Support additional params for nimble append

bbimber · bbimber · commit 46f5727e5815 · 2025-01-26T12:53:31.000-08:00
diff --git a/singlecell/resources/chunks/AppendNimble.R b/singlecell/resources/chunks/AppendNimble.R
@@ -19,7 +19,8 @@ for (datasetId in names(seuratObjects)) {
   for (genomeId in names(nimbleGenomes)) {
     maxAmbiguityAllowed <- nimbleGenomeAmbiguousPreference[[genomeId]]
     queryDatabaseForLineageUpdates <- queryDatabaseForLineageUpdatesPreference[[genomeId]]
-    seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, ensureSamplesShareAllGenomes = ensureSamplesShareAllGenomes, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, maxAmbiguityAllowed = maxAmbiguityAllowed, maxLibrarySizeRatio = maxLibrarySizeRatio, queryDatabaseForLineageUpdates = queryDatabaseForLineageUpdates)
+    replaceExistingAssayData <- replaceExistingAssayDataByGenome[[genomeId]]
+    seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, ensureSamplesShareAllGenomes = ensureSamplesShareAllGenomes, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, maxAmbiguityAllowed = maxAmbiguityAllowed, maxLibrarySizeRatio = maxLibrarySizeRatio, queryDatabaseForLineageUpdates = queryDatabaseForLineageUpdates, replaceExistingAssayData = replaceExistingAssayData)
   }
 
   saveData(seuratObj, datasetId)
diff --git a/singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js b/singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js
@@ -10,7 +10,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 	initComponent: function(){
 		Ext4.apply(this, {
 			style: 'padding: 10px;margins: 5px;',
-            minWidth: 950,
+            minWidth: 1025,
 			border: true,
 			items: [{
 				html: 'This step will query nimble results for the selected genome(s). It will then append these results to the seurat object on the target assay.',
@@ -20,7 +20,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 			},{
 				xtype: 'ldk-gridpanel',
 				clicksToEdit: 1,
-				width: 875,
+				width: 1000,
 				tbar: [{
 					text: 'Add',
 					handler: function(btn){
@@ -40,7 +40,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 				},LABKEY.ext4.GRIDBUTTONS.DELETERECORD()],
 				store: {
 					type: 'array',
-					fields: ['genomeId', 'targetAssay','maxAmbiguityAllowed', 'queryDatabaseForLineageUpdates']
+					fields: ['genomeId', 'targetAssay','maxAmbiguityAllowed', 'queryDatabaseForLineageUpdates', 'replaceExistingAssayData']
 				},
 				columns: [{
 					dataIndex: 'genomeId',
@@ -86,6 +86,16 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 						allowBlank: true,
 						value: false
 					}
+				},{
+					dataIndex: 'replaceExistingAssayData',
+					width: 150,
+					header: 'Replace Existing Data?',
+					editor: {
+						xtype: 'checkbox',
+						allowBlank: true,
+						value: true
+					}
+
 				}]
 			}]
 		});
@@ -96,7 +106,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 	getValue: function(){
 		var ret = [];
 		this.down('ldk-gridpanel').store.each(function(r, i) {
-			ret.push([r.data.genomeId, r.data.targetAssay, r.data.maxAmbiguityAllowed ?? '', !!r.data.queryDatabaseForLineageUpdates]);
+			ret.push([r.data.genomeId, r.data.targetAssay, r.data.maxAmbiguityAllowed ?? '', !!r.data.queryDatabaseForLineageUpdates], !!r.data.replaceExistingAssayData);
 		}, this);
 
 		return Ext4.isEmpty(ret) ? null : JSON.stringify(ret);
@@ -133,7 +143,8 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 					genomeId: row[0],
 					targetAssay: row[1],
 					maxAmbiguityAllowed: row[2],
-					queryDatabaseForLineageUpdates: !!row[3]
+					queryDatabaseForLineageUpdates: !!row[3],
+					replaceExistingAssayData: !!row[4]
 				});
 				grid.store.add(rec);
 			}, this);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java
@@ -77,7 +77,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         for (int i = 0; i < json.length(); i++)
         {
             JSONArray arr = json.getJSONArray(i);
-            if (arr.length() != 4)
+            if (arr.length() != 5)
             {
                 throw new PipelineJobException("Unexpected value: " + json.get(i));
             }
@@ -96,7 +96,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         for (int i = 0; i < json.length(); i++)
         {
             JSONArray arr = json.getJSONArray(i);
-            if (arr.length() < 3)
+            if (arr.length() != 5)
             {
                 throw new PipelineJobException("Unexpected value: " + json.getString(i));
             }
@@ -118,13 +118,32 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         for (int i = 0; i < json.length(); i++)
         {
             JSONArray arr = json.getJSONArray(i);
-            if (arr.length() != 4)
+            if (arr.length() != 5)
             {
                 throw new PipelineJobException("Unexpected value: " + json.getString(i));
             }
 
             int genomeId = arr.getInt(0);
-            String valStr = arr.get(2) == null ? null : StringUtils.trimToNull(String.valueOf(arr.get(2)));
+            String valStr = arr.get(3) == null ? null : StringUtils.trimToNull(String.valueOf(arr.get(2)));
+            boolean val = Boolean.parseBoolean(valStr);
+
+            ret.bodyLines.add("\t" + delim + "'" + genomeId + "' = " + (val ? "TRUE" : "FALSE"));
+            delim = ",";
+        }
+        ret.bodyLines.add(")");
+
+        ret.bodyLines.add("replaceExistingAssayDataByGenome <- list(");
+        delim = "";
+        for (int i = 0; i < json.length(); i++)
+        {
+            JSONArray arr = json.getJSONArray(i);
+            if (arr.length() != 5)
+            {
+                throw new PipelineJobException("Unexpected value: " + json.getString(i));
+            }
+
+            int genomeId = arr.getInt(0);
+            String valStr = arr.get(4) == null ? null : StringUtils.trimToNull(String.valueOf(arr.get(2)));
             boolean val = Boolean.parseBoolean(valStr);
 
             ret.bodyLines.add("\t" + delim + "'" + genomeId + "' = " + (val ? "TRUE" : "FALSE"));

