.collections[aidID]["sample-spectra associations"];
+	var samplespecs = IFD.getCollection(aidID)["sample-spectra associations"];
 	var items = IFD.items[aidID].samplespectra;
 	for (var i = 0; i < items.length; i++) {
 		var assoc = samplespecs[items[i]];
@@ -67,11 +71,11 @@ IFD.getSpectrumIDsForSample = function(aidID,id) {
 }
 
 IFD.getCompoundIndexesForText = function(aidID, text) {
-	var compounds = IFD.collections[aidID].compounds;	
+	var compounds = IFD.getCollection(aidID).compounds;
 	var keys = IFD.getCompoundCollectionKeys();
 	var ids = [];
-	var citems = IFD.items[aidID].compounds;
 	text = text.toLowerCase();
+	var citems = IFD.items[aidID].compounds;
 	for (var i = 0; i < citems.length; i++) {
 		var assoc = compounds[citems[i]];
 		var found = false;
@@ -90,8 +94,8 @@ var testText = function(s, text) {
 }
 
 IFD.getCompoundIndexesForStructures = function(aidID, strucIDs) {
-	var compounds = IFD.collections[aidID].compounds;
-	var structures = IFD.collections[aidID].structures;
+	var compounds = IFD.getCollection(aidID).compounds;
+	var structures = IFD.getCollection(aidID).structures;
 	var keys = IFD.getCompoundCollectionKeys();
 	var ids = [];
 	var citems = IFD.items[aidID].compounds;
@@ -112,7 +116,7 @@ IFD.getCompoundIndexesForStructures = function(aidID, strucIDs) {
 }
 
 IFD.getStructureIDsForSpectra = function(aidID, specIDs) {
-	var compounds = IFD.collections[aidID].compounds;
+	var compounds = IFD.getCollection(aidID).compounds;
 	var keys = IFD.getCompoundCollectionKeys();
 	var ids = [];
 	var items = IFD.items[aidID].compounds;
@@ -236,6 +240,8 @@ IFD.getCollectionSetById = function(aid) {
 	IFD.collectionKeys = {};
 	var collections = aid.collectionSet.itemsByID || aid.collectionSet.items;
 	var dc = IFD.collections[aid.id] = {};
+	if (IFD.findingAidID == '.')
+		IFD.collections['.'] = dc;
 	for (var i in collections) {
 		c = collections[i];
 		dc[c.id] = c.items || c.itemsByID;
@@ -246,6 +252,29 @@ IFD.getCollectionSetById = function(aid) {
 	return dc;
 }
 
+IFD.getCollectionSetItems = function(aid) {
+	var dc = IFD.getCollectionSetById(aid);
+	var dItems = IFD.items[aid.id] = {};
+	if (IFD.findingAidID == '.')
+		IFD.items['.'] = dItems;
+	if (dc[IFD.MODE_SAMPLES]) {
+		dItems[IFD.MODE_SAMPLES] = IFD.getIDs(dc[IFD.MODE_SAMPLES]);
+	}
+	if (dc[IFD.MODE_COMPOUNDS]) {
+		dItems[IFD.MODE_COMPOUNDS] = IFD.getIDs(dc[IFD.MODE_COMPOUNDS]);
+	}
+	if (dc[IFD.MODE_STRUCTURES]) {
+		dItems[IFD.MODE_STRUCTURES] = IFD.getIDs(dc[IFD.MODE_STRUCTURES]);
+	}
+	if (dc[IFD.MODE_SPECTRA]) {
+		dItems[IFD.MODE_SPECTRA] = IFD.getIDs(dc[IFD.MODE_SPECTRA]);
+	}
+	if (dc["sample-spectra associations"]) {
+		dItems[IFD.MODE_SAMPLESPECTRA] = IFD.getIDs(dc["sample-spectra associations"]);
+	}
+	return dItems;
+}
+
 IFD.getCompoundCollectionKeys = function() {
 	var ckeys = IFD.collectionKeys.compounds;
 	if (ckeys && !ckeys[0]) {
@@ -272,7 +301,7 @@ IFD.getSMILES = function(aidID, retIDs, retSMILES, allowReactions, withAidID) {
 	var structureIDs = IFD.items[aidID]["structures"];
 	for (var i = 0; i < structureIDs.length; i++) {
 		var id = structureIDs[i];
-		var struc = IFD.collections[aidID].structures[id];
+		var struc = IFD.getCollection(aidID).structures[id];
 		var reps = struc.representations;
 		var types = IFD.getRepTypes(reps, "smiles");
 		if (types.smiles) {
diff --git a/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-gui.js b/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-gui.js
index 5edfc6c..87fa4f3 100644
--- a/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-gui.js
+++ b/src/main/java/com/integratedgraphics/html/site/assets/FAIRSpec-gui.js
@@ -19,11 +19,7 @@
 	var MAIN_SEARCH_PROP = "main_search_prop";
 	var MAIN_SEARCH     = "main_search";
 	var MAIN_SUMMARY    = "main_summary";
-	var MODE_NONE       = "none";
-	var MODE_COMPOUNDS  = "compounds";
-	var MODE_STRUCTURES = "structures";
-	var MODE_SPECTRA    = "spectra";
-	var MODE_SAMPLES  = "samples";
+	
 	var NMRDB_PREDICT_SMILES = "https://www.nmrdb.org/service.php?name=%TYPE%-prediction&smiles=%SMILES%";
 	// where type = 1h, 13c, cosy, hmbc, hsqc
 	
