@platforma-open/milaboratories.top-antibodies.workflow 1.17.6 → 2.0.1

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@1.17.6 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@2.0.1 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/assembling-fasta.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,22 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 2.0.1
+
+### Patch Changes
+
+- 140ce30: Support custom block label
+
+## 2.0.0
+
+### Major Changes
+
+- 590699a: Introduce diverisified ranking, in-vivo score estimation and workflow presets
+
+### Patch Changes
+
+- Updated dependencies [590699a]
+  - @platforma-open/milaboratories.top-antibodies.sample-clonotypes@2.0.0
+
 ## 1.17.6
 
 ### Patch Changes

package/dist/tengo/lib/sampled-cols-conv.lib.tengo

@@ -1,6 +1,6 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 
-getColumns := func(datasetSpec, addRanking) {
+getColumns := func(datasetSpec, addRanking, addInVivoScore) {
   columns := [{
         column: "top",
         id: "link",
@@ -32,7 +32,21 @@ getColumns := func(datasetSpec, addRanking) {
         }
       }]
   }
-
+  if addInVivoScore {
+    columns = columns + [{
+        column: "inVivoScore",
+        spec: {
+          name: "pl7.app/vdj/inVivoScore",
+          valueType: "Float",
+          domain: {},
+          annotations: {
+            "pl7.app/label": "In Vivo Score",
+            "pl7.app/table/visibility": "optional",
+            "pl7.app/format": ".2f"
+          }
+        }
+      }]
+  }
 
   return {
     axes: [

package/dist/tengo/lib/sampled-export-conv.lib.tengo

@@ -1,16 +1,16 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 json := import("json")
 
-getColumns := func(datasetSpec, filterMap, rankingMap, disableClusterRanking, clusterColumn, topClonotypes) {
+getColumns := func(datasetSpec, filterMap, rankingMap, diversificationColumn, topClonotypes) {
 
 
   domain := {
     "pl7.app/vdj/filter-map": string(json.encode(filterMap)),
-    "pl7.app/vdj/ranking-map": string(json.encode(rankingMap)),            
+    "pl7.app/vdj/ranking-map": string(json.encode(rankingMap)),
     "pl7.app/vdj/top-clonotypes": string(topClonotypes)
   }
-  if !disableClusterRanking && clusterColumn != undefined && clusterColumn != "" {
-    domain["pl7.app/vdj/diversity-column"] = string(json.encode(clusterColumn))
+  if diversificationColumn != undefined && diversificationColumn != "" {
+    domain["pl7.app/vdj/diversity-column"] = string(json.encode(diversificationColumn))
   }
 
   columns := [{

package/dist/tengo/lib/utils.lib.tengo

@@ -5,6 +5,13 @@ json := import("json")
 
 
 
+inVivoScoreSourceColumns := {
+    "fractionCDR": "pl7.app/vdj/sequence/fractionCDRMutations",
+    "nMutations": "pl7.app/vdj/sequence/nMutations"
+}
+
+
+
 
 
 
@@ -175,12 +182,12 @@ buildSortedLinkers := func(columns, datasetSpec) {
 
 
 resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
-    if is_undefined(args.clusterColumn) {
+    if is_undefined(args.diversificationColumn) {
         return undefined
     }
-    
 
-    selectedLinkerSpec := columns.getSpec(args.clusterColumn)
+
+    selectedLinkerSpec := columns.getSpec(args.diversificationColumn)
     if is_undefined(selectedLinkerSpec) {
         return undefined
     }
@@ -273,6 +280,21 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
     if len(args.rankingOrder) > 0 {
         for i, col in args.rankingOrder {
 
