@platforma-open/milaboratories.top-antibodies.workflow 1.17.3 → 1.17.5

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.top-antibodies.workflow@1.17.3 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@1.17.5 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/assembling-fasta.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,19 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 1.17.5
+
+### Patch Changes
+
+- ff606b5: Implement multi-selection filters
+- Updated dependencies [ff606b5]
+  - @platforma-open/milaboratories.top-antibodies.sample-clonotypes@1.9.3
+
+## 1.17.4
+
+### Patch Changes
+
+- 605fdf0: Add domain to exported filter
+
 ## 1.17.3
 
 ### Patch Changes

package/dist/tengo/lib/sampled-cols-conv.lib.tengo

@@ -6,11 +6,11 @@ getColumns := func(datasetSpec, addRanking) {
         id: "link",
         allowNA: false,
         spec: {
-          name: "pl7.app/vdj/sampling-column",
+          name: "pl7.app/vdj/lead-selection",
           valueType: "Int",
           domain: {},
           annotations: {
-            "pl7.app/label": "Sampling column",
+            "pl7.app/label": "Selected Leads",
             "pl7.app/table/visibility": "hidden",
             "pl7.app/isSubset": "true"
           }

package/dist/tengo/lib/sampled-export-conv.lib.tengo

@@ -1,6 +1,18 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
+json := import("json")
+
+getColumns := func(datasetSpec, filterMap, rankingMap, disableClusterRanking, clusterColumn, topClonotypes) {
+
+
+  domain := {
+    "pl7.app/vdj/filter-map": string(json.encode(filterMap)),
+    "pl7.app/vdj/ranking-map": string(json.encode(rankingMap)),            
+    "pl7.app/vdj/top-clonotypes": string(topClonotypes)
+  }
+  if !disableClusterRanking && clusterColumn != undefined && clusterColumn != "" {
+    domain["pl7.app/vdj/diversity-column"] = string(json.encode(clusterColumn))
+  }
 
-getColumns := func(datasetSpec) {
   columns := [{
         column: "top",
         id: "link",
@@ -8,7 +20,7 @@ getColumns := func(datasetSpec) {
         spec: {
           name: "pl7.app/vdj/lead-selection",
           valueType: "Int",
-          domain: {},
+          domain: domain,
           annotations: {
             "pl7.app/label": "Selected Leads",
             "pl7.app/table/visibility": "hidden",

package/dist/tengo/lib/utils.lib.tengo

@@ -1,6 +1,7 @@
 
 
 slices := import("@platforma-sdk/workflow-tengo:slices")
+json := import("json")
 
 
 
@@ -545,6 +546,89 @@ initializeAssemSeqTable := func(pframes, columns, datasetSpec, isSingleCell) {
     }
 }
 
+
+filterOperatorMap := {
+    "number_greaterThan": ">",
+    "number_greaterThanOrEqualTo": ">=",
+    "number_lessThan": "<",
+    "number_lessThanOrEqualTo": "<=",
+    "number_equals": "=",
+    "number_notEquals": "!=",
+    "string_equals": "=",
+    "string_notEquals": "!=",
+    "string_contains": "contains",
+    "string_doesNotContain": "not contains",
+    "string_in": "in",
+    "string_notIn": "not in"
+}
+
+
+
+
+
+
+
+
+
+formatFilterDescription := func(columnLabel, filter) {
+    if is_undefined(filter) || is_undefined(filter.type) {
+        return columnLabel
+    }
+
+
+    op := filterOperatorMap[filter.type]
+    if is_undefined(op) {
+        op = filter.type
+    }
+
+    ref := filter.reference
+
+    if filter.type == "string_in" || filter.type == "string_notIn" {
+        values := json.decode(string(ref))
+        valStr := "["
+        for i, v in values {
+            if i > 0 {
+                valStr = valStr + ", "
+            }
+            valStr = valStr + string(v)
+        }
+        ref = valStr + "]"
+    }
+
+    return columnLabel + " " + op + " " + string(ref)
+}
+
+
+
+
+
+
+
+
+
+buildFilterTraceLabel := func(filters, columns) {
+    result := ""
+    count := 0
+    for filter in filters {
+        if !is_undefined(filter.value) {
+            colSpec := columns.getSpec(filter.value.column)
+            if !is_undefined(colSpec) {
+                colLabel := colSpec.annotations["pl7.app/label"]
+                if is_undefined(colLabel) {
+                    colLabel = colSpec.name
+                }
+                desc := formatFilterDescription(colLabel, filter.filter)
+                if count > 0 {
+                    result = result + ", "
+                }
+                result = result + desc
+                count = count + 1
+            }
+        }
+    }
+    return result
+}
+
 export {
     clusterAxisDomainsMatch: clusterAxisDomainsMatch,
     findMatchingLinkerIndex: findMatchingLinkerIndex,
@@ -555,5 +639,7 @@ export {
     makeHeaderName: makeHeaderName,
     initializeCdr3SeqTable: initializeCdr3SeqTable,
     detectBulkChain: detectBulkChain,
-    initializeAssemSeqTable: initializeAssemSeqTable
+    initializeAssemSeqTable: initializeAssemSeqTable,
+    formatFilterDescription: formatFilterDescription,
+    buildFilterTraceLabel: buildFilterTraceLabel
 }

