@platforma-open/milaboratories.samples-and-data.workflow 2.3.0 → 2.4.0

package/dist/tengo/lib/ds-bulk-count-matrix.lib.tengo

@@ -37,6 +37,10 @@ getSamples := func(dataset, importFile) {
     return result
 }
 
+createGroupAxis := func(groupIdAxis, _) {
+    return copy(groupIdAxis)
+}
+
 createDataset := func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
     
     extension :=  dataset.content.xsvType + (dataset.content.gzipped ? ".gz" : "")
@@ -64,5 +68,6 @@ createDataset := func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
 export {
     isGrouped: true,
     getSamples: getSamples,
+    createGroupAxis: createGroupAxis,
     createDataset: createDataset
 }

package/dist/tengo/lib/ds-h5.lib.tengo

@@ -0,0 +1,10 @@
+util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
+
+createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
+    return util.createFileDataset(blockId, sampleIdAxis, dataset, importFile, "h5")
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
+}

package/dist/tengo/lib/ds-h5ad.lib.tengo

@@ -1,34 +1,10 @@
-
-ll := import("@platforma-sdk/workflow-tengo:ll")
-pColumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
-
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
 createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
-    extension := "h5ad"
-    
-    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
-    spec.axesSpec = [sampleIdAxis]
-
-    data := pColumn.resourceMapBuilder(1)
-    for sampleId, importHandle in dataset.content.data {
-        if !importHandle {
-            ll.panic("File handle not set for sample %v", sampleId)
-        }
-        data.add([sampleId], importFile(importHandle))
-    }
-
-    result := {}
-    result["dataset." + dataset.id] = {
-        spec: spec,
-        data: data.build()
-    }
-
-    return result
+    return util.createFileDataset(blockId, sampleIdAxis, dataset, importFile, "h5ad")
 }
 
 export {
     isGrouped: false,
     createDataset: createDataset
 }
-

package/dist/tengo/lib/ds-multiplexed-fastq.lib.tengo

@@ -5,6 +5,10 @@ json := import("json")
 smart := import("@platforma-sdk/workflow-tengo:smart")
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
+createGroupAxis := func(groupIdAxis, _) {
+    return copy(groupIdAxis)
+}
+
 createDataset := func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
 	extension :=  dataset.content.gzipped ? "fastq.gz" : "fastq"
 	
@@ -50,6 +54,7 @@ getSamples := func(dataset, importFile) {
 
 export {
     isGrouped: true,
+    createGroupAxis: createGroupAxis,
     createDataset: createDataset,
 	getSamples: getSamples
 }

package/dist/tengo/lib/ds-multisample-h5ad.lib.tengo

@@ -18,10 +18,7 @@ getColumns := func(fImport, importFile) {
 
 getSamples := func(dataset, importFile) {
     result := {}
-    sampleColumnName := dataset.content.sampleColumnName
-    if !sampleColumnName {
-        sampleColumnName = "sample"
-    }
+    sampleColumnName := util.getSampleColumnName(dataset)
     for groupId, importHandle in dataset.content.data {
         if !importHandle {
             ll.panic("File handle not set for group %v", groupId)
@@ -36,6 +33,13 @@ getSamples := func(dataset, importFile) {
     return result
 }
 
+createGroupAxis := func(groupIdAxis, dataset) {
+    sampleColumnName := util.getSampleColumnName(dataset)
+    result := copy(groupIdAxis)
+    result.annotations["pl7.app/sampleColumnName"] = sampleColumnName
+    return result
+}
+
 createDataset := func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
         
     extension := "h5ad"
@@ -64,6 +68,7 @@ export {
     isGrouped: true,
     getColumns: getColumns,
     getSamples: getSamples,
+    createGroupAxis: createGroupAxis,
     createDataset: createDataset
 }
 

package/dist/tengo/lib/ds-multisample-seurat.lib.tengo

@@ -18,10 +18,7 @@ getColumns := func(fImport, importFile) {
 
 getSamples := func(dataset, importFile) {
     result := {}
-    sampleColumnName := dataset.content.sampleColumnName
-    if !sampleColumnName {
-        sampleColumnName = "sample"
-    }
+    sampleColumnName := util.getSampleColumnName(dataset)
     for groupId, importHandle in dataset.content.data {
         if !importHandle {
             ll.panic("File handle not set for group %v", groupId)
@@ -36,6 +33,13 @@ getSamples := func(dataset, importFile) {
     return result
 }
 
