From 22034c2b4ea96e7a54280893d0c27af0350cbf65 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Thu, 23 Jan 2025 13:25:14 -0800
Subject: [PATCH] Allow nimble append to support queryDatabaseForLineageUpdates

---
 singlecell/resources/chunks/AppendNimble.R    |  5 +++--
 .../web/singlecell/panel/NimbleAppendPanel.js | 16 +++++++++++---
 .../pipeline/singlecell/AppendNimble.java     | 21 ++++++++++++++++++-
 3 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/singlecell/resources/chunks/AppendNimble.R b/singlecell/resources/chunks/AppendNimble.R
index 7a913d757..97023dea0 100644
--- a/singlecell/resources/chunks/AppendNimble.R
+++ b/singlecell/resources/chunks/AppendNimble.R
@@ -17,8 +17,9 @@ for (datasetId in names(seuratObjects)) {
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
   for (genomeId in names(nimbleGenomes)) {
-    maxAmbiguityAllowed <- !nimbleGenomeAmbiguousPreference[[genomeId]]
-    seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, ensureSamplesShareAllGenomes = ensureSamplesShareAllGenomes, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, maxAmbiguityAllowed = maxAmbiguityAllowed, maxLibrarySizeRatio = maxLibrarySizeRatio)
+    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)
   }
 
   saveData(seuratObj, datasetId)
diff --git a/singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js b/singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js
index f01e307ce..7712dc1c0 100644
--- a/singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js
+++ b/singlecell/resources/web/singlecell/panel/NimbleAppendPanel.js
@@ -40,7 +40,7 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 				},LABKEY.ext4.GRIDBUTTONS.DELETERECORD()],
 				store: {
 					type: 'array',
-					fields: ['genomeId', 'targetAssay','maxAmbiguityAllowed']
+					fields: ['genomeId', 'targetAssay','maxAmbiguityAllowed', 'queryDatabaseForLineageUpdates']
 				},
 				columns: [{
 					dataIndex: 'genomeId',
@@ -77,6 +77,15 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 						allowBlank: true,
 						minValue: 0
 					}
+				},{
+					dataIndex: 'queryDatabaseForLineageUpdates',
+					width: 175,
+					header: 'Check for Lineage Updates',
+					editor: {
+						xtype: 'checkbox',
+						allowBlank: true,
+						value: false
+					}
 				}]
 			}]
 		});
@@ -87,7 +96,7 @@ 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 ?? '']);
+			ret.push([r.data.genomeId, r.data.targetAssay, r.data.maxAmbiguityAllowed ?? '', !!r.data.queryDatabaseForLineageUpdates]);
 		}, this);
 
 		return Ext4.isEmpty(ret) ? null : JSON.stringify(ret);
@@ -123,7 +132,8 @@ Ext4.define('SingleCell.panel.NimbleAppendPanel', {
 				var rec = grid.store.createModel({
 					genomeId: row[0],
 					targetAssay: row[1],
-					maxAmbiguityAllowed: row[2]
+					maxAmbiguityAllowed: row[2],
+					queryDatabaseForLineageUpdates: !!row[3]
 				});
 				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
index 2fade274d..67b24280a 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java
@@ -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() < 3)
             {
                 throw new PipelineJobException("Unexpected value: " + json.getString(i));
             }
@@ -113,6 +113,25 @@ protected Chunk createParamChunk(SequenceOutputHandler.JobContext ctx, List<Seur
         }
         ret.bodyLines.add(")");
 
+        ret.bodyLines.add("queryDatabaseForLineageUpdatesPreference <- list(");
+        delim = "";
+        for (int i = 0; i < json.length(); i++)
+        {
+            JSONArray arr = json.getJSONArray(i);
+            if (arr.length() != 4)
+            {
+                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)));
+            boolean val = Boolean.parseBoolean(valStr);
+
+            ret.bodyLines.add("\t" + delim + "'" + genomeId + "' = " + (val ? "TRUE" : "FALSE"));
+            delim = ",";
+        }
+        ret.bodyLines.add(")");
+
         return ret;
     }