@platforma-open/milaboratories.humanization-score.model 0.2.0 → 0.3.0

package/.turbo/turbo-build.log

@@ -1,18 +1,18 @@
  WARN  Issue while reading "/home/runner/work/humanization-score/humanization-score/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.humanization-score.model@0.2.0 build /home/runner/work/humanization-score/humanization-score/model
+> @platforma-open/milaboratories.humanization-score.model@0.3.0 build /home/runner/work/humanization-score/humanization-score/model
 > ts-builder build --target block-model && block-tools build-model
 
 Building block-model project...
 ↳ cli.mjs -c /home/runner/work/humanization-score/humanization-score/node_modules/.pnpm/@milaboratories+ts-builder@1.5.0_@types+node@24.5.2_rollup@4.55.1_vue@3.5.26_typescript@5.6.3__yaml@2.8.2/node_modules/@milaboratories/ts-builder/dist/configs/rolldown.block-model.config.js
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+[log] <DIR>/index.d.ts.map  asset │ size:  0.40 kB
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+[log] <DIR>/bundle.js      chunk │ size: 363.08 kB
 [log]
-[success] rolldown v1.0.0-rc.18 Finished in 2.02 s
+[success] rolldown v1.0.0-rc.18 Finished in 3.04 s
 Build completed successfully

package/.turbo/turbo-lint.log

@@ -1,5 +1,5 @@
  WARN  Issue while reading "/home/runner/work/humanization-score/humanization-score/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.humanization-score.model@0.2.0 lint /home/runner/work/humanization-score/humanization-score/model
+> @platforma-open/milaboratories.humanization-score.model@0.3.0 lint /home/runner/work/humanization-score/humanization-score/model
 > eslint .
 

package/.turbo/turbo-type-check.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/humanization-score/humanization-score/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.humanization-score.model@0.2.0 type-check /home/runner/work/humanization-score/humanization-score/model
+> @platforma-open/milaboratories.humanization-score.model@0.3.0 type-check /home/runner/work/humanization-score/humanization-score/model
 > ts-builder type-check --target block-model
 
 ↳ tsc --noEmit --project ./tsconfig.json --customConditions ,

package/CHANGELOG.md

@@ -1,5 +1,22 @@
 # @platforma-open/milaboratories.humanization-score.model
 
+## 0.3.0
+
+### Minor Changes
+
+- 5c4b4f0: Initial release of the Humanization Score block.
+
+  Scores antibody sequences for humanness relative to natural human antibody
+  repertoires using the offline OASis/SwissProt databases bundled with the
+  `promb` Python runtime environment.
+
+  - **workflow**: Tengo templates that run per-clonotype humanness scoring over
+    the input dataset.
+  - **software**: Python scoring scripts (Parquet in/out) wrapping `promb`.
+  - **model**: block configuration, inputs/outputs, and result columns.
+  - **ui**: results UI with humanness score table, histogram, and sample boxplot
+    pages.
+
 ## 0.2.0
 
 Initial release.

