@platforma-open/milaboratories.immune-assay-data.workflow 1.8.0 → 1.9.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/immune-assay-data/immune-assay-data/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.immune-assay-data.workflow@1.8.0 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
+> @platforma-open/milaboratories.immune-assay-data.workflow@1.9.0 build /home/runner/work/immune-assay-data/immune-assay-data/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/analysis.tpl.tengo"...
@@ -9,6 +9,7 @@ Processing "src/check-content-empty.tpl.tengo"...
 Processing "src/extract-unique-values.tpl.tengo"...
 Processing "src/get-unique-values.tpl.tengo"...
 Processing "src/main.tpl.tengo"...
+Processing "src/prerun.tpl.tengo"...
 Processing "src/process-outputs.tpl.tengo"...
 Processing "src/run-alignment.tpl.tengo"...
 No syntax errors found.
@@ -17,6 +18,7 @@ No syntax errors found.
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/check-content-empty.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/extract-unique-values.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/get-unique-values.plj.gz
+  info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/prerun.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/process-outputs.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/run-alignment.plj.gz
   info:   - writing /home/runner/work/immune-assay-data/immune-assay-data/workflow/dist/tengo/tpl/analysis.plj.gz

package/CHANGELOG.md

@@ -1,5 +1,23 @@
 # @platforma-open/milaboratories.immune-assay-data.workflow
 
+## 1.9.0
+
+### Minor Changes
+
+- 4a7083b: Fix assay file import to support remote (non-local) files
+
+  Previously, column detection used `lsDriver.getLocalFileContent()` which only works for locally-mounted files. Files from remote storages would silently fail, leaving the block unconfigurable.
+
+  Now uses a prerun workflow step to import the file and expose it as a blob, and `ReactiveFileContent` in the UI to read it via `blobDriver` — the same pattern used by samples-and-data. This works for both local and remote files.
+
+## 1.8.1
+
+### Patch Changes
+
+- 36ed105: Improve empty input detection
+- Updated dependencies [36ed105]
+  - @platforma-open/milaboratories.immune-assay-data.check-content-empty@1.0.1
+
 ## 1.8.0
 
 ### Minor Changes

package/dist/index.cjs

@@ -3,6 +3,7 @@ module.exports = { Templates: {
   'check-content-empty': { type: 'from-file', path: require.resolve('./tengo/tpl/check-content-empty.plj.gz') },
   'extract-unique-values': { type: 'from-file', path: require.resolve('./tengo/tpl/extract-unique-values.plj.gz') },
   'get-unique-values': { type: 'from-file', path: require.resolve('./tengo/tpl/get-unique-values.plj.gz') },
+  'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
   'process-outputs': { type: 'from-file', path: require.resolve('./tengo/tpl/process-outputs.plj.gz') },
   'run-alignment': { type: 'from-file', path: require.resolve('./tengo/tpl/run-alignment.plj.gz') },
   'analysis': { type: 'from-file', path: require.resolve('./tengo/tpl/analysis.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-outputs" | "check-content-empty" | "extract-unique-values" | "get-unique-values" | "process-outputs" | "run-alignment" | "analysis" | "main";
+declare type TplName = "build-outputs" | "check-content-empty" | "extract-unique-values" | "get-unique-values" | "prerun" | "process-outputs" | "run-alignment" | "analysis" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -4,6 +4,7 @@ export const Templates = {
   'check-content-empty': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/check-content-empty.plj.gz') },
   'extract-unique-values': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/extract-unique-values.plj.gz') },
   'get-unique-values': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/get-unique-values.plj.gz') },
+  'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
   'process-outputs': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/process-outputs.plj.gz') },
   'run-alignment': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/run-alignment.plj.gz') },
   'analysis': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/analysis.plj.gz') },

package/package.json

@@ -1,19 +1,20 @@
 {
   "name": "@platforma-open/milaboratories.immune-assay-data.workflow",
-  "version": "1.8.0",
+  "version": "1.9.0",
   "type": "module",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.9.1",
+    "@platforma-sdk/workflow-tengo": "5.10.1",
     "@platforma-open/soedinglab.software-mmseqs2": "1.18.3",
-    "@platforma-open/milaboratories.immune-assay-data.add-header": "1.1.3",
     "@platforma-open/milaboratories.immune-assay-data.prepare-fasta": "1.1.3",
     "@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc": "1.2.0",
+    "@platforma-open/milaboratories.immune-assay-data.add-header": "1.1.3",
     "@platforma-open/milaboratories.immune-assay-data.fasta-to-tsv": "1.1.3",
+    "@platforma-open/milaboratories.immune-assay-data.check-content-empty": "1.0.1",
     "@platforma-open/milaboratories.immune-assay-data.xlsx-to-csv": "1.1.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.27"
+    "@platforma-sdk/tengo-builder": "2.4.30"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",

