@platforma-open/milaboratories.mixcr-shm-trees.workflow 3.8.0 → 3.9.0

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@3.8.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
+> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.9.0 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
 
+## 3.9.0
+
+### Minor Changes
+
+- 1ba80e7: Fix for basket feature with new axis structure
+
+## 3.8.1
+
+### Patch Changes
+
+- b992b42: Fix for bug introduced in "Sequence Search" after migrating to new processColumn API
+
 ## 3.8.0
 
 ### Minor Changes

package/dist/tengo/lib/export-settings.lib.tengo

@@ -717,6 +717,21 @@ shmTreeNodesWithClones := func(dataDescription, donorColumn) {
         }
     })
 
+    cmdArgs = append(cmdArgs, "-cloneId")
+    axes = append(axes, {
+        column: "cloneId",
+        id: "clone-id",
+
+
+        filterOutRegex: "^$",
+        spec: {
+            name: "pl7.app/vdj/cloneId",
+            type: "Long",
+
+            annotations: addTableAnnotations(70000, true, "Clone id", {})
+        }
+    })
+
     cmdArgs = append(cmdArgs, "-fileName")
     axes = append(axes, {
         column: "fileName",
@@ -735,21 +750,6 @@ shmTreeNodesWithClones := func(dataDescription, donorColumn) {
         })
     })
 
-    cmdArgs = append(cmdArgs, "-cloneId")
-    axes = append(axes, {
-        column: "cloneId",
-        id: "clone-id",
-
-
-        filterOutRegex: "^$",
-        spec: {
-            name: "pl7.app/vdj/cloneId",
-            type: "Long",
-
-            annotations: addTableAnnotations(70000, true, "Clone id", {})
-        }
-    })
-
     if dataDescription.hasCellTags {
         cmdArgs = append(cmdArgs, "-uniqueTagCount", "Cell")
         columns = append(columns, {

package/package.json

@@ -1,20 +1,20 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "3.8.0",
+  "version": "3.9.0",
   "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": "^4.2.2"
+    "@platforma-sdk/workflow-tengo": "^4.4.4"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.3",
     "@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": "^1.30.9",
+    "@platforma-open/milaboratories.software-ptransform": "^1.4.3",
+    "@platforma-sdk/test": "^1.30.32",
     "vitest": "~2.1.8",
     "typescript": "~5.6.3"
   },

package/src/export-settings.lib.tengo

@@ -717,6 +717,21 @@ shmTreeNodesWithClones := func(dataDescription, donorColumn) {
         }
     })
 
+    cmdArgs = append(cmdArgs, "-cloneId")
+    axes = append(axes, {
+        column: "cloneId",
+        id: "clone-id",
+        // allowNA: true,
+        // filtering off records without clones because we are not interested in them here
+        filterOutRegex: "^$",
+        spec: {
+            name: "pl7.app/vdj/cloneId",
+            type: "Long",
+            // TODO domain with blockId
+            annotations: addTableAnnotations(70000, true, "Clone id", {})
+        }
+    })
+
     cmdArgs = append(cmdArgs, "-fileName")
     axes = append(axes, {
         column: "fileName",
@@ -735,21 +750,6 @@ shmTreeNodesWithClones := func(dataDescription, donorColumn) {
         })
     })
 
-    cmdArgs = append(cmdArgs, "-cloneId")
-    axes = append(axes, {
-        column: "cloneId",
-        id: "clone-id",
-        // allowNA: true,
-        // filtering off records without clones because we are not interested in them here
-        filterOutRegex: "^$",
-        spec: {
-            name: "pl7.app/vdj/cloneId",
-            type: "Long",
-            // TODO domain with blockId
-            annotations: addTableAnnotations(70000, true, "Clone id", {})
-        }
-    })
-
     if dataDescription.hasCellTags {
         cmdArgs = append(cmdArgs, "-uniqueTagCount", "Cell")
         columns = append(columns, {

package/src/process.tpl.tengo

@@ -236,14 +236,6 @@ self.body(func(inputs) {
 
 	// ll.print("__THE_LOG__ " + string(json.encode(additionalArgsForImportTsv)))
 
-	trees := exportResults.xsvOutputFrame("trees")
-
-	treeNodes := exportResults.xsvOutputFrame("treeNodes")
-
-	treeNodesWithClones := exportResults.xsvOutputFrame("treeNodesWithClones")
-
-	treeNodesUniqueIsotype := exportResults.xsvOutputFrame("treeNodesUniqueIsotype")
-
 	// Running SOI search for the data
 	soiNodesResults := {}
 	soiTreesResults := {}
@@ -270,8 +262,8 @@ self.body(func(inputs) {
 			ll.panic("unknown target feature: " + soiDb.parameters.targetFeature)
 		}
 
-		querySpec := treeNodes[columnId + ".spec"]
-		queryData := treeNodes[columnId + ".data"]
+		querySpec := exportResults.outputSpec("treeNodes", columnId)
+		queryData := exportResults.outputData("treeNodes", columnId)
 
 		soiResult := render.create(soiTpl, {
 			querySpec: querySpec,
@@ -283,6 +275,15 @@ self.body(func(inputs) {
 		soiTreesResults[soiDb.parameters.id] = soiResult.output("treesResult")
 	}
 
+
+	trees := exportResults.xsvOutputFrame("trees")
+
+	treeNodes := exportResults.xsvOutputFrame("treeNodes")
+
+	treeNodesWithClones := exportResults.xsvOutputFrame("treeNodesWithClones")
+
+	treeNodesUniqueIsotype := exportResults.xsvOutputFrame("treeNodesUniqueIsotype")
+
     return {
 		alleles: shmtResults.output("alleles"),
 		downsampled: shmtResults.output("downsampled"),