package/dist/bundle.js

@@ -4960,6 +4960,9 @@
 			Sequence: "pl7.app/vdj/sequence"
 		}
 	};
+	function isLabelColumn(column) {
+		return column.axesSpec.length === 1 && column.name === PColumnName.Label;
+	}
 	/** Get column id and spec from a column */
 	function getColumnIdAndSpec(column) {
 		return {
@@ -8196,6 +8199,198 @@
 		}
 	};
 	//#endregion
+	//#region ../node_modules/.pnpm/@platforma-sdk+model@1.77.15/node_modules/@platforma-sdk/model/dist/pframe_utils/axes.js
+	/** Create id for column copy with added keys in axes domains */
+	const colId = (id, domains, contextDomains) => {
+		let wid = id.toString();
+		domains?.forEach((domain) => {
+			if (domain) for (const [k, v] of Object.entries(domain)) {
+				wid += k;
+				wid += v;
+			}
+		});
+		contextDomains?.forEach((contextDomain) => {
+			if (contextDomain) for (const [k, v] of Object.entries(contextDomain)) {
+				wid += k;
+				wid += v;
+			}
+		});
+		return wid;
+	};
+	/** All combinations with 1 key from each list */
+	function getKeysCombinations(idsLists) {
+		if (!idsLists.length) return [];
+		let result = [[]];
+		idsLists.forEach((list) => {
+			const nextResult = [];
+			list.forEach((key) => {
+				nextResult.push(...result.map((resultItem) => [...resultItem, key]));
+			});
+			result = nextResult;
+		});
+		return result;
+	}
+	function getAvailableWithLinkersAxes(linkerColumns, blockAxes) {
+		const availableAxes = LinkerMap.fromColumns(linkerColumns.map(getColumnIdAndSpec)).getReachableByLinkersAxesFromAxesNormalized([...blockAxes.values()], (linkerKeyId, sourceAxisId) => matchAxisId(sourceAxisId, linkerKeyId));
+		return new Map(availableAxes.map((axisSpec) => {
+			return [canonicalizeJson(getAxisId(axisSpec)), axisSpec];
+		}));
+	}
+	/** Add columns with fully compatible axes created from partial compatible ones */
+	function enrichCompatible(blockAxes, columns) {
+		return columns.flatMap((column) => getAdditionalColumnsForColumn(blockAxes, column));
+	}
+	function getAdditionalColumnsForColumn(blockAxes, column) {
+		const columnAxesIds = column.spec.axesSpec.map(getAxisId);
+		if (columnAxesIds.every((id) => blockAxes.has(canonicalizeJson(id)))) return [column];
+		const secondaryIdsVariants = getKeysCombinations(columnAxesIds.map((id) => {
+			const result = [];
+			for (const [_, mainId] of blockAxes) if (matchAxisId(mainId, id) && !matchAxisId(id, mainId)) result.push(mainId);
+			return result;
+		}));
+		const allAddedDomainValues = /* @__PURE__ */ new Set();
+		const addedNotToAllVariantsDomainValues = /* @__PURE__ */ new Set();
+		const addedByVariantsDomainValues = secondaryIdsVariants.map((idsList) => {
+			const addedSet = /* @__PURE__ */ new Set();
+			idsList.map((axisId, idx) => {
+				const d1 = column.spec.axesSpec[idx].domain;
+				const d2 = axisId.domain;
+				Object.entries(d2 ?? {}).forEach(([key, value]) => {
+					if (d1?.[key] === void 0) {
+						const item = JSON.stringify([key, value]);
+						addedSet.add(item);
+						allAddedDomainValues.add(item);
+					}
+				});
+				const cd1 = column.spec.axesSpec[idx].contextDomain;
+				const cd2 = axisId.contextDomain;
+				Object.entries(cd2 ?? {}).forEach(([key, value]) => {
+					if (cd1?.[key] === void 0) {
+						const item = JSON.stringify(["ctx:" + key, value]);
+						addedSet.add(item);
+						allAddedDomainValues.add(item);
+					}
+				});
+				return {
+					...axisId,
+					annotations: column.spec.axesSpec[idx].annotations
+				};
+			});
+			return addedSet;
+		});
+		[...allAddedDomainValues].forEach((addedPart) => {
+			if (addedByVariantsDomainValues.some((s) => !s.has(addedPart))) addedNotToAllVariantsDomainValues.add(addedPart);
+		});
