@platforma-open/milaboratories.rarefaction.workflow 1.1.3 → 1.1.5

package/.turbo/turbo-build.log

@@ -1,11 +1,13 @@
  WARN  Issue while reading "/home/runner/work/rarefaction/rarefaction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.rarefaction.workflow@1.1.3 build /home/runner/work/rarefaction/rarefaction/workflow
+> @platforma-open/milaboratories.rarefaction.workflow@1.1.5 build /home/runner/work/rarefaction/rarefaction/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/main.tpl.tengo"...
+Processing "src/rarefaction-calculation.tpl.tengo"...
 No syntax errors found.
   info: Compiling 'dist'...
+  info:   - writing /home/runner/work/rarefaction/rarefaction/workflow/dist/tengo/tpl/rarefaction-calculation.plj.gz
   info:   - writing /home/runner/work/rarefaction/rarefaction/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.rarefaction.workflow
 
+## 1.1.5
+
+### Patch Changes
+
+- 8e56508: Show running state for tables and graphs
+- Updated dependencies [8e56508]
+  - @platforma-open/milaboratories.rarefaction.software@1.2.4
+
+## 1.1.4
+
+### Patch Changes
+
+- 602e87e: Fix deduplication
+
 ## 1.1.3
 
 ### Patch Changes

package/dist/index.cjs

@@ -1,3 +1,4 @@
 module.exports = { Templates: {
+  'rarefaction-calculation': { type: 'from-file', path: require.resolve('./tengo/tpl/rarefaction-calculation.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 = "main";
+declare type TplName = "rarefaction-calculation" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -1,4 +1,5 @@
 import { resolve } from 'node:path';
 export const Templates = {
+  'rarefaction-calculation': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/rarefaction-calculation.plj.gz') },
   'main': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/main.plj.gz') }
 };

package/package.json

@@ -1,20 +1,18 @@
 {
   "name": "@platforma-open/milaboratories.rarefaction.workflow",
-  "version": "1.1.3",
+  "version": "1.1.5",
   "type": "module",
-  "description": "Block Workflow",
+  "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.4.2",
-    "@platforma-open/milaboratories.rarefaction.software": "1.2.3"
+    "@platforma-sdk/workflow-tengo": "5.8.0",
+    "@platforma-open/milaboratories.rarefaction.software": "1.2.4"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.3.2",
-    "@platforma-sdk/test": "^1.44.19",
-    "vitest": "^2.1.8"
+    "@platforma-sdk/tengo-builder": "2.4.8"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",
-    "test": "vitest",
-    "format": "/usr/bin/env emacs --script ./format.el"
+    "format": "/usr/bin/env emacs --script ./format.el",
+    "do-pack": "rm -f *.tgz && pnpm pack && mv *.tgz package.tgz"
   }
 }

package/src/main.tpl.tengo

@@ -1,13 +1,13 @@
 wf := import("@platforma-sdk/workflow-tengo:workflow")
-exec := import("@platforma-sdk/workflow-tengo:exec")
 assets := import("@platforma-sdk/workflow-tengo:assets")
 ll := import("@platforma-sdk/workflow-tengo:ll")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
 xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec")
 maps := import("@platforma-sdk/workflow-tengo:maps")
+render := import("@platforma-sdk/workflow-tengo:render")
 
-rarefactionSw := assets.importSoftware("@platforma-open/milaboratories.rarefaction.software:main")
+rarefactionTpl := assets.importTemplate(":rarefaction-calculation")
 
 getSpec := func(abundanceSpec, args) {
 	return {
@@ -98,8 +98,6 @@ wf.prepare(func(args) {
 })
 
 wf.body(func(args) {
-    infile := "rarefaction-input.tsv"
-    outfile := "rarefaction-output.tsv"
 
 	datasetSpec := args.columns.getSpec(args.datasetRef)
     tsvBuilder := pframes.tsvFileBuilder()
@@ -107,23 +105,19 @@ wf.body(func(args) {
     tsvBuilder.setAxisHeader(datasetSpec.axesSpec[1].name, "clonotypeKey")
     tsv := tsvBuilder.build()
 
