@platforma-open/milaboratories.top-antibodies.workflow 1.15.0 → 1.16.0

package/src/prerun.tpl.tengo

@@ -1,493 +0,0 @@
-// Prerun template for clonotype filtering
-wf := import("@platforma-sdk/workflow-tengo:workflow")
-exec := import("@platforma-sdk/workflow-tengo:exec")
-assets := import("@platforma-sdk/workflow-tengo:assets")
-xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
-pframes := import("@platforma-sdk/workflow-tengo:pframes")
-slices := import("@platforma-sdk/workflow-tengo:slices")
-render := import("@platforma-sdk/workflow-tengo:render")
-ll := import("@platforma-sdk/workflow-tengo:ll")
-kabatConv := import(":pf-kabat-conv")
-
-spectratypeConv := import(":pf-spectratype-conv")
-vjUsageConv := import(":pf-vj-usage-conv")
-
-filterAndSampleTpl := assets.importTemplate(":filter-and-sample")
-
-wf.prepare(func(args){
-	if is_undefined(args.inputAnchor) {
-        return {
-            columns: wf.createPBundleBuilder().build()
-        }
-    }
-	// We need a table with cluster ID (optional) | clonotype id | selected ranking columns
-    bundleBuilder := wf.createPBundleBuilder()
-    bundleBuilder.ignoreMissingDomains() // to make query work for both bulk and single cell data
-    bundleBuilder.addAnchor("main", args.inputAnchor) 
-    
-    validRanks := false
-    if len(args.rankingOrder) > 0 {
-        for col in args.rankingOrder {
-            // For cases where the user is selecting the table to filter
-            if col.value != undefined {
-                bundleBuilder.addAnchor(col.value.anchorName, col.value.anchorRef)
-                bundleBuilder.addSingle(col.value.column)
-                validRanks = true
-            }
-        }
-    } 
-    if !validRanks {
-        // @TODO: this is a temporal patch for issue where rankingOrderDefault 
-        // are not defined by the time prerun works
-        // prerun sometimes runs before this variable is ready
-        if args.rankingOrderDefault.value != undefined {
-            bundleBuilder.addAnchor(args.rankingOrderDefault.value.anchorName, 
-                                    args.rankingOrderDefault.value.anchorRef)
-            bundleBuilder.addSingle(args.rankingOrderDefault.value.column)
-        }
-    }
-
-    // Load filter columns
-    if len(args.filters) > 0 {
-        for filter in args.filters {
-            if filter.value != undefined {
-                bundleBuilder.addAnchor(filter.value.anchorName, filter.value.anchorRef)
-                bundleBuilder.addSingle(filter.value.column)
-            }
-        }
-    }
-    
-
-    // Add linker column
-    bundleBuilder.addMulti({
-        axes: [{ anchor: "main", idx: 1 }], // this will do partial axes match (unlike in the model)
-        annotations: { "pl7.app/isLinkerColumn": "true" },
-        partialAxesMatch: true
-    }, "linkers")
-
-    // Add cluster size columns from clustering blocks
-    bundleBuilder.addMulti({
-        name: "pl7.app/vdj/clustering/clusterSize",
-        partialAxesMatch: true
-    }, "clusterSizes")
-
-    // Add CDR3 sequences
-	bundleBuilder.addMulti({
-		axes: [{ anchor: "main", idx: 1 }], // Clonotype axis
-		name: "pl7.app/vdj/sequence",
-		domain: {
-			"pl7.app/alphabet": "aminoacid",
-			"pl7.app/vdj/feature": "CDR3"    // Specify CDR3 feature
-		}
-	}, "cdr3Sequences") // New collection name for CDR3 sequences
-
-	// Add V gene
-	bundleBuilder.addMulti({
-		axes: [{ anchor: "main", idx: 1 }], // Clonotype axis
-		name: "pl7.app/vdj/geneHit",
-		domain: {
-			"pl7.app/vdj/reference": "VGene"
-		}
-	}, "VGenes")
-
-	// Add J gene
-	bundleBuilder.addMulti({
-		axes: [{ anchor: "main", idx: 1 }], // Clonotype axis
-		name: "pl7.app/vdj/geneHit",
-		domain: {
-			"pl7.app/vdj/reference": "JGene"
-		}
-	}, "JGenes")
-
-	// Add assembling feature aminoacid sequences (bulk, sc, scFv)
-	bundleBuilder.addMulti({
-		axes: [{ anchor: "main", idx: 1 }], // Clonotype axis
-		annotations: { "pl7.app/vdj/isAssemblingFeature": "true" },
-		domain: { "pl7.app/alphabet": "aminoacid" }
-	}, "assemblingAaSeqs")
-    
-    return {
-        columns: bundleBuilder.build()
-    }
-})
-
-wf.body(func(args) {
-	// output containers 
-	outputs := {}
-
-    if !is_undefined(args.inputAnchor) {
-        // Input arguments
-        columns := args.columns
-        datasetSpec := columns.getSpec(args.inputAnchor)
-        topClonotypes := args.topClonotypes
-
-        // Needed conditional variable
-	    isSingleCell := datasetSpec.axesSpec[1].name == "pl7.app/vdj/scClonotypeKey"
-    
-        ////////// Clonotype Filtering //////////
-        // Build clonotype table
