@platforma-open/milaboratories.top-antibodies.workflow 1.17.2 → 1.17.3

package/.turbo/turbo-build.log

@@ -1,7 +1,7 @@
  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@1.17.2 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
-> rm -rf dist && pl-tengo check && pl-tengo build
+> @platforma-open/milaboratories.top-antibodies.workflow@1.17.3 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"...
 Processing "src/filter-and-sample.tpl.tengo"...
@@ -10,6 +10,7 @@ Processing "src/pf-kabat-conv.lib.tengo"...
 Processing "src/pf-spectratype-conv.lib.tengo"...
 Processing "src/pf-vj-usage-conv.lib.tengo"...
 Processing "src/sampled-cols-conv.lib.tengo"...
+Processing "src/sampled-export-conv.lib.tengo"...
 Processing "src/utils.lib.tengo"...
 No syntax errors found.
   info: Compiling 'dist'...
@@ -17,6 +18,7 @@ No syntax errors found.
   info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/pf-spectratype-conv.lib.tengo
   info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/pf-vj-usage-conv.lib.tengo
   info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/sampled-cols-conv.lib.tengo
+  info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/sampled-export-conv.lib.tengo
   info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/lib/utils.lib.tengo
   info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/tpl/assembling-fasta.plj.gz
   info:   - writing /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow/dist/tengo/tpl/filter-and-sample.plj.gz

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 1.17.3
+
+### Patch Changes
+
+- 535be8f: Exporte selected Leads
+
 ## 1.17.2
 
 ### Patch Changes

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

@@ -0,0 +1,34 @@
+ll := import("@platforma-sdk/workflow-tengo:ll")
+
+getColumns := func(datasetSpec) {
+  columns := [{
+        column: "top",
+        id: "link",
+        allowNA: false,
+        spec: {
+          name: "pl7.app/vdj/lead-selection",
+          valueType: "Int",
+          domain: {},
+          annotations: {
+            "pl7.app/label": "Selected Leads",
+            "pl7.app/table/visibility": "hidden",
+            "pl7.app/isSubset": "true"
+          }
+        }
+      }]
+
+  return {
+    axes: [
+      {
+        column: "clonotypeKey",
+        spec: datasetSpec.axesSpec[1]
+      }],
+    columns: columns,
+    storageFormat: "Parquet",
+    partitionKeyLength: 0
+  }
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.17.2",
+  "version": "1.17.3",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.7.3",
+    "@platforma-sdk/workflow-tengo": "5.8.1",
     "@platforma-open/milaboratories.software-anarci": "^0.0.3",
     "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.9.2",
     "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.1",
@@ -13,11 +13,11 @@
     "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.8"
+    "@platforma-sdk/tengo-builder": "2.4.13"
   },
   "scripts": {
-    "build": "rm -rf dist && pl-tengo check && pl-tengo build",
+    "build": "shx rm -rf dist && pl-tengo check && pl-tengo build",
     "format": "/usr/bin/env emacs --script ./format.el",
-    "do-pack": "rm -f *.tgz && pnpm pack && mv *.tgz package.tgz"
+    "do-pack": "shx rm -f *.tgz && pnpm pack && shx mv *.tgz package.tgz"
   }
 }

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

@@ -6,9 +6,10 @@ pframes := import("@platforma-sdk/workflow-tengo:pframes")
 xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 render := import("@platforma-sdk/workflow-tengo:render")
 sampledColsConv := import(":sampled-cols-conv")
+sampledExportConv := import(":sampled-export-conv")
 json := import("json")
 
-self.defineOutputs("sampledRows", "finalClonotypes")
+self.defineOutputs("sampledRows", "finalClonotypes", "sampledColumnsExport")
 
 self.body(func(inputs) {
 
@@ -87,5 +88,11 @@ self.body(func(inputs) {
 
     outputs["finalClonotypes"] = finalClonotypes
 
+    // Export only the sampling column to be used as a filter downstream
+    sampledExportsParams := sampledExportConv.getColumns(datasetSpec)
+    sampledColumnsOnlyPf := xsv.importFile(finalClonotypes, "parquet", sampledExportsParams,
+                                        {cpu: 1, mem: "16GiB"})
+    outputs["sampledColumnsExport"] = sampledColumnsOnlyPf
+
     return outputs
 }) 

package/src/main.tpl.tengo

@@ -110,6 +110,7 @@ wf.prepare(func(args){
 wf.body(func(args) {
 	// output containers 
 	outputs := {}
+    exports := {}
 
     if !is_undefined(args.inputAnchor) {
         // Input arguments
@@ -154,7 +155,10 @@ wf.body(func(args) {
 
             // Get the filtered and sampled clonotypes P-frame from the template result
             finalClonotypes := filterSampleResult.output("finalClonotypes", 24 * 60 * 60 * 1000)
-            
+
+            // Export only the sampling column for downstream (built inside sub-template to avoid hang)
+            exports["sampledColumnsPf"] = filterSampleResult.output("sampledColumnsExport", 24 * 60 * 60 * 1000)
+
             ////////// CDR3 Length Calculation //////////
             // Initialize and build CDR3 sequence table
             cdr3SeqTableBuilt := utils.initializeCdr3SeqTable(pframes, columns, datasetSpec, isSingleCell)
@@ -230,6 +234,6 @@ wf.body(func(args) {
 
 	return {
 		outputs: outputs,
-		exports: {}
+		exports: exports
 	}
 })

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

@@ -0,0 +1,34 @@
+ll := import("@platforma-sdk/workflow-tengo:ll")
+
+getColumns := func(datasetSpec) {
+  columns := [{
+        column: "top",
+        id: "link",
+        allowNA: false,
+        spec: {
+          name: "pl7.app/vdj/lead-selection",
+          valueType: "Int",
+          domain: {},
+          annotations: {
+            "pl7.app/label": "Selected Leads",
+            "pl7.app/table/visibility": "hidden",
+            "pl7.app/isSubset": "true"
+          }
+        }
+      }]
+
+  return {
+    axes: [
+      {
+        column: "clonotypeKey",
+        spec: datasetSpec.axesSpec[1]
+      }],
+    columns: columns,
+    storageFormat: "Parquet",
+    partitionKeyLength: 0
+  }
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})