+		return [column, ...secondaryIdsVariants.map((idsList, idx) => {
+			const id = colId(column.id, idsList.map((id) => id.domain), idsList.map((id) => id.contextDomain));
+			const label = readAnnotation(column.spec, Annotation.Label) ?? "";
+			const labelDomainPart = [...addedByVariantsDomainValues[idx]].filter((str) => addedNotToAllVariantsDomainValues.has(str)).sort().map((v) => JSON.parse(v)?.[1]).join(" / ");
+			const annotations = {
+				...column.spec.annotations,
+				[Annotation.Graph.IsVirtual]: stringifyJson(true)
+			};
+			if (label || labelDomainPart) annotations[Annotation.Label] = label && labelDomainPart ? label + " / " + labelDomainPart : label + labelDomainPart;
+			return {
+				...column,
+				id,
+				spec: {
+					...column.spec,
+					axesSpec: idsList.map((axisId, idx) => ({
+						...axisId,
+						annotations: column.spec.axesSpec[idx].annotations
+					})),
+					annotations
+				}
+			};
+		})];
+	}
+	//#endregion
+	//#region ../node_modules/.pnpm/@platforma-sdk+model@1.77.15/node_modules/@platforma-sdk/model/dist/pframe_utils/columns.js
+	function getAllRelatedColumns(ctx, predicate) {
+		const columns = new PColumnCollection();
+		columns.addColumnProvider(ctx.resultPool);
+		const allColumns = columns.getColumns(predicate, {
+			dontWaitAllData: true,
+			overrideLabelAnnotation: false
+		}) ?? [];
+		return enrichCompatible(new Map(allColumns.flatMap((column) => getNormalizedAxesList(column.spec.axesSpec)).map((axisSpec) => {
+			return [canonicalizeJson(getAxisId(axisSpec)), axisSpec];
+		})), allColumns);
+	}
+	function getRelatedColumns(ctx, { columns: rootColumns, predicate }) {
+		const columns = new PColumnCollection();
+		columns.addColumnProvider(ctx.resultPool);
+		columns.addColumns(rootColumns);
+		const blockAxes = /* @__PURE__ */ new Map();
+		const allAxes = /* @__PURE__ */ new Map();
+		for (const c of rootColumns) for (const spec of getNormalizedAxesList(c.spec.axesSpec)) {
+			const aid = getAxisId(spec);
+			blockAxes.set(canonicalizeJson(aid), spec);
+			allAxes.set(canonicalizeJson(aid), spec);
+		}
+		const availableWithLinkersAxes = getAvailableWithLinkersAxes(columns.getColumns((spec) => predicate(spec) && isLinkerColumn(spec), { dontWaitAllData: true }) ?? [], blockAxes);
+		for (const item of availableWithLinkersAxes) {
+			blockAxes.set(...item);
+			allAxes.set(...item);
+		}
+		const blockAxesArr = Array.from(blockAxes.values());
+		let compatibleWithoutLabels = (columns.getColumns((spec) => predicate(spec) && spec.axesSpec.some((axisSpec) => {
+			const axisId = getAxisId(axisSpec);
+			return blockAxesArr.some((selectorAxisSpec) => matchAxisId(getAxisId(selectorAxisSpec), axisId));
+		}), {
+			dontWaitAllData: true,
+			overrideLabelAnnotation: false
+		}) ?? []).filter((column) => !isLabelColumn(column.spec));
+		for (const c of compatibleWithoutLabels) for (const spec of getNormalizedAxesList(c.spec.axesSpec)) {
+			const aid = getAxisId(spec);
+			allAxes.set(canonicalizeJson(aid), spec);
+		}
+		const allAxesArr = Array.from(allAxes.values());
+		compatibleWithoutLabels = (columns.getColumns((spec) => predicate(spec) && spec.axesSpec.every((axisSpec) => {
+			const axisId = getAxisId(axisSpec);
+			return allAxesArr.some((selectorAxisSpec) => matchAxisId(getAxisId(selectorAxisSpec), axisId));
+		}), {
+			dontWaitAllData: true,
+			overrideLabelAnnotation: false
+		}) ?? []).filter((column) => !isLabelColumn(column.spec));
+		const compatibleLabels = (columns.getColumns((spec) => predicate(spec) && spec.axesSpec.some((axisSpec) => {
+			const axisId = getAxisId(axisSpec);
+			return allAxesArr.some((selectorAxisSpec) => matchAxisId(getAxisId(selectorAxisSpec), axisId));
+		}), {
