@platforma-open/milaboratories.immune-assay-data.model 1.0.1

package/src/index.ts

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+import type {
+  ImportFileHandle,
+  InferOutputsType,
+  PlDataTableState,
+  PlRef,
+  SUniversalPColumnId,
+} from '@platforma-sdk/model';
+import {
+  BlockModel,
+  createPlDataTableV2,
+} from '@platforma-sdk/model';
+
+type Settings = {
+  coverageThreshold: number; // fraction of aligned residues required
+  coverageMode: 0 | 1 | 2 | 3 | 4 | 5; // MMseqs2 coverage modes
+};
+
+export type ImportColumnInfo = {
+  header: string;
+  type: 'Int' | 'Double' | 'String';
+  /** If this column is a sequence column, the type of the sequence */
+  sequenceType?: 'nucleotide' | 'aminoacid';
+};
+
+export type BlockArgs = {
+  datasetRef?: PlRef;
+  targetRef?: SUniversalPColumnId;
+  fileHandle?: ImportFileHandle;
+  fileExtension?: string;
+  importColumns?: ImportColumnInfo[];
+  sequenceColumnHeader?: string;
+  settings: Settings;
+};
+
+export type UiState = {
+  title: string;
+  fileImportError?: string;
+  tableState: PlDataTableState;
+};
+
+export const model = BlockModel.create()
+
+  .withArgs<BlockArgs>({
+    settings: {
+      coverageMode: 2, // default to coverage of clone,
+      coverageThreshold: 0.95, // default value matching MMseqs2 default
+    },
+  })
+
+  .withUiState<UiState>({
+    title: 'Immune Assay Data',
+    tableState: {
+      gridState: {},
+    },
+  })
+
+  .argsValid((ctx) =>
+    ctx.args.datasetRef !== undefined
+    && ctx.args.fileHandle !== undefined
+    && ctx.args.importColumns !== undefined
+    && ctx.args.sequenceColumnHeader !== undefined
+    && ctx.args.targetRef !== undefined
+    && ctx.uiState.fileImportError === undefined,
+  )
+
+  .output('datasetOptions', (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' },
+    }], { refsWithEnrichments: true }),
+  )
+
+  .output('targetOptions', (ctx) => {
+    const ref = ctx.args.datasetRef;
+    if (ref === undefined) return undefined;
+
+    const isSingleCell = ctx.resultPool.getPColumnSpecByRef(ref)?.axesSpec[1].name === 'pl7.app/vdj/scClonotypeKey';
+    const sequenceMatchers = [];
+    const allowedFeatures = ['CDR1', 'CDR2', 'CDR3', 'FR1', 'FR2',
+      'FR3', 'FR4', 'VDJRegion'];
+    for (const feature of allowedFeatures) {
+      if (isSingleCell) {
+        sequenceMatchers.push({
+          axes: [{ anchor: 'main', idx: 1 }],
+          name: 'pl7.app/vdj/sequence',
+          domain: {
+            'pl7.app/vdj/feature': feature,
+            'pl7.app/vdj/scClonotypeChain/index': 'primary',
+          },
+        });
+      } else {
+        sequenceMatchers.push({
+          axes: [{ anchor: 'main', idx: 1 }],
+          name: 'pl7.app/vdj/sequence',
+          domain: {
+            'pl7.app/vdj/feature': feature,
+          },
+        });
+      }
+    }
+
+    return ctx.resultPool.getCanonicalOptions(
+      { main: ref },
+      sequenceMatchers,
+      {
+        ignoreMissingDomains: true,
+        labelOps: {
+          includeNativeLabel: true,
+        },
+      });
+  })
+
+  .output(
+    'dataImportHandle',
+    (ctx) => ctx.outputs?.resolve('dataImportHandle')?.getImportProgress(),
+    { isActive: true },
+  )
+
+  .output('table', (ctx) => {
+    const cols = ctx.outputs?.resolve('table')?.getPColumns();
+    if (cols === undefined)
+      return undefined;
+
+    return createPlDataTableV2(
+      ctx,
+      cols,
+      (_) => true,
+      ctx.uiState.tableState,
+    );
+  })
+
+  .output('isRunning', (ctx) => ctx.outputs?.getIsReadyOrError() === false)
+
+  .title((ctx) => ctx.uiState.title)
+
+  .sections((_ctx) => ([
+    { type: 'link', href: '/', label: 'Main' },
+  ]))
+
+  .done();
+
+export type BlockOutputs = InferOutputsType<typeof model>;

package/tsconfig.json

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+{
+  "compilerOptions": {
+    "target": "es2022",
+    "module": "commonjs",
+    "moduleResolution": "node",
+    "esModuleInterop": true,
+    "strict": true,
+    "outDir": "./dist",
+    "rootDir": "./src",
+    "sourceMap": true,
+    "declaration": true
+  },
+  "types": [],
+  "include": ["src/**/*"],
+  "exclude": ["node_modules", "dist"]
+}

package/vite.config.mts

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+import { defineConfig } from 'vite';
+
+export default defineConfig({
+  build: {
+    emptyOutDir: false,
+    lib: {
+      entry: 'src/index.ts',
+      name: 'model',
+      fileName: (format) => `my-lib.${format}.js`
+    },
+    minify: false,
+    sourcemap: true,
+    rollupOptions: {
+      output: {
+        format: 'iife',
+        entryFileNames: 'bundle.js'
+      }
+    }
+  }
+});