wip (pl error)

platforma-open · Sep 1, 2024 · 3b60d12 · 3b60d12
1 parent 05f5d6a
commit 3b60d12
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Showing 14 changed files with 469 additions and 226 deletions.
diff --git a/model/src/helpers.ts b/model/src/helpers.ts
@@ -4,6 +4,7 @@
 
 import { z } from 'zod';
 import { base32Encode } from './base32-encode';
+import { PValueInt, TreeNodeAccessor } from '@milaboratory/sdk-ui';
 
 /** Number of raw bytes in the PlId. */
 export const PlIdBytes = 15;
@@ -33,3 +34,66 @@ export async function digestPlId(data: string): Promise<PlId> {
   const bytes = await crypto.subtle.digest('SHA-256', encoder.encode(data));
   return plId(new Uint8Array(bytes.slice(0, 15)));
 }
+
+export const ResourceMapResourceTypeName = 'PColumnData/ResourceMap';
+export const ResourceMapResourcePartitionedTypeName = 'PColumnData/Partitioned/ResourceMap';
+
+export type PColumnKey = (string | number)[];
+
+export type PColumnResourceMapEntry<T> = {
+  key: PColumnKey;
+  value: T;
+};
+
+export type PColumnResourceMapData<T> = {
+  isComplete: boolean;
+  data: PColumnResourceMapEntry<T>[];
+};
+
+function populateResourceMapData<T>(
+  acc: TreeNodeAccessor | undefined,
+  resourceParser: (acc: TreeNodeAccessor) => T | undefined,
+  data: PColumnResourceMapEntry<T>[],
+  keyPrefix: PColumnKey = []
+): boolean {
+  if (acc === undefined) return false;
+  switch (acc.resourceType.name) {
+    case ResourceMapResourceTypeName: {
+      let isComplete = acc.getInputsLocked();
+      for (const keyStr of acc.listInputFields()) {
+        const value = acc.resolve({ field: keyStr, assertFieldType: 'Input' });
+        if (value === undefined) isComplete = false;
+        else {
+          const key = [...keyPrefix, ...JSON.parse(keyStr)] as PColumnKey;
+          const converted = resourceParser(value);
+          if (converted === undefined) isComplete = false;
+          else data.push({ key, value: converted });
+        }
+      }
+      return isComplete;
+    }
+    case ResourceMapResourcePartitionedTypeName: {
+      let isComplete = acc.getInputsLocked();
+      for (const keyStr of acc.listInputFields()) {
+        const value = acc.resolve({ field: keyStr, assertFieldType: 'Input' });
+        if (value === undefined) isComplete = false;
+        else {
+          const key = [...keyPrefix, ...JSON.parse(keyStr)] as PColumnKey;
+          isComplete = isComplete && populateResourceMapData(value, resourceParser, data, key);
+        }
+      }
+      return isComplete;
+    }
+    default:
+      throw new Error(`Unknown resource type: ${acc.resourceType.name}`);
+  }
+}
+
+export function parseResourceMap<T>(
+  acc: TreeNodeAccessor | undefined,
+  resourceParser: (acc: TreeNodeAccessor) => T | undefined
+): PColumnResourceMapData<NonNullable<T>> {
+  const data: PColumnResourceMapEntry<NonNullable<T>>[] = [];
+  const isComplete = populateResourceMapData(acc, resourceParser, data, []);
+  return { isComplete, data };
+}
diff --git a/model/src/index.ts b/model/src/index.ts
@@ -6,34 +6,48 @@ import {
   type InferOutputsType
 } from '@milaboratory/sdk-ui';
 import { BlockArgs, BlockArgsValid } from './args';
+import { parseResourceMap } from './helpers';
 
 export const platforma = BlockModel.create<BlockArgs>('Heavy')
 
   .initialArgs({})
 
   .output('presets', (ctx) =>
-    ctx.precalc?.resolve({ field: 'presets', assertFieldType: 'Input' })?.getFileHandle()
+    ctx.prerun?.resolve({ field: 'presets', assertFieldType: 'Input' })?.getFileHandle()
   )
 
   .output('preset', (ctx) =>
-    ctx.precalc?.resolve({ field: 'preset', assertFieldType: 'Input' })?.getDataAsString()
+    ctx.prerun?.resolve({ field: 'preset', assertFieldType: 'Input' })?.getDataAsString()
   )
 
   .output('qc', (ctx) =>
-    ctx.outputs?.resolve({ field: 'qc', assertFieldType: 'Input' })?.getDataAsJson()
+    parseResourceMap(ctx.outputs?.resolve({ field: 'qc', assertFieldType: 'Input' }), (acc) =>
+      acc.getRemoteFileHandle()
+    )
+  )
+
+  .output('reports', (ctx) =>
+    parseResourceMap(ctx.outputs?.resolve({ field: 'reports', assertFieldType: 'Input' }), (acc) =>
+      acc.getRemoteFileHandle()
+    )
+  )
+
+  .output('clones', (ctx) =>
+    parseResourceMap(ctx.outputs?.resolve({ field: 'clones', assertFieldType: 'Input' }), (acc) =>
+      acc.listInputFields()
+    )
   )
 
   .output('inputOptions', (ctx) => {
-    const spectFromPool = ctx.resultPool
-      .getSpecsFromResultPool();
+    const spectFromPool = ctx.resultPool.getSpecsFromResultPool();
     return ctx.resultPool
       .getSpecsFromResultPool()
       .entries.filter((v) => {
         if (!isPColumnSpec(v.obj)) return false;
         const domain = v.obj.domain;
         return (
           v.obj.name === 'pl7.app/sequencing/data' &&
-          ((v.obj.valueType as string) === 'blob' || (v.obj.valueType as string) === 'file') &&
+          (v.obj.valueType as string) === 'File' &&
           domain !== undefined &&
           (domain['pl7.app/fileExtension'] === 'fastq' ||
             domain['pl7.app/fileExtension'] === 'fastq.gz')

diff --git a/package.json b/package.json
@@ -54,11 +54,16 @@
         "@milaboratory/tengo-sdk": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/tengo-sdk/milaboratory-tengo-sdk-1.0.14.tgz",
         "@milaboratory/tengo-template-builder": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/tengo-template-builder"
       }
+    },
+    "pnpm2": {
+      "overrides": {
+        "@milaboratory/tengo-sdk": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/tengo-sdk",
+        "@milaboratory/pl-middle-layer": "file:/Volumes/Data/Projects/MiLaboratory/platforma/ts-pl-middle-layer",
+        "@milaboratory/sdk-ui": "file:/Volumes/Data/Projects/MiLaboratory/platforma/ts-sdk-ui"
+      }
     }
   },
   "pnpm": {
-    "overrides": {
-      "@milaboratory/tengo-sdk": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/tengo-sdk"
-    }
+    "overrides": {}
   }
 }