-        cloneTable := pframes.csvFileBuilder() 
-        cloneTable.setAxisHeader(datasetSpec.axesSpec[1], "clonotypeKey")
-
-        // Add Filters to table
-        addedAxes := []
-        filterMap := {}
-        rankingMap := {}
-        addedCols := false
-        if len(args.filters) > 0 {
-            for i, filter in args.filters {
-                if filter.value != undefined {
-                    // Columns added here might also be in ranking list, so we add default IDs
-                    cloneTable.add(columns.getColumn(filter.value.column), 
-                                    {header: "Filter_" + string(i), id: "filter_" + string(i)})
-                    addedCols = true
-                    // Store reference value and filter type associated to this column
-                    filterMap["Filter_" + string(i)] = filter.filter
-                    filterMap["Filter_" + string(i)]["valueType"] = columns.getSpec(filter.value.column).valueType
-                
-                    // If column does not have main anchor axis we have to include theirs
-                    colsSpec := columns.getSpec(filter.value.column)
-                    axesNames := slices.map(colsSpec.axesSpec, func (a) { return a.name})
-                    if !slices.hasElement(axesNames, datasetSpec.axesSpec[1].name) {
-                        for na, ax in colsSpec.axesSpec {
-                            if ax.name != datasetSpec.axesSpec[1].name {
-                                cloneTable.setAxisHeader(ax, "cluster_" + string(i) + string(na))
-                                addedAxes = append(addedAxes, ax.name)
-                            }
-                        }
-                    }	
-                }
-            }
-        }
-
-        // Add ranking columns to table
-        validRanks := false
-        if len(args.rankingOrder) > 0 {
-            for i, col in args.rankingOrder {
-                if col.value != undefined {
-                    validRanks = true
-                    cloneTable.add(columns.getColumn(col.value.column), {header: "Col" + string(i)})
-                    addedCols = true
-                    // Store ranking order for this column
-                    rankingMap["Col" + string(i)] = col.rankingOrder
-                
-                    // If column does not have main anchor axis we have to include theirs
-                    colsSpec := columns.getSpec(col.value.column)
-                    axesNames := slices.map(colsSpec.axesSpec, func (a) { return a.name})
-                    if !slices.hasElement(axesNames, datasetSpec.axesSpec[1].name) {
-                        for na, ax in colsSpec.axesSpec {
-                            if ax.name != datasetSpec.axesSpec[1].name && !slices.hasElement(addedAxes, ax.name) {
-                                cloneTable.setAxisHeader(ax, "cluster_" + string(i) + string(na))
-                            }
-                        }
-                    }	
-                }
-            }
-        }
-        // If we didn't have any ranking column or all where not valid
-        if !validRanks {
-            // @TODO: this is a temporal patch for issue where rankingOrderDefault 
-            // are not defined by the time prerun works
-            if args.rankingOrderDefault.value != undefined {
-                i := 0
-                cloneTable.add(columns.getColumn(args.rankingOrderDefault.value.column), {header: "Col" + string(i)})
-                addedCols = true
-                // Store default ranking order
-                rankingMap["Col" + string(i)] = args.rankingOrderDefault.rankingOrder
-            
-                // If column does not have main anchor axis we have to include theirs
-                colsSpec := columns.getSpec(args.rankingOrderDefault.value.column)
-                axesNames := slices.map(colsSpec.axesSpec, func (a) { return a.name})
-                if !slices.hasElement(axesNames, datasetSpec.axesSpec[1].name) {
-                    for na, ax in colsSpec.axesSpec {
-                        if ax.name != datasetSpec.axesSpec[1].name {
-                            cloneTable.setAxisHeader(ax, "cluster_" + string(i) + string(na))
-                        }
-                    }
-                }	
-            }
-        }
-
-        // Get linker columns if needed
-        linkerAxisSpec := {}
-        linkerClusterIdAxes := []
-        if len(columns.getColumns("linkers")) > 0 {
-            for i, col in columns.getColumns("linkers") {
-                clusterIdAxis := undefined
-                if datasetSpec.axesSpec[1].name == col.spec.axesSpec[1].name {
