@platforma-open/milaboratories.top-antibodies.workflow 2.2.2 → 3.0.0

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@2.2.2 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@3.0.0 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 +1,11 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 3.0.0
+
+### Major Changes
+
+- c2c2b06: VDJ Integration support, BlockV3 api migration
+
 ## 2.2.2
 
 ### Patch Changes

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

@@ -339,9 +339,61 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
     }
 
 
+
+    usedNonMainAxes := {}
+    for i, filter in args.filters {
+        if filter.value != undefined {
+            colSpec := columns.getColumn(filter.value.column)
+            if !is_undefined(colSpec) && !is_undefined(colSpec.spec) {
+                for ax in colSpec.spec.axesSpec {
+                    if ax.name != datasetSpec.axesSpec[1].name {
+                        usedNonMainAxes[ax.name] = true
+                    }
+                }
+            }
+        }
+    }
+    for i, col in args.rankingOrder {
+        if col.value != undefined && col.value.column != "pl7.app/vdj/inVivoScore" {
+            colSpec := columns.getColumn(col.value.column)
+            if !is_undefined(colSpec) && !is_undefined(colSpec.spec) {
+                for ax in colSpec.spec.axesSpec {
+                    if ax.name != datasetSpec.axesSpec[1].name {
+                        usedNonMainAxes[ax.name] = true
+                    }
+                }
+            }
+        }
+    }
+
+    if !is_undefined(args.diversificationColumn) {
+        selectedLinkerSpec := columns.getSpec(args.diversificationColumn)
+        if !is_undefined(selectedLinkerSpec) {
+            for ax in selectedLinkerSpec.axesSpec {
+                if ax.name != datasetSpec.axesSpec[1].name {
+                    usedNonMainAxes[ax.name] = true
+                }
+            }
+        }
+    }
+
+
     linkerClusterIdAxesWithIdx := []
-    
+
     for linkerIdx, col in sortedLinkers {
+
+        otherAxis := undefined
+        if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
+            otherAxis = col.spec.axesSpec[0]
+        } else if datasetSpec.axesSpec[1].name == col.spec.axesSpec[0].name {
+            otherAxis = col.spec.axesSpec[1]
+        }
+
+
+        if is_undefined(otherAxis) || is_undefined(usedNonMainAxes[otherAxis.name]) {
+            continue
+        }
+
         clusterIdAxis := undefined
         if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
 
@@ -421,7 +473,7 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
     if addedCols {
         cloneTable.mem("16GiB")
         cloneTable.cpu(1)
-        builtTable = cloneTable.build()
+        builtTable = cloneTable.build({joinType: "Inner"})
         
 
         clusterColumnHeader = resolveClusterColumnHeader(args, columns, sortedLinkers)

package/package.json

@@ -1,19 +1,19 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "2.2.2",
+  "version": "3.0.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.11.0",
-    "@platforma-open/milaboratories.software-anarci": "1.0.1",
+    "@platforma-sdk/workflow-tengo": "5.13.1",
+    "@platforma-open/milaboratories.software-anarci": "^0.0.3",
     "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "2.1.1",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.2",
-    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.4.2",
     "@platforma-open/milaboratories.top-antibodies.umap": "1.2.2",
-    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.1"
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.2",
+    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.1",
+    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.4.2"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.5.2"
+    "@platforma-sdk/tengo-builder": "2.5.8"
   },
   "scripts": {
     "build": "shx rm -rf dist && pl-tengo check && pl-tengo build",

package/src/main.tpl.tengo

@@ -45,7 +45,6 @@ wf.prepare(func(args){
                     validRanks = true
                     continue
                 }
-                bundleBuilder.addAnchor(col.value.anchorName, col.value.anchorRef)
                 bundleBuilder.addSingle(col.value.column)
                 validRanks = true
             }
@@ -56,14 +55,15 @@ wf.prepare(func(args){
     if len(args.filters) > 0 {
         for filter in args.filters {
             if filter.value != undefined {
-                bundleBuilder.addAnchor(filter.value.anchorName, filter.value.anchorRef)
                 bundleBuilder.addSingle(filter.value.column)
             }
         }
     }
     
 
-    // Add linker columns
+    // Add linker columns — always fetch them for metadata,
+    // but initializeCloneTable only adds linkers to the join when needed
+    // by filter/ranking columns or diversification.
     bundleBuilder.addMulti({
         axes: [{ anchor: "main", idx: 1 }], // this will do partial axes match (unlike in the model)
         annotations: { "pl7.app/isLinkerColumn": "true" },

package/src/utils.lib.tengo

@@ -338,10 +338,62 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
         }
     }
 
-    // Get linker columns and add them to the table
+    // Collect axes used by filter/ranking columns (excluding clonotypeKey)
+    // to determine which linkers are actually needed
+    usedNonMainAxes := {}
+    for i, filter in args.filters {
+        if filter.value != undefined {
+            colSpec := columns.getColumn(filter.value.column)
+            if !is_undefined(colSpec) && !is_undefined(colSpec.spec) {
+                for ax in colSpec.spec.axesSpec {
+                    if ax.name != datasetSpec.axesSpec[1].name {
+                        usedNonMainAxes[ax.name] = true
+                    }
+                }
+            }
+        }
+    }
+    for i, col in args.rankingOrder {
+        if col.value != undefined && col.value.column != "pl7.app/vdj/inVivoScore" {
+            colSpec := columns.getColumn(col.value.column)
+            if !is_undefined(colSpec) && !is_undefined(colSpec.spec) {
+                for ax in colSpec.spec.axesSpec {
+                    if ax.name != datasetSpec.axesSpec[1].name {
+                        usedNonMainAxes[ax.name] = true
+                    }
+                }
+            }
+        }
+    }
+    // Diversification also needs its linker
+    if !is_undefined(args.diversificationColumn) {
+        selectedLinkerSpec := columns.getSpec(args.diversificationColumn)
+        if !is_undefined(selectedLinkerSpec) {
+            for ax in selectedLinkerSpec.axesSpec {
+                if ax.name != datasetSpec.axesSpec[1].name {
+                    usedNonMainAxes[ax.name] = true
+                }
+            }
+        }
+    }
+
+    // Get linker columns — only add to clone table if their non-main axis is used
     linkerClusterIdAxesWithIdx := []
-    
+
     for linkerIdx, col in sortedLinkers {
+        // Determine the linker's non-clonotypeKey axis
+        otherAxis := undefined
+        if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
+            otherAxis = col.spec.axesSpec[0]
+        } else if datasetSpec.axesSpec[1].name == col.spec.axesSpec[0].name {
+            otherAxis = col.spec.axesSpec[1]
+        }
+
+        // Skip this linker if its non-main axis is not used by any filter/ranking/diversification
+        if is_undefined(otherAxis) || is_undefined(usedNonMainAxes[otherAxis.name]) {
+            continue
+        }
+
         clusterIdAxis := undefined
         if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
             // clonotypeKey is in second axis
@@ -421,7 +473,7 @@ initializeCloneTable := func(pframes, columns, args, datasetSpec) {
     if addedCols {
         cloneTable.mem("16GiB")
         cloneTable.cpu(1)
-        builtTable = cloneTable.build()
+        builtTable = cloneTable.build({joinType: "Inner"})
         
         // Resolve diversificationColumn ref to header name
         clusterColumnHeader = resolveClusterColumnHeader(args, columns, sortedLinkers)