@platforma-open/milaboratories.antibody-variant-designer.block 1.0.0 → 1.1.0

package/dist/index.js

@@ -12727,55 +12727,68 @@ const ErrorShape = objectType({
 });
 //#endregion
 //#region ../model/dist/index.js
-const dataModel = new DataModelBuilder().from("v1").init(() => ({
-	dataset: void 0,
+/** Every scalar `BlockData` field's default value, in one place: `.init()`
+*  seeds a new project from it, `.args()` falls back to it for a project
+*  persisted before a field existed, and the settings panel shows it in the
+*  field the operator has not touched. */
+const BLOCK_DATA_DEFAULTS = {
+	runMode: "liabilities",
 	rsasaBuriedCutoff: .075,
 	actOnFixability: ["fixable", "easily_fixable"],
-	maxEditsPerVariant: 5,
-	frConfThresh: 4,
-	cdrConfThresh: 6,
-	variantsPerParent: 10,
+	maxLiabilityEdits: 10,
+	maxFrameworkEdits: 20,
+	frConfidenceThreshold: 4,
+	cdrConfidenceThreshold: 6,
+	variantsPerParent: 100,
 	candidateResiduesPerPosition: 3,
+	structuralWeight: 1,
+	objectiveWeight: 1,
+	nonHumanPriorMargin: .05,
+	maxNewLiabilities: 0,
+	humanizationIgnoredLiabilities: [],
 	lowToleranceFloor: 3,
-	epistasisRescoreTopK: 20,
+	epistasisRescoreTopK: 20
+};
+const dataModel = new DataModelBuilder().from("v1").init(() => ({
+	dataset: void 0,
+	...BLOCK_DATA_DEFAULTS,
 	variantsTableState: createPlDataTableStateV2(),
-	liabilitiesTableState: createPlDataTableStateV2()
+	liabilitiesTableState: createPlDataTableStateV2(),
+	alignmentModel: {}
 }));
 const STRUCTURE_PDB_COLUMN = "pl7.app/structure/pdb";
 const LEAD_SELECTION_COLUMN = "pl7.app/lead-selection";
 function isStructuresDataset(spec) {
 	return spec.kind === "PColumn" && spec.name === STRUCTURE_PDB_COLUMN && spec.annotations?.["pl7.app/isAnchor"] === "true";
 }
-/** One step's skip TSV: `clonotypeKey \t reason \t detail`, header row
-*  first, reason and detail empty when that clonotype passed. Absent and
-*  empty are equivalent to the reduce below, so only non-empty-reason rows
-*  are kept. */
-function parseSkipRows(tsv) {
+const DEFAULT_REJECTION_OBJECTIVE = "liability";
+function parseRejectionRows(tsv) {
 	const rows = /* @__PURE__ */ new Map();
 	for (const line of tsv.split("\n").slice(1)) {
 		if (line.length === 0) continue;
-		const [clonotypeKey, reason, detail] = line.split("	");
-		if (reason) rows.set(clonotypeKey, {
+		const [clonotypeKey, reason, detail, rejectedType, objective] = line.split("	");
+		if (reason) rows.set(`${clonotypeKey}\t${objective || DEFAULT_REJECTION_OBJECTIVE}`, {
 			reason,
-			detail: detail ?? ""
+			detail: detail ?? "",
+			rejectedType: rejectedType || "parent",
+			objective: objective || DEFAULT_REJECTION_OBJECTIVE
 		});
 	}
 	return rows;
 }
-/** Per clonotype, the first non-empty reason (and its detail) in step
-*  order: index-and-scan, then read-tolerance, then build-variants. A
-*  clonotype named in more than one file is kept once, at its earliest
-*  step. */
-function reduceSkips(stepSkipTsvs) {
-	const byClonotype = /* @__PURE__ */ new Map();
-	for (const tsv of stepSkipTsvs) for (const [clonotypeKey, row] of parseSkipRows(tsv)) if (!byClonotype.has(clonotypeKey)) byClonotype.set(clonotypeKey, row);
-	return byClonotype;
-}
-function reduceSkippedClonotypes(stepSkipTsvs) {
-	return [...reduceSkips(stepSkipTsvs)].map(([clonotypeKey, { reason, detail }]) => ({
-		clonotypeKey,