-                    cloneTable.add(col, {header: "linker." + string(i)})
-                    cloneTable.setAxisHeader(col.spec.axesSpec[0], "cluster_" + string(i))
-                    linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[0]
-                    clusterIdAxis = col.spec.axesSpec[0]
-                } else if datasetSpec.axesSpec[1].name == col.spec.axesSpec[0].name {
-                    cloneTable.add(col, {header: "linker." + string(i)})
-                    cloneTable.setAxisHeader(col.spec.axesSpec[1], "cluster_" + string(i))
-                    linkerAxisSpec["cluster_" + string(i)] = col.spec.axesSpec[1]
-                    clusterIdAxis = col.spec.axesSpec[1]
-                }
-                // Collect clusterId axes from linker columns to match cluster size columns
-                if !is_undefined(clusterIdAxis) && clusterIdAxis.name == "pl7.app/vdj/clusterId" {
-                    linkerClusterIdAxes = append(linkerClusterIdAxes, clusterIdAxis)
-                }
-                addedCols = true
-            }
-        }
-
-        // Add cluster size columns if available, but only those matching linker columns' clusterId axes
-        // This ensures we only join columns from the same clustering run
-        if len(columns.getColumns("clusterSizes")) > 0 {
-            clusterSizeIdx := 0
-            for col in columns.getColumns("clusterSizes") {
-                // Find the clusterId axis in this cluster size column
-                clusterSizeClusterIdAxis := undefined
-                for axis in col.spec.axesSpec {
-                    if axis.name == "pl7.app/vdj/clusterId" {
-                        clusterSizeClusterIdAxis = axis
-                        break
-                    }
-                }
-                
-                // Only add if we have linker columns and this cluster size matches one of them
-                shouldAdd := false
-                if len(linkerClusterIdAxes) > 0 && !is_undefined(clusterSizeClusterIdAxis) {
-                    // Check if this cluster size column matches any linker's clusterId axis
-                    for linkerAxis in linkerClusterIdAxes {
-                        // Compare domains - they must match exactly for same clustering run
-                        if clusterSizeClusterIdAxis.name == linkerAxis.name &&
-                           clusterSizeClusterIdAxis.type == linkerAxis.type {
-                            // Check if domains match
-                            domainsMatch := true
-                            if is_undefined(clusterSizeClusterIdAxis.domain) != is_undefined(linkerAxis.domain) {
-                                domainsMatch = false
-                            } else if !is_undefined(clusterSizeClusterIdAxis.domain) && !is_undefined(linkerAxis.domain) {
-                                // Compare domain keys and values
-                                if len(clusterSizeClusterIdAxis.domain) != len(linkerAxis.domain) {
-                                    domainsMatch = false
-                                } else {
-                                    for k, v in clusterSizeClusterIdAxis.domain {
-                                        if is_undefined(linkerAxis.domain[k]) || linkerAxis.domain[k] != v {
-                                            domainsMatch = false
-                                            break
-                                        }
-                                    }
-                                }
-                            }
-                            if domainsMatch {
-                                shouldAdd = true
-                                break
-                            }
-                        }
-                    }
-                }
-                
-                // Only add cluster size columns that match a linker column's clustering run
-                if shouldAdd {
-                    // Trace elements are already present in col.spec from the clustering block.
-                    // deriveLabels (in label.ts) will use these existing trace elements to construct
-                    // distinguishing labels when multiple clustering blocks are joined, similar to
-                    // how LabelTypeFull ('__LABEL__@1') works. The trace includes:
-                    // - Original dataset trace
-                    // - "milaboratories.clonotype-clustering.sequences" trace element
-                    // - "milaboratories.clonotype-clustering.clustering" trace element
-                    // No modification needed - just preserve the existing trace.
