@platforma-open/milaboratories.samples-and-data.workflow 2.0.0 → 2.1.0

package/dist/index.cjs

@@ -1,5 +1,6 @@
 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') },
   '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" | "prerun" | "main";
+declare type TplName = "parse-bulk-count-matrix" | "parse-multisample-h5ad" | "prerun" | "main";
 declare const Templates: Record<TplName, TemplateFromFile>;
 export { Templates };

package/dist/index.js

@@ -1,6 +1,7 @@
 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') },
   '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

@@ -1,4 +1,3 @@
-
 ll := import("@platforma-sdk/workflow-tengo:ll")
 pt := import("@platforma-sdk/workflow-tengo:pt")
 render := import("@platforma-sdk/workflow-tengo:render")
@@ -9,59 +8,61 @@ parseHeaderTpl := assets.importTemplate("@platforma-open/milaboratories.samples-
 
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
-export {
-    isGrouped: true,
-    
-    getSamples: func(dataset, importFile) {
-
-        result := {}
-        for groupId, importHandle in dataset.content.data {
-            if !importHandle {
-                ll.panic("File handle not set for group %v", groupId)
-            }
-            
-            headerContent := txt.head(importFile(importHandle), {lines: 1})
+getSamples := func(dataset, importFile) {
 
-            separator := "\t"
-            if dataset.content.xsvType == "tsv" {
-                separator = "\t"
-            } else if dataset.content.xsvType == "csv" {
-                separator = ","
-            } else {
-                ll.panic("Unsupported file extension: " + dataset.content.xsvType)
-            }
-            
-            samples := render.create(parseHeaderTpl, {
-                header: headerContent,
-                delimiter: separator
-            }).output("samples")
-            
-            result[groupId] = samples
+    result := {}
+    for groupId, importHandle in dataset.content.data {
+        if !importHandle {
+            ll.panic("File handle not set for group %v", groupId)
         }
-        return result
-    },
+        
+        headerContent := txt.head(importFile(importHandle), {lines: 1})
 
-    createDataset: func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
+        separator := "\t"
+        if dataset.content.xsvType == "tsv" {
+            separator = "\t"
+        } else if dataset.content.xsvType == "csv" {
+            separator = ","
+        } else {
+            ll.panic("Unsupported file extension: " + dataset.content.xsvType)
+        }
         
-        extension :=  dataset.content.xsvType + (dataset.content.gzipped ? ".gz" : "")
+        samples := render.create(parseHeaderTpl, {
+            header: headerContent,
+            delimiter: separator
+        }).output("samples")
         
-        spec := util.datasetColumnSpecBase(blockId, dataset, extension)
-        spec.axesSpec = [groupIdAxis]
+        result[groupId] = samples
+    }
+    return result
+}
 
-        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))
-        }
+createDataset := func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
+    
+    extension :=  dataset.content.xsvType + (dataset.content.gzipped ? ".gz" : "")
+    
+    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
+    spec.axesSpec = [groupIdAxis]
 
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
+    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))
+    }
 
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: true,
+    getSamples: getSamples,
+    createDataset: createDataset
 }

package/dist/tengo/lib/ds-cellranger-mtx.lib.tengo

@@ -5,43 +5,44 @@ util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
 cellRangerMtxRoles := ["matrix.mtx", "features.tsv", "barcodes.tsv"]
 
-export {
-    isGrouped: false,
+createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
+    compression := dataset.content.gzipped ? "gz" : "none"
 
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        compression := dataset.content.gzipped ? "gz" : "none"
+    spec := util.datasetColumnSpecBase(blockId, dataset, undefined)
+    spec.domain["pl7.app/compression"] = compression
 
-        spec := util.datasetColumnSpecBase(blockId, dataset, undefined)
-        spec.domain["pl7.app/compression"] = compression
-
-        cellRangerFileRoleAxisSpec := {
-            type: "String",
-            name: "pl7.app/sc/cellRangerFileRole",
-            annotations: {
-                "pl7.app/label": "Role"
-            }
+    cellRangerFileRoleAxisSpec := {
+        type: "String",
+        name: "pl7.app/sc/cellRangerFileRole",
+        annotations: {
+            "pl7.app/label": "Role"
         }
+    }
 