+createGroupAxis := func(groupIdAxis, dataset) {
+    sampleColumnName := util.getSampleColumnName(dataset)
+    result := copy(groupIdAxis)
+    result.annotations["pl7.app/sampleColumnName"] = sampleColumnName
+    return result
+}
+
 createDataset := func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
     
     extension := "rds"
@@ -64,6 +68,7 @@ export {
     isGrouped: true,
     getColumns: getColumns,
     getSamples: getSamples,
+    createGroupAxis: createGroupAxis,
     createDataset: createDataset
 }
 

package/dist/tengo/lib/ds-seurat.lib.tengo

@@ -1,34 +1,10 @@
-
-ll := import("@platforma-sdk/workflow-tengo:ll")
-pColumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
-
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
+createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
+    return util.createFileDataset(blockId, sampleIdAxis, dataset, importFile, "rds")
+}
+
 export {
     isGrouped: false,
-    
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        extension := "rds"
-        
-        spec := util.datasetColumnSpecBase(blockId, dataset, extension)
-        spec.axesSpec = [sampleIdAxis]
-
-        data := pColumn.resourceMapBuilder(1)
-        for sampleId, importHandle in dataset.content.data {
-            if !importHandle {
-                ll.panic("File handle not set for sample %v", sampleId)
-            }
-            data.add([sampleId], importFile(importHandle))
-        }
-
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
-        }
-
-        return result
-    }
+    createDataset: createDataset
 }
-
-

package/dist/tengo/lib/util.lib.tengo

@@ -2,6 +2,8 @@ json := import("json")
 maps := import("@platforma-sdk/workflow-tengo:maps")
 smart := import("@platforma-sdk/workflow-tengo:smart")
 consts := import("@platforma-sdk/workflow-tengo:pframes.constants")
+ll := import("@platforma-sdk/workflow-tengo:ll")
+pColumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
 
 RTYPE_P_COLUMN_DATA_JSON := consts.RTYPE_P_COLUMN_DATA_JSON
 
@@ -72,9 +74,39 @@ sampleGroupsLinkerColumn := func(blockId, dataset, sampleIdAxis, groupIdAxis) {
     }
 }
 
+getSampleColumnName := func(dataset) {
+    sampleColumnName := dataset.content.sampleColumnName
+    if !sampleColumnName {
+        return "sample"
+    }
+    return sampleColumnName
+}
+
+createFileDataset := func(blockId, sampleIdAxis, dataset, importFile, extension) {
+    spec := datasetColumnSpecBase(blockId, dataset, extension)
+    spec.axesSpec = [sampleIdAxis]
+
+    data := pColumn.resourceMapBuilder(1)
+    for sampleId, importHandle in dataset.content.data {
+        if !importHandle {
+            ll.panic("File handle not set for sample %v", sampleId)
+        }
+        data.add([sampleId], importFile(importHandle))
+    }
+
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
+    }
+
+    return result
+}
 
 export {
     createJsonPColumnData: createJsonPColumnData,
     datasetColumnSpecBase: datasetColumnSpecBase,
-    sampleGroupsLinkerColumn: sampleGroupsLinkerColumn
+    sampleGroupsLinkerColumn: sampleGroupsLinkerColumn,
+    getSampleColumnName: getSampleColumnName,
+    createFileDataset: createFileDataset
 }

package/package.json

@@ -1,18 +1,18 @@
 {
   "name": "@platforma-open/milaboratories.samples-and-data.workflow",
-  "version": "2.3.0",
+  "version": "2.4.0",
   "type": "module",
   "files": [
     "./dist/**/*"
   ],
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.6.1",
+    "@platforma-sdk/workflow-tengo": "5.6.3",
     "@platforma-open/milaboratories.samples-and-data.parse-h5ad": "1.1.1",
     "@platforma-open/milaboratories.samples-and-data.parse-seurat": "1.1.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.3.10"
+    "@platforma-sdk/tengo-builder": "2.3.13"
   },
   "scripts": {
     "build": "rm -rf dist/* && pl-tengo check && pl-tengo build",