@platforma-open/milaboratories.mixcr-shm-trees.workflow 3.4.0 → 3.5.1

package/.turbo/turbo-build.log

@@ -1,5 +1,5 @@
 
-> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.4.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
+> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.5.1 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
 
+## 3.5.1
+
+### Patch Changes
+
+- 089219e: dependency upgrade
+
+## 3.5.0
+
+### Minor Changes
+
+- 591630e: Descrete columns annotation
+
 ## 3.4.0
 
 ### Minor Changes

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

@@ -1,18 +1,18 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
 text := import("text")
 
-// ==============================================
-//
-// Every function in this file will return:
-//   pfconvParams - params to run xsv.importFileMap on exported files
-//   cmdArgs - additional args for MiXCR to specify what fields to extract
-//
-// ==============================================
-
-// TODO: TMP
+
+
+
+
+
+
+
+
+
 allowNA := true
 
-// export of threes whithout nodes
+
 shmTreeTableOptions := func(dataDescription) {
     axes := []
     columns := []
@@ -149,6 +149,7 @@ shmTreeTableOptions := func(dataDescription) {
             annotations: {
                 type: "V gene name",
                 "pl7.app/label": "V gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "30000"
             }
@@ -169,6 +170,7 @@ shmTreeTableOptions := func(dataDescription) {
             annotations: {
                 type: "J gene name",
                 "pl7.app/label": "J gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "29000"
             }
@@ -185,6 +187,8 @@ shmTreeTableOptions := func(dataDescription) {
             name: "pl7.app/vdj/chain",
             annotations: {
                 "pl7.app/label": "Chain",
+                "pl7.app/isDiscreteFilter": "true",
+                "pl7.app/discreteValues": "['TRA', 'TRB', 'TRG', 'TRD', 'IGH', 'IGK', 'IGL']",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "40000"
             }
@@ -296,7 +300,7 @@ shmTreeTableOptions := func(dataDescription) {
     }
 }
 
-// export data that is uniq for node
+
 shmTreeNodesTableOptions := func(dataDescription) {
     axes := []
     columns := []
@@ -357,10 +361,12 @@ shmTreeNodesTableOptions := func(dataDescription) {
         allowNA: false,
         spec: {
             name: "pl7.app/dendrogram/isObserved",
-            // TODO change to Boolean when it will be supported
+
             valueType: "String",
             annotations: {
                 "pl7.app/label": "Is observed in data",
+                "pl7.app/isDiscreteFilter": "true",
+                "pl7.app/discreteValues": "['true', 'false']",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "85000"
             }
@@ -672,6 +678,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
             annotations: {
                 type: "V gene name",
                 "pl7.app/label": "V gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "49000"
             }
@@ -692,6 +699,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
             annotations: {
                 type: "J gene name",
                 "pl7.app/label": "J gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "47000"
             }
@@ -803,8 +811,8 @@ shmTreeNodesTableOptions := func(dataDescription) {
     }
 }
 
-// export data that is unique for clones, but not unique for a node
-// (different clones could be in the same topology node, for example, different time points)
+
+
 shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     donorColumnSpec := donorColumn.spec
 