-                    
-                    cloneTable.add(col, {header: "clusterSize." + string(clusterSizeIdx)})
-                    addedCols = true
-                    // Add the cluster axis header
-                    for axisIdx, axis in col.spec.axesSpec {
-                        if axis.name != datasetSpec.axesSpec[1].name {
-                            cloneTable.setAxisHeader(axis, "clusterAxis_" + string(clusterSizeIdx) + "_" + string(axisIdx))
-                        }
-                    }
-                    clusterSizeIdx = clusterSizeIdx + 1
-                }
-            }
-        }
-
-        // Continue only if we have at least a column
-        // This condition prevents temporal intermittent error while filters are 
-        // being processed and possibly in other situations too
-        if addedCols {
-            cloneTable.mem("16GiB")
-            cloneTable.cpu(1)
-            cloneTable = cloneTable.build()
-
-            // Use ender.create to call the filter-clonotypes template
-            filterSampleResult := render.create(filterAndSampleTpl, {
-                inputAnchor: args.inputAnchor,
-                cloneTable: cloneTable,
-                rankingOrder: args.rankingOrder,
-                rankingOrderDefault: args.rankingOrderDefault,
-                filters: args.filters,
-                filterMap: filterMap,
-                rankingMap: rankingMap,
-                datasetSpec: datasetSpec,
-                topClonotypes: args.topClonotypes
-            })
-            
-            // Get the filtered clonotypes from the template result
-            outputs["sampledRows"] = filterSampleResult.output("sampledRows", 24 * 60 * 60 * 1000)
-
-            // Get the filtered and sampled clonotypes P-frame and CSV from the template result
-            finalClonotypesCsv := filterSampleResult.output("finalClonotypesCsv", 24 * 60 * 60 * 1000)
-            // outputs["sampledRows"] = filterSampleResult.output("sampledRows", 24 * 60 * 60 * 1000)
-            
-            ////////// CDR3 Length Calculation //////////
-                
-            cdr3SeqTable := pframes.tsvFileBuilder()
-            cdr3SeqTable.setAxisHeader(datasetSpec.axesSpec[1].name, "clonotypeKey")
-
-            // Must deal with multiple CDR3 sequences (two for each cell in single cell data)
-            // Chain will be added in the header as cdr3Sequence.chain and used in python script
-            // Notice chain is in spec.domain for single cell data and spec.axesSpec[0].domain for bulk data
-
-            // Helper function to add chain information to the headers dynamically
-            chainMapping := {
-                "IG": { "A": "Heavy", "B": "Light" },
-                "TCRAB": { "A": "TRA", "B": "TRB" },
-                "TCRGD": { "A": "TRG", "B": "TRD" }
-            }
-
-            makeHeaderName := func(col, baseHeaderName, isSingleCell) {
-                if isSingleCell {
-                    chain := col.spec.domain["pl7.app/vdj/scClonotypeChain"]  // e.g., "A", "B"
-                    receptor := col.spec.axesSpec[0].domain["pl7.app/vdj/receptor"]  // e.g., "IG", "TCRAB", "TCRGD"
-                    chainLabel := chainMapping[receptor][chain]
-                    return baseHeaderName + "." + chainLabel // e.g., "cdr3Sequence.Heavy"
-                } else {
-                    // For bulk, if chain info is available (e.g. IGH, IGK, IGL)
-                    chainFromDomain := col.spec.axesSpec[0].domain["pl7.app/vdj/chain"] // e.g. "IGH", "IGK"
-                    if chainFromDomain != undefined {
-                        return baseHeaderName + "." + chainFromDomain // e.g., "cdr3Sequence.IGH"
-                    }
-                }
-                return baseHeaderName
-            };
-
-            // Process CDR3 sequences
-            cdr3Sequences := columns.getColumns("cdr3Sequences")
-
-            for col in cdr3Sequences {
-                headerName := makeHeaderName(col, "cdr3Sequence", isSingleCell)
-                if isSingleCell {
-                    if col.spec.domain["pl7.app/vdj/scClonotypeChain/index"] == "primary" {
-                        cdr3SeqTable.add(col, {header: headerName})
-                    }
-                } else {
-                    cdr3SeqTable.add(col, {header: headerName})
-                }
-            }
-
-            // Process V genes
-            vGenes := columns.getColumns("VGenes")	
-
-            for col in vGenes {
-                headerName := makeHeaderName(col, "vGene", isSingleCell)
-                cdr3SeqTable.add(col, {header: headerName})
-            }
-
-            // Process J genes
-            jGenes := columns.getColumns("JGenes")	
-
-            for col in jGenes {
-                headerName := makeHeaderName(col, "jGene", isSingleCell)
-                cdr3SeqTable.add(col, {header: headerName})
-            }
-
-            cdr3SeqTable.mem("16GiB")
-            cdr3SeqTable.cpu(1)
-            cdr3SeqTableBuilt := cdr3SeqTable.build()
-
-            cdr3VspectratypeCmd := exec.builder().
-                software(assets.importSoftware("@platforma-open/milaboratories.top-antibodies.spectratype:main")).
