@platforma-open/milaboratories.mixcr-shm-trees.workflow 3.0.0 → 3.1.0

package/.turbo/turbo-build.log

@@ -1,5 +1,5 @@
 
-> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.0.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
+> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.1.0 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 +1,23 @@
 # @platforma-open/milaboratories.mixcr-shm-trees.workflow
 
+## 3.1.0
+
+### Minor Changes
+
+- c558d62: Initial implementation of node baskets
+
+### Patch Changes
+
+- 2086db2: Fixes error if empty sequence search list is used
+- 2086db2: Fixes error if sample name is used as donor
+- 954ec46: Filter off all not-observed records form the node-clonotypes table
+
+## 3.0.1
+
+### Patch Changes
+
+- 5e814a5: SDK upgrade, minor fixes
+
 ## 3.0.0
 
 ### Major Changes

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

@@ -271,7 +271,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
     cmdArgs = append(cmdArgs, "-isObserved")
     columns = append(columns, {
         "column": "isObserved",
-        "id": "is-node-obsered",
+        "id": "is-node-observed",
         "allowNA": false,
         "spec": {
             "name": "pl7.app/dendrogram/isObserved",
@@ -495,7 +495,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     axes = append(axes, {
         "column": "fileName",
         // in case of single cell trees, not all subtrees will be filled for nodes with observed
-        "allowNA": true,
+        // "allowNA": true,
         "preProcess": [
             {
                 "type": "regexpReplace",
@@ -510,7 +510,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     axes = append(axes, {
         "column": "cloneId",
         "id": "clone-id",
-        "allowNA": true,
+        // "allowNA": true,
+        // filtering off records without clones because we are not interested in them here
+        filterOutRegex: "^$",
         "spec": {
             "name": "pl7.app/vdj/cloneId",
             "type": "Long",

package/dist/tengo/lib/prepare-donor-column.lib.tengo

@@ -1,5 +1,6 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 smart := import("@platforma-sdk/workflow-tengo:smart")
+maps := import("@platforma-sdk/workflow-tengo:maps")
 
 json := import("json")
 
@@ -24,7 +25,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
 
     sampleIdAxis := donorColumnSpec.axesSpec[0]
 
-    resultSpec := {
+    resultSpec := maps.clone({
         kind: "PColumn",
         name: "mixcr.com/clns",
         valueType: "File",
@@ -46,13 +47,13 @@ groupDataByDonorId := func(donorColumn, datasets) {
                 }
             }
         ]
-    }
+    }, { removeUndefs: true })
 
     // creating sample to donor map
 
     sampleToDonor := {}
 
-    // columns with meta could be fetched as data direcctly
+    // columns with meta could be fetched as data directly
 	for k, v in donorColumn.data.getDataAsJson()["data"] {
         sampleId := json.decode(k)[0]
         sampleToDonor[sampleId] = v

package/package.json

@@ -1,20 +1,20 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "3.0.0",
+  "version": "3.1.0",
   "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"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^1.17.4",
-    "@platforma-sdk/workflow-tengo": "^2.8.2",
+    "@platforma-sdk/tengo-builder": "^1.17.5",
+    "@platforma-sdk/workflow-tengo": "^2.8.8",
     "@milaboratories/software-pframes-conv": "^2.1.2",
-    "@platforma-open/milaboratories.software-small-binaries": "^1.15.0",
-    "@platforma-open/milaboratories.software-mixcr": "4.7.0-133-develop",
+    "@platforma-open/milaboratories.software-small-binaries": "^1.15.6",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-139-develop",
     "@platforma-open/milaboratories.software-mitool": "2.3.1-2-main",
     "@platforma-open/milaboratories.software-paggregate": "^1.0.1",
-    "@platforma-sdk/test": "^1.20.9",
+    "@platforma-sdk/test": "^1.21.0",
     "vitest": "^2.1.8",
     "typescript": "~5.6.3"
   },