package/package.json

@@ -1,19 +1,19 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "1.17.3",
+  "version": "1.17.5",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "5.8.1",
+    "@platforma-sdk/workflow-tengo": "5.8.2",
     "@platforma-open/milaboratories.software-anarci": "^0.0.3",
-    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.9.2",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.1",
+    "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "1.9.3",
     "@platforma-open/milaboratories.top-antibodies.umap": "1.2.1",
-    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.3.0",
-    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.0"
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.1",
+    "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.0",
+    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.3.0"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "2.4.13"
+    "@platforma-sdk/tengo-builder": "2.4.18"
   },
   "scripts": {
     "build": "shx rm -rf dist && pl-tengo check && pl-tengo build",

package/src/filter-and-sample.tpl.tengo

@@ -4,6 +4,7 @@ exec := import("@platforma-sdk/workflow-tengo:exec")
 assets := import("@platforma-sdk/workflow-tengo:assets")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
 xsv := import("@platforma-sdk/workflow-tengo:pframes.xsv")
+pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec")
 render := import("@platforma-sdk/workflow-tengo:render")
 sampledColsConv := import(":sampled-cols-conv")
 sampledExportConv := import(":sampled-export-conv")
@@ -89,10 +90,25 @@ self.body(func(inputs) {
     outputs["finalClonotypes"] = finalClonotypes
 
     // Export only the sampling column to be used as a filter downstream
-    sampledExportsParams := sampledExportConv.getColumns(datasetSpec)
+    sampledExportsParams := sampledExportConv.getColumns(datasetSpec, filterMap,
+        rankingMap, inputs.disableClusterRanking, inputs.rawClusterColumn, topClonotypes)
     sampledColumnsOnlyPf := xsv.importFile(finalClonotypes, "parquet", sampledExportsParams,
                                         {cpu: 1, mem: "16GiB"})
-    outputs["sampledColumnsExport"] = sampledColumnsOnlyPf
+
+    // Create trace with filter descriptions and inject into exported column
+    traceLabel := inputs.filterTraceLabel
+    if is_undefined(traceLabel) || traceLabel == "" {
+        traceLabel = "Selected Leads"
+    }
+    trace := pSpec.makeTrace(datasetSpec,
+        {
+            type: "milaboratories.antibody-tcr-lead-selection",
+            importance: 30,
+            label: traceLabel
+        })
+    exportPf := pframes.pFrameBuilder()
+    exportPf.add("link", trace.inject(sampledColumnsOnlyPf["link.spec"]), sampledColumnsOnlyPf["link.data"])
+    outputs["sampledColumnsExport"] = exportPf.build()
 
     return outputs
 }) 

package/src/main.tpl.tengo

@@ -6,6 +6,7 @@ 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")
+pSpec := import("@platforma-sdk/workflow-tengo:pframes.spec")
 ll := import("@platforma-sdk/workflow-tengo:ll")
 kabatConv := import(":pf-kabat-conv")
 
@@ -132,10 +133,13 @@ wf.body(func(args) {
         addedCols := tableInit.addedCols
 
         // Continue only if we have at least a column
-        // This condition prevents temporal intermittent error while filters are 
+        // This condition prevents temporal intermittent error while filters are
         // being processed and possibly in other situations too
         if addedCols {
 
+            // Build trace label from filter descriptions
+            filterTraceLabel := utils.buildFilterTraceLabel(args.filters, columns)
+
             // Use ender.create to call the filter-clonotypes template
             filterSampleResult := render.create(filterAndSampleTpl, {
                 inputAnchor: args.inputAnchor,
@@ -147,9 +151,11 @@ wf.body(func(args) {
                 datasetSpec: datasetSpec,
                 topClonotypes: args.topClonotypes,
                 disableClusterRanking: args.disableClusterRanking,
-                clusterColumn: clusterColumnHeader
+                clusterColumn: clusterColumnHeader,
+                rawClusterColumn: args.clusterColumn,
+                filterTraceLabel: filterTraceLabel
             })
-            
+
             // Get the filtered clonotypes from the template result
             outputs["sampledRows"] = filterSampleResult.output("sampledRows", 24 * 60 * 60 * 1000)
 

package/src/sampled-cols-conv.lib.tengo

@@ -6,11 +6,11 @@ getColumns := func(datasetSpec, addRanking) {
         id: "link",
         allowNA: false,
         spec: {
-          name: "pl7.app/vdj/sampling-column",
+          name: "pl7.app/vdj/lead-selection",
           valueType: "Int",
           domain: {},
           annotations: {
-            "pl7.app/label": "Sampling column",
+            "pl7.app/label": "Selected Leads",
             "pl7.app/table/visibility": "hidden",
             "pl7.app/isSubset": "true"
           }