+			dontWaitAllData: true,
+			overrideLabelAnnotation: false
+		}) ?? []).filter((column) => isLabelColumn(column.spec));
+		return enrichCompatible(blockAxes, [...compatibleWithoutLabels, ...compatibleLabels]);
+	}
+	//#endregion
+	//#region ../node_modules/.pnpm/@platforma-sdk+model@1.77.15/node_modules/@platforma-sdk/model/dist/components/PFrameForGraphs.js
+	function isHiddenFromGraphColumn(column) {
+		return !!readAnnotationJson(column, Annotation.HideDataFromGraphs);
+	}
+	function isHiddenFromUIColumn(column) {
+		return !!readAnnotationJson(column, Annotation.HideDataFromUi);
+	}
+	/**
+	The aim of createPFrameForGraphs: to create pframe with block’s columns and all compatible columns from result pool
+	(including linker columns and all label columns).
+	Block’s columns are added to pframe as is.
+	Other columns are added basing on set of axes of block’s columns, considering available with linker columns.
+	Compatible columns must have at least one axis from block’s axes set. This axis of the compatible column from
+	result pool must satisfy matchAxisId (it can have less domain keys than in block’s axis, but without conflicting values
+	among existing ones).
+	In requests to pframe (calculateTableData) columns must have strictly the same axes. For compatibility in case
+	of partially matched axis we add to pframe a copy of this column with modified axis (with filled missed domains)
+	and modified label (with added domain values in case if more than one copy with different domains exist).
+	*/
+	function createPFrameForGraphs(ctx, blockColumns) {
+		const suitableSpec = (spec) => !isHiddenFromUIColumn(spec) && !isHiddenFromGraphColumn(spec);
+		if (!blockColumns) return ctx.createPFrame(getAllRelatedColumns(ctx, suitableSpec));
+		return ctx.createPFrame(getRelatedColumns(ctx, {
+			columns: blockColumns,
+			predicate: suitableSpec
+		}));
+	}
+	//#endregion
 	//#region ../node_modules/.pnpm/@platforma-sdk+model@1.77.15/node_modules/@platforma-sdk/model/dist/columns/column_selector.js
 	function normalizeStringMatchers(input) {
 		if (typeof input === "string") return [{
@@ -10170,29 +10365,45 @@
 	});
 	//#endregion
 	//#region src/index.ts
+	const HUMANNESS_SCORE_COLUMN = "pl7.app/humannessScore";
+	const defaultGraphStateHistogram = () => ({
+		title: "Humanness Score Distribution",
+		template: "bins",
+		currentTab: null,
+		axesSettings: { other: { binsCount: 20 } }
+	});
+	const defaultGraphStateBoxplot = () => ({
+		title: "Humanness by Sample",
+		template: "box",
+		currentTab: null
+	});
+	const inputSelectors = [{
+		axes: [{ name: "pl7.app/sampleId" }, { name: "pl7.app/vdj/clonotypeKey" }],
+		annotations: { "pl7.app/isAnchor": "true" }
+	}, {
+		axes: [{ name: "pl7.app/sampleId" }, { name: "pl7.app/vdj/scClonotypeKey" }],
+		annotations: { "pl7.app/isAnchor": "true" }
+	}];
 	const dataModel = new DataModelBuilder().from("v1").upgradeLegacy(({ args, uiState }) => ({
 		...args,
-		tableState: uiState.tableState
+		tableState: uiState.tableState,
+		graphStateHistogram: uiState.graphStateHistogram ?? defaultGraphStateHistogram(),
+		graphStateBoxplot: uiState.graphStateBoxplot ?? defaultGraphStateBoxplot()
 	})).init(() => ({
 		customBlockLabel: "",
-		tableState: createPlDataTableStateV2()
+		tableState: createPlDataTableStateV2(),
+		graphStateHistogram: defaultGraphStateHistogram(),
+		graphStateBoxplot: defaultGraphStateBoxplot()
 	}));
-	//#endregion
-	exports.platforma = BlockModelV3.create(dataModel).args((data) => {
+	const platforma$1 = BlockModelV3.create(dataModel).args((data) => {
 		if (!data.inputAnchor) throw new Error("Input anchor is required");
 		return {
-			customBlockLabel: data.customBlockLabel || "Humanness Score",