-        spec.axesSpec = [sampleIdAxis, cellRangerFileRoleAxisSpec]
+    spec.axesSpec = [sampleIdAxis, cellRangerFileRoleAxisSpec]
 
-        data := pColumn.resourceMapBuilder(2)
-        for sampleId, fileGroup in dataset.content.data {
-            for role in cellRangerMtxRoles {
-                importHandle := fileGroup[role]
-                if !importHandle {
-                    ll.panic("File handle not set for %v in sample %v", role, sampleId)
-                }
-                data.add([sampleId, role], importFile(importHandle))
+    data := pColumn.resourceMapBuilder(2)
+    for sampleId, fileGroup in dataset.content.data {
+        for role in cellRangerMtxRoles {
+            importHandle := fileGroup[role]
+            if !importHandle {
+                ll.panic("File handle not set for %v in sample %v", role, sampleId)
             }
+            data.add([sampleId, role], importFile(importHandle))
         }
+    }
 
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
-        }
-
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
 }
 

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

@@ -4,29 +4,30 @@ 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 :=  dataset.content.gzipped ? "fasta.gz" : "fasta"
     
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        extension :=  dataset.content.gzipped ? "fasta.gz" : "fasta"
-        
-        spec := util.datasetColumnSpecBase(blockId, dataset, extension)
-        spec.axesSpec = [sampleIdAxis]
+    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()
+    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))
+    }
 
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
 }

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

@@ -4,48 +4,49 @@ pColumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
 json := import("json")
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
-export {
-    isGrouped: false,
+createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
+    extension :=  dataset.content.gzipped ? "fastq.gz" : "fastq"
     
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        extension :=  dataset.content.gzipped ? "fastq.gz" : "fastq"
-        
-        spec := util.datasetColumnSpecBase(blockId, dataset, extension)
+    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
 
-        readIndexAxisSpec := {
-			type: "String",
-			name: "pl7.app/sequencing/readIndex",
-			annotations: {
-				"pl7.app/label": "Read Index"
-			},
-			domain: {
+    readIndexAxisSpec := {
+		type: "String",
+		name: "pl7.app/sequencing/readIndex",
+		annotations: {
+			"pl7.app/label": "Read Index"
+		},
+		domain: {
 
 
 
 
-				"pl7.app/readIndices": string(json.encode(dataset.content.readIndices))
-			}
+			"pl7.app/readIndices": string(json.encode(dataset.content.readIndices))
 		}
+	}
 
-        spec.axesSpec = [sampleIdAxis, readIndexAxisSpec]
+    spec.axesSpec = [sampleIdAxis, readIndexAxisSpec]
 
-        data := pColumn.resourceMapBuilder(2)
-        for sampleId, fileGroup in dataset.content.data {
-            for _, readIndex in dataset.content.readIndices {
-                importHandle := fileGroup[readIndex]
-                if !importHandle {
-                    ll.panic("File handle not set for %v in sample %v", readIndex, sampleId)
-                }
-                data.add([sampleId, readIndex], importFile(importHandle))
+    data := pColumn.resourceMapBuilder(2)
+    for sampleId, fileGroup in dataset.content.data {
+        for _, readIndex in dataset.content.readIndices {
+            importHandle := fileGroup[readIndex]
+            if !importHandle {
+                ll.panic("File handle not set for %v in sample %v", readIndex, sampleId)
             }
+            data.add([sampleId, readIndex], importFile(importHandle))
         }
+    }
 
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
-        }
-
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
 }

package/dist/tengo/lib/ds-h5ad.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")
+
+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
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
+}
+

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

@@ -4,58 +4,59 @@ pColumn := import("@platforma-sdk/workflow-tengo:pframes.pcolumn")
 json := import("json")
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
-export {
-    isGrouped: false,
+createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
+    extension :=  dataset.content.gzipped ? "fastq.gz" : "fastq"
     
