@platforma-open/milaboratories.top-antibodies.workflow 1.1.0 → 1.1.1

package/.turbo/turbo-build.log

@@ -1,13 +1,13 @@
  WARN  Issue while reading "/home/runner/work/top-antibodies/top-antibodies/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.top-antibodies.workflow@1.1.0 build /home/runner/work/top-antibodies/top-antibodies/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@1.1.1 build /home/runner/work/top-antibodies/top-antibodies/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
-  info: Skipping unknown file type: wf.test.ts
 Processing "src/main.tpl.tengo"...
+Processing "src/sampled-cols-conv.lib.tengo"...
 No syntax errors found.
-  info: Skipping unknown file type: wf.test.ts
   info: Compiling 'dist'...
+  info:   - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/lib/sampled-cols-conv.lib.tengo
   info:   - writing /home/runner/work/top-antibodies/top-antibodies/workflow/dist/tengo/tpl/main.plj.gz
-  info: 
+  info: Template Pack build done.
   info: Template Pack build done.

package/CHANGELOG.md

@@ -1,5 +1,13 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 1.1.1
+
+### Patch Changes
+
+- 339a780: Main backbone
+- Updated dependencies [339a780]
+  - @platforma-open/milaboratories.top-antibodies.software@1.0.1
+
 ## 1.1.0
 
 ### Minor Changes

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

@@ -0,0 +1,46 @@
+ll := import("@platforma-sdk/workflow-tengo:ll")
+
+getColumns := func(datasetSpec, linkerAxisSpec) {
+  axes := [
+      {
+        "column": "clonotypeKey",
+        "spec": datasetSpec.axesSpec[1]
+      }]
+
+  if len(linkerAxisSpec) > 0 {
+    for key, val in linkerAxisSpec {
+      axes.push([
+      {
+        "column": key,
+        "spec": val
+      }])
+    }
+    
+  }
+  return {
+    "axes": axes,
+    "columns": [
+      {
+        "column": "top",
+        "id": "link",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/link",
+          "valueType": "Int",
+          "domain": {},
+          "annotations": {
+            "pl7.app/isLinkerColumn": "true",
+            "pl7.app/label": "Linker column",
+            "pl7.app/table/visibility": "optional"
+          }
+        }
+      }
+    ],
+    "storageFormat": "Binary",
+    "partitionKeyLength": 0
+  }
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})

package/package.json

@@ -1,14 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.0.2"
+    "@platforma-sdk/workflow-tengo": "^4.3.2",
+    "@platforma-open/milaboratories.top-antibodies.software": "1.0.1"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.0.3",
-    "@platforma-sdk/test": "^1.27.10",
+    "@platforma-sdk/tengo-builder": "^2.1.3",
+    "@platforma-sdk/test": "^1.30.19",
     "vitest": "^2.1.8"
   },
   "scripts": {

package/src/main.tpl.tengo

@@ -1,10 +1,87 @@
 // light block with no workflow
 wf := import("@platforma-sdk/workflow-tengo:workflow")
+exec := import("@platforma-sdk/workflow-tengo:exec")
+assets:= import("@platforma-sdk/workflow-tengo:assets")
+xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
+pframes := import("@platforma-sdk/workflow-tengo:pframes")
+sampledColsConv := import(":sampled-cols-conv")
+
+
+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) 
+	
+	for col in args.rankingOrder {
+		bundleBuilder.addSingle(col)
+	}
+
+	bundleBuilder.addMulti({
+		axes: [{ anchor: "main", idx: 1 }],
+		partialAxesMatch: true,
+		annotations: { "pl7.app/isLinkerColumn": "true" }
+		},
+		"linker")
+
+	return {
+		columns: bundleBuilder.build()
+	}
+})
 
 wf.body(func(args) {
 
+	columns := args.columns
+	datasetSpec := columns.getSpec(args.inputAnchor)
+	topClonotypes := args.topClonotypes
+	
+
+	clonoTable := columns.xsvTableBuilder()
+	clonoTable.setAxisHeader(datasetSpec.axesSpec[1].name, "clonotypeKey")
+	
+	for i, col in args.rankingOrder {
+		clonoTable.add(col, {header: "Col" + string(i)})
+	}
+
+	// Columns gotten by query require .key
+	linkerAxisSpec := {}
+	for i, col in columns.getColumns("linker") {
+		if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
+			clonoTable.add(col.key, {header: "linker." + string(i)})
+			clonoTable.setAxisHeader(col.spec.axesSpec[0].name, "cluster_" + string(i))
+			linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[0]
+		} else if datasetSpec.axesSpec[1].name == col.spec.axesSpec[0].name {
+			clonoTable.add(col.key, {header: "linker." + string(i)})
+			clonoTable.setAxisHeader(col.spec.axesSpec[1].name, "cluster_" + string(i))
+			linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[1]
+		}
+		
+	}
+
+	clonoTable = clonoTable.build("csv")
+
+	sampleClones := exec.builder().
+		software(assets.importSoftware("@platforma-open/milaboratories.top-antibodies.software:sample-clonotypes")).
+		addFile("filteredClonotypes.csv", clonoTable).
+		arg("--csv").arg("filteredClonotypes.csv").
+		arg("--n").arg(string(topClonotypes)).
+		arg("--out").arg("sampledClonotypes.csv").
+		saveFile("sampledClonotypes_top.csv").
+		printErrStreamToStdout().
+		saveStdoutContent().
+		cache(24 * 60 * 60 * 1000).
+		run()
+	
+	sampledColsParams := sampledColsConv.getColumns(datasetSpec, linkerAxisSpec)
+	sampledColumnsPf := xsv.importFile(sampleClones.getFile("sampledClonotypes_top.csv"), "csv", sampledColsParams)
+
+	// we need to output all filtered data axis
+
 	return {
-		outputs: {},
+		outputs: {
+			"sampledColumns": pframes.exportFrame(sampledColumnsPf)
+		},
 		exports: {}
 	}
 })

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

@@ -0,0 +1,46 @@
+ll := import("@platforma-sdk/workflow-tengo:ll")
+
+getColumns := func(datasetSpec, linkerAxisSpec) {
+  axes := [
+      {
+        "column": "clonotypeKey",
+        "spec": datasetSpec.axesSpec[1]
+      }]
+
+  if len(linkerAxisSpec) > 0 {
+    for key, val in linkerAxisSpec {
+      axes.push([
+      {
+        "column": key,
+        "spec": val
+      }])
+    }
+    
+  }
+  return {
+    "axes": axes,
+    "columns": [
+      {
+        "column": "top",
+        "id": "link",
+        "allowNA": false,
+        "spec": {
+          "name": "pl7.app/vdj/link",
+          "valueType": "Int",
+          "domain": {},
+          "annotations": {
+            "pl7.app/isLinkerColumn": "true",
+            "pl7.app/label": "Linker column",
+            "pl7.app/table/visibility": "optional"
+          }
+        }
+      }
+    ],
+    "storageFormat": "Binary",
+    "partitionKeyLength": 0
+  }
+}
+
+export ll.toStrict({
+	getColumns: getColumns
+})

package/src/wf.test.ts

@@ -1,13 +0,0 @@
-import { tplTest } from "@platforma-sdk/test";
-
-tplTest(
-  'should return a concatenated string',
-  async ({ helper, expect }) => {
-    const results = await helper.renderWorkflow("main", false, {
-      name: 'World'
-    });
-
-    const tengoMessage = results.output("tengoMessage", (a) => a?.getDataAsJson<string>());
-    expect(await tengoMessage.awaitStableValue()).eq('Hello from Tengo, World!');
-  }
-);