+            if col.value != undefined && col.value.column == "pl7.app/vdj/inVivoScore" {
+
+                cloneTable.setAxisHeader(datasetSpec.axesSpec[0], "sampleId")
+                cloneTable.add(columns.getColumn(args.inputAnchor), {header: "inVivo_primaryAbundance"})
+                addedCols = true
+                for key, _ in inVivoScoreSourceColumns {
+                    for srcCol in columns.getColumns("inVivo_" + key) {
+                        cloneTable.add(srcCol, {header: "inVivo_" + key})
+                        addedCols = true
+                    }
+                }
+                rankingMap["inVivoScore"] = col.rankingOrder
+                continue
+            }
+
             if col.value != undefined && columns.getColumn(col.value.column).spec != undefined {
 
                 colsSpec := columns.getSpec(col.value.column)
@@ -641,5 +663,6 @@ export {
     detectBulkChain: detectBulkChain,
     initializeAssemSeqTable: initializeAssemSeqTable,
     formatFilterDescription: formatFilterDescription,
-    buildFilterTraceLabel: buildFilterTraceLabel
+    buildFilterTraceLabel: buildFilterTraceLabel,
+    inVivoScoreSourceColumns: inVivoScoreSourceColumns
 }

package/package.json

@@ -1,16 +1,16 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.17.6",
+  "version": "2.0.1",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.8.2",
     "@platforma-open/milaboratories.software-anarci": "^0.0.3",
-    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.9.3",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.1",
+    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "2.0.0",
     "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.0",
+    "@platforma-open/milaboratories.top-antibodies.umap": "1.2.1",
     "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.3.0",
-    "@platforma-open/milaboratories.top-antibodies.umap": "1.2.1"
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.1"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "2.4.18"

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

@@ -40,8 +40,16 @@ self.body(func(inputs) {
     // Save filtered parquet file
     filteredClonotypes := filterResult.getFile("filteredClonotypes.parquet")
 
-    // Store outputs 
-    sampledColsParams := sampledColsConv.getColumns(datasetSpec, false) // No ranking column
+    // Check if In Vivo Score is in the ranking map
+    hasInVivoScore := false
+    for key, _ in rankingMap {
+        if key == "inVivoScore" {
+            hasInVivoScore = true
+        }
+    }
+
+    // Store outputs
+    sampledColsParams := sampledColsConv.getColumns(datasetSpec, false, false) // No ranking column
     filteredClonotypesPf := xsv.importFile(filteredClonotypes, "parquet", sampledColsParams,
                                         {cpu: 1, mem: "16GiB"})
 
@@ -62,12 +70,9 @@ self.body(func(inputs) {
 			arg("--n").arg(string(topClonotypes)).
 			arg("--ranking-map").arg(string(json.encode(rankingMap)))
 
-		// Add optional parameters if provided in block args
-		if inputs.disableClusterRanking {
-			builder = builder.arg("--disable-cluster-ranking")
-		}
-		if inputs.clusterColumn != undefined && inputs.clusterColumn != "" {
-			builder = builder.arg("--cluster-column").arg(inputs.clusterColumn)
+		// Add diversification column if provided
+		if inputs.diversificationColumn != undefined && inputs.diversificationColumn != "" {
+			builder = builder.arg("--diversification-column").arg(inputs.diversificationColumn)
 		}
 
 		sampleClones := builder.
@@ -80,8 +85,8 @@ self.body(func(inputs) {
 		// Save top clonotypes parquet file
 		finalClonotypes = sampleClones.getFile("sampledClonotypes_top.parquet")
 		
-		// Store outputs 
-        sampledColsParams := sampledColsConv.getColumns(datasetSpec, true) // Add ranking column
+		// Store outputs
+        sampledColsParams := sampledColsConv.getColumns(datasetSpec, true, hasInVivoScore) // Add ranking column
 		sampledColumnsPf := xsv.importFile(finalClonotypes, "parquet", sampledColsParams,
 											{cpu: 1, mem: "16GiB"})
 		outputs["sampledRows"] = pframes.exportFrame(sampledColumnsPf)
@@ -91,7 +96,7 @@ self.body(func(inputs) {
 
     // Export only the sampling column to be used as a filter downstream
     sampledExportsParams := sampledExportConv.getColumns(datasetSpec, filterMap,
-        rankingMap, inputs.disableClusterRanking, inputs.rawClusterColumn, topClonotypes)
+        rankingMap, inputs.diversificationColumn, topClonotypes)
     sampledColumnsOnlyPf := xsv.importFile(finalClonotypes, "parquet", sampledExportsParams,
                                         {cpu: 1, mem: "16GiB"})
 
