wip

model/src/index.ts

@@ -31,28 +31,39 @@ export const platforma = BlockModel.create<BlockArgs>('Heavy')
 
   .output('qc', (ctx) =>
     parseResourceMap(ctx.outputs?.resolve({ field: 'qc', assertFieldType: 'Input' }), (acc) =>
-      acc.getRemoteFileHandle()
+      acc.getFileHandle()
     )
   )
 
   .output('reports', (ctx) =>
     parseResourceMap(ctx.outputs?.resolve({ field: 'reports', assertFieldType: 'Input' }), (acc) =>
-      acc.getRemoteFileHandle()
+      acc.getFileHandle()
     )
   )
 
   .output('logs', (ctx) => {
-    return parseResourceMap(
-      ctx.outputs?.resolve({ field: 'logs', assertFieldType: 'Input' }),
-      (acc) => acc.getLogHandle()
-    );
+    return ctx.outputs !== undefined
+      ? parseResourceMap(ctx.outputs?.resolve({ field: 'logs', assertFieldType: 'Input' }), (acc) =>
+          acc.getLogHandle()
+        )
+      : undefined;
   })
 
   .output('progress', (ctx) => {
-    return parseResourceMap(
-      ctx.outputs?.resolve({ field: 'logs', assertFieldType: 'Input' }),
-      (acc) => acc.getProgressLog(ProgressPrefix)
-    );
+    return ctx.outputs !== undefined
+      ? parseResourceMap(ctx.outputs?.resolve({ field: 'logs', assertFieldType: 'Input' }), (acc) =>
+          acc.getProgressLog(ProgressPrefix)
+        )
+      : undefined;
+  })
+
+  .output('done', (ctx) => {
+    return ctx.outputs !== undefined
+      ? parseResourceMap(
+          ctx.outputs?.resolve({ field: 'clns', assertFieldType: 'Input' }),
+          (acc) => true
+        ).data.map((e) => e.key[0] as string)
+      : undefined;
   })
 
   .output('clones', (ctx) => {
@@ -124,11 +135,19 @@ export const platforma = BlockModel.create<BlockArgs>('Heavy')
 
     // if (sampleLabelsObj.obj.data.resourceType.name !== 'PColumn/Json') return undefined;
 
-    return sampleLabelsObj.obj.data.getDataAsJson();
+    return Object.fromEntries(
+      Object.entries(sampleLabelsObj.obj.data.getDataAsJson<Record<string, string>>()).map((e) => [
+        JSON.parse(e[0])[0],
+        e[1]
+      ])
+    ) satisfies Record<string, string>;
   })
 
   .sections((ctx) => {
-    return [{ type: 'link', href: '/', label: 'Settings' }];
+    return [
+      { type: 'link', href: '/', label: 'Settings' },
+      { type: 'link', href: '/reports', label: 'Reports' }
+    ];
   })
 
   .inputsValid((ctx) => BlockArgsValid.safeParse(ctx.args).success)
@@ -139,4 +158,5 @@ export type BlockOutputs = InferOutputsType<typeof platforma>;
 export type Href = InferHrefType<typeof platforma>;
 export * from './args';
 export * from './helpers';
+export * from './logs';
 export { BlockArgs };

package.json

@@ -61,6 +61,7 @@
         "@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",
         "@milaboratory/sdk-test": "file:/Volumes/Data/Projects/MiLaboratory/platforma/ts-sdk-test",
+        "@milaboratory/sdk-vue": "file:/Volumes/Data/Projects/MiLaboratory/platforma/sdk-vue",
         "@milaboratory/milaboratories.samples-and-data.workflow": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/block-samples-and-data/workflow"
       }
     }

pnpm-workspace.yaml

@@ -10,15 +10,15 @@ catalog:
   '@milaboratory/pl-block-tools': ^2.1.5
   '@milaboratory/block-builder': ^1.2.3
 
-  '@milaboratory/sdk-ui': ^0.12.21
+  '@milaboratory/sdk-ui': ^0.12.22
   '@milaboratory/sdk-test': ^1.5.5
 
   '@milaboratory/tengo-sdk': ^1.2.1
   '@milaboratory/pframes-conv': ^0.4.25
 
-  '@milaboratory/mixcr': 4.7.0-68-develop
+  '@milaboratory/mixcr': 4.7.0-70-develop
 
-  '@milaboratory/platforma-uikit': ^1.1.2
+  '@milaboratory/platforma-uikit': ^1.1.4
   '@milaboratory/sdk-vue': ^1.1.1
   '@milaboratory/helpers': ^1.5.3
 

test/assets/expected_results/mixcr.sh

@@ -2,5 +2,7 @@
 
 set -e
 
-mixcr exportPreset --preset-name milab-human-dna-xcr-7genes-multiplex preset.json
-mixcr analyze milab-human-dna-xcr-7genes-multiplex ../small_data_R1.fastq.gz ../small_data_R2.fastq.gz result
+mixcr exportPreset --preset-name milab-human-dna-xcr-7genes-multiplex -f preset.json
+
+# --add-step assembleContigs 
+mixcr analyze milab-human-dna-xcr-7genes-multiplex -f ../small_data_R1.fastq.gz ../small_data_R2.fastq.gz result

test/src/wf.test.ts

@@ -87,7 +87,7 @@ blockTest(
       ]
     } satisfies SamplesAndDataBlockArgs);
     await project.runBlock(sndBlockId);
-    await helpers.awaitBlockDone(sndBlockId);
+    await helpers.awaitBlockDone(sndBlockId, 4000);
     const sndBlockState = project.getBlockState(sndBlockId);
     const clonotypingBlockState = project.getBlockState(clonotypingBlockId);
 
@@ -128,9 +128,9 @@ blockTest(
     )) as InferBlockState<typeof platforma>;
 
     const outputs2 = wrapOutputs<BlockOutputs>(clonotypingStableState2.outputs);
-    console.dir(outputs2.sampleLabