@platforma-open/milaboratories.mixcr-library-builder.workflow 1.0.2

package/.turbo/turbo-build.log

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+ WARN  Issue while reading "/home/runner/work/mixcr-library-builder/mixcr-library-builder/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
+
+> @platforma-open/milaboratories.mixcr-library-builder.workflow@1.0.2 build /home/runner/work/mixcr-library-builder/mixcr-library-builder/workflow
+> rm -rf dist && pl-tengo check && pl-tengo build
+
+Processing "src/main.tpl.tengo"...
+No syntax errors found.
+  info: Compiling 'dist'...
+  info:   - writing /home/runner/work/mixcr-library-builder/mixcr-library-builder/workflow/dist/tengo/tpl/main.plj.gz
+  info: 
+  info: Template Pack build done.

package/CHANGELOG.md

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+# @platforma-open/milaboratories.mixcr-library-builder.workflow
+
+## 1.0.2
+
+### Patch Changes
+
+- d46bab1: chore: change npmjs repo
+
+## 1.0.1
+
+### Patch Changes
+
+- 344b5fc: chore: inital release

package/dist/index.cjs

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

package/dist/index.d.ts

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

package/dist/index.js

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

package/format.el

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+;; This program formats all files inside src directory. Usage: emacs --script ./format.el
+
+(defun install-go-mode ()
+  "Installs go-mode"
+  (require 'package)
+  (add-to-list 'package-archives
+               '("melpa-stable" . "https://stable.melpa.org/packages/"))
+  (package-initialize)
+  (unless package-archive-contents
+    (package-refresh-contents))
+
+  (package-install 'go-mode t)
+  (require 'go-mode))
+
+;; spaces -> tabs only at the beginning of lines
+(setq tabify-regexp "^\t* [ \t]+")
+
+(defun format-file (file)
+  "Formats a file according to slightly changed Go rules"
+  (message "Format %s" file)
+  (save-excursion
+    (find-file file)
+    (delete-trailing-whitespace)            ;; deletes whitespaces
+    (go-mode)                               ;; sets golang rules for indentation
+    (tabify (point-min) (point-max))        ;; spaces -> tabs in the whole file
+    (indent-region (point-min) (point-max)) ;; indentation in the whole file
+    (save-buffer)))                         ;; save file
+
+(install-go-mode)
+
+;; change syntax of a standard go-mode a bit
+(advice-add
+ 'go--in-composite-literal-p
+ :filter-return
+ (lambda (&rest r) t))
+
+;; find all files in src
+(setq files (directory-files-recursively "src" "\\.tengo\\'"))
+
+;; call format on every file.
+(dolist (file files)
+  (format-file file))
+

package/index.d.ts

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+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

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

package/package.json

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+{
+  "name": "@platforma-open/milaboratories.mixcr-library-builder.workflow",
+  "version": "1.0.2",
+  "type": "module",
+  "description": "Block Workflow",
+  "dependencies": {},
+  "devDependencies": {
+    "@platforma-sdk/tengo-builder": "^1.17.7",
+    "@platforma-sdk/workflow-tengo": "^2.12.1",
+    "@platforma-open/milaboratories.software-small-binaries": "^1.15.6",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-139-develop",
+    "@platforma-sdk/test": "^1.22.49",
+    "vitest": "^3.0.5"
+  },
+  "scripts": {
+    "build": "rm -rf dist && pl-tengo check && pl-tengo build",
+    "test": "vitest",
+    "format": "/usr/bin/env emacs --script ./format.el"
+  }
+}