@@ -862,8 +870,8 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     cmdArgs = append(cmdArgs, "-fileName")
     axes = append(axes, {
         column: "fileName",
-        // in case of single cell trees, not all subtrees will be filled for nodes with observed
-        // allowNA: true,
+
+
         preProcess: [
             {
                 type: "regexpReplace",
@@ -874,6 +882,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
         spec: donorColumnSpec.axesSpec[0],
         annotations: {
             "pl7.app/label": "Sample name",
+            "pl7.app/isDiscreteFilter": "true",
             "pl7.app/table/visibility": "default",
             "pl7.app/table/orderPriority": "110000"
         }
@@ -883,13 +892,13 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
     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: {
                 "pl7.app/label": "Clone id",
                 "pl7.app/table/visibility": "default",
@@ -980,6 +989,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
             annotations: {
                 type: "D gene name",
                 "pl7.app/label": "Best D hit",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "48000"
             }
@@ -1000,6 +1010,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
             annotations: {
                 type: "C gene name",
                 "pl7.app/label": "Best C hit",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "46000"
             }
@@ -1016,6 +1027,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
           name: "pl7.app/vdj/isotype",
           annotations: {
             "pl7.app/label": "IG isotype",
+            "pl7.app/isDiscreteFilter": "true",
             "pl7.app/table/visibility": "default",
             "pl7.app/table/orderPriority": "50000"
           }
@@ -1106,6 +1118,7 @@ shmTreeNodesUniqueIsotypeTableOptions := func(dataDescription) {
           name: "pl7.app/vdj/isotype",
           annotations: {
             "pl7.app/label": "Top IG isotype",
+            "pl7.app/isDiscreteFilter": "true",
             "pl7.app/table/visibility": "optional",
             "pl7.app/table/orderPriority": "50000"
           }
@@ -1122,7 +1135,7 @@ shmTreeNodesUniqueIsotypeTableOptions := func(dataDescription) {
     }
 }
 
-// to use the file as a library, we should explicitly export functions
+
 export ll.toStrict({
 	shmTreeTableOptions: shmTreeTableOptions,
     shmTreeNodesTableOptions: shmTreeNodesTableOptions,

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

@@ -7,19 +7,19 @@ json := import("json")
 _P_COLUMN_DATA_RESOURCE_MAP := { Name: "PColumnData/ResourceMap", Version: "1" }
 
 groupDataByDonorId := func(donorColumn, datasets) {
-    // we need to form a pColumn with two axes:
-	//    axes[0]: donorId
-	//    axes[1]: sampleId
-	//    axes[2]: mixcrclonotypingBlockId
-	//      value: fileRef resource
-
-	// we have:
-	//    column of donorIds:
-	//        axes[0]: sampleId
-	//          value: donorId
-	//    several columns of clns:
-	//        axes[0]: sampleId
-	//          value: fileRef resource
+
+
+
+
+
+
+
+
+
+
+
+
+
 
     donorColumnSpec := donorColumn.spec
 
@@ -30,7 +30,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
         name: "mixcr.com/clns",
         valueType: "File",
 
-        // annotations and domain could differ between datasets
+
         axesSpec: [
             {
                 name: donorColumnSpec.name,
@@ -49,20 +49,20 @@ groupDataByDonorId := func(donorColumn, datasets) {
         ]
     }, { removeUndefs: true })
 
-    // creating sample to donor map
+
 
     sampleToDonor := {}
 
-    // 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
 	}
 
-    // build pColumn by hand
+
     dataBuilder := smart.structBuilder(_P_COLUMN_DATA_RESOURCE_MAP, json.encode({ keyLength: 3 }))
 
-    // collect all the clns files that we have into pColumn
+
 	for clonotypingBlockId, dataset in datasets {
 		for sKey, fileRef in dataset.data.inputs() {
             sampleId := json.decode(sKey)[0]
@@ -77,7 +77,7 @@ groupDataByDonorId := func(donorColumn, datasets) {
     }
 }
 
-// to use the file as a library, we should explicitly export functions
+
 export ll.toStrict({
 	groupDataByDonorId: groupDataByDonorId
 })

package/dist/tengo/lib/tablesAggregation.lib.tengo

@@ -4,7 +4,7 @@ assets := import("@platforma-sdk/workflow-tengo:assets")
 json := import("json")
 paggregateSw := assets.importSoftware("@platforma-open/milaboratories.software-ptransform:main")
 
