@platforma-open/milaboratories.3d-structure-prediction.workflow 1.0.5 → 1.0.7

package/.turbo/turbo-build.log

@@ -1,12 +1,13 @@
  WARN  Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.3d-structure-prediction.workflow@1.0.5 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow
+> @platforma-open/milaboratories.3d-structure-prediction.workflow@1.0.7 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: wf.test.ts
 Processing "src/build-pdbs-map.tpl.tengo"...
 Processing "src/main.tpl.tengo"...
 Processing "src/predict-batch.tpl.tengo"...
+Processing "src/prerun.tpl.tengo"...
 Processing "src/structure-cols-conv.lib.tengo"...
 No syntax errors found.
   info: Skipping unknown file type: wf.test.ts
@@ -14,6 +15,7 @@ No syntax errors found.
   info:   - writing /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow/dist/tengo/lib/structure-cols-conv.lib.tengo
   info:   - writing /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow/dist/tengo/tpl/build-pdbs-map.plj.gz
   info:   - writing /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow/dist/tengo/tpl/predict-batch.plj.gz
+  info:   - writing /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow/dist/tengo/tpl/prerun.plj.gz
   info:   - writing /home/runner/work/3d-structure-prediction/3d-structure-prediction/workflow/dist/tengo/tpl/main.plj.gz
   info: Template Pack build done.
   info: Template Pack build done.

package/CHANGELOG.md

@@ -1,5 +1,19 @@
 # @platforma-open/milaboratories.3d-structure-prediction.workflow
 
+## 1.0.7
+
+### Patch Changes
+
+- 49b6d30: Update workflow version
+- Updated dependencies [49b6d30]
+  - @platforma-open/milaboratories.3d-structure-prediction.software@1.0.6
+
+## 1.0.6
+
+### Patch Changes
+
+- 0aae4c9: Add a pre-flight clonotype-count check. The prerun counts distinct clonotypes in the selected dataset (after the optional filter) and disables Run with an explanatory alert when the count exceeds 10 000.
+
 ## 1.0.5
 
 ### Patch Changes

package/dist/index.cjs

@@ -1,5 +1,6 @@
 module.exports = { Templates: {
   'build-pdbs-map': { type: 'from-file', path: require.resolve('./tengo/tpl/build-pdbs-map.plj.gz') },
   'predict-batch': { type: 'from-file', path: require.resolve('./tengo/tpl/predict-batch.plj.gz') },
+  'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: require.resolve('./tengo/tpl/main.plj.gz') }
 }};

package/dist/index.d.ts

@@ -1,4 +1,4 @@
 declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "build-pdbs-map" | "predict-batch" | "main";
+declare type TplName = "build-pdbs-map" | "predict-batch" | "prerun" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -2,5 +2,6 @@ import { resolve } from 'node:path';
 export const Templates = {
   'build-pdbs-map': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/build-pdbs-map.plj.gz') },
   'predict-batch': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/predict-batch.plj.gz') },
+  'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/main.plj.gz') }
 };

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

@@ -165,7 +165,7 @@ getPredictionSuccessfulSettings := func(clonotypeAxisSpec, clonotypeAxisName) {
 				valueType: "Int",
 				name: "pl7.app/structure/predictionSuccessful",
 				annotations: {
-					"pl7.app/label": "Structure predicted",
+					"pl7.app/label": "All structures",
 					"pl7.app/isSubset": "true",
 					"pl7.app/table/visibility": "hidden"
 				}
@@ -177,7 +177,7 @@ getPredictionSuccessfulSettings := func(clonotypeAxisSpec, clonotypeAxisName) {
 
 
 
-getConfidentSettings := func(clonotypeAxisSpec, clonotypeAxisName, confidenceMetric, threshold) {
+getConfidentSettings := func(clonotypeAxisSpec, clonotypeAxisName) {
 	return {
 		axes: [{ column: clonotypeAxisName, spec: clonotypeAxisSpec }],
 		columns: [{
@@ -186,7 +186,7 @@ getConfidentSettings := func(clonotypeAxisSpec, clonotypeAxisName, confidenceMet
 				valueType: "Int",
 				name: "pl7.app/structure/confident",
 				annotations: {
-					"pl7.app/label": "Confident structure (" + confidenceMetric + " ≤ " + string(threshold) + " Å)",
+					"pl7.app/label": "Confident structures",
 					"pl7.app/isSubset": "true",
 					"pl7.app/table/visibility": "hidden"
 				}

package/package.json

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.3d-structure-prediction.workflow",
-  "version": "1.0.5",
+  "version": "1.0.7",
   "description": "Block Workflow",
   "type": "module",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.21.0",
-    "@platforma-open/milaboratories.3d-structure-prediction.software": "1.0.5"
+    "@platforma-sdk/workflow-tengo": "5.25.0",
+    "@platforma-open/milaboratories.3d-structure-prediction.software": "1.0.6"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.5.26",
-    "@platforma-sdk/test": "1.75.6"
+    "@platforma-sdk/tengo-builder": "3.0.1",
+    "@platforma-sdk/test": "1.77.5"
   },
   "peerDependencies": {
     "vitest": "*"

package/src/main.tpl.tengo

@@ -14,6 +14,8 @@ structureColsConv := import(":structure-cols-conv")
 predictBatchTpl := assets.importTemplate(":predict-batch")
 immuneBuilderSw := assets.importSoftware("@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict")
 