@@ -100,6 +105,10 @@ self.body(func(inputs) {
     if is_undefined(traceLabel) || traceLabel == "" {
         traceLabel = "Selected Leads"
     }
+    customBlockLabel := inputs.customBlockLabel
+    if !is_undefined(customBlockLabel) && customBlockLabel != "" {
+        traceLabel = customBlockLabel + " / " + traceLabel
+    }
     trace := pSpec.makeTrace(datasetSpec,
         {
             type: "milaboratories.antibody-tcr-lead-selection",

package/src/main.tpl.tengo

@@ -32,6 +32,19 @@ wf.prepare(func(args){
         for col in args.rankingOrder {
             // For cases where the user is selecting the table to filter
             if col.value != undefined {
+                // In Vivo Score is computed from source columns, not a real PColumn
+                if col.value.column == "pl7.app/vdj/inVivoScore" {
+                    // Primary abundance is the input anchor itself — already added above.
+                    // Fetch the remaining source columns by name.
+                    for key, name in utils.inVivoScoreSourceColumns {
+                        bundleBuilder.addMulti({
+                            axes: [{ anchor: "main", idx: 1 }],
+                            name: name
+                        }, "inVivo_" + key)
+                    }
+                    validRanks = true
+                    continue
+                }
                 bundleBuilder.addAnchor(col.value.anchorName, col.value.anchorRef)
                 bundleBuilder.addSingle(col.value.column)
                 validRanks = true
@@ -57,9 +70,9 @@ wf.prepare(func(args){
         partialAxesMatch: true
     }, "linkers")
     
-    // Add clusterColumn as a named anchor for matching in body phase
-    if !is_undefined(args.clusterColumn) {
-        bundleBuilder.addAnchor("selectedCluster", args.clusterColumn)
+    // Add diversificationColumn as a named anchor for matching in body phase
+    if !is_undefined(args.diversificationColumn) {
+        bundleBuilder.addAnchor("selectedCluster", args.diversificationColumn)
     }
 
     // Add cluster size columns from clustering blocks
@@ -150,10 +163,9 @@ wf.body(func(args) {
                 rankingMap: rankingMap,
                 datasetSpec: datasetSpec,
                 topClonotypes: args.topClonotypes,
-                disableClusterRanking: args.disableClusterRanking,
-                clusterColumn: clusterColumnHeader,
-                rawClusterColumn: args.clusterColumn,
-                filterTraceLabel: filterTraceLabel
+                diversificationColumn: clusterColumnHeader,
+                filterTraceLabel: filterTraceLabel,
+                customBlockLabel: args.customBlockLabel
             })
 
             // Get the filtered clonotypes from the template result

package/src/sampled-cols-conv.lib.tengo

@@ -1,6 +1,6 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 
-getColumns := func(datasetSpec, addRanking) {
+getColumns := func(datasetSpec, addRanking, addInVivoScore) {
   columns := [{
         column: "top",
         id: "link",
@@ -32,7 +32,21 @@ getColumns := func(datasetSpec, addRanking) {
         }
       }]
   }
-
+  if addInVivoScore {
+    columns = columns + [{
+        column: "inVivoScore",
+        spec: {
+          name: "pl7.app/vdj/inVivoScore",
+          valueType: "Float",
+          domain: {},
+          annotations: {
+            "pl7.app/label": "In Vivo Score",
+            "pl7.app/table/visibility": "optional",
+            "pl7.app/format": ".2f"
+          }
+        }
+      }]
+  }
 
   return {
     axes: [

package/src/sampled-export-conv.lib.tengo

@@ -1,16 +1,16 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 json := import("json")
 
-getColumns := func(datasetSpec, filterMap, rankingMap, disableClusterRanking, clusterColumn, topClonotypes) {
+getColumns := func(datasetSpec, filterMap, rankingMap, diversificationColumn, topClonotypes) {
 
   // Define domain
   domain := {
     "pl7.app/vdj/filter-map": string(json.encode(filterMap)),
-    "pl7.app/vdj/ranking-map": string(json.encode(rankingMap)),            
+    "pl7.app/vdj/ranking-map": string(json.encode(rankingMap)),
     "pl7.app/vdj/top-clonotypes": string(topClonotypes)
   }
-  if !disableClusterRanking && clusterColumn != undefined && clusterColumn != "" {
-    domain["pl7.app/vdj/diversity-column"] = string(json.encode(clusterColumn))
+  if diversificationColumn != undefined && diversificationColumn != "" {
+    domain["pl7.app/vdj/diversity-column"] = string(json.encode(diversificationColumn))
   }
 
   columns := [{

package/src/utils.lib.tengo

@@ -3,6 +3,13 @@
 slices := import("@platforma-sdk/workflow-tengo:slices")
 json := import("json")
 
+// PColumn names used as source columns for In Vivo Score computation.
+// Primary abundance is resolved separately via specific annotations.
+inVivoScoreSourceColumns := {
+    "fractionCDR": "pl7.app/vdj/sequence/fractionCDRMutations",
+    "nMutations": "pl7.app/vdj/sequence/nMutations"
+}
+
 /**
  * Checks if two clusterId axes have matching domains.
  * Used to determine if two columns belong to the same clustering run.
@@ -169,18 +176,18 @@ buildSortedLinkers := func(columns, datasetSpec) {
 /**
  * Resolves cluster column reference to header name by matching against sortedLinkers.
  * 
- * @param args - Arguments containing clusterColumn
+ * @param args - Arguments containing diversificationColumn
  * @param columns - PBundle containing all columns
  * @param sortedLinkers - List of linker columns in proper order
  * @return Cluster column header string or undefined
  */
 resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
-    if is_undefined(args.clusterColumn) {
+    if is_undefined(args.diversificationColumn) {
         return undefined
     }
-    
-    // Get the spec for the selected cluster column
-    selectedLinkerSpec := columns.getSpec(args.clusterColumn)
+
+    // Get the spec for the selected diversification column
+    selectedLinkerSpec := columns.getSpec(args.diversificationColumn)
     if is_undefined(selectedLinkerSpec) {
         return undefined
     }
@@ -220,7 +227,7 @@ resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
  * 
  * @param pframes - PFrames import
  * @param columns - PBundle containing all columns
- * @param args - Arguments containing filters, rankingOrder, clusterColumn
+ * @param args - Arguments containing filters, rankingOrder, diversificationColumn
  * @param datasetSpec - Dataset specification with axes
  * @return Map with keys: cloneTable, filterMap, rankingMap, sortedLinkers, clusterColumnHeader, addedCols
  */
@@ -272,6 +279,21 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
     
     if len(args.rankingOrder) > 0 {
         for i, col in args.rankingOrder {
+            // In Vivo Score: add source columns to the clone table for later computation
+            if col.value != undefined && col.value.column == "pl7.app/vdj/inVivoScore" {
+                // Primary abundance is the input anchor itself; it introduces the sampleId axis
+                cloneTable.setAxisHeader(datasetSpec.axesSpec[0], "sampleId")
+                cloneTable.add(columns.getColumn(args.inputAnchor), {header: "inVivo_primaryAbundance"})
+                addedCols = true
+                for key, _ in inVivoScoreSourceColumns {
+                    for srcCol in columns.getColumns("inVivo_" + key) {
+                        cloneTable.add(srcCol, {header: "inVivo_" + key})
+                        addedCols = true
+                    }
+                }
+                rankingMap["inVivoScore"] = col.rankingOrder
+                continue
+            }
             // we check for value presence and for actual pcolumn (cases where upstream block is deleted)
             if col.value != undefined && columns.getColumn(col.value.column).spec != undefined {
                 // Process the ranking column to determine header and cluster axis
@@ -401,7 +423,7 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
         cloneTable.cpu(1)
         builtTable = cloneTable.build()
         
-        // Resolve clusterColumn ref to header name
+        // Resolve diversificationColumn ref to header name
         clusterColumnHeader = resolveClusterColumnHeader(args, columns, sortedLinkers)
     }
     
@@ -641,5 +663,6 @@ export {
     detectBulkChain: detectBulkChain,
     initializeAssemSeqTable: initializeAssemSeqTable,
     formatFilterDescription: formatFilterDescription,
-    buildFilterTraceLabel: buildFilterTraceLabel
+    buildFilterTraceLabel: buildFilterTraceLabel,
+    inVivoScoreSourceColumns: inVivoScoreSourceColumns
 }