wip: test passes

model/src/index.ts

@@ -15,6 +15,10 @@ export const platforma = BlockModel.create<BlockArgs>('Heavy')
     ctx.precalc?.resolve({ field: 'presets', assertFieldType: 'Input' })?.getFileHandle()
   )
 
+  .output('preset', (ctx) =>
+    ctx.precalc?.resolve({ field: 'preset', assertFieldType: 'Input' })?.getDataAsString()
+  )
+
   .output('qc', (ctx) =>
     ctx.outputs?.resolve({ field: 'qc', assertFieldType: 'Input' })?.getDataAsJson()
   )

test/src/wf.test.ts

@@ -13,11 +13,10 @@ import * as tp from 'node:timers/promises';
 
 blockTest('empty imputs', { timeout: 10000 }, async ({ rawPrj: project, ml, helpers, expect }) => {
   const blockId = await project.addBlock('Block', myBlockSpec);
-  await project.runBlock(blockId);
-  const stableState = await helpers.awaitBlockDoneAndGetStableBlockState<typeof platforma>(
-    blockId,
+  const stableState = await awaitStableState(
+    project.getBlockState(blockId),
     5000
-  );
+  ) as InferBlockState<typeof platforma>;
   expect(stableState.outputs).toMatchObject({ inputOptions: { ok: true, value: [] } });
   const presetsOutput = wrapOutputs(stableState.outputs).presets;
   const presetsStr = Buffer.from(
@@ -27,6 +26,22 @@ blockTest('empty imputs', { timeout: 10000 }, async ({ rawPrj: project, ml, help
   expect(presets).length.gt(10);
 });
 
+blockTest(
+  'preset content',
+  { timeout: 10000 },
+  async ({ rawPrj: project, ml, helpers, expect }) => {
+    const blockId = await project.addBlock('Block', myBlockSpec);
+    await project.setBlockArgs(blockId, {
+      preset: 'milab-human-dna-xcr-7genes-multiplex'
+    } satisfies BlockArgs);
+    const stableState = await awaitStableState(
+      project.getBlockState(blockId),
+      5000
+    ) as InferBlockState<typeof platforma>;
+    expect(stableState.outputs).toMatchObject({ preset: { ok: true } });
+  }
+);
+
 blockTest(
   'simple project',
   { timeout: 20000 },

workflow/package.json

@@ -4,7 +4,7 @@
   "type": "module",
   "description": "Tengo-based template",
   "scripts": {
-    "build": "rm -rf dist && pl-tengo check && pl-tengo build",
+    "build": "node ./scripts/build-static.mjs src/pfconv_params.json src/pfconv_params.lib.tengo && rm -rf dist && pl-tengo check && pl-tengo build",
     "format": "/usr/bin/env emacs --script ./format.el"
   },
   "devDependencies": {

workflow/scripts/build-static.mjs

@@ -0,0 +1,4 @@
+import fs from 'node:fs/promises'
+
+const jsonContent = await fs.readFile(process.argv[2])
+fs.writeFile(process.argv[3], "export " + jsonContent)

workflow/src/calculate-pfconv-params.tpl.tengo

@@ -0,0 +1,16 @@
+// calculate-pfconv-params
+
+self := import("@milaboratory/tengo-sdk:tpl")
+
+pvconfParams := import(":pfconv_params")
+
+self.defineOutputs("params")
+
+self.body(func(inputs) {
+	// preset content
+	preset := inputs.preset
+
+	return {
+		params: pvconfParams
+	}
+})

workflow/src/get-preset.tpl.tengo

@@ -0,0 +1,31 @@
+// get preset
+
+self := import("@milaboratory/tengo-sdk:tpl")
+ll := import("@milaboratory/tengo-sdk:ll")
+exec := import("@milaboratory/tengo-sdk:exec")
+
+self.defineOutputs("preset")
+
+self.body(func(inputs) {
+	preset := inputs.preset
+
+	if !is_string(preset) {
+		ll.panic("preset is not string: %v", preset)
+	}
+
+	mixcrCmd := exec.builder().
+					printErrStreamToStdout().
+					cmd("mixcr").
+					arg("exportPreset").
+					arg("--preset-name").
+					arg(preset).
+					arg("preset.json").
+					saveFileContent("preset.json").
+					run()
+
+	presetContent := mixcrCmd.getFileContent("preset.json")
+
+	return {
+		preset: presetContent
+	}
+})