@@ -146,8 +142,8 @@
 	//external
 	IFD.showSamples = function(aidID, ids) {
 		IFD.select(aidID);
-		setMode(MODE_SAMPLES);
-		ids || (ids = IFD.items[aidID][MODE_SAMPLES]);
+		setMode(IFD.MODE_SAMPLES);
+		ids || (ids = IFD.items[aidID][IFD.MODE_SAMPLES]);
 		var s = "<table>";
 		for (var i = 0; i < ids.length; i++) {
 			s += "<tr class=\"tableRow" + (i%2) + "\">" + showSample(aidID,ids[i]) + "</tr>";
@@ -160,13 +156,18 @@
 	IFD.showCompounds = function(aidID, ids) {
 		loadMainSummary(IFD.aid, false);
 		IFD.select(aidID);
-		setMode(MODE_COMPOUNDS);
-		ids || (ids = IFD.items[aidID][MODE_COMPOUNDS]);
-		var s = "<table>";
-		for (var i = 0; i < ids.length; i++) {
-			s += "<tr class=\"tablerow" + (i%2) + "\">" + showCompound(aidID,ids[i]) + "</tr>";
+		setMode(IFD.MODE_COMPOUNDS);
+		ids || (ids = IFD.items[aidID][IFD.MODE_COMPOUNDS]);
+		var s;
+		if (ids.length == 0) {
+			s = "no compounds found";
+		} else {
+			s = "<table>";
+			for (var i = 0; i < ids.length; i++) {
+				s += "<tr class=\"tablerow" + (i%2) + "\">" + showCompound(aidID,ids[i]) + "</tr>";
+			}
+			s += "</table>";
 		}
-		s += "</table>";
 		setResults(s);
 	} 
 	
@@ -174,8 +175,8 @@
 	IFD.showSpectra = function(aidID, ids) {
 		loadMainSummary(IFD.aid, false);
 		IFD.select(aidID);
-		setMode(MODE_SPECTRA);
-		ids || (ids = IFD.items[aidID][MODE_SPECTRA]);
+		setMode(IFD.MODE_SPECTRA);
+		ids || (ids = IFD.items[aidID][IFD.MODE_SPECTRA]);
 		var s = "<table>";
 		for (var i = 0; i < ids.length; i++) {
 			s += "<tr class=\"tableRow" + (i%2) + "\">" + showSpectrum(aidID,ids[i]) + "</tr>";
@@ -188,8 +189,8 @@
 	IFD.showStructures = function(aidID, ids) {
 		loadMainSummary(IFD.aid, false);
 		IFD.select(aidID);
-		setMode(MODE_STRUCTURES);
-		ids || ids === false || (ids = IFD.getItems(aidID, MODE_STRUCTURES));
+		setMode(IFD.MODE_STRUCTURES);
+		ids || ids === false || (ids = IFD.getItems(aidID, IFD.MODE_STRUCTURES));
 		var s = showCompoundStructures(aidID,ids, false, true);
 		setResults(s);
 	} 	
@@ -413,41 +414,39 @@
 	}
 
 	var addTopRow = function(aid) {
-		var dc = IFD.getCollectionSetById(aid);
+		var dItems = IFD.getCollectionSetItems(aid);
 		var id = aid.id;
-		var dItems = IFD.items[id] = {};
 		var sep = "&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;" 
-			//+ ==&gt;
 			+ "&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;";
 		var s = "";
-		if (dc.samples) {
+		var items = dItems[IFD.MODE_SAMPLES];
+		if (items) {
 			if (s)
 				s += sep;
-			var items = dItems[MODE_SAMPLES] = IFD.getIDs(dc.samples);
 			s += "<a href=\"javascript:IFD.showSamples('"+aid.id+"')\">Samples(" + items.length + ")</a>";
 		}
-		if (dc.compounds) {
-			var items = dItems[MODE_COMPOUNDS] = IFD.getIDs(dc.compounds);
+		items = dItems[IFD.MODE_COMPOUNDS];
+		if (items) {
 			if (s)
 				s += sep;
 			s += "<a href=\"javascript:IFD.showCompounds('"+id+"')\">Compounds(" + items.length + ")</a>";
 		}
-		if (dc.structures) {
-			var items = dItems[MODE_STRUCTURES] = IFD.getIDs(dc.structures);
+		items = dItems[IFD.MODE_STRUCTURES];
+		if (items) {
 			if (s)
 				s += sep;
 			s += "<a href=\"javascript:IFD.showStructures('"+aid.id+"')\">Structures(" + items.length + ")</a>";
 		}
-		if (dc.spectra) {
-			var items = dItems[MODE_SPECTRA] = IFD.getIDs(dc.spectra);
+		items = dItems[IFD.MODE_SPECTRA];
+		if (items) {
 			if (s)
 				s += sep;
 			s += "<a href=\"javascript:IFD.showSpectra('"+id+"')\">Spectra(" + items.length + ")</a>";
 		}
 