Original file line number	Diff line number	Diff line change
`@@ -19,7 +19,8 @@ for (datasetId in names(seuratObjects)) {`
`19`	`19`	`for (genomeId in names(nimbleGenomes)) {`
`20`	`20`	`maxAmbiguityAllowed <- nimbleGenomeAmbiguousPreference[[genomeId]]`
`21`	`21`	`queryDatabaseForLineageUpdates <- queryDatabaseForLineageUpdatesPreference[[genomeId]]`
`22`		`- seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, ensureSamplesShareAllGenomes = ensureSamplesShareAllGenomes, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, maxAmbiguityAllowed = maxAmbiguityAllowed, maxLibrarySizeRatio = maxLibrarySizeRatio, queryDatabaseForLineageUpdates = queryDatabaseForLineageUpdates)`
	`22`	`+ replaceExistingAssayData <- replaceExistingAssayDataByGenome[[genomeId]]`
	`23`	`+ seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, ensureSamplesShareAllGenomes = ensureSamplesShareAllGenomes, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, maxAmbiguityAllowed = maxAmbiguityAllowed, maxLibrarySizeRatio = maxLibrarySizeRatio, queryDatabaseForLineageUpdates = queryDatabaseForLineageUpdates, replaceExistingAssayData = replaceExistingAssayData)`
`23`	`24`	`}`
`24`	`25`
`25`	`26`	`saveData(seuratObj, datasetId)`
Original file line number	Diff line number	Diff line change
`@@ -77,7 +77,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur`
`77`	`77`	`for (int i = 0; i < json.length(); i++)`
`78`	`78`	`{`
`79`	`79`	`JSONArray arr = json.getJSONArray(i);`
`80`		`- if (arr.length() != 4)`
	`80`	`+ if (arr.length() != 5)`
`81`	`81`	`{`
`82`	`82`	`throw new PipelineJobException("Unexpected value: " + json.get(i));`
`83`	`83`	`}`
`@@ -96,7 +96,7 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur`
`96`	`96`	`for (int i = 0; i < json.length(); i++)`
`97`	`97`	`{`
`98`	`98`	`JSONArray arr = json.getJSONArray(i);`
`99`		`- if (arr.length() < 3)`
	`99`	`+ if (arr.length() != 5)`
`100`	`100`	`{`
`101`	`101`	`throw new PipelineJobException("Unexpected value: " + json.getString(i));`
`102`	`102`	`}`
`@@ -118,13 +118,32 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur`
`118`	`118`	`for (int i = 0; i < json.length(); i++)`
`119`	`119`	`{`
`120`	`120`	`JSONArray arr = json.getJSONArray(i);`
`121`		`- if (arr.length() != 4)`
	`121`	`+ if (arr.length() != 5)`
`122`	`122`	`{`
`123`	`123`	`throw new PipelineJobException("Unexpected value: " + json.getString(i));`
`124`	`124`	`}`
`125`	`125`
`126`	`126`	`int genomeId = arr.getInt(0);`
`127`		`- String valStr = arr.get(2) == null ? null : StringUtils.trimToNull(String.valueOf(arr.get(2)));`
	`127`	`+ String valStr = arr.get(3) == null ? null : StringUtils.trimToNull(String.valueOf(arr.get(2)));`
	`128`	`+ boolean val = Boolean.parseBoolean(valStr);`
	`129`	`+`
	`130`	`+ ret.bodyLines.add("\t" + delim + "'" + genomeId + "' = " + (val ? "TRUE" : "FALSE"));`
	`131`	`+ delim = ",";`
	`132`	`+ }`
	`133`	`+ ret.bodyLines.add(")");`
	`134`	`+`
	`135`	`+ ret.bodyLines.add("replaceExistingAssayDataByGenome <- list(");`
	`136`	`+ delim = "";`
	`137`	`+ for (int i = 0; i < json.length(); i++)`
	`138`	`+ {`
	`139`	`+ JSONArray arr = json.getJSONArray(i);`
	`140`	`+ if (arr.length() != 5)`
	`141`	`+ {`
	`142`	`+ throw new PipelineJobException("Unexpected value: " + json.getString(i));`
	`143`	`+ }`
	`144`	`+`
	`145`	`+ int genomeId = arr.getInt(0);`
	`146`	`+ String valStr = arr.get(4) == null ? null : StringUtils.trimToNull(String.valueOf(arr.get(2)));`
`128`	`147`	`boolean val = Boolean.parseBoolean(valStr);`
`129`	`148`
`130`	`149`	`ret.bodyLines.add("\t" + delim + "'" + genomeId + "' = " + (val ? "TRUE" : "FALSE"));`