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        extension :=  dataset.content.gzipped ? "fastq.gz" : "fastq"
-        
-        spec := util.datasetColumnSpecBase(blockId, dataset, extension)
-
-		laneAxisSpec := {
-			type: "String",
-			name: "pl7.app/sequencing/lane",
-			annotations: {
-				"pl7.app/label": "Lane"
-			}
+    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
+
+	laneAxisSpec := {
+		type: "String",
+		name: "pl7.app/sequencing/lane",
+		annotations: {
+			"pl7.app/label": "Lane"
 		}
+	}
 
-        readIndexAxisSpec := {
-			type: "String",
-			name: "pl7.app/sequencing/readIndex",
-			annotations: {
-				"pl7.app/label": "Read Index"
-			},
-			domain: {
+    readIndexAxisSpec := {
+		type: "String",
+		name: "pl7.app/sequencing/readIndex",
+		annotations: {
+			"pl7.app/label": "Read Index"
+		},
+		domain: {
 
 
 
 
-				"pl7.app/readIndices": string(json.encode(dataset.content.readIndices))
-			}
+			"pl7.app/readIndices": string(json.encode(dataset.content.readIndices))
 		}
+	}
 
-        spec.axesSpec = [sampleIdAxis, laneAxisSpec, readIndexAxisSpec]
-
-        data := pColumn.resourceMapBuilder(3)
-        for sampleId, laneData in dataset.content.data {
-            for laneId, fileGroup in laneData {
-                for _, readIndex in dataset.content.readIndices {
-                    importHandle := fileGroup[readIndex]
-                    if !importHandle {
-                        ll.panic("File handle not set for %v, lane %v in sample %v", readIndex, laneId, sampleId)
-                    }
-                    data.add([sampleId, laneId, readIndex], importFile(importHandle))
+    spec.axesSpec = [sampleIdAxis, laneAxisSpec, readIndexAxisSpec]
+
+    data := pColumn.resourceMapBuilder(3)
+    for sampleId, laneData in dataset.content.data {
+        for laneId, fileGroup in laneData {
+            for _, readIndex in dataset.content.readIndices {
+                importHandle := fileGroup[readIndex]
+                if !importHandle {
+                    ll.panic("File handle not set for %v, lane %v in sample %v", readIndex, laneId, sampleId)
                 }
+                data.add([sampleId, laneId, readIndex], importFile(importHandle))
             }
         }
+    }
 
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
-        }
-
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
 }

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

@@ -0,0 +1,69 @@
+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")
+parseH5adTpl := assets.importTemplate("@platforma-open/milaboratories.samples-and-data.workflow:parse-multisample-h5ad")
+
+util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
+
+getColumns := func(fImport, importFile) {
+    h5adFile := importFile(fImport)
+    columnsCsv := render.create(parseH5adTpl, {
+        h5adFile: h5adFile,
+        sampleColumnName:  "sample"
+    }).output("columnsCsv")
+
+    return columnsCsv
+}
+
+getSamples := func(dataset, importFile) {
+    result := {}
+    sampleColumnName := dataset.content.sampleColumnName
+    if !sampleColumnName {
+        sampleColumnName = "sample"
+    }
+    for groupId, importHandle in dataset.content.data {
+        if !importHandle {
+            ll.panic("File handle not set for group %v", groupId)
+        }
+        h5adFile := importFile(importHandle)
+        samplesCsv := render.create(parseH5adTpl, {
+            h5adFile: h5adFile,
+            sampleColumnName: sampleColumnName
+        }).output("samplesCsv")
+        result[groupId] = samplesCsv
+    }
+    return result
+}
+
+createDataset := func(blockId, sampleIdAxis, groupIdAxis, dataset, importFile) {
+        
+    extension := "h5ad"
+    
+    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,
+    createDataset: createDataset
+}
+

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

@@ -5,92 +5,93 @@ maps := import("@platforma-sdk/workflow-tengo:maps")
 json := import("json")
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
-export {
-    isGrouped: false,
+createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
+    extension :=  dataset.content.gzipped ? "fastq.gz" : "fastq"
     
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        extension :=  dataset.content.gzipped ? "fastq.gz" : "fastq"
-        
-        spec := util.datasetColumnSpecBase(blockId, dataset, extension)
-
-        axesSpec := [sampleIdAxis]
-
-        for tag in dataset.content.tags {
-            axesSpec = append(axesSpec, {
-                type: "String",
-                name: "pl7.app/sequencing/tag",
-                domain: {
-                    "pl7.app/sequencing/tag": tag
-                },
-                annotations: {
-                    "pl7.app/label": tag + " tag"
-                }
-            })
-        }
+    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
 