-	// TODO fold this information into "samples"
-		if (dc["sample-spectra associations"]) {
-			var items = dItems["samplespectra"] = IFD.getIDs(dc["sample-spectra associations"]);
+		items = dItems[IFD.MODE_SAMPLESPECTRA];
+		if (items) {
+			// TODO fold this information into "samples"
 //			s += "<a href=\"javascript:IFD.showSampleSpectraAssociations('"+aid.id+"')\">Sample-Spectra Associations(" + items.length + ")</a>";
 		}
 		return "<tr><td><b>Collections:</b>&nbsp;&nbsp;</td><td>"
@@ -455,7 +454,7 @@
 	}
 
 	var showSample = function(aidID,id) {
-		var sample = IFD.collections[aidID].samples[id];
+		var sample = IFD.getCollection(aidID).samples[id];
 		var specids = IFD.getSpectrumIDsForSample(aidID, id);
 		var structureIDs = IFD.getStructureIDsForSpectra(aidID,specids);
 		var s = getHeader("Sample/s", "Sample " + id); 
@@ -496,7 +495,7 @@
 	}
 
 	var showSpectrum = function(aidID,id) {
-		var spec = IFD.collections[aidID].spectra[id];
+		var spec = IFD.getCollection(aidID).spectra[id];
 		var structureIDs = IFD.getStructureIDsForSpectra(aidID, [id]);
 		var sampleID = spec.properties && spec.properties.originating_sample_id;
 		var sid = (IFD.byID ? id : spec.id); 
@@ -524,7 +523,7 @@
 	}
 
 	var showCompound = function(aidID,id) {
-		var cmpd = IFD.collections[aidID].compounds[id];
+		var cmpd = IFD.getCollection(aidID).compounds[id];
 		var keys = IFD.getCompoundCollectionKeys();
 		var structureIDs = cmpd[IFD.itemsKey][keys.structures];
 		var spectraIDs = cmpd[IFD.itemsKey][keys.spectra];
@@ -577,7 +576,7 @@
 	var showCompoundStructure = function(aidID, id, showID, tableRow) {
 		var cl = (tableRow > 0 ? " class=tablerow" + (tableRow%2) : "");
 		var s = "<td" + cl + "><table cellpadding=10><tr>";
-		var struc = IFD.collections[aidID].structures[id];
+		var struc = IFD.getCollection(aidID).structures[id];
 		var sid = struc.id;
 		var props = struc.properties;
 		var reps = struc.representations;
@@ -585,7 +584,7 @@
 		s += "<td rowspan=2 valign=\"top\">";
 		if (showID) {
 			var h = (id.indexOf("Structure") == 0 ? removeUnderline(sid) : "Structure " + sid);
-			s += "<span class=structurehead>"+ (IFD.resultsMode == MODE_STRUCTURES ? getHeader("Structure/s", h) : h) + "</span><br>";
+			s += "<span class=structurehead>"+ (IFD.resultsMode == IFD.MODE_STRUCTURES ? getHeader("Structure/s", h) : h) + "</span><br>";
 		}
 		v = IFD.getStructureVisual(reps);
 		if (v){
@@ -606,7 +605,7 @@
 	}
 
 	var showCompoundSpectra = function(aidID,ids,smiles,withTitle) {
-		ids || (ids = IFD.items[aidID][MODE_SPECTRA]);
+		ids || (ids = IFD.items[aidID][IFD.MODE_SPECTRA]);
 		var s = "<table>"
 			if (withTitle)
 				s += "<tr><td style=\"width:100px\" valign=top><span class=spectitle>Spectra</span></td></tr>";
@@ -632,7 +631,7 @@
 
 	var setResults = function(s) {
 		addOrAppendJQ("#results",s, true);
-		loadContents(!!s);
+		loadContents(s && !s.startsWith("no "));
 	}
 
 	var loadContents = function(hasContent) {
@@ -754,7 +753,7 @@
 	}
 
 	var addCompoundSpectrumRow = function(aidID, id, smiles, tableRow) {
-		var spec = IFD.collections[aidID].spectra[id];
+		var spec = IFD.getCollection(aidID).spectra[id];
 		var cl = (tableRow > 0 ? " class=tablerow" + (tableRow%2) : "");
 		var s = "<tr><td"+ cl + " id='q1' rowspan=2 style=\"width:100px\" valign=top>" 
 			+ (IFD.byID ? id : "")