package/src/analysis.tpl.tengo

@@ -12,6 +12,7 @@ fastaToTsvSw := assets.importSoftware("@platforma-open/milaboratories.immune-ass
 addHeaderSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.add-header:main")
 covModeCalcSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.coverage-mode-calc:main")
 xlsxToCsvSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.xlsx-to-csv:main")
+checkContentEmptySw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.check-content-empty:main")
 
 runAlignmentTpl := assets.importTemplate(":run-alignment")
 checkContentEmptyTpl := assets.importTemplate(":check-content-empty")
@@ -274,16 +275,24 @@ self.body(func(args) {
 		arg("-o").arg("results_with_header.tsv").
 		addFile("results.tsv", mmseqsOutput).
 		saveFile("results_with_header.tsv").
-		saveFileContent("results_with_header.tsv").
 		run()
 
 	mmseqsResultTsv := addHeaderRun.getFile("results_with_header.tsv")
-	mmseqsResultContent := addHeaderRun.getFileContent("results_with_header.tsv")
 
-	// Use subtemplate to check if file is empty
+	// Check if results are empty (only header line or nothing)
+	checkResultsRun := exec.builder().
+		software(checkContentEmptySw).
+		arg("-i").arg("input.file").
+		arg("-n").arg("2"). // Require at least 2 non-empty lines (header + 1 data line)
+		addFile("input.file", mmseqsResultTsv).
+		saveStdoutContent().
+		mem("8GiB").
+		cpu(1).
+		inLightQueue().
+		run()
+
 	checkResult := render.create(checkContentEmptyTpl, {
-		content: mmseqsResultContent,
-		mode: "headerOnly"
+		content: checkResultsRun.getStdoutContent()
 	})
 	emptyResults := checkResult.output("result")
 

package/src/check-content-empty.tpl.tengo

@@ -4,18 +4,6 @@ text := import("text")
 self.defineOutputs("result")
 
 self.body(func(args) {
-    content := string(args.content.getData())
-    mode := args.mode
-
-    isEmpty := false
-    if mode == "raw" {
-        // No header line (e.g. FASTA): empty content means no data
-        isEmpty = text.trim_space(content) == ""
-    } else if mode == "headerOnly" {
-        // File has a header line (e.g. TSV with added header): empty means <= 1 line
-        lines := text.split(text.trim_space(content), "\n")
-        isEmpty = len(lines) <= 1
-    }
-
-    return { result: isEmpty }
+    // 'content' is the stdout of the check-software (already a "true"/"false" string)
+    return { result: text.trim_space(string(args.content.getData())) == "true" }
 })

package/src/main.tpl.tengo

@@ -11,11 +11,15 @@ text := import("text")
 render := import("@platforma-sdk/workflow-tengo:render")
 strings := import("@platforma-sdk/workflow-tengo:strings")
 
+prerunTpl := assets.importTemplate(":prerun")
 analysisTpl := assets.importTemplate(":analysis")
 processOutputsTpl := assets.importTemplate(":process-outputs")
 checkContentEmptyTpl := assets.importTemplate(":check-content-empty")
 
+wf.setPreRun(prerunTpl)
+
 prepareFastaSw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.prepare-fasta:main")
+checkContentEmptySw := assets.importSoftware("@platforma-open/milaboratories.immune-assay-data.check-content-empty:main")
 
 wf.prepare(func(args){
 	bundleBuilder := wf.createPBundleBuilder()
@@ -103,15 +107,23 @@ wf.body(func(args) {
 		arg("--seq_col").arg("sequence").
 		arg("--id_col").arg("seqId").
 		saveFile("output.fasta").
-		saveFileContent("output.fasta").
 		run()
 	clonesFasta := clonesFastaRun.getFile("output.fasta")
-	clonesFastaContent := clonesFastaRun.getFileContent("output.fasta")
 
 	// Check if clones are empty before running mmseqs2
+	checkClonesRun := exec.builder().
+		software(checkContentEmptySw).
+		arg("-i").arg("input.file").
+		arg("-n").arg("1").
+		addFile("input.file", clonesFasta).
+		saveStdoutContent().
+		mem("8GiB").
+		cpu(1).
+		inLightQueue().
+		run()
+
 	checkClonesResult := render.create(checkContentEmptyTpl, {
-		content: clonesFastaContent,
-		mode: "raw"
+		content: checkClonesRun.getStdoutContent()
 	})
 	emptyClonesInput := checkClonesResult.output("result")
 

package/src/prerun.tpl.tengo

@@ -0,0 +1,17 @@
+wf := import("@platforma-sdk/workflow-tengo:workflow")
+file := import("@platforma-sdk/workflow-tengo:file")
+
+wf.body(func(args) {
+	if is_undefined(args.fileHandle) {
+		return { outputs: {}, exports: {} }
+	}
+
+	importedFile := file.importFile(args.fileHandle)
+
+	return {
+		outputs: {
+			assayFile: file.exportFile(importedFile.file)
+		},
+		exports: {}
+	}
+})