-        if dataset.content.hasLanes {
-            laneAxisSpec := {
-                type: "String",
-                name: "pl7.app/sequencing/lane",
-                annotations: {
-                    "pl7.app/label": "Lane"
-                }
+    axesSpec := [sampleIdAxis]
+
+    for tag in dataset.content.tags {
+        axesSpec = append(axesSpec, {
+            type: "String",
+            name: "pl7.app/sequencing/tag",
+            domain: {
+                "pl7.app/sequencing/tag": tag
+            },
+            annotations: {
+                "pl7.app/label": tag + " tag"
             }
+        })
+    }
 
-            axesSpec = append(axesSpec, laneAxisSpec)
+    if dataset.content.hasLanes {
+        laneAxisSpec := {
+            type: "String",
+            name: "pl7.app/sequencing/lane",
+            annotations: {
+                "pl7.app/label": "Lane"
+            }
         }
 
-        readIndexAxisSpec := {
-			type: "String",
-			name: "pl7.app/sequencing/readIndex",
-			annotations: {
-				"pl7.app/label": "Read Index"
-			},
-			domain: {
+        axesSpec = append(axesSpec, laneAxisSpec)
+    }
 
+    readIndexAxisSpec := {
+		type: "String",
+		name: "pl7.app/sequencing/readIndex",
+		annotations: {
+			"pl7.app/label": "Read Index"
+		},
+		domain: {
 
 
 
-				"pl7.app/readIndices": string(json.encode(dataset.content.readIndices))
-			}
+
+			"pl7.app/readIndices": string(json.encode(dataset.content.readIndices))
 		}
+	}
 
-        axesSpec = append(axesSpec, readIndexAxisSpec)
-        spec.axesSpec = axesSpec
-
-        data := pColumn.resourceMapBuilder(len(axesSpec))
-        
-        for sampleId, records in dataset.content.data {
-            for record in records {
-                keyPrefix := [sampleId]
-                for tag in dataset.content.tags {
-                    tagValue := record.tags[tag]
-                    if !tagValue {
-                        ll.panic("No tag value for %v in sample %v", tag, sampleId)
-                    }
-                    keyPrefix = append(keyPrefix, tagValue)
-                }
-                if dataset.content.hasLanes {
-                    keyPrefix = append(keyPrefix, record.lane)
+    axesSpec = append(axesSpec, readIndexAxisSpec)
+    spec.axesSpec = axesSpec
+
+    data := pColumn.resourceMapBuilder(len(axesSpec))
+    
+    for sampleId, records in dataset.content.data {
+        for record in records {
+            keyPrefix := [sampleId]
+            for tag in dataset.content.tags {
+                tagValue := record.tags[tag]
+                if !tagValue {
+                    ll.panic("No tag value for %v in sample %v", tag, sampleId)
                 }
-                for readIndex in dataset.content.readIndices {
-                    importHandle := record.files[readIndex]
-                    key := maps.clone(keyPrefix)
-                    key = append(key, readIndex)
-                    if !importHandle {
-                        ll.panic("File handle not set for key %v", key)
-                    }
-                    data.add(key, importFile(importHandle))
+                keyPrefix = append(keyPrefix, tagValue)
+            }
+            if dataset.content.hasLanes {
+                keyPrefix = append(keyPrefix, record.lane)
+            }
+            for readIndex in dataset.content.readIndices {
+                importHandle := record.files[readIndex]
+                key := maps.clone(keyPrefix)
+                key = append(key, readIndex)
+                if !importHandle {
+                    ll.panic("File handle not set for key %v", key)
                 }
+                data.add(key, importFile(importHandle))
             }
         }
+    }
 
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
-        }
-
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
 }

package/dist/tengo/lib/ds-tagged-xsv.lib.tengo

@@ -5,59 +5,60 @@ maps := import("@platforma-sdk/workflow-tengo:maps")
 
 util := import("@platforma-open/milaboratories.samples-and-data.workflow:util")
 
