@platforma-open/milaboratories.mixcr-shm-trees.workflow 3.6.0 → 3.7.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-shm-trees/mixcr-shm-trees/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.6.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
+> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.7.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/export-settings.lib.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-shm-trees.workflow
 
+## 3.7.0
+
+### Minor Changes
+
+- cf34335: Fix to work with built-in library
+
+## 3.6.1
+
+### Patch Changes
+
+- 9e53ea9: Fix for await criteria
+
 ## 3.6.0
 
 ### Minor Changes

package/package.json

@@ -1,20 +1,20 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "3.6.0",
+  "version": "3.7.0",
   "type": "module",
   "description": "Tengo-based template",
   "//": {
     "build": "node ./scripts/build-static.mjs src/pfconv_params.json src/pfconv_params.lib.tengo && rm -rf dist && pl-tengo check && pl-tengo build && ./create_tags.sh"
   },
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.2.0"
+    "@platforma-sdk/workflow-tengo": "^4.2.2"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.3",
-    "@platforma-open/milaboratories.software-mixcr": "4.7.0-139-develop",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-165-develop",
     "@platforma-open/milaboratories.software-mitool": "2.3.1-5-main",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
-    "@platforma-sdk/test": "^1.30.4",
+    "@platforma-sdk/test": "^1.30.9",
     "vitest": "~2.1.8",
     "typescript": "~5.6.3"
   },

package/src/main.tpl.tengo

@@ -31,9 +31,6 @@ wf.body(func(args) {
 
 	donorColumn := wf.resolve(args.donorColumn)
 
-	// The problem is that refs for data is not resolved.
-	// To deal with it, we should call resolve resolve that will return feature.
-	// Then to resolve feature we should call another templete where we will describe what's to wait
 	results := render.createEphemeral(processTpl, {
 		datasets: datasets,
 		donorColumn: donorColumn,

package/src/process.tpl.tengo

@@ -21,7 +21,14 @@ self.awaitState("datasets", { wildcard: "*" }, "AllInputsSet")
 self.awaitState("datasets", { wildcard: "*" }, "data", "InputsLocked")
 // but we need spec already
 self.awaitState("datasets", { wildcard: "*" }, "spec", "ResourceReady")
-self.awaitState("library", "spec", "ResourceReady")
+
+// Using match instead of exact name to make fields effectively optional,
+// in cases where built-in library is used, null resource is passed as library.
+// Match don't throw error if no fields matched, opposite to exact name.
+self.awaitState("library", { match: "^spec$" }, "ResourceReady")
+self.awaitState("library", { match: "^data$" }, "AllInputsSet") // change to InputsLocked after fix
+// self.awaitState({ match: "^library$" }, "BQueryResultMulti")
+
 self.awaitState("donorColumn", "ResourceReady")
 self.awaitState("params", "ResourceReady")
 

package/src/reconstruct-shm-trees.tpl.tengo

@@ -36,10 +36,6 @@ self.body(func(inputs) {
     library := inputs.library
     libraryFormat := globalParams.libraryFormat
 
-    // ll.print("__THE_LOG__ " + json.encode(datasetTypes))
-    // ll.print("__THE_LOG__ " + json.encode(downsampling))
-    // ll.print("__THE_LOG__ " + json.encode(libraryFormat))
-
     ll.assert(!is_undefined(datasetTypes), "datasetTypes undefined")
 
     addLibraryFile := func(cmdBuilder) {
@@ -119,8 +115,6 @@ self.body(func(inputs) {
             ll.panic("Unknown downsampling type: " + downsampling.type)
         }
 
-        // ll.print("__THE_LOG__ " + downsamplingParam)
-
         for input in toProcess {
             if datasetTypes[input.clonotypingBlockId] == "bulk" {
                 downsamplingCmdBuilder := exec.builder().

package/src/request-library.tpl.tengo

@@ -17,8 +17,11 @@ self.body(func(args) {
 
 	for _, dataset in datasets {
 		dsLibraryId := dataset.spec.annotations["pl7.app/vdj/libraryId"]
+		if is_undefined(dsLibraryId) {
+			dsLibraryId = ""
+		}
 		if is_undefined(libraryId) {
-			libraryId = !is_undefined(dsLibraryId) ? dsLibraryId : ""
+			libraryId = dsLibraryId
 		} else {
 			if libraryId != dsLibraryId {
 				ll.panic("All datasets should have the same libraryId. Got " + libraryId + " and " + dsLibraryId)