-//// aggregating by-nodes output to make it uniquely addressable by it's native key
+
 ensureUniqueness := func(inputTsv, pfConvParams, ...aggParams) {
     keyColumns := []
     for axis in pfConvParams.axes {

package/package.json

@@ -1,20 +1,22 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "3.4.0",
+  "version": "3.5.1",
   "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": "^3.1.0"
+  },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^1.17.5",
-    "@platforma-sdk/workflow-tengo": "^2.9.9",
-    "@milaboratories/software-pframes-conv": "^2.1.8",
-    "@platforma-open/milaboratories.software-small-binaries": "^1.15.6",
+    "@platforma-sdk/tengo-builder": "^2.0.2",
+    "@milaboratories/software-pframes-conv": "^2.1.20",
+    "@platforma-open/milaboratories.software-small-binaries": "^1.15.19",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-139-develop",
     "@platforma-open/milaboratories.software-mitool": "2.3.1-5-main",
-    "@platforma-open/milaboratories.software-ptransform": "^1.1.0",
-    "@platforma-sdk/test": "^1.22.6",
+    "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
+    "@platforma-sdk/test": "^1.25.0",
     "vitest": "^2.1.8",
     "typescript": "~5.6.3"
   },

package/src/export-settings.lib.tengo

@@ -149,6 +149,7 @@ shmTreeTableOptions := func(dataDescription) {
             annotations: {
                 type: "V gene name",
                 "pl7.app/label": "V gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "30000"
             }
@@ -169,6 +170,7 @@ shmTreeTableOptions := func(dataDescription) {
             annotations: {
                 type: "J gene name",
                 "pl7.app/label": "J gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "29000"
             }
@@ -185,6 +187,8 @@ shmTreeTableOptions := func(dataDescription) {
             name: "pl7.app/vdj/chain",
             annotations: {
                 "pl7.app/label": "Chain",
+                "pl7.app/isDiscreteFilter": "true",
+                "pl7.app/discreteValues": "['TRA', 'TRB', 'TRG', 'TRD', 'IGH', 'IGK', 'IGL']",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "40000"
             }
@@ -361,6 +365,8 @@ shmTreeNodesTableOptions := func(dataDescription) {
             valueType: "String",
             annotations: {
                 "pl7.app/label": "Is observed in data",
+                "pl7.app/isDiscreteFilter": "true",
+                "pl7.app/discreteValues": "['true', 'false']",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "85000"
             }
@@ -672,6 +678,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
             annotations: {
                 type: "V gene name",
                 "pl7.app/label": "V gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "49000"
             }
@@ -692,6 +699,7 @@ shmTreeNodesTableOptions := func(dataDescription) {
             annotations: {
                 type: "J gene name",
                 "pl7.app/label": "J gene",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "47000"
             }
@@ -874,6 +882,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
         spec: donorColumnSpec.axesSpec[0],
         annotations: {
             "pl7.app/label": "Sample name",
+            "pl7.app/isDiscreteFilter": "true",
             "pl7.app/table/visibility": "default",
             "pl7.app/table/orderPriority": "110000"
         }
@@ -980,6 +989,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
             annotations: {
                 type: "D gene name",
                 "pl7.app/label": "Best D hit",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "48000"
             }
@@ -1000,6 +1010,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
             annotations: {
                 type: "C gene name",
                 "pl7.app/label": "Best C hit",
+                "pl7.app/isDiscreteFilter": "true",
                 "pl7.app/table/visibility": "default",
                 "pl7.app/table/orderPriority": "46000"
             }
@@ -1016,6 +1027,7 @@ shmTreeNodesWithClonesTableOptions := func(dataDescription, donorColumn) {
           name: "pl7.app/vdj/isotype",
           annotations: {
             "pl7.app/label": "IG isotype",
+            "pl7.app/isDiscreteFilter": "true",
             "pl7.app/table/visibility": "default",
             "pl7.app/table/orderPriority": "50000"
           }
@@ -1106,6 +1118,7 @@ shmTreeNodesUniqueIsotypeTableOptions := func(dataDescription) {
           name: "pl7.app/vdj/isotype",
           annotations: {
             "pl7.app/label": "Top IG isotype",
+            "pl7.app/isDiscreteFilter": "true",
             "pl7.app/table/visibility": "optional",
             "pl7.app/table/orderPriority": "50000"
           }