-export {
-    isGrouped: false,
+createDataset := func(blockId, sampleIdAxis, dataset, importFile) {
     
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        
-        extension :=  dataset.content.xsvType + (dataset.content.gzipped ? ".gz" : "")
-        
-        spec := util.datasetColumnSpecBase(blockId, dataset, extension)
-        
-        axesSpec := [sampleIdAxis]
-
-         for tag in dataset.content.tags {
-            axesSpec = append(axesSpec, {
-                type: "String",
-                name: "pl7.app/sequencing/tag",
-                domain: {
-                    "pl7.app/sequencing/tag": tag
-                },
-                annotations: {
-                    "pl7.app/label": tag + " tag"
-                }
-            })
-        }
+    extension :=  dataset.content.xsvType + (dataset.content.gzipped ? ".gz" : "")
+    
+    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
+    
+    axesSpec := [sampleIdAxis]
 
-        spec.axesSpec = axesSpec
-
-        data := pColumn.resourceMapBuilder(len(axesSpec))
-        
-        for sampleId, records in dataset.content.data {
-            for record in records {
-                key := [sampleId]
-                for tag in dataset.content.tags {
-                    tagValue := record.tags[tag]
-                    if !tagValue {
-                        ll.panic("No tag value for %v in sample %v", tag, sampleId)
-                    }
-                    key = append(key, tagValue)
-                }
+     for tag in dataset.content.tags {
+        axesSpec = append(axesSpec, {
+            type: "String",
+            name: "pl7.app/sequencing/tag",
+            domain: {
+                "pl7.app/sequencing/tag": tag
+            },
+            annotations: {
+                "pl7.app/label": tag + " tag"
+            }
+        })
+    }
 
-                importHandle := record.file
-                if !importHandle {
-                    ll.panic("File handle not set for key %v", key)
+    spec.axesSpec = axesSpec
+
+    data := pColumn.resourceMapBuilder(len(axesSpec))
+    
+    for sampleId, records in dataset.content.data {
+        for record in records {
+            key := [sampleId]
+            for tag in dataset.content.tags {
+                tagValue := record.tags[tag]
+                if !tagValue {
+                    ll.panic("No tag value for %v in sample %v", tag, sampleId)
                 }
-                data.add(key, importFile(importHandle))
+                key = append(key, tagValue)
             }
-        }
 
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
+            importHandle := record.file
+            if !importHandle {
+                ll.panic("File handle not set for key %v", key)
+            }
+            data.add(key, importFile(importHandle))
         }
+    }
 
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
 }

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

@@ -4,30 +4,31 @@ 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) {
     
-    createDataset: func(blockId, sampleIdAxis, dataset, importFile) {
-        
-        extension :=  dataset.content.xsvType + (dataset.content.gzipped ? ".gz" : "")
-        
-        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))
-        }
+    extension :=  dataset.content.xsvType + (dataset.content.gzipped ? ".gz" : "")
+    
+    spec := util.datasetColumnSpecBase(blockId, dataset, extension)
+    spec.axesSpec = [sampleIdAxis]
 
-        result := {}
-        result["dataset." + dataset.id] = {
-            spec: spec,
-            data: data.build()
+    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))
+    }
 
-        return result
+    result := {}
+    result["dataset." + dataset.id] = {
+        spec: spec,
+        data: data.build()
     }
+
+    return result
+}
+
+export {
+    isGrouped: false,
+    createDataset: createDataset
 }

package/package.json

@@ -1,16 +1,17 @@
 {
   "name": "@platforma-open/milaboratories.samples-and-data.workflow",
-  "version": "2.0.0",
+  "version": "2.1.0",
   "type": "module",
   "files": [
     "./dist/**/*"
   ],
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^5.4.5"
+    "@platforma-sdk/workflow-tengo": "5.5.15",
+    "@platforma-open/milaboratories.samples-and-data.parse-h5ad": "1.1.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.3.2"
+    "@platforma-sdk/tengo-builder": "2.3.3"
   },
   "scripts": {
     "build": "rm -rf dist/* && pl-tengo check && pl-tengo build",