workflow/src/list-presets.tpl.tengo

@@ -0,0 +1,22 @@
+// list presets
+
+self := import("@milaboratory/tengo-sdk:tpl")
+ll := import("@milaboratory/tengo-sdk:ll")
+exec := import("@milaboratory/tengo-sdk:exec")
+file := import("@milaboratory/tengo-sdk:file")
+
+self.defineOutputs("presets")
+
+self.body(func(inputs) {
+	listPresets := exec.builder().
+						cmd("mixcr").
+						arg("listPresetSpecificationsForUI").
+						arg("presets.json").
+						inUiQueue().
+						saveFile("presets.json").
+						run()
+
+	return {
+		presets: file.exportFile(listPresets.getFile("presets.json"))
+	}
+})

workflow/src/main.tpl.tengo

@@ -7,10 +7,13 @@ ll := import("@milaboratory/tengo-sdk:ll")
 smart := import("@milaboratory/tengo-sdk:smart")
 file := import("@milaboratory/tengo-sdk:file")
 llPFrames := import("@milaboratory/tengo-sdk:pframes.ll")
+exec := import("@milaboratory/tengo-sdk:exec")
 
 json := import("json")
 
-runMixcrTpl := ll.importTemplate(":run-mixcr")
+getPresetTpl := ll.importTemplate(":get-preset")
+calculatePfconvParamsTpl := ll.importTemplate(":calculate-pfconv-params")
+processTpl := ll.importTemplate(":process")
 
 wf.setPreRun(ll.importTemplate(":prerun"))
 
@@ -21,10 +24,22 @@ wf.body(func(args) {
 
 	input := wf.resolve(inputRef)
 
-	runMixcr := render.createEphemeral(runMixcrTpl, {
+	getPreset := render.create(getPresetTpl, {
+		preset: args.preset
+	})
+	presetContent := getPreset.output("preset", 24 * 60 * 60 * 1000)
+
+	calculatePfconvParams := render.create(calculatePfconvParamsTpl, {
+		preset: presetContent
+	})
+	pfconvParams := calculatePfconvParams.output("params", 24 * 60 * 60 * 1000)
+
+	runMixcr := render.createEphemeral(processTpl, {
 		params: smart.createJsonResource({
 			preset: preset
 		}),
+		presetContent: presetContent,
+		pfconvParams: pfconvParams,
 		inputSpec: input.getFutureInputField("spec"),
 		inputData: input.getFutureInputField("data")
 	})

workflow/src/mixcr-analyze.tpl.tengo

@@ -11,11 +11,22 @@ self.defineOutputs("qc")
 
 self.body(func(inputs) {
 	inputData := inputs[pConstants.VALUE_FIELD_NAME]
-	params := inputs.params
 
+	params := inputs.params
 	preset := params.preset
 	fileExtension := params.fileExtension
 
+	presetContent := inputs.presetContent.getDataAsJson()
+	pfconvParams := inputs.pfconvParams // already in JSON
+
+	if !is_map(presetContent) {
+		ll.panic("malformed presetContent %v", presetContent)
+	}
+
+	if !is_map(pfconvParams) {
+		ll.panic("malformed pfconvParams %v", pfconvParams)
+	}
+
 	inputDataMeta := inputData.getDataAsJson()
 
 	if inputDataMeta.keyLength == 1 {

workflow/src/pfconv_params.lib.tengo

@@ -0,0 +1,36 @@
+export {
+  "axes": [
+    {
+      "column": "cloneId",
+      "spec": {
+        "name": "pl7.app/vdj/cloneId",
+        "type": "Long"
+      }
+    }
+  ],
+  "columns": [
+    {
+      "column": "readCount",
+      "id": "read-count",
+      "name": "pl7.app/vdj/readCount",
+      "type": "Long",
+      "annotations": {
+        "pl7.app/label": "Number Of Reads"
+      }
+    },
+    {
+      "column": "nSeqCDR3",
+      "id": "n-seq-cdr3",
+      "type": "String",
+      "name": "pl7.app/vdj/nucleotideSequence",
+      "domain": {
+        "pl7.app/vdj/feature": "CDR3"
+      },
+      "annotations": {
+        "pl7.app/label": "CDR3 Nucleotide Sequence"
+      }
+    }
+  ],
+  "storageFormat": "Binary",
+  "partitionKeyLength": 0
+}

workflow/src/prerun.tpl.tengo

@@ -1,22 +1,28 @@
+// pre-run
+
 wf := import("@milaboratory/tengo-sdk:workflow")
-exec := import("@milaboratory/tengo-sdk:exec")
-file := import("@milaboratory/tengo-sdk:file")
+render := import("@milaboratory/tengo-sdk:render")
+ll := import("@milaboratory/tengo-sdk:ll")
+
+listPresetsTpl := ll.importTemplate(":list-presets")
+getPresetTpl := ll.importTemplate(":get-preset")
 
 wf.body(func(args) {
 
-	listPresets := exec.builder().
-						cmd("mixcr").
-						arg("listPresetSpecificationsForUI").
-						arg("presets.json").
-						inUiQueue().
-						cache(24 * 60 * 60 * 1000).
-						saveFile("presets.json").
-						run()
+	outputs := {}
+
+	listPresets := render.create(listPresetsTpl, {})
+	outputs.presets = listPresets.output("presets", 24 * 60 * 60 * 1000)
+
+	if is_string(args.preset) {
+		getPreset := render.create(getPresetTpl, {
+			preset: args.preset
+		})
+		outputs.preset = getPreset.output("preset", 24 * 60 * 60 * 1000)
+	}
 
 	return {
-		outputs: {
-			presets: file.exportFile(listPresets.getFile("presets.json"))
-		},
+		outputs: outputs,
 		exports: {}
 	}
 })

workflow/src/run-mixcr.tpl.tengo → workflow/src/process.tpl.tengo

@@ -1,4 +1,4 @@
-// run-mixcr
+// process
 
 self := import("@milaboratory/tengo-sdk:tpl")
 
@@ -9,7 +9,7 @@ llPFrames := import("@milaboratory/tengo-sdk:pframes.ll")
 
 json := import("json")
 
-mixcrAggTpl := ll.importTemplate(":mixcr-analyze")
+mixcrAnalyzeTpl := ll.importTemplate(":mixcr-analyze")
 
 self.awaitState("InputsLocked")
 self.awaitState("params", "ResourceReady")
@@ -20,17 +20,30 @@ self.body(func(inputs) {
 	preset := params.preset
 	inputSpec := self.rawInputs().inputSpec.getValue().getDataAsJson()
 
+	presetContent := self.rawInputs().presetContent
+	pfconvParams := self.rawInputs().pfconvParams
+
+	if is_undefined(presetContent) {
+		ll.panic("no presetContent")
+	}
+
+	if is_undefined(pfconvParams) {
+		ll.panic("no pfconvParams")
+	}
+
 	fileExtension := inputSpec.domain["pl7.app/fileExtension"]
 
 	mixcrResults := llPFrames.aggregate(
-			self.rawInputs().inputData, [1], mixcrAggTpl,
+			self.rawInputs().inputData, [1], mixcrAnalyzeTpl,
 			["qc"],
 			false,
 			{
 				params: smart.createJsonResource({
 					preset: preset,
 					fileExtension: fileExtension
-				})
+				}),
+				presetContent: presetContent,
+				pfconvParams: pfconvParams
 			}
 		)