@platforma-open/milaboratories.top-antibodies.workflow 4.0.0 → 4.0.1

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@4.0.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@4.0.1 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 +1,15 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 4.0.1
+
+### Patch Changes
+
+- dd754ae: Accept both pre- and post-peptide-adaptation spec names from upstream blocks so projects using either version remain functional:
+
+  - Preset filter/ranking allowlists now include `pl7.app/enrichment*` (clonotype-enrichment) and `pl7.app/developability*` (antibody-sequence-liabilities) alongside the legacy `pl7.app/vdj/`-prefixed names.
+  - Diversification dropdown, cluster-axis matching, hidden cluster-mapping column, and workflow-side linker matching now recognize both `pl7.app/clusterId` and `pl7.app/vdj/clusterId` axis names (clonotype-clustering rename).
+  - Cluster-size query uses a namePattern matching both `pl7.app/clustering/clusterSize` and `pl7.app/vdj/clustering/clusterSize`.
+
 ## 4.0.0
 
 ### Major Changes

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

@@ -13,6 +13,13 @@ inVivoScoreSourceColumns := {
 
 
 
+isClusterIdAxis := func(name) {
+    return name == "pl7.app/clusterId" || name == "pl7.app/vdj/clusterId"
+}
+
+
+
+
 
 
 
@@ -61,7 +68,7 @@ findMatchingLinkerIndex := func(colsSpec, linkerColumns) {
 
     rankingClusterIdAxis := undefined
     for axis in colsSpec.axesSpec {
-        if axis.name == "pl7.app/clusterId" {
+        if isClusterIdAxis(axis.name) {
             rankingClusterIdAxis = axis
             break
         }
@@ -76,7 +83,7 @@ findMatchingLinkerIndex := func(colsSpec, linkerColumns) {
 
         linkerClusterIdAxis := undefined
         for axis in linkerCol.spec.axesSpec {
-            if axis.name == "pl7.app/clusterId" {
+            if isClusterIdAxis(axis.name) {
                 linkerClusterIdAxis = axis
                 break
             }
@@ -195,7 +202,7 @@ resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
 
     selectedClusterIdAxis := undefined
     for axis in selectedLinkerSpec.axesSpec {
-        if axis.name == "pl7.app/clusterId" {
+        if isClusterIdAxis(axis.name) {
             selectedClusterIdAxis = axis
             break
         }
@@ -209,7 +216,7 @@ resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
     for linkerIdx, col in sortedLinkers {
 
         for axis in col.spec.axesSpec {
-            if axis.name == "pl7.app/clusterId" {
+            if isClusterIdAxis(axis.name) {
 
                 if clusterAxisDomainsMatch(selectedClusterIdAxis, axis) {
                     return "clusterAxis_" + string(linkerIdx) + "_0"
@@ -409,7 +416,7 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
             addedCols = true
         }
 
-        if !is_undefined(clusterIdAxis) && clusterIdAxis.name == "pl7.app/clusterId" {
+        if !is_undefined(clusterIdAxis) && isClusterIdAxis(clusterIdAxis.name) {
             linkerClusterIdAxesWithIdx = append(linkerClusterIdAxesWithIdx, {
                 axis: clusterIdAxis,
                 linkerIdx: linkerIdx
@@ -423,7 +430,7 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
 
             clusterSizeClusterIdAxis := undefined
             for axis in col.spec.axesSpec {
-                if axis.name == "pl7.app/clusterId" {
+                if isClusterIdAxis(axis.name) {
                     clusterSizeClusterIdAxis = axis
                     break
                 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "4.0.0",
+  "version": "4.0.1",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
@@ -8,9 +8,9 @@
     "@platforma-open/milaboratories.software-anarci": "^0.0.3",
     "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "2.1.2",
     "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.2",
+    "@platforma-open/milaboratories.top-antibodies.umap": "1.2.3",
     "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.4.3",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.3",
-    "@platforma-open/milaboratories.top-antibodies.umap": "1.2.3"
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.3"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "2.5.20"

package/src/main.tpl.tengo

@@ -75,9 +75,11 @@ wf.prepare(func(args){
         bundleBuilder.addAnchor("selectedCluster", args.diversificationColumn)
     }
 
