@platforma-open/milaboratories.top-antibodies 4.3.0 → 4.3.2

package/dist/index.js

@@ -13996,13 +13996,57 @@ 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-${s.id}`,
 		value: matchToColumnId(s, anchorRef),
@@ -14471,14 +14515,14 @@ const CLUSTER_ID_SELECTORS = [...CLUSTER_ID_AXIS_NAMES].map((name) => ({ name: e
 const OWN_PLUMBING_SELECTORS = [{ name: exactMatch("pl7.app/selectionStage") }, { name: exactMatch("pl7.app/lead-selection") }];
 /**
 * Adapt column recipes to `PColumn`s for the helpers that still take
-* materialised `PColumn[]` and have no id form (`createPFrameForGraphs`,
-* `PColumnIdAndSpec`).
+* materialised `PColumn[]` and have no id form (`getRelatedColumns`,
+* `createPFrameForGraphs`, `PColumnIdAndSpec`).
 *
 * Only bare leaves qualify: `PColumn.id` is typed `PObjectId`, which no wrapper
 * recipe carries — hence `isDataColumn` rather than `hasReachableData`, which
-* also admits spec-overrides over a leaf. Deduped by id: the same leaf can be
-* reachable via more than one path and `createPFrameForGraphs` rejects
-* duplicates.
+* also admits spec-overrides over a leaf. Deduped by id: these lists travel as
+* block columns, and a repeated id aborts the collection scan inside
+* `getRelatedColumns`.
 */
 function toGraphColumns(recipes) {
 	return dedupColumns(recipes.filter(isDataColumn).map((c) => ({
@@ -14492,32 +14536,38 @@ function accessorGraphColumns(accessor) {
 	if (!accessor) return void 0;
 	return toGraphColumns(ColumnsCollection([accessor]).getColumns());
 }
+function umapPoolColumns(ctx) {
+	const clonotypeAxisName = getSpecByRef(getInputAnchorRef(ctx.data))?.axesSpec[1]?.name;
+	if (clonotypeAxisName === void 0) return void 0;
+	const umap = ColumnsCollection(["result_pool"]).filter({ include: {
+		name: "^pl7\\.app/umap[12]$",
+		axes: [{ name: exactMatch(clonotypeAxisName) }]
+	} }).getColumns();
+	if (umap.length === 0) return void 0;
+	return toGraphColumns(umap);
+}
 /**
-* UMAP columns from the sequence-space block plus this block's own sampled-rows
-* markers, materialised for `createPFrameForGraphs` / `PColumnIdAndSpec`.
+* Ids of the columns that join the UMAP projection, discovered once per UMAP
+* column and unioned, so a second clonotype-space block keyed on its own axis
+* still contributes.
 *
-* The legacy `{ anchor: "main", idx: 1 }` axis binding has no selector form, so
-* the clonotype axis name is read off the resolved anchor spec and matched by
-* name. Omitting `partialAxesMatch` keeps the old exact-axis-set semantics.
+* Anchors are specs, never ids, so the pool's own copy of a UMAP column cannot
+* collide with one handed in here.
 */
-function umapGraphColumns(ctx) {
-	const anchorSpec = getSpecByRef(getInputAnchorRef(ctx.data));
-	const clonotypeAxisName = anchorSpec?.axesSpec[1]?.name;
-	if (anchorSpec === void 0 || clonotypeAxisName === void 0) return void 0;
-	const umap = ColumnsCollection(["result_pool"]).discover({
-		anchors: { main: anchorSpec },
-		include: {
-			name: "^pl7\\.app/umap[12]$",
-			axes: [{ name: exactMatch(clonotypeAxisName) }]
-		}
-	}).getColumns();
-	if (umap.length === 0) return void 0;
-	const sampledRows = ColumnsCollection([ctx.outputs?.resolve({
+function umapRelatedIds(umap) {
+	return [...new Set(umap.flatMap((c) => ColumnsCollection().discover({
+		mode: "enrichment",
+		maxHops: 4,
+		anchors: { main: c.spec },
+		exclude: [{ annotations: { [Annotation.HideDataFromUi]: exactMatch("true") } }, { annotations: { [Annotation.HideDataFromGraphs]: exactMatch("true") } }]
+	}).getColumnIds()))];
+}
+function sampledRowsGraphColumns(ctx) {
+	return accessorGraphColumns(ctx.outputs?.resolve({
 		field: "sampledRows",
 		assertFieldType: "Input",
 		allowPermanentAbsence: true
-	})].filter((a) => a !== void 0)).getColumns();
-	return toGraphColumns([...umap, ...sampledRows]);
+	}));
 }
 const platforma$1 = BlockModelV3.create({
 	dataModel: blockDataModel,
@@ -14581,7 +14631,7 @@ 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);
@@ -14806,13 +14856,14 @@ const platforma$1 = BlockModelV3.create({
 	if (ctx.outputs.getIsReadyOrError() === false) return true;
 	return false;
 }).outputWithStatus("umapPf", (ctx) => {
-	const pCols = umapGraphColumns(ctx);
-	if (pCols === void 0) return void 0;
-	return createPFrameForGraphs(ctx, pCols);
+	const umap = umapPoolColumns(ctx);
+	if (umap === void 0) return void 0;
+	if (umap.some((c) => c.data === void 0)) return void 0;
+	return ctx.createPFrame([...umapRelatedIds(umap), ...umap.map((c) => c.id)]);
 }).outputWithStatus("umapPcols", (ctx) => {
-	const pCols = umapGraphColumns(ctx);
-	if (pCols === void 0) return void 0;
-	return pCols.map((c) => ({
+	const umap = umapPoolColumns(ctx);
+	if (umap === void 0) return void 0;
+	return [...umap, ...sampledRowsGraphColumns(ctx) ?? []].map((c) => ({
 		columnId: c.id,
 		spec: c.spec
 	}));
@@ -14864,9 +14915,9 @@ 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",
@@ -14884,7 +14935,7 @@ 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"