package/src/main.tpl.tengo

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+// "hello world"
+wf := import("@platforma-sdk/workflow-tengo:workflow")
+exec := import("@platforma-sdk/workflow-tengo:exec")
+ll := import("@platforma-sdk/workflow-tengo:ll")
+assets := import("@platforma-sdk/workflow-tengo:assets")
+file := import("@platforma-sdk/workflow-tengo:file")
+times := import("times")
+json := import("json")
+rand := import("rand")
+
+mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:main")
+
+wf.body(func(args) {
+
+	if is_undefined(args.vFastaFile) && is_undefined(args.vSpecies) {
+		
+		ll.panic("expected to have either `fastaFile` or `built in`; provided no any")
+	}
+
+	if is_undefined(args.jFastaFile) && is_undefined(args.jSpecies) {
+		
+	 	ll.panic("expected to have either `fastaFile` or `built in`; provided no any")
+	}
+
+	outputs := {}
+
+	species := args.species
+	chain := args.chain
+
+	libraryBuilderCmdBuilder := undefined
+
+	taxonId := string(rand.intn(9000) + 1000)
+	libraryBuilderCmdBuilder = exec.builder().
+		software(mixcrSw).
+		secret("MI_LICENSE", "MI_LICENSE").
+	 	arg("buildLibrary").
+	 	arg("--debug").
+	 	arg("--species").arg(species).
+	 	arg("--chain").arg(chain).
+	 	arg("--taxon-id").arg(taxonId)
+	if !is_undefined(args.vFastaFile) {
+	 	vImport := file.importFile(args.vFastaFile)
+		outputs.vImportHandle = vImport.handle
+	 	libraryBuilderCmdBuilder.arg("--v-gene-feature").arg("VRegion").
+	 	arg("--v-genes-from-fasta").arg("v.fasta").
+	 	addFile("v.fasta", vImport.file)
+	} else {
+	 	libraryBuilderCmdBuilder.arg("--v-genes-from-species").arg(args.vSpecies)
+	}
+
+	if !is_undefined(args.jFastaFile) {
+	 	jImport := file.importFile(args.jFastaFile)
+		outputs.jImportHandle = jImport.handle
+	 	libraryBuilderCmdBuilder.arg("--j-genes-from-fasta").arg("j.fasta").
+	 		addFile("j.fasta", jImport.file)
+	} else {
+	 	libraryBuilderCmdBuilder.arg("--j-genes-from-species").arg(args.jSpecies)
+	}
+
+	if !is_undefined(args.dFastaFile) {
+	 	dImport := file.importFile(args.dFastaFile)
+		outputs.dImportHandle = dImport.handle
+	 	libraryBuilderCmdBuilder.arg("--d-genes-from-fasta").arg("d.fasta").
+	 	addFile("d.fasta", dImport.file)
+	} else if !is_undefined(args.dSpecies) {
+	 	libraryBuilderCmdBuilder.arg("--d-genes-from-species").arg(args.dSpecies)
+	}
+
+	if !is_undefined(args.cFastaFile) {
+		cImport := file.importFile(args.cFastaFile)
+		outputs.cImportHandle = cImport.handle
+	 	libraryBuilderCmdBuilder.arg("--c-genes-from-fasta").arg("c.fasta").
+	 	addFile("c.fasta", cImport.file)
+	} else if !is_undefined(args.cSpecies) {
+	 	libraryBuilderCmdBuilder.arg("--c-genes-from-species").arg(args.cSpecies)
+	}
+
+	libraryBuilderCmdBuilder.arg("library.json").
+		saveFile("library.json").
+		printErrStreamToStdout()
+	libraryBuilderCmd := libraryBuilderCmdBuilder.run()
+	
+	debugOutput := libraryBuilderCmd.getStdoutStream()
+	library := libraryBuilderCmd.getFile("library.json")
+
+	outputs.debugOutput = debugOutput
+
+	exports := {
+		library : {
+			data: library,
+			spec: {
+				kind: "File",
+				annotations: {
+					"pl7.app/species": species,
+					"pl7.app/vdj/chain": chain,
+					"pl7.app/vdj/isLibrary": "true",
+					"pl7.app/label": species + "_" + chain + "_library"
+				}
+			}		
+	 	}
+	}
+		
+	return {
+		outputs: outputs,
+		exports: exports
+	}
+})
+

package/src/wf.test.ts

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+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!');
+  }
+);

package/tsconfig.json

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+{
+  "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

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