-    // Add cluster size columns from clustering blocks
+    // Add cluster size columns from clustering blocks. The namePattern matches
+    // both the post-peptide-adaptation name and the pre-peptide `pl7.app/vdj/`
+    // variant so older clonotype-clustering instances remain usable.
     bundleBuilder.addMulti({
-        name: "pl7.app/vdj/clustering/clusterSize",
+        namePattern: "^pl7\\.app/(vdj/)?clustering/clusterSize$",
         partialAxesMatch: true
     }, "clusterSizes")
 

package/src/utils.lib.tengo

@@ -10,6 +10,13 @@ inVivoScoreSourceColumns := {
     "nMutations": "pl7.app/vdj/sequence/nMutations"
 }
 
+// Cluster-id axis names — both unprefixed (post-peptide-adaptation) and
+// `pl7.app/vdj/`-prefixed (pre-peptide) so older clonotype-clustering
+// instances remain selectable as diversification linkers.
+isClusterIdAxis := func(name) {
+    return name == "pl7.app/clusterId" || name == "pl7.app/vdj/clusterId"
+}
+
 /**
  * Checks if two clusterId axes have matching domains.
  * Used to determine if two columns belong to the same clustering run.
@@ -61,7 +68,7 @@ findMatchingLinkerIndex := func(colsSpec, linkerColumns) {
     // Find the clusterId axis in the ranking column
     rankingClusterIdAxis := undefined
     for axis in colsSpec.axesSpec {
-        if axis.name == "pl7.app/clusterId" {
+        if isClusterIdAxis(axis.name) {
             rankingClusterIdAxis = axis
             break
         }
@@ -76,7 +83,7 @@ findMatchingLinkerIndex := func(colsSpec, linkerColumns) {
         // Get the clusterId axis from the linker column
         linkerClusterIdAxis := undefined
         for axis in linkerCol.spec.axesSpec {
-            if axis.name == "pl7.app/clusterId" {
+            if isClusterIdAxis(axis.name) {
                 linkerClusterIdAxis = axis
                 break
             }
@@ -195,7 +202,7 @@ resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
     // Find the clusterId axis in the selected linker
     selectedClusterIdAxis := undefined
     for axis in selectedLinkerSpec.axesSpec {
-        if axis.name == "pl7.app/clusterId" {
+        if isClusterIdAxis(axis.name) {
             selectedClusterIdAxis = axis
             break
         }
@@ -209,7 +216,7 @@ resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
     for linkerIdx, col in sortedLinkers {
         // Get the clusterId axis from this linker
         for axis in col.spec.axesSpec {
-            if axis.name == "pl7.app/clusterId" {
+            if isClusterIdAxis(axis.name) {
                 // Use clusterAxisDomainsMatch for proper domain comparison
                 if clusterAxisDomainsMatch(selectedClusterIdAxis, axis) {
                     return "clusterAxis_" + string(linkerIdx) + "_0"
@@ -409,7 +416,7 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
             addedCols = true
         }
         // Collect clusterId axes from linker columns to match cluster size columns
-        if !is_undefined(clusterIdAxis) && clusterIdAxis.name == "pl7.app/clusterId" {
+        if !is_undefined(clusterIdAxis) && isClusterIdAxis(clusterIdAxis.name) {
             linkerClusterIdAxesWithIdx = append(linkerClusterIdAxesWithIdx, {
                 axis: clusterIdAxis,
                 linkerIdx: linkerIdx
@@ -423,7 +430,7 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
             // Find the clusterId axis in this cluster size column
             clusterSizeClusterIdAxis := undefined
             for axis in col.spec.axesSpec {
-                if axis.name == "pl7.app/clusterId" {
+                if isClusterIdAxis(axis.name) {
                     clusterSizeClusterIdAxis = axis
                     break
                 }