@platforma-open/milaboratories.top-antibodies.workflow 1.9.0 → 1.10.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.top-antibodies.workflow@1.9.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@1.10.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/filter-and-sample.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,16 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 1.10.0
+
+### Minor Changes
+
+- c282203: Improved block performance. Fixed increasing ranking order and cluster size ranking
+
+### Patch Changes
+
+- Updated dependencies [c282203]
+  - @platforma-open/milaboratories.top-antibodies.sample-clonotypes@1.3.0
+
 ## 1.9.0
 
 ### Minor Changes

package/package.json

@@ -1,13 +1,13 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.9.0",
+  "version": "1.10.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^4.9.2",
-    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.2.0",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.4.0",
-    "@platforma-open/milaboratories.top-antibodies.umap": "1.0.3"
+    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.3.0",
+    "@platforma-open/milaboratories.top-antibodies.umap": "1.0.3",
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.4.0"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.12",

package/src/filter-and-sample.tpl.tengo

@@ -15,6 +15,7 @@ self.body(func(inputs) {
     cloneTable := inputs.cloneTable
     datasetSpec := inputs.datasetSpec
     filterMap := inputs.filterMap
+    rankingMap := inputs.rankingMap
     topClonotypes := inputs.topClonotypes
 
     outputs := {}
@@ -58,6 +59,7 @@ self.body(func(inputs) {
 			addFile("filteredClonotypes.csv", filteredClonotypesCsv).
 			arg("--csv").arg("filteredClonotypes.csv").
 			arg("--n").arg(string(topClonotypes)).
+			arg("--ranking-map").arg(string(json.encode(rankingMap))).
 			arg("--out").arg("sampledClonotypes_top.csv").
 			saveFile("sampledClonotypes_top.csv").
 			printErrStreamToStdout().

package/src/main.tpl.tengo

@@ -49,6 +49,12 @@ wf.prepare(func(args){
         partialAxesMatch: true
     }, "linkers")
 
+    // Add cluster size columns from clustering blocks
+    bundleBuilder.addMulti({
+        name: "pl7.app/vdj/clustering/clusterSize",
+        partialAxesMatch: true
+    }, "clusterSizes")
+
     // Add CDR3 sequences
 	bundleBuilder.addMulti({
 		axes: [{ anchor: "main", idx: 1 }], // Clonotype axis
@@ -104,6 +110,7 @@ wf.body(func(args) {
 	// AnchoredColumnId {anchorRef: PlRef, anchorName: string, column: SUniversalPColumnId (unique column id)}
 	addedAxes := [] // Keep track of axes that are added to the table to prevent duplicates
 	filterMap := {} // Map column headers to filter criteria
+	rankingMap := {} // Map column headers to ranking order (increasing/decreasing)
 	if len(args.filters) > 0 {
 		for i, filter in args.filters {
 			if filter.value != undefined {
@@ -132,6 +139,8 @@ wf.body(func(args) {
 	if len(args.rankingOrder) > 0 {
 		for i, col in args.rankingOrder {
 			cloneTable.add(columns.getColumn(col.value.column), {header: "Col" + string(i)})
+			// Store ranking order for this column
+			rankingMap["Col" + string(i)] = col.rankingOrder
 		
 			// If column does not have main anchor axis we have to include theirs (columns coming from clustering blocks for example)
 			colsSpec := columns.getSpec(col.value.column)
@@ -147,6 +156,8 @@ wf.body(func(args) {
 	} else {
 		i := 0
 		cloneTable.add(columns.getColumn(args.rankingOrderDefault.value.column), {header: "Col" + string(i)})
+		// Store default ranking order
+		rankingMap["Col" + string(i)] = args.rankingOrderDefault.rankingOrder
 	