-		reason,
-		detail
+/** Per (clonotype, objective) pair, the first non-empty reason (and its detail) in step
+*  order: index-and-scan, then read-tolerance, then build-variants. A pair named in more than
+*  one file is kept once, at its earliest step — a parent named by two objectives keeps both
+*  rows, and one named twice by the same objective keeps only its earliest. */
+function reduceRejections(stepRejectionTsvs) {
+	const byPair = /* @__PURE__ */ new Map();
+	for (const tsv of stepRejectionTsvs) for (const [pairKey, row] of parseRejectionRows(tsv)) if (!byPair.has(pairKey)) byPair.set(pairKey, row);
+	return byPair;
+}
+function reduceRejectedClonotypes(stepRejectionTsvs) {
+	return [...reduceRejections(stepRejectionTsvs)].map(([pairKey, row]) => ({
+		clonotypeKey: pairKey.slice(0, pairKey.lastIndexOf("	")),
+		...row
 	}));
 }
 function tableFromAccessorOutput(ctx, outputName, tableState) {
@@ -12784,31 +12797,47 @@ function tableFromAccessorOutput(ctx, outputName, tableState) {
 	const provider = AccessorColumnsProvider(acc);
 	const snapshots = provider.getColumns();
 	if (snapshots.length === 0) return void 0;
-	const anchorSpec = (snapshots.find((s) => s.getSpec().name !== "pl7.app/label") ?? snapshots[0]).getSpec();
+	const anchorSpec = (snapshots.find((s) => s.getSpec().name !== "pl7.app/label" && s.getSpec().annotations?.["pl7.app/isLinkerColumn"] !== "true") ?? snapshots[0]).getSpec();
 	return createPlDataTableV3(ctx, {
 		columns: {
 			sources: [provider],
 			anchors: { main: anchorSpec },
 			selector: {
 				mode: "enrichment",
-				maxHops: 0
+				maxHops: 1
 			}
 		},
 		tableState
 	});
 }
+/** The alignment group's PColumns, or undefined when the result was computed by
+*  a build that did not yet write this output. */
+function alignmentColumns(ctx) {
+	return ctx.outputs?.resolve({
+		field: "alignmentData",
+		assertFieldType: "Input",
+		allowPermanentAbsence: true
+	})?.getPColumns();
+}
 const platforma$1 = BlockModelV3.create(dataModel).args((data) => {
 	if (!data.dataset?.primary?.column) throw new Error("Pick a 3D structures dataset");
 	return {
 		primaryRef: data.dataset.primary,
 		subsetRef: data.dataset.primary.filter,
+		runMode: data.runMode ?? BLOCK_DATA_DEFAULTS.runMode,
 		rsasaBuriedCutoff: data.rsasaBuriedCutoff,
 		actOnFixability: [...new Set(data.actOnFixability)].sort(),
-		maxEditsPerVariant: data.maxEditsPerVariant,
-		frConfThresh: data.frConfThresh,
-		cdrConfThresh: data.cdrConfThresh,
+		maxLiabilityEdits: data.maxLiabilityEdits ?? data.maxEditsPerVariant ?? BLOCK_DATA_DEFAULTS.maxLiabilityEdits,
+		maxFrameworkEdits: data.maxFrameworkEdits ?? BLOCK_DATA_DEFAULTS.maxFrameworkEdits,
+		frConfidenceThreshold: data.frConfidenceThreshold ?? data.frConfThresh ?? BLOCK_DATA_DEFAULTS.frConfidenceThreshold,
+		cdrConfidenceThreshold: data.cdrConfidenceThreshold ?? data.cdrConfThresh ?? BLOCK_DATA_DEFAULTS.cdrConfidenceThreshold,
 		variantsPerParent: data.variantsPerParent,
 		candidateResiduesPerPosition: data.candidateResiduesPerPosition,
+		structuralWeight: data.structuralWeight ?? data.wStruct ?? BLOCK_DATA_DEFAULTS.structuralWeight,
+		objectiveWeight: data.objectiveWeight ?? data.wObj ?? BLOCK_DATA_DEFAULTS.objectiveWeight,
+		nonHumanPriorMargin: data.nonHumanPriorMargin ?? BLOCK_DATA_DEFAULTS.nonHumanPriorMargin,