-                mem("16GiB").
-                cpu(1).
-                addFile("cdr3_sequences_input.tsv", cdr3SeqTableBuilt).
-                arg("--input_tsv").arg("cdr3_sequences_input.tsv").
-                arg("--spectratype_tsv").arg("spectratype.tsv").
-                arg("--vj_usage_tsv").arg("vj_usage.tsv") // no dot here
-
-            // Add top clonotypes argument and file to the builder if provided
-            if finalClonotypesCsv != undefined {
-                cdr3VspectratypeCmd = cdr3VspectratypeCmd.
-                    arg("--final_clonotypes_csv").arg("finalClonotypes.csv").
-                    addFile("finalClonotypes.csv", finalClonotypesCsv)
-            }
-
-            cdr3VspectratypeCmd = cdr3VspectratypeCmd. // continue building the command
-                saveFile("spectratype.tsv").
-                saveFile("vj_usage.tsv").
-                printErrStreamToStdout().
-                cache(24 * 60 * 60 * 1000).
-                run()
-
-
-            // Spectratype PFrame structure is [chain][cdr3Length][vGene] -> count
-
-            cdr3VspectratypePf := xsv.importFile(cdr3VspectratypeCmd.getFile("spectratype.tsv"), 
-                                                "tsv", spectratypeConv.getColumns(),
-                                                {cpu: 1, mem: "16GiB"})
-            outputs["cdr3VspectratypePf"] = pframes.exportFrame(cdr3VspectratypePf) 
-
-            // For vjUsage structure is [chain][vGene][jGene] -> count
-            vjUsagePf := xsv.importFile(cdr3VspectratypeCmd.getFile("vj_usage.tsv"), 
-                                        "tsv", vjUsageConv.getColumns(), 
-                                        {cpu: 1, mem: "16GiB"})
-            outputs["vjUsagePf"] = pframes.exportFrame(vjUsagePf)
-
-            if args.kabatNumbering == true {
-            ////////// Assembling AA sequences //////////
-                assemSeqTable := pframes.tsvFileBuilder()
-                keyHeader := "clonotypeKey"
-                assemSeqTable.setAxisHeader(datasetSpec.axesSpec[1].name, keyHeader)
-
-                seqCols := columns.getColumns("assemblingAaSeqs")
-                for col in seqCols {
-                    headerName := makeHeaderName(col, "assemblingFeature", isSingleCell)
-                    assemSeqTable.add(col, {header: headerName})
-                }
-
-                assemSeqTable.mem("16GiB")
-                assemSeqTable.cpu(1)
-                assemSeqTableBuilt := assemSeqTable.build()
-
-                // Convert assembling feature sequences to FASTA via sub-template
-                assemFastaTpl := assets.importTemplate(":assembling-fasta")
-                bulkChain := undefined
-                if !isSingleCell {
-                    // infer bulk chain by header names of incoming seq columns (domain uses IGHeavy / IGLight)
-                    chainDetected := "KL"
-                    for col in seqCols {
-                        ch := col.spec.axesSpec[0].domain["pl7.app/vdj/chain"] // e.g., IGHeavy, IGLight
-                        if ch == "IGHeavy" { chainDetected = "H"; break }
-                        if ch == "IGLight" { chainDetected = "KL" }
-                    }
-                    bulkChain = chainDetected
-                }
-                assem := render.create(assemFastaTpl, {
-                    inputTsv: assemSeqTableBuilt,
-                    keyColumn: "clonotypeKey",
-                    finalClonotypesCsv: finalClonotypesCsv,
-                    isSingleCell: isSingleCell,
-                    bulkChain: bulkChain
-                })
-                //outputs["assemblingAnarci"] = assem.output("anarci", 24 * 60 * 60 * 1000)
-                kabatFile := assem.output("kabat", 24 * 60 * 60 * 1000)
-                // Derive feature name from assembling feature columns (prefer first column's feature)
-                featName := ""
-                if len(seqCols) > 0 {
-                    f := seqCols[0].spec.domain["pl7.app/vdj/feature"]
-                    if f != undefined { featName = f }
-                }
-                // Convert kabat.tsv to PFrame with proper specs (bulk: select heavy/light)
-                kabatPf := xsv.importFile(kabatFile, "tsv", kabatConv.getColumns(datasetSpec, featName, bulkChain), {cpu: 1, mem: "8GiB"})
-                outputs["assemblingKabatPf"] = pframes.exportFrame(kabatPf)
-            }
-        }
-    }
-
-	return {
-		outputs: outputs,
-		exports: {}
-	}
-})