 		// If column does not have main anchor axis we have to include theirs
 		colsSpec := columns.getSpec(args.rankingOrderDefault.value.column)
@@ -175,6 +186,20 @@ wf.body(func(args) {
 			}
 		}
 	}
+
+	// Add cluster size columns if available
+	if len(columns.getColumns("clusterSizes")) > 0 {
+		for i, col in columns.getColumns("clusterSizes") {
+			cloneTable.add(col, {header: "clusterSize." + string(i)})
+			// Add the cluster axis header
+			for axisIdx, axis in col.spec.axesSpec {
+				if axis.name != datasetSpec.axesSpec[1].name {
+					cloneTable.setAxisHeader(axis.name, "clusterAxis_" + string(i) + "_" + string(axisIdx))
+				}
+			}
+		}
+	}
+
 	cloneTable.mem("16GiB")
 	cloneTable.cpu(1)
 	cloneTable = cloneTable.build()
@@ -187,6 +212,7 @@ wf.body(func(args) {
 		rankingOrderDefault: args.rankingOrderDefault,
 		filters: args.filters,
 		filterMap: filterMap,
+		rankingMap: rankingMap,
 		datasetSpec: datasetSpec,
 		topClonotypes: args.topClonotypes
 	})

package/src/prerun.tpl.tengo

@@ -51,6 +51,12 @@ wf.prepare(func(args){
         partialAxesMatch: true
     }, "linkers")
 
+    // Add cluster size columns from clustering blocks
+    bundleBuilder.addMulti({
+        name: "pl7.app/vdj/clustering/clusterSize",
+        partialAxesMatch: true
+    }, "clusterSizes")
+
     // Add CDR3 sequences
 	bundleBuilder.addMulti({
 		axes: [{ anchor: "main", idx: 1 }], // Clonotype axis
@@ -100,6 +106,7 @@ wf.body(func(args) {
         // Add Filters to table
         addedAxes := []
         filterMap := {}
+        rankingMap := {}
         if len(args.filters) > 0 {
             for i, filter in args.filters {
                 if filter.value != undefined {
@@ -129,6 +136,8 @@ wf.body(func(args) {
             for i, col in args.rankingOrder {
                 if col.value != undefined {
                     cloneTable.add(columns.getColumn(col.value.column), {header: "Col" + string(i)})
+                    // Store ranking order for this column
+                    rankingMap["Col" + string(i)] = col.rankingOrder
                 
                     // If column does not have main anchor axis we have to include theirs
                     colsSpec := columns.getSpec(col.value.column)
@@ -148,6 +157,8 @@ wf.body(func(args) {
             if args.rankingOrderDefault.value != undefined {
                 i := 0
                 cloneTable.add(columns.getColumn(args.rankingOrderDefault.value.column), {header: "Col" + string(i)})
+                // Store default ranking order
+                rankingMap["Col" + string(i)] = args.rankingOrderDefault.rankingOrder
             
                 // If column does not have main anchor axis we have to include theirs
                 colsSpec := columns.getSpec(args.rankingOrderDefault.value.column)
@@ -177,6 +188,20 @@ wf.body(func(args) {
                 }
             }
         }
+
+        // Add cluster size columns if available
+        if len(columns.getColumns("clusterSizes")) > 0 {
+            for i, col in columns.getColumns("clusterSizes") {
+                cloneTable.add(col, {header: "clusterSize." + string(i)})
+                // Add the cluster axis header
+                for axisIdx, axis in col.spec.axesSpec {
+                    if axis.name != datasetSpec.axesSpec[1].name {
+                        cloneTable.setAxisHeader(axis.name, "clusterAxis_" + string(i) + "_" + string(axisIdx))
+                    }
+                }
+            }
+        }
+
         cloneTable.mem("16GiB")
         cloneTable.cpu(1)
         cloneTable = cloneTable.build()
@@ -190,6 +215,7 @@ wf.body(func(args) {
             rankingOrderDefault: args.rankingOrderDefault,
             filters: args.filters,
             filterMap: filterMap,
+            rankingMap: rankingMap,
             datasetSpec: datasetSpec
         })