+		maxNewLiabilities: data.maxNewLiabilities ?? BLOCK_DATA_DEFAULTS.maxNewLiabilities,
+		humanizationIgnoredLiabilities: [...new Set(data.humanizationIgnoredLiabilities ?? BLOCK_DATA_DEFAULTS.humanizationIgnoredLiabilities)].sort(),
 		lowToleranceFloor: data.lowToleranceFloor,
 		epistasisRescoreTopK: data.epistasisRescoreTopK,
 		indexAndScanCpu: data.indexAndScanCpu,
@@ -12837,15 +12866,20 @@ const platforma$1 = BlockModelV3.create(dataModel).args((data) => {
 		case "stale-selection": return "The selected structures dataset is no longer available. Pick it again, or add a 3D Structure Prediction block upstream.";
 		default: return cause;
 	}
-}).outputWithStatus("variantsTable", (ctx) => tableFromAccessorOutput(ctx, "variantsData", ctx.data.variantsTableState)).outputWithStatus("liabilitiesTable", (ctx) => tableFromAccessorOutput(ctx, "liabilitiesData", ctx.data.liabilitiesTableState)).output("synthesisCsv", (ctx) => ctx.outputs?.resolve("synthesisCsv")?.getRemoteFileHandle()).output("skippedClonotypes", (ctx) => {
-	const liabilitiesSkip = ctx.outputs?.resolve("liabilitiesSkip")?.getDataAsString();
-	const toleranceSkip = ctx.outputs?.resolve("toleranceSkip")?.getDataAsString();
-	const variantsSkip = ctx.outputs?.resolve("variantsSkip")?.getDataAsString();
-	if (liabilitiesSkip === void 0 || toleranceSkip === void 0 || variantsSkip === void 0) return;
-	return reduceSkippedClonotypes([
-		liabilitiesSkip,
-		toleranceSkip,
-		variantsSkip
+}).outputWithStatus("variantsTable", (ctx) => tableFromAccessorOutput(ctx, "variantsData", ctx.data.variantsTableState)).outputWithStatus("liabilitiesTable", (ctx) => tableFromAccessorOutput(ctx, "liabilitiesData", ctx.data.liabilitiesTableState)).output("synthesisCsv", (ctx) => ctx.outputs?.resolve("synthesisCsv")?.getRemoteFileHandle()).outputWithStatus("rejectedClonotypes", (ctx) => {
+	const rejectedTsv = (name) => ctx.outputs?.resolve({
+		field: name,
+		assertFieldType: "Input",
+		allowPermanentAbsence: true
+	})?.getDataAsString();
+	const liabilitiesRejected = rejectedTsv("liabilitiesRejected");
+	const toleranceRejected = rejectedTsv("toleranceRejected");
+	const variantsRejected = rejectedTsv("variantsRejected");
+	if (liabilitiesRejected === void 0 || toleranceRejected === void 0 || variantsRejected === void 0) return;
+	return reduceRejectedClonotypes([
+		liabilitiesRejected,
+		toleranceRejected,
+		variantsRejected
 	]);
 }).output("clonotypeLabelsPf", (ctx) => {
 	const pCols = ctx.outputs?.resolve("liabilitiesData")?.getPColumns();
@@ -12855,6 +12889,12 @@ const platforma$1 = BlockModelV3.create(dataModel).args((data) => {
 	const axis = (ctx.outputs?.resolve("liabilitiesData")?.getPColumns())?.[0]?.spec.axesSpec[0];
 	if (axis === void 0) return void 0;
 	return getAxisId(axis);
+}).output("alignmentPf", (ctx) => {
+	const pCols = alignmentColumns(ctx);
+	if (pCols === void 0 || pCols.length === 0) return void 0;
+	return ctx.createPFrame(pCols);
+}).output("alignmentAxisSpec", (ctx) => {
+	return alignmentColumns(ctx)?.[0]?.spec.axesSpec[0];
 }).sections(() => [
 	{
 		type: "link",
@@ -12868,8 +12908,8 @@ const platforma$1 = BlockModelV3.create(dataModel).args((data) => {
 	},
 	{
 		type: "link",
-		href: "/skipped",
-		label: "Skipped"
+		href: "/rejection-causes",
+		label: "Objective Findings"
 	}
 ]).done();
 //#endregion