fixes and improvements

platforma-open · Sep 7, 2024 · 7ef00a2 · 7ef00a2
1 parent ae0a61a
commit 7ef00a2
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Showing 5 changed files with 749 additions and 713 deletions.
diff --git a/test/src/wf.test.ts b/test/src/wf.test.ts
@@ -165,6 +165,14 @@ blockTest(
 
     const clonesPfColumnList = await ml.driverKit.pFrameDriver.listColumns(clonesPfHandle);
 
+    expect(
+      clonesPfColumnList[0].spec.axesSpec.find((s: any) => s.name === 'pl7.app/vdj/cloneId')
+    ).toMatchObject({
+      domain: {
+        'pl7.app/blockId': clonotypingBlockId
+      }
+    });
+
     // console.log(clonesPfColumnList);
     expect(clonesPfColumnList).length.to.greaterThanOrEqual(7);
 

diff --git a/workflow/src/calculate-pfconv-params.tpl.tengo b/workflow/src/calculate-pfconv-params.tpl.tengo
@@ -1,14 +1,26 @@
 // calculate-pfconv-params
 self := import("@milaboratory/tengo-sdk:tpl")
+// validation := import("@milaboratory/tengo-sdk:validation")
 
-pvconfParams := import(":pfconv_params")
+pvconfParamsLib := import(":pfconv_params")
 
 json := import("json")
 
+// self.validateInputs({
+// 	"__options__,closed": "",
+// 	"request": {
+// 		"__options__,closed": "",
+// 		"blockId": ["not", validation.resource()],
+// 		"specs,omitempty": ["not", validation.resource()]
+// 	}
+// })
+
 self.defineOutputs("params")
 
 self.body(func(inputs) {
 
+	blockId := inputs.blockId
+
 	// filter function
 	filter := func(list, predicate) {
 		result := []
@@ -33,6 +45,7 @@ self.body(func(inputs) {
 	// get specs and preset data
 	specs := inputs.specs.getDataAsJson()
 	preset := inputs.preset.getDataAsJson()
+
 	//if using readCount or umiCount
 	columnsList := []
 	columnsOrder := []
@@ -63,6 +76,8 @@ self.body(func(inputs) {
 		}
 	}
 
+	pvconfParams := pvconfParamsLib.getColumns(blockId)
+
 	// filter pvconfParams by column name and get a list of fields from it
 	columns := []
 	for col in columnsList {

diff --git a/workflow/src/main.tpl.tengo b/workflow/src/main.tpl.tengo
@@ -20,6 +20,8 @@ processTpl := assets.importTemplate(":process")
 wf.setPreRun(assets.importTemplate(":prerun"))
 
 wf.body(func(args) {
+	blockId := wf.blockId().getDataAsJson()
+
 	inputRef := args.input
 
 	preset := args.preset
@@ -38,6 +40,7 @@ wf.body(func(args) {
 	specsContent := getPreset.output("presetSpecForBack", 24 * 60 * 60 * 1000)
 
 	calculatePfconvParams := render.create(calculatePfconvParamsTpl, {
+		blockId: blockId,
 		preset: presetContent,
 		specs: specsContent
 	})
@@ -46,7 +49,8 @@ wf.body(func(args) {
 	runMixcr := render.createEphemeral(processTpl, {
 		params: smart.createJsonResource({
 			preset: preset,
-			species: species
+			species: species,
+			blockId: blockId
 		}),
 		presetContent: specsContent,
 		pfconvParams: pfconvParams,
@@ -63,7 +67,11 @@ wf.body(func(args) {
 			spec: runMixcr.output("reports.spec"),
 			data: runMixcr.output("reports.data")
 		},
-		clones: runMixcr.output("clones")
+		clones: runMixcr.output("clones"),
+		clns: {
+			spec: runMixcr.output("clns.spec"),
+			data: runMixcr.output("clns.data")
+		}
 	}
 
 	outputs := {