+wf.setPreRun(assets.importTemplate(":prerun"))
+
 wf.prepare(func(args) {
 	// args.dataset is a PrimaryRef { __isPrimaryRef: "v1", column: PlRef, filter?: PlRef }.
 	// `addAnchor` resolves the dataset column (also gives us its spec for the
@@ -208,7 +210,7 @@ wf.body(func(args) {
 
 	confidentPf := xsv.importFile(
 		subsetRun.getFile("confident.tsv"), "tsv",
-		structureColsConv.getConfidentSettings(clonotypeAxisSpec, clonotypeAxisName, confidenceMetric, threshold),
+		structureColsConv.getConfidentSettings(clonotypeAxisSpec, clonotypeAxisName),
 		{ splitDataAndSpec: true })
 
 	// Final structures pframe: confidence + subset columns. The label column

package/src/predict-batch.tpl.tengo

@@ -70,4 +70,4 @@ self.body(func(inputs) {
 		confidence: predictRun.getFile("confidence.tsv"),
 		pdbsMap: predictRun.getProcessorResult("pdbsMap")
 	}
-})
+})

package/src/prerun.tpl.tengo

@@ -0,0 +1,54 @@
+// Pre-flight check for the 3D Structure Prediction workflow.
+//
+// Counts the number of distinct clonotype-axis values in the selected
+// heavy-chain column AFTER applying the optional dataset filter. The result
+// is surfaced to the model so the UI can warn / disable Run when the input
+// would generate too many batches to be feasible.
+//
+// Mirrors `main.tpl.tengo`'s primary-source plumbing: the optional filter is
+// applied via the ResolvedPrimaryRef shape, so the count reflects exactly
+// what the main `pframes.processColumn` would batch over.
+
+wf := import("@platforma-sdk/workflow-tengo:workflow")
+pt := import("@platforma-sdk/workflow-tengo:pt")
+
+wf.prepare(func(args) {
+	bb := wf.createPBundleBuilder()
+	bb.ignoreMissingDomains()
+	bb.addAnchor("main", args.dataset.column)
+	bb.addSingle(args.heavyChainRef)
+	if !is_undefined(args.dataset.filter) {
+		bb.addRef(args.dataset.filter)
+	}
+	return { columns: bb.build() }
+})
+
+wf.body(func(args) {
+	columns := args.columns
+	heavy := columns.getColumn(args.heavyChainRef)
+
+	// Counting workflow: load heavy chain, optionally inner-join the filter
+	// on the (shared) clonotype axis, then count rows. Heavy chain is keyed
+	// solely by the clonotype axis, so the row count equals the number of
+	// distinct clonotypes that the main batch run would fan out over.
+	countWf := pt.workflow().mem("1GiB").cpu(1)
+	heavyEntry := pt.p.column("heavy", { spec: heavy.spec, data: heavy.data })
+
+	pEntry := heavyEntry
+	if !is_undefined(args.dataset.filter) {
+		filterCol := columns.getColumn(args.dataset.filter)
+		filterEntry := pt.p.column("filterValue", { spec: filterCol.spec, data: filterCol.data })
+		pEntry = pt.p.inner(heavyEntry, filterEntry)
+	}
+
+	df := countWf.frame(pEntry)
+	df.select(pt.col("heavy").count().alias("count")).saveContent("count.tsv")
+	countRun := countWf.run()
+
+	return {
+		outputs: {
+			clonotypeCount: countRun.getFileContent("count.tsv")
+		},
+		exports: {}
+	}
+})

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

@@ -165,7 +165,7 @@ getPredictionSuccessfulSettings := func(clonotypeAxisSpec, clonotypeAxisName) {
 				valueType: "Int",
 				name: "pl7.app/structure/predictionSuccessful",
 				annotations: {
-					"pl7.app/label": "Structure predicted",
+					"pl7.app/label": "All structures",
 					"pl7.app/isSubset": "true",
 					"pl7.app/table/visibility": "hidden"
 				}
@@ -177,7 +177,7 @@ getPredictionSuccessfulSettings := func(clonotypeAxisSpec, clonotypeAxisName) {
 
 // xsv.importFile settings for the `confident` subset PColumn — 1 when the
 // user-selected confidence metric is ≤ threshold AND prediction succeeded.
-getConfidentSettings := func(clonotypeAxisSpec, clonotypeAxisName, confidenceMetric, threshold) {
+getConfidentSettings := func(clonotypeAxisSpec, clonotypeAxisName) {
 	return {
 		axes: [{ column: clonotypeAxisName, spec: clonotypeAxisSpec }],
 		columns: [{
@@ -186,7 +186,7 @@ getConfidentSettings := func(clonotypeAxisSpec, clonotypeAxisName, confidenceMet
 				valueType: "Int",
 				name: "pl7.app/structure/confident",
 				annotations: {
-					"pl7.app/label": "Confident structure (" + confidenceMetric + " ≤ " + string(threshold) + " Å)",
+					"pl7.app/label": "Confident structures",
 					"pl7.app/isSubset": "true",
 					"pl7.app/table/visibility": "hidden"
 				}