@platforma-open/milaboratories.top-antibodies 4.3.1 → 4.3.3

package/block-pack/published.json

@@ -3,6 +3,6 @@
   "id": {
     "organization": "milaboratories",
     "name": "top-antibodies",
-    "version": "4.3.1"
+    "version": "4.3.3"
   }
 }

package/dist/index.js

@@ -13809,6 +13809,13 @@ function isProducedByLeadSelection(spec) {
 	const trace = readAnnotationJson(spec, Annotation.Trace);
 	return Array.isArray(trace) && trace.length > 0 && trace[trace.length - 1]?.type === LEAD_SELECTION_TRACE_TYPE;
 }
+/** Repertoire-labeling emits one such column per label. `PColumnName` has no entry for it. */
+const LABELING_TAG_COLUMN_NAME = "pl7.app/tag";
+/** `pl7.app/isSubset` marks both a dataset restriction and a presence-only column. A labeling
+*  tag is only the second, so the dataset picker must not offer it. */
+function isDatasetScopingSubset(spec) {
+	return isPColumnSpec(spec) && spec.name !== LABELING_TAG_COLUMN_NAME;
+}
 /**
 * True when a column carries no readable value. Presence is the whole signal.
 *
@@ -13996,13 +14003,57 @@ function computeDefaultFilters(scores, anchorRef) {
 	}
 	return defaultFilters;
 }
+/**
+* Which pipeline produced the anchor's records, from the run-id key on its record axis:
+*
+*   pl7.app/peptide/extractionRunId      peptide-extraction
+*   pl7.app/repertoire/extractionRunId   synthetic-repertoire-profiler
+*   pl7.app/vdj/clonotypingRunId         MiXCR, and import-vdj-data's imported sets
+*
+* Reads the domain, not the axis name: clonotypeKey and scClonotypeKey are migrating to
+* pl7.app/variantKey, after which the name discriminates nothing. The axis-name checks below are
+* a fallback for producers that have not migrated yet.
+*
+* Does not say how a receptor dataset arrived. Uploaded sequences and MiXCR output are both
+* `vdj`. Whether specific columns exist is a separate question — see {@link hasGeneCalls}.
+*/
+function recordSource(anchorSpec) {
+	const keyAxis = anchorSpec.axesSpec[1];
+	if (keyAxis === void 0) return "unknown";
+	const domain = keyAxis.domain ?? {};
+	if (domain["pl7.app/peptide/extractionRunId"] !== void 0) return "peptide";
+	if (domain["pl7.app/repertoire/extractionRunId"] !== void 0) return "amplicon";
+	if (domain["pl7.app/vdj/clonotypingRunId"] !== void 0) return "vdj";
+	if (keyAxis.name === "pl7.app/vdj/clonotypeKey" || keyAxis.name === "pl7.app/vdj/scClonotypeKey") return "vdj";
+	return "unknown";
+}
+/** True for the two producers whose records are peptides or synthetic variants, not receptors. */
+function isPeptideOrAmplicon(anchorSpec) {
+	const source = recordSource(anchorSpec);
+	return source === "peptide" || source === "amplicon";
+}
+/**
+* Whether the dataset carries V/J gene calls — needed by CDR3 V Spectratype, V/J Gene Usage and
+* Kabat renumbering.
+*
+* Separate from {@link recordSource} on purpose: an uploaded set and a MiXCR set are both `vdj`,
+* but only MiXCR's has gene calls.
+*
+* TEMPORARY. This infers from the axis, and no variantKey producer emits gene calls today. When
+* MiXCR migrates to that axis this returns false for MiXCR too and both sections silently
+* disappear. Nothing structural separates the cases then — same axis name, same
+* clonotypingRunId — so replace it with a result-pool query for the gene columns.
+*/
+function hasGeneCalls(anchorSpec) {
+	return anchorSpec.axesSpec[1]?.name !== "pl7.app/variantKey";
+}
 function computePresets(scores, defaultFilters, anchorRef, anchorSpec) {
-	const isPeptide = anchorSpec.axesSpec[1]?.name === "pl7.app/variantKey";
+	const usesPeptidePreset = isPeptideOrAmplicon(anchorSpec);
 	const repertoireScore = scores.find((s) => s.getSpec().name === REPERTOIRE_SCORE_COLUMN_NAME);
 	const hasRepertoireScore = repertoireScore !== void 0;
 	const isEnrichmentColumn = (name) => name.startsWith("pl7.app/enrichment") || name.startsWith("pl7.app/vdj/enrichment");
 	const hasEnrichmentScores = scores.some((s) => isEnrichmentColumn(s.getSpec().name));
