@platforma-open/milaboratories.top-antibodies.workflow 4.1.2 → 4.2.0

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@4.1.2 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@4.2.0 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
 
+## 4.2.0
+
+### Minor Changes
+
+- 8edddd1: Add dataset selector with optional filter dropdown. Replaces the plain dataset dropdown with `PlDatasetSelector`, and inner-joins the selected filter column into the clone table so it narrows every downstream stage (final clonotypes, spectratype, Kabat).
+
 ## 4.1.2
 
 ### Patch Changes

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

@@ -239,20 +239,32 @@ resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
 
 
 
-initializeCloneTable := func(pframes, columns, args, datasetSpec) {
+
+
+
+initializeCloneTable := func(pframes, columns, args, datasetSpec, inputFilterColumn) {
 
     cloneTable := pframes.parquetFileBuilder()
     cloneTable.setAxisHeader(datasetSpec.axesSpec[1], "clonotypeKey")
-    
+
 
     sortedLinkers := buildSortedLinkers(columns, datasetSpec)
-    
+
 
     addedAxes := []
     filterMap := {}
     rankingMap := {}
     addedCols := false
-    
+
+
+
+
+
+    if !is_undefined(inputFilterColumn) {
+        cloneTable.add(inputFilterColumn, {header: "primary_filter"})
+        addedCols = true
+    }
+
     if len(args.filters) > 0 {
         for i, filter in args.filters {
 

package/package.json

@@ -1,19 +1,19 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "4.1.2",
+  "version": "4.2.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.21.0",
+    "@platforma-sdk/workflow-tengo": "5.26.0",
     "@platforma-open/milaboratories.software-anarci": "^0.0.3",
     "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "2.1.4",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.5",
     "@platforma-open/milaboratories.top-antibodies.umap": "1.2.5",
+    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.4",
     "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.4.5",
-    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.4"
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.5"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.5.26"
+    "@platforma-sdk/tengo-builder": "3.0.3"
   },
   "scripts": {
     "build": "shx rm -rf dist && pl-tengo check && pl-tengo build",

package/src/main.tpl.tengo

@@ -7,6 +7,7 @@ pframes := import("@platforma-sdk/workflow-tengo:pframes")
 slices := import("@platforma-sdk/workflow-tengo:slices")
 render := import("@platforma-sdk/workflow-tengo:render")
 pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec")
+smart := import("@platforma-sdk/workflow-tengo:smart")
 ll := import("@platforma-sdk/workflow-tengo:ll")
 kabatConv := import(":pf-kabat-conv")
 
@@ -25,8 +26,15 @@ wf.prepare(func(args){
 	// We need a table with cluster ID (optional) | clonotype id | selected ranking columns
     bundleBuilder := wf.createPBundleBuilder()
     bundleBuilder.ignoreMissingDomains() // to make query work for both bulk and single cell data
-    bundleBuilder.addAnchor("main", args.inputAnchor) 
-    
+    bundleBuilder.addAnchor("main", args.inputAnchor)
+
+    // Optional primary filter from PlDatasetSelector — inner-joined into the
+    // clone table below so the filter narrows every downstream stage
+    // (finalClonotypes, spectratype, Kabat, etc.).
+    if !is_undefined(args.inputFilter) {
+        bundleBuilder.addRef(args.inputFilter)
+    }
+
     validRanks := false
     if len(args.rankingOrder) > 0 {
         for col in args.rankingOrder {
@@ -149,10 +157,15 @@ wf.prepare(func(args){
 })
 
 wf.body(func(args) {
-	// output containers 
+	// output containers
 	outputs := {}
     exports := {}
 
+    // Expose this block's own id so the model can drop self-produced filter
+    // entries from the dataset selector — without this the just-finished
+    // sampled subset shows up as a filter option on the next configuration.
+    outputs["selfBlockId"] = smart.createJsonResource(wf.getBlockId())
+
     if !is_undefined(args.inputAnchor) {
         // Input arguments
         columns := args.columns
@@ -164,8 +177,14 @@ wf.body(func(args) {
 	    isPeptide := datasetSpec.axesSpec[1].name == "pl7.app/variantKey"
     
         ////////// Clonotype Filtering //////////
-        // Initialize and build clone table with all columns
-        tableInit := utils.initializeCloneTable(pframes, columns, args, datasetSpec)
+        // Initialize and build clone table with all columns. When the user
+        // picked an optional primary filter in PlDatasetSelector, fetch the
+        // resolved column so initializeCloneTable can inner-join it.
+        inputFilterColumn := undefined
+        if !is_undefined(args.inputFilter) {
+            inputFilterColumn = columns.getColumn(args.inputFilter)
+        }
+        tableInit := utils.initializeCloneTable(pframes, columns, args, datasetSpec, inputFilterColumn)
         cloneTable := tableInit.cloneTable
         filterMap := tableInit.filterMap
         rankingMap := tableInit.rankingMap

package/src/utils.lib.tengo

@@ -232,27 +232,39 @@ resolveClusterColumnHeader := func(args, columns, sortedLinkers) {
 /**
  * Initializes and builds complete clone table with all columns.
  * Handles filters, ranking columns, linkers, cluster sizes, and fallback columns.
- * 
+ *
  * @param pframes - PFrames import
  * @param columns - PBundle containing all columns
  * @param args - Arguments containing filters, rankingOrder, diversificationColumn
  * @param datasetSpec - Dataset specification with axes
+ * @param inputFilterColumn - Optional resolved column from the primary filter
+ *        (PlDatasetSelector). Added with an inner join so missing keys are
+ *        dropped from the clone table — narrows every downstream stage.
  * @return Map with keys: cloneTable, filterMap, rankingMap, sortedLinkers, clusterColumnHeader, addedCols
  */
-initializeCloneTable := func(pframes, columns, args, datasetSpec) {
+initializeCloneTable := func(pframes, columns, args, datasetSpec, inputFilterColumn) {
     // Build clonotype table
     cloneTable := pframes.parquetFileBuilder()
     cloneTable.setAxisHeader(datasetSpec.axesSpec[1], "clonotypeKey")
-    
+
     // Build linker list in SAME ORDER as model
     sortedLinkers := buildSortedLinkers(columns, datasetSpec)
-    
+
     // Add Filters to table
     addedAxes := []
     filterMap := {}
     rankingMap := {}
     addedCols := false
-    
+
+    // Apply the optional primary filter from PlDatasetSelector first. The
+    // builder's inner-join keeps the rows where every added column has a
+    // value, so once this column is present rows missing from the filter are
+    // dropped from the entire pipeline.
+    if !is_undefined(inputFilterColumn) {
+        cloneTable.add(inputFilterColumn, {header: "primary_filter"})
+        addedCols = true
+    }
+
     if len(args.filters) > 0 {
         for i, filter in args.filters {
             // we check for value presence and for actual pcolumn (cases where upstream block is deleted)