package/src/export-settings.lib.tengo

@@ -271,7 +271,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
     cmdArgs = append(cmdArgs, "-isObserved")
     columns = append(columns, {
         "column": "isObserved",
-        "id": "is-node-obsered",
+        "id": "is-node-observed",
         "allowNA": false,
         "spec": {
             "name": "pl7.app/dendrogram/isObserved",
@@ -495,7 +495,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     axes = append(axes, {
         "column": "fileName",
         // in case of single cell trees, not all subtrees will be filled for nodes with observed
-        "allowNA": true,
+        // "allowNA": true,
         "preProcess": [
             {
                 "type": "regexpReplace",
@@ -510,7 +510,9 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     axes = append(axes, {
         "column": "cloneId",
         "id": "clone-id",
-        "allowNA": true,
+        // "allowNA": true,
+        // filtering off records without clones because we are not interested in them here
+        filterOutRegex: "^$",
         "spec": {
             "name": "pl7.app/vdj/cloneId",
             "type": "Long",

package/src/prepare-donor-column.lib.tengo

@@ -1,5 +1,6 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 smart := import("@platforma-sdk/workflow-tengo:smart")
+maps := import("@platforma-sdk/workflow-tengo:maps")
 
 json := import("json")
 
@@ -24,7 +25,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
 
     sampleIdAxis := donorColumnSpec.axesSpec[0]
 
-    resultSpec := {
+    resultSpec := maps.clone({
         kind: "PColumn",
         name: "mixcr.com/clns",
         valueType: "File",
@@ -46,13 +47,13 @@ groupDataByDonorId := func(donorColumn, datasets) {
                 }
             }
         ]
-    }
+    }, { removeUndefs: true })
 
     // creating sample to donor map
 
     sampleToDonor := {}
 
-    // columns with meta could be fetched as data direcctly
+    // columns with meta could be fetched as data directly
 	for k, v in donorColumn.data.getDataAsJson()["data"] {
         sampleId := json.decode(k)[0]
         sampleToDonor[sampleId] = v

package/src/process.tpl.tengo

@@ -7,6 +7,7 @@ assets := import("@platforma-sdk/workflow-tengo:assets")
 render := import("@platforma-sdk/workflow-tengo:render")
 xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
 text := import("text")
+json := import("json")
 exportSettings := import(":export-settings")
 prepareDonorColumn := import(":prepare-donor-column")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
@@ -133,6 +134,8 @@ self.body(func(inputs) {
 		additionalAxesSpec: dataGroupedByDonorId["spec"]["axesSpec"][:1]
 	}
 
+	ll.print("__THE_LOG__ " + string(json.encode(additionalArgsForImportTsv)))
+
 	trees := xsv.importFileMap(
         mixcrResults.output("trees"),
         "tsv",
@@ -159,6 +162,10 @@ self.body(func(inputs) {
 	soiTreesResults := {}
 	for soiDb in inputs.params.sequencesOfInterest {
 
+		if len(soiDb.sequences) == 0 {
+			continue
+		}
+
 		columnId := ""
 		if soiDb.parameters.type == "nucleotide" {
 			columnId = "n-seq-"

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

@@ -28,8 +28,8 @@ self.body(func(inputs) {
     datasetTypes := globalParams.datasetTypes
     downsampling := globalParams.downsampling
 
-    ll.print("__THE_LOG__ " + json.encode(datasetTypes))
-    ll.print("__THE_LOG__ " + json.encode(downsampling))
+    // ll.print("__THE_LOG__ " + json.encode(datasetTypes))
+    // ll.print("__THE_LOG__ " + json.encode(downsampling))
 
     ll.assert(!is_undefined(datasetTypes), "datasetTypes undefined")
 
@@ -98,7 +98,7 @@ self.body(func(inputs) {
             ll.panic("Unknown downsampling type: " + downsampling.type)
         }
 
-        ll.print("__THE_LOG__ " + downsamplingParam)
+        // ll.print("__THE_LOG__ " + downsamplingParam)
 
         for input in toProcess {
             if datasetTypes[input.clonotypingBlockId] == "bulk" {