+			customBlockLabel: data.customBlockLabel || "",
 			inputAnchor: data.inputAnchor,
 			mem: data.mem
 		};
-	}).output("inputOptions", (ctx) => ctx.resultPool.getOptions([{
-		axes: [{ name: "pl7.app/sampleId" }, { name: "pl7.app/vdj/clonotypeKey" }],
-		annotations: { "pl7.app/isAnchor": "true" }
-	}, {
-		axes: [{ name: "pl7.app/sampleId" }, { name: "pl7.app/vdj/scClonotypeKey" }],
-		annotations: { "pl7.app/isAnchor": "true" }
-	}])).outputWithStatus("pt", (ctx) => {
-		const pCols = ctx.outputs?.resolve("outputLiabilities")?.getPColumns();
+	}).output("inputOptions", (ctx) => ctx.resultPool.getOptions(inputSelectors)).outputWithStatus("pt", (ctx) => {
+		const pCols = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
 		if (pCols === void 0) return;
 		return createPlDataTableV3(ctx, {
 			tableState: ctx.data.tableState,
@@ -10201,11 +10412,85 @@
 				isPrimary: true
 			}))
 		});
-	}).output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false).title(() => "Humanness Score").subtitle((ctx) => ctx.data.customBlockLabel || "Humanness Score").sections((_) => [{
-		type: "link",
-		href: "/",
-		label: "Table"
-	}]).done();
+	}).outputWithStatus("histogramPf", (ctx) => {
+		const pCols = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
+		if (pCols === void 0) return void 0;
+		return createPFrameForGraphs(ctx, pCols);
+	}).output("histogramPfPcols", (ctx) => {
+		const pCols = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
+		if (pCols === void 0 || pCols.length === 0) return void 0;
+		return pCols.map((c) => ({
+			columnId: c.id,
+			spec: c.spec
+		}));
+	}).outputWithStatus("perSamplePf", (ctx) => {
+		const humanness = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
+		if (humanness === void 0) return void 0;
+		const ref = ctx.data.inputAnchor;
+		if (ref === void 0) return void 0;
+		const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{
+			axes: [{
+				anchor: "main",
+				idx: 0
+			}, {
+				anchor: "main",
+				idx: 1
+			}],
+			annotations: {
+				"pl7.app/isAbundance": "true",
+				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": "true"
+			}
+		}]);
+		return createPFrameForGraphs(ctx, [...humanness, ...abundance ?? []]);
+	}).output("perSamplePfPcols", (ctx) => {
+		const humanness = ctx.outputs?.resolve("outputHumanness")?.getPColumns();
+		if (humanness === void 0 || humanness.length === 0) return void 0;
+		const ref = ctx.data.inputAnchor;
+		if (ref === void 0) return void 0;
+		const abundance = ctx.resultPool.getAnchoredPColumns({ main: ref }, [{
+			axes: [{
+				anchor: "main",
+				idx: 0
+			}, {
+				anchor: "main",
+				idx: 1
+			}],
+			annotations: {
+				"pl7.app/isAbundance": "true",
+				"pl7.app/abundance/normalized": "false",
+				"pl7.app/abundance/isPrimary": "true"
+			}
+		}]);
+		return [...humanness, ...abundance ?? []].map((c) => ({
+			columnId: c.id,
+			spec: c.spec
+		}));
+	}).output("isRunning", (ctx) => ctx.outputs?.getIsReadyOrError() === false).title(() => "Humanization Score").subtitle((ctx) => {
+		if (ctx.data.customBlockLabel) return ctx.data.customBlockLabel;
+		return "Humanization Score";
+	}).sections((_) => [
+		{
+			type: "link",
+			href: "/",
+			label: "Table"
+		},
+		{
+			type: "link",
+			href: "/histogram",
+			label: "Score Distribution"
+		},
+		{
+			type: "link",
+			href: "/by-sample",
+			label: "By Sample"
+		}
+	]).done();
+	//#endregion
+	exports.HUMANNESS_SCORE_COLUMN = HUMANNESS_SCORE_COLUMN;
+	exports.defaultGraphStateBoxplot = defaultGraphStateBoxplot;
+	exports.defaultGraphStateHistogram = defaultGraphStateHistogram;
+	exports.platforma = platforma$1;
 });
 
 //# sourceMappingURL=bundle.js.map