-	const detectedPreset = isPeptide ? "peptide" : hasRepertoireScore ? "in-vivo" : hasEnrichmentScores ? "in-vitro" : void 0;
+	const detectedPreset = usesPeptidePreset ? "peptide" : hasRepertoireScore ? "in-vivo" : hasEnrichmentScores ? "in-vitro" : void 0;
 	const defaultRankingOrder = scores.filter((s) => s.getSpec().valueType !== "String").filter((s) => !hasRepertoireScore || s.getSpec().name !== "pl7.app/vdj/repertoireScore").filter((s) => !hasRepertoireScore || !IN_VIVO_MUTATION_COLUMNS.has(s.getSpec().name)).map((s) => ({
 		id: `default-rank-${s.id}`,
 		value: matchToColumnId(s, anchorRef),
@@ -14560,14 +14611,17 @@ const platforma$1 = BlockModelV3.create({
 		diversificationColumn: data.diversificationColumn
 	};
 }).output("datasetOptions", (ctx) => {
-	const opts = buildDatasetOptions(ctx, { primary: (spec) => {
-		if (!isPColumnSpec(spec)) return false;
-		if (spec.annotations?.[Annotation.IsAnchor] !== "true") return false;
-		if (spec.axesSpec.length < 2) return false;
-		if (spec.axesSpec[0]?.name !== "pl7.app/sampleId") return false;
-		const rowAxis = spec.axesSpec[1]?.name;
-		return rowAxis === "pl7.app/vdj/clonotypeKey" || rowAxis === "pl7.app/vdj/scClonotypeKey" || rowAxis === "pl7.app/variantKey";
-	} });
+	const opts = buildDatasetOptions(ctx, {
+		primary: (spec) => {
+			if (!isPColumnSpec(spec)) return false;
+			if (spec.annotations?.[Annotation.IsAnchor] !== "true") return false;
+			if (spec.axesSpec.length < 2) return false;
+			if (spec.axesSpec[0]?.name !== "pl7.app/sampleId") return false;
+			const rowAxis = spec.axesSpec[1]?.name;
+			return rowAxis === "pl7.app/vdj/clonotypeKey" || rowAxis === "pl7.app/vdj/scClonotypeKey" || rowAxis === "pl7.app/variantKey";
+		},
+		filter: isDatasetScopingSubset
+	});
 	if (!opts) return opts;
 	const selfBlockId = ctx.outputs?.resolve({
 		field: "selfBlockId",
@@ -14587,7 +14641,7 @@ const platforma$1 = BlockModelV3.create({
 }, { retentive: true }).output("modality", (ctx) => {
 	const spec = getSpecByRef(getInputAnchorRef(ctx.data));
 	if (!spec) return void 0;
-	return spec.axesSpec[1]?.name === "pl7.app/variantKey" ? "peptide" : "antibody_tcr";
+	return isPeptideOrAmplicon(spec) ? "peptide" : "antibody_tcr";
 }, { retentive: true }).output("filterConfig", (ctx) => {
 	const inputAnchor = getInputAnchorRef(ctx.data);
 	const result = buildCollection(inputAnchor);
@@ -14871,9 +14925,9 @@ const platforma$1 = BlockModelV3.create({
 	if (numbered === 0) return "Kabat numbering could not be applied to any clonotype. The framework regions may be too divergent from known germline sequences. Kabat sequence columns will be empty.";
 	return `Kabat numbering was applied to ${numbered.toLocaleString()} clonotype${numbered === 1 ? "" : "s"}. Clonotypes that could not be numbered will have empty Kabat sequence columns.`;
 }).output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false).title(() => "Lead Selection").subtitle((ctx) => ctx.data.customBlockLabel || ctx.data.defaultBlockLabel).sections((ctx) => {
-	const keyAxis = getSpecByRef(getInputAnchorRef(ctx.data))?.axesSpec[1];
-	const isPeptide = keyAxis?.name === "pl7.app/variantKey";
-	const spaceLabel = isPeptide && keyAxis?.domain?.["pl7.app/repertoire/extractionRunId"] !== void 0 ? "Variant Space" : isPeptide ? "Peptide Space" : "Clonotype Space";
+	const anchorSpec = getSpecByRef(getInputAnchorRef(ctx.data));
+	const source = anchorSpec !== void 0 ? recordSource(anchorSpec) : "unknown";
+	const spaceLabel = source === "amplicon" ? "Variant Space" : source === "peptide" ? "Peptide Space" : "Clonotype Space";
 	const sections = [
 		{
 			type: "link",
@@ -14891,7 +14945,7 @@ const platforma$1 = BlockModelV3.create({
 			label: "Selection Plot"
 		}
 	];
-	if (!isPeptide) sections.push({
+	if (anchorSpec !== void 0 && hasGeneCalls(anchorSpec)) sections.push({
 		type: "link",
 		href: "/spectratype",
 		label: "CDR3 V Spectratype"