-	rarefactionCmd := exec.builder().
-		software(rarefactionSw).
-		mem(string(args.mem) + "GiB").
-		cpu(args.cpu).
-		arg(infile).
-        addFile(infile, tsv).
-		arg(outfile).
-        arg(args.numPoints).
-        arg(args.numIterations).
-        arg(string(args.extrapolation)).
-        saveFile(outfile).
-		dontSaveStdoutOrStderr().
-        cacheMinutes(24*60).
-        printErrStreamToStdout().
-		run()
+	// Call UMAP calculation subtemplate
+	rarefactionRender := render.create(rarefactionTpl, {
+		inputTsv: tsv,
+		numPoints: args.numPoints,
+		numIterations: args.numIterations,
+		extrapolation: args.extrapolation,
+		metaInputs: {
+			mem: args.mem,
+			cpu: args.cpu
+		}
+	})
 
-    rarefactionPFrame := xsv.importFile(rarefactionCmd.getFile(outfile), "tsv", getSpec(datasetSpec, args), {
+    rarefactionPFrame := xsv.importFile(rarefactionRender.output("rarefactionOutput"), "tsv", getSpec(datasetSpec, args), {
 		splitDataAndSpec: true
 	})
     

package/src/rarefaction-calculation.tpl.tengo

@@ -0,0 +1,52 @@
+self := import("@platforma-sdk/workflow-tengo:tpl")
+exec := import("@platforma-sdk/workflow-tengo:exec")
+assets := import("@platforma-sdk/workflow-tengo:assets")
+
+rarefactionSw := assets.importSoftware("@platforma-open/milaboratories.rarefaction.software:main")
+
+self.validateInputs({
+    "__options__,closed": "",
+    inputTsv: "any",
+    numPoints: "string",
+    numIterations: "string",
+    extrapolation: "boolean",
+    metaInputs: {
+        "__options__,closed": "",
+        "mem,?": "number",
+        "cpu,?": "number"
+    }
+})
+
+self.defineOutputs("rarefactionOutput")
+
+self.body(func(args) {
+    // Get input parameters
+    cpu := args.metaInputs.cpu
+    mem := args.metaInputs.mem
+    numPoints := args.numPoints
+    numIterations := args.numIterations
+    extrapolation := args.extrapolation
+    inputTsv := args.inputTsv
+
+    infile := "rarefaction-input.tsv"
+    outfile := "rarefaction-output.tsv"
+
+    rarefactionCmd := exec.builder().
+            software(rarefactionSw).
+            mem(string(mem) + "GiB").
+            cpu(cpu).
+            arg(infile).
+            addFile(infile, inputTsv).
+            arg(outfile).
+            arg(numPoints).
+            arg(numIterations).
+            arg(string(extrapolation)).
+            saveFile(outfile).
+            cacheMinutes(4*60).
+            printErrStreamToStdout().
+            run()
+
+    return {
+        rarefactionOutput: rarefactionCmd.getFile(outfile)
+    }
+})

package/index.d.ts

@@ -1,4 +0,0 @@
-declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "main";
-declare const Templates: Record<TplName, TemplateFromFile>;
-export { Templates };

package/index.js

@@ -1,3 +0,0 @@
-module.exports = { Templates: {
-  'main': { type: 'from-file', path: require.resolve('./dist/tengo/tpl/main.plj.gz') }
-}}

package/tsconfig.json

@@ -1,16 +0,0 @@
-{
-  "compilerOptions": {
-    "target": "es2022",
-    "module": "commonjs",
-    "moduleResolution": "node",
-    "esModuleInterop": true,
-    "strict": true,
-    "outDir": "./dist",
-    "rootDir": "./src",
-    "sourceMap": true,
-    "declaration": true
-  },
-  "types": [],
-  "include": ["src/**/*"],
-  "exclude": ["node_modules", "dist"]
-}

package/vitest.config.mts

@@ -1,9 +0,0 @@
-import { defineConfig } from 'vitest/config';
-
-export default defineConfig({
-  test: {
-    watch: false,
-    maxConcurrency: 3,
-    testTimeout: 5000
-  }
-});