@platforma-open/milaboratories.immune-assay-data.model 1.5.1 → 1.5.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.immune-assay-data.model",
-  "version": "1.5.1",
+  "version": "1.5.3",
   "description": "Block model",
   "type": "module",
   "main": "./dist/index.js",
@@ -15,13 +15,13 @@
     "./dist/model.json": "./dist/model.json"
   },
   "dependencies": {
-    "@platforma-sdk/model": "1.51.6",
-    "@milaboratories/graph-maker": "1.1.211"
+    "@platforma-sdk/model": "1.53.3",
+    "@milaboratories/graph-maker": "1.1.216"
   },
   "devDependencies": {
-    "@milaboratories/ts-builder": "1.2.2",
+    "@milaboratories/ts-builder": "1.2.4",
     "@milaboratories/ts-configs": "1.2.0",
-    "@platforma-sdk/block-tools": "2.6.29",
+    "@platforma-sdk/block-tools": "2.6.36",
     "@platforma-sdk/eslint-config": "1.2.0",
     "eslint": "^9.25.1",
     "typescript": "~5.6.3",

package/src/index.ts

@@ -1,14 +1,23 @@
 import type {
+  DataInfo,
   ImportFileHandle,
+  PColumn,
+  PColumnSpec,
+  PColumnValues,
   PlDataTableStateV2,
+  PlMultiSequenceAlignmentModel,
   PlRef,
+  RenderCtxLegacy,
   SUniversalPColumnId,
+  TreeNodeAccessor,
 } from '@platforma-sdk/model';
 import {
   BlockModel,
+  createPFrameForGraphs,
   createPlDataTableStateV2,
   createPlDataTableV2,
 } from '@platforma-sdk/model';
+import { getDefaultBlockLabel } from './label';
 
 type Settings = {
   coverageThreshold: number; // fraction of aligned residues required
@@ -39,12 +48,47 @@ export type BlockArgs = {
 export type UiState = {
   fileImportError?: string;
   tableState: PlDataTableStateV2;
+  alignmentModel: PlMultiSequenceAlignmentModel;
 };
 
+type Column = PColumn<DataInfo<TreeNodeAccessor> | TreeNodeAccessor | PColumnValues>;
+
+type Columns = {
+  props: Column[];
+};
+
+function getColumns(ctx: RenderCtxLegacy<BlockArgs, UiState>): Columns | undefined {
+  const anchor = ctx.args.datasetRef;
+  if (anchor === undefined)
+    return undefined;
+
+  const anchorSpec = ctx.resultPool.getPColumnSpecByRef(anchor);
+  if (anchorSpec === undefined)
+    return undefined;
+
+  // all clone properties
+  const props = (ctx.resultPool.getAnchoredPColumns(
+    { main: anchor },
+    [
+      {
+        axes: [{ anchor: 'main', idx: 1 }],
+      },
+    ]) ?? [])
+    .filter((p) => p.spec.annotations?.['pl7.app/sequence/isAnnotation'] !== 'true');
+
+  return {
+    props: props,
+  };
+}
+
 export const model = BlockModel.create()
 
   .withArgs<BlockArgs>({
-    defaultBlockLabel: '',
+    defaultBlockLabel: getDefaultBlockLabel({
+      similarityType: 'alignment-score',
+      identity: 0.9,
+      coverageThreshold: 0.95,
+    }),
     customBlockLabel: '',
     settings: {
       coverageThreshold: 0.95, // default value matching MMseqs2 default
@@ -56,6 +100,7 @@ export const model = BlockModel.create()
 
   .withUiState<UiState>({
     tableState: createPlDataTableStateV2(),
+    alignmentModel: {},
   })
 
   .argsValid((ctx) =>
@@ -143,6 +188,48 @@ export const model = BlockModel.create()
     );
   })
 
+  .output('pf', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {
+      return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+      return undefined;
+
+    return createPFrameForGraphs(ctx, cols);
+  })
+
+  .output('assaySequenceSpec', (ctx): PColumnSpec | undefined => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {
+      return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+      return undefined;
+    // Return only sequence column
+    return cols.find((c) => c.spec.name === 'pl7.app/vdj/sequence'
+      && c.spec.axesSpec[0].name === 'pl7.app/vdj/assay/sequenceId')?.spec;
+  })
+
+  .output('msaPf', (ctx) => {
+    if (ctx.outputs?.resolve('emptyResults')?.getDataAsJson<boolean>()) {
+      return undefined;
+    }
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+      return undefined;
+
+    const msaCols = ctx.outputs?.resolve('assayLinkerPframe')?.getPColumns();
+    if (!msaCols) return undefined;
+
+    const columns = getColumns(ctx);
+    if (columns === undefined) {
+      return undefined;
+    }
+
+    return createPFrameForGraphs(ctx, [...msaCols, ...cols, ...columns.props]);
+  })
+
   .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)
 
   .title(() => 'Immune Assay Data')
@@ -154,3 +241,5 @@ export const model = BlockModel.create()
   ]))
 
   .done(2);
+
+export { getDefaultBlockLabel } from './label';

package/src/label.ts

@@ -0,0 +1,27 @@
+export function getDefaultBlockLabel(data: {
+  fileName?: string;
+  similarityType: 'alignment-score' | 'sequence-identity';
+  identity: number;
+  coverageThreshold: number;
+}) {
+  const parts: string[] = [];
+
+  // Add file name if available
+  if (data.fileName) {
+    parts.push(data.fileName);
+  }
+
+  // Add similarity type label
+  const similarityLabel = data.similarityType === 'alignment-score' ? 'BLOSUM' : 'Exact Match';
+  if (similarityLabel) {
+    parts.push(similarityLabel);
+  }
+
+  // Add identity threshold
+  parts.push(`ident:${data.identity}`);
+
+  // Add coverage threshold
+  parts.push(`cov:${data.coverageThreshold}`);
+
+  return parts.filter(Boolean).join(', ');
+}