@platforma-open/milaboratories.samples-and-data.workflow 2.2.1 → 2.3.1

package/dist/index.cjs

@@ -1,6 +1,7 @@
 module.exports = { Templates: {
   'parse-bulk-count-matrix': { type: 'from-file', path: require.resolve('./tengo/tpl/parse-bulk-count-matrix.plj.gz') },
   'parse-multisample-h5ad': { type: 'from-file', path: require.resolve('./tengo/tpl/parse-multisample-h5ad.plj.gz') },
+  'parse-multisample-seurat': { type: 'from-file', path: require.resolve('./tengo/tpl/parse-multisample-seurat.plj.gz') },
   'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: require.resolve('./tengo/tpl/main.plj.gz') }
 }};

package/dist/index.d.ts

@@ -1,4 +1,4 @@
 declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
-declare type TplName = "parse-bulk-count-matrix" | "parse-multisample-h5ad" | "prerun" | "main";
+declare type TplName = "parse-bulk-count-matrix" | "parse-multisample-h5ad" | "parse-multisample-seurat" | "prerun" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -2,6 +2,7 @@ import { resolve } from 'node:path';
 export const Templates = {
   'parse-bulk-count-matrix': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/parse-bulk-count-matrix.plj.gz') },
   'parse-multisample-h5ad': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/parse-multisample-h5ad.plj.gz') },
+  'parse-multisample-seurat': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/parse-multisample-seurat.plj.gz') },
   'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
   'main': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/main.plj.gz') }
 };

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-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

@@ -0,0 +1,75 @@
+ll := import("@platforma-sdk/workflow-tengo:ll")
+render := import("@platforma-sdk/workflow-tengo:render")
+assets := import("@platforma-sdk/workflow-tengo:assets")
+pColumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
+parseSeuratTpl := assets.importTemplate("@platforma-open/milaboratories.samples-and-data.workflow:parse-multisample-seurat")
+
+util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
+
+getColumns := func(fImport, importFile) {
+    seuratFile := importFile(fImport)
+    columnsCsv := render.create(parseSeuratTpl, {
+        seuratFile: seuratFile,
+        sampleColumnName:  "sample"
+    }).output("columnsCsv")
+
+    return columnsCsv
+}
+
+getSamples := func(dataset, importFile) {
+    result := {}
+    sampleColumnName := util.getSampleColumnName(dataset)
+    for groupId, importHandle in dataset.content.data {
+        if !importHandle {
+            ll.panic("File handle not set for group %v", groupId)
+        }
+        seuratFile := importFile(importHandle)
+        samplesCsv := render.create(parseSeuratTpl, {
+            seuratFile: seuratFile,
+            sampleColumnName: sampleColumnName
+        }).output("samplesCsv")
+        result[groupId] = samplesCsv
+    }
+    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"
+    
+    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
+    spec.axesSpec = [groupIdAxis]
+
+    data := pColumn.resourceMapBuilder(1)
+    for groupId, importHandle in dataset.content.data {
+        if !importHandle {
+            ll.panic("File handle not set for sample %v", groupId)
+        }
+        data.add([groupId], importFile(importHandle))
+    }
+
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
+    }
+
+    return result
+}
+
+export {
+    isGrouped: true,
+    getColumns: getColumns,
+    getSamples: getSamples,
+    createGroupAxis: createGroupAxis,
+    createDataset: createDataset
+}
+
+

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

@@ -0,0 +1,34 @@
+
+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")
+
+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
+    }
+}
+
+

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

@@ -72,9 +72,18 @@ sampleGroupsLinkerColumn := func(blockId, dataset, sampleIdAxis, groupIdAxis) {
     }
 }
 
+getSampleColumnName := func(dataset) {
+    sampleColumnName := dataset.content.sampleColumnName
+    if !sampleColumnName {
+        return "sample"
+    }
+    return sampleColumnName
+}
+
 
 export {
     createJsonPColumnData: createJsonPColumnData,
     datasetColumnSpecBase: datasetColumnSpecBase,
-    sampleGroupsLinkerColumn: sampleGroupsLinkerColumn
+    sampleGroupsLinkerColumn: sampleGroupsLinkerColumn,
+    getSampleColumnName: getSampleColumnName
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.samples-and-data.workflow",
-  "version": "2.2.1",
+  "version": "2.3.1",
   "type": "module",
   "files": [
     "./dist/**/*"
@@ -8,10 +8,11 @@
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "5.6.1",
-    "@platforma-open/milaboratories.samples-and-data.parse-h5ad": "1.1.1"
+    "@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": "2.3.9"
+    "@platforma-sdk/tengo-builder": "2.3.10"
   },
   "scripts": {
     "build": "rm -rf dist/* && pl-tengo check && pl-tengo build",