package/src/sampled-export-conv.lib.tengo

@@ -1,6 +1,18 @@
 ll := import("@platforma-sdk/workflow-tengo:ll")
+json := import("json")
+
+getColumns := func(datasetSpec, filterMap, rankingMap, disableClusterRanking, clusterColumn, topClonotypes) {
+
+  // Define domain
+  domain := {
+    "pl7.app/vdj/filter-map": string(json.encode(filterMap)),
+    "pl7.app/vdj/ranking-map": string(json.encode(rankingMap)),            
+    "pl7.app/vdj/top-clonotypes": string(topClonotypes)
+  }
+  if !disableClusterRanking && clusterColumn != undefined && clusterColumn != "" {
+    domain["pl7.app/vdj/diversity-column"] = string(json.encode(clusterColumn))
+  }
 
-getColumns := func(datasetSpec) {
   columns := [{
         column: "top",
         id: "link",
@@ -8,7 +20,7 @@ getColumns := func(datasetSpec) {
         spec: {
           name: "pl7.app/vdj/lead-selection",
           valueType: "Int",
-          domain: {},
+          domain: domain,
           annotations: {
             "pl7.app/label": "Selected Leads",
             "pl7.app/table/visibility": "hidden",

package/src/utils.lib.tengo

@@ -1,6 +1,7 @@
 // Utility functions for antibody-tcr-lead-selection workflow
 
 slices := import("@platforma-sdk/workflow-tengo:slices")
+json := import("json")
 
 /**
  * Checks if two clusterId axes have matching domains.
@@ -545,6 +546,89 @@ initializeAssemSeqTable := func(pframes, columns, datasetSpec, isSingleCell) {
     }
 }
 
+// Maps filter type to short operator symbol for trace labels.
+filterOperatorMap := {
+    "number_greaterThan": ">",
+    "number_greaterThanOrEqualTo": ">=",
+    "number_lessThan": "<",
+    "number_lessThanOrEqualTo": "<=",
+    "number_equals": "=",
+    "number_notEquals": "!=",
+    "string_equals": "=",
+    "string_notEquals": "!=",
+    "string_contains": "contains",
+    "string_doesNotContain": "not contains",
+    "string_in": "in",
+    "string_notIn": "not in"
+}
+
+/**
+ * Formats a single filter as a short description for trace labels.
+ * e.g. "Min quality FR1 > 0", "Productive = true", "Chain in Heavy, Light"
+ *
+ * @param columnLabel - Human-readable column name
+ * @param filter - Filter object with type and reference fields
+ * @return Formatted filter description string
+ */
+formatFilterDescription := func(columnLabel, filter) {
+    if is_undefined(filter) || is_undefined(filter.type) {
+        return columnLabel
+    }
+
+    // Return filter.type if short operator is not found
+    op := filterOperatorMap[filter.type]
+    if is_undefined(op) {
+        op = filter.type
+    }
+
+    ref := filter.reference
+    // In multiple select filters, parse JSON array and join values
+    if filter.type == "string_in" || filter.type == "string_notIn" {
+        values := json.decode(string(ref))
+        valStr := "["
+        for i, v in values {
+            if i > 0 {
+                valStr = valStr + ", "
+            }
+            valStr = valStr + string(v)
+        }
+        ref = valStr + "]"
+    }
+
+    return columnLabel + " " + op + " " + string(ref)
+}
+
+/**
+ * Builds a comma-separated filter description string for use in trace labels.
+ * e.g. "Min quality FR1 > 0, Productive = true, Chain in Heavy, Light"
+ *
+ * @param filters - Array of filter objects from block args
+ * @param columns - PBundle to look up column specs for labels
+ * @return Filter description string, or empty string if no valid filters
+ */
+buildFilterTraceLabel := func(filters, columns) {
+    result := ""
+    count := 0
+    for filter in filters {
+        if !is_undefined(filter.value) {
+            colSpec := columns.getSpec(filter.value.column)
+            if !is_undefined(colSpec) {
+                colLabel := colSpec.annotations["pl7.app/label"]
+                if is_undefined(colLabel) {
+                    colLabel = colSpec.name
+                }
+                desc := formatFilterDescription(colLabel, filter.filter)
+                if count > 0 {
+                    result = result + ", "
+                }
+                result = result + desc
+                count = count + 1
+            }
+        }
+    }
+    return result
+}
+
 export {
     clusterAxisDomainsMatch: clusterAxisDomainsMatch,
     findMatchingLinkerIndex: findMatchingLinkerIndex,
@@ -555,5 +639,7 @@ export {
     makeHeaderName: makeHeaderName,
     initializeCdr3SeqTable: initializeCdr3SeqTable,
     detectBulkChain: detectBulkChain,
-    initializeAssemSeqTable: initializeAssemSeqTable
+    initializeAssemSeqTable: initializeAssemSeqTable,
+    formatFilterDescription: formatFilterDescription,
+    buildFilterTraceLabel: buildFilterTraceLabel
 }