wip: mixcr successfully runs for input samples

model/src/index.ts

@@ -28,7 +28,7 @@ export const platforma = BlockModel.create<BlockArgs>('Heavy')
         if (!isPColumnSpec(v.obj)) return false;
         const domain = v.obj.domain;
         return (
-          v.obj.name === 'pl7.app/data/sequencing' &&
+          v.obj.name === 'pl7.app/sequencing/data' &&
           ((v.obj.valueType as string) === 'blob' || (v.obj.valueType as string) === 'file') &&
           domain !== undefined &&
           (domain['pl7.app/fileExtension'] === 'fastq' ||

package.json

@@ -42,10 +42,17 @@
     "@milaboratory/pl-block-tools": "catalog:",
     "@changesets/cli": "catalog:"
   },
-  "//": {},
-  "pnpm": {
-    "overrides": {
-      "@milaboratory/pl-middle-layer": "file:/Volumes/Data/Projects/MiLaboratory/platforma/ts-pl-middle-layer/milaboratory-pl-middle-layer-1.9.30.tgz"
+  "//": {
+    "pnpm": {
+      "overrides": {
+        "@milaboratory/pl-middle-layer": "file:/Volumes/Data/Projects/MiLaboratory/platforma/ts-pl-middle-layer/milaboratory-pl-middle-layer-1.9.30.tgz"
+      }
+    },
+    "pnpm1": {
+      "overrides": {
+        "@milaboratory/pl-middle-layer": "1.9.30",
+        "@milaboratory/tengo-sdk": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/tengo-sdk"
+      }
     }
   }
 }

pnpm-workspace.yaml

@@ -11,11 +11,11 @@ catalog:
   '@milaboratory/block-builder': ^1.2.3
 
   '@milaboratory/sdk-ui': ^0.12.18
-  '@milaboratory/sdk-test': ^1.4.11
+  '@milaboratory/sdk-test': ^1.4.12
 
-  '@milaboratory/tengo-sdk': ^1.0.14
+  '@milaboratory/tengo-sdk': ^1.0.15
 
-  '@milaboratory/platforma-uikit': ^1.0.24
+  '@milaboratory/platforma-uikit': ^1.0.25
   '@milaboratory/sdk-vue': ^1.0.33
   '@milaboratory/helpers': ^1.5.2
 

test/src/wf.test.ts

@@ -29,7 +29,7 @@ blockTest('empty imputs', { timeout: 10000 }, async ({ rawPrj: project, ml, help
 
 blockTest(
   'simple project',
-  { timeout: 10000 },
+  { timeout: 20000 },
   async ({ rawPrj: project, ml, helpers, expect }) => {
     const sndBlockId = await project.addBlock('Samples & Data', samplesAndDataBlockSpec);
     const clonotypingBlockId = await project.addBlock('MiXCR Clonotyping', myBlockSpec);
@@ -115,7 +115,8 @@ blockTest(
     } satisfies BlockArgs);
     await project.runBlock(clonotypingBlockId);
     const clonotypingStableState2 = await helpers.awaitBlockDoneAndGetStableBlockState(
-      clonotypingBlockId
+      clonotypingBlockId,
+      10000
     );
     console.dir(clonotypingStableState2, { depth: 5 });
   }

workflow/src/main.tpl.tengo

@@ -1,5 +1,7 @@
 wf := import("@milaboratory/tengo-sdk:workflow")
 
+render := import("@milaboratory/tengo-sdk:render")
+
 maps := import("@milaboratory/tengo-sdk:maps")
 ll := import("@milaboratory/tengo-sdk:ll")
 smart := import("@milaboratory/tengo-sdk:smart")
@@ -8,7 +10,7 @@ llPFrames := import("@milaboratory/tengo-sdk:pframes.ll")
 
 json := import("json")
 
-mixcrAggTpl := ll.importTemplate(":mixcr-analyze")
+runMixcrTpl := ll.importTemplate(":run-mixcr")
 
 wf.setPreRun(ll.importTemplate(":prerun"))
 
@@ -19,22 +21,19 @@ wf.body(func(args) {
 
 	input := wf.resolve(inputRef)
 
-	mixcrResults := llPFrames.aggregate(
-			input.getFutureInputField("data"), [1], mixcrAggTpl,
-			["qc"],
-			false,
-			{
-				params: smart.createJsonResource({
-					preset: preset
-				})
-			}
-		)
+	runMixcr := render.createEphemeral(runMixcrTpl, {
+		params: smart.createJsonResource({
+			preset: preset
+		}),
+		inputSpec: input.getFutureInputField("spec"),
+		inputData: input.getFutureInputField("data")
+	})
 
 	exports := {}
 
 	return {
 		outputs: {
-			qc: mixcrResults.output("qc")
+			qc: runMixcr.output("qc")
 		},
 		exports: exports
 	}

workflow/src/mixcr-analyze.tpl.tengo

@@ -5,6 +5,8 @@ pConstants := import("@milaboratory/tengo-sdk:pframes.constants")
 ll := import("@milaboratory/tengo-sdk:ll")
 exec := import("@milaboratory/tengo-sdk:exec")
 
+json := import("json")
+
 self.defineOutputs("qc")
 
 self.body(func(inputs) {
@@ -18,15 +20,18 @@ self.body(func(inputs) {
 
 	if inputDataMeta.keyLength == 1 {
 		mixcrCmdBuilder := exec.builder().
+								printErrStreamToStdout().
 						        cmd("mixcr").
 						        arg("analyze").
 								arg(preset)
 
-		for r, inputFile in inputData.inputs() {
+		for sKey, inputFile in inputData.inputs() {
+			key := json.decode(sKey)
+			r := key[0]
 			if (r[0] != 'R' && r[0] != "I") || (r[1] != '1' && r[1] != '2') || len(r) != 2 {
 				ll.panic("malformed read index: %v", r)
 			}
-			fileName := "input_" + r + fileExtension
+			fileName := "input_" + r + "." + fileExtension
 			mixcrCmdBuilder.addFile(fileName, inputFile).
 							arg(fileName)
 		}

workflow/src/prerun.tpl.tengo

@@ -8,6 +8,7 @@ wf.body(func(args) {
 						cmd("mixcr").
 						arg("listPresetSpecificationsForUI").
 						arg("presets.json").
+						inUiQueue().
 						cache(24 * 60 * 60 * 1000).
 						saveFile("presets.json").
 						run()

workflow/src/run-mixcr.tpl.tengo

@@ -0,0 +1,40 @@
+// run-mixcr
+
+self := import("@milaboratory/tengo-sdk:tpl")
+
+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")
+
+json := import("json")
+
+mixcrAggTpl := ll.importTemplate(":mixcr-analyze")
+
+self.awaitState("InputsLocked")
+self.awaitState("params", "ResourceReady")
+self.awaitState("inputSpec", "ResourceReady")
+
+self.body(func(inputs) {
+	params := inputs.params
+	preset := params.preset
+	inputSpec := self.rawInputs().inputSpec.getValue().getDataAsJson()
+
+	fileExtension := inputSpec.domain["pl7.app/fileExtension"]
+
+	mixcrResults := llPFrames.aggregate(
+			self.rawInputs().inputData, [1], mixcrAggTpl,
+			["qc"],
+			false,
+			{
+				params: smart.createJsonResource({
+					preset: preset,
+					fileExtension: fileExtension
+				})
+			}
+		)
+
+	return {
+		qc: mixcrResults.output("qc")
+	}
+})