@platforma-open/milaboratories.top-antibodies 4.2.2 → 4.3.1

package/dist/index.js

@@ -13809,6 +13809,21 @@ 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;
 }
+/**
+* True when a column carries no readable value. Presence is the whole signal.
+*
+* Requires the annotation. Requires axes that are a subset of the anchor's. Axis identity
+* is name, type, domain and context-domain. An axis that differs in any of them is a
+* different axis. A column that carries one is not presence-only.
+*
+* `matchAxisId` accepts an extra domain key on the column axis. This check does not.
+* A column reached through a linker keeps its own axes and reads as not presence-only.
+*/
+function isPresenceOnlyColumn(spec, anchorSpec) {
+	if (spec.annotations?.[Annotation.IsSubset] !== "true") return false;
+	const anchorAxes = new Set(anchorSpec.axesSpec.map(canonicalizeAxisId));
+	return spec.axesSpec.every((axis) => anchorAxes.has(canonicalizeAxisId(axis)));
+}
 /** JS post-filter for the residual predicates that {@link discoveryExcludeSelectors}
 *  can't express host-side: File value type (`File` is not a matchable `ValueType`)
 *  and columns produced by a lead-selection block (last-trace-step check on parsed
@@ -13817,6 +13832,17 @@ function isSelectableMatch(c) {
 	return !isProducedByLeadSelection(c.getSpec());
 }
 /**
+* Whether the ranking options include a discovered column.
+*
+* Presence-only columns carry nothing to order by. A column the saved ranking names stays
+* in the options. Dropping the last one resets the list to preset defaults.
+*/
+function isRankableMatch(c, anchorSpec, rankedColumnIds) {
+	if (!isSelectableMatch(c)) return false;
+	if (rankedColumnIds.has(extractPObjectId(c.id))) return true;
+	return !isPresenceOnlyColumn(c.getSpec(), anchorSpec);
+}
+/**
 * Collapses discovery results to one recipe per storage column, first hit wins.
 *
 * Restores the pre-migration shape of a discovery result. The old
@@ -14445,14 +14471,14 @@ 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) => ({
@@ -14466,32 +14492,38 @@ 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,
@@ -14566,14 +14598,18 @@ const platforma$1 = BlockModelV3.create({
 	}).getColumns()).filter(isSelectableMatch);
 	const labels = deriveDistinctLabels(filterableMatches.map((c) => c.getSpec()), { includeNativeLabel: true });
 	return {
-		options: filterableMatches.map((c, i) => ({
-			label: labels[i],
-			value: matchToColumnId(c, inputAnchor),
-			column: {
-				id: c.id,
-				spec: c.getSpec()
-			}
-		})),
+		options: filterableMatches.map((c, i) => {
+			const spec = c.getSpec();
+			return {
+				label: labels[i],
+				value: matchToColumnId(c, inputAnchor),
+				column: {
+					id: c.id,
+					spec
+				},
+				presenceOnly: isPresenceOnlyColumn(spec, result.anchorSpec)
+			};
+		}),
 		defaults: result.meta.defaultFilters,
 		inVivoDefaults: result.meta.inVivoDefaults.filters,
 		inVitroDefaults: result.meta.inVitroDefaults.filters,
@@ -14583,10 +14619,11 @@ const platforma$1 = BlockModelV3.create({
 	const inputAnchor = getInputAnchorRef(ctx.data);
 	const result = buildCollection(inputAnchor);
 	if (!result) return void 0;
+	const rankedColumnIds = new Set(ctx.data.rankingOrder.flatMap((r) => r.value ? [r.value.column] : []));
 	const rankableMatches = dedupByLeafId(result.collection.discover({
 		anchors: { main: result.anchorSpec },
 		exclude: [...discoveryExcludeSelectors(result.sampleAxisName), { type: "String" }]
-	}).getColumns()).filter(isSelectableMatch);
+	}).getColumns()).filter((c) => isRankableMatch(c, result.anchorSpec, rankedColumnIds));
 	const labels = deriveDistinctLabels(rankableMatches.map((c) => c.getSpec()), { includeNativeLabel: true });
 	return {
 		options: rankableMatches.map((c, i) => ({
@@ -14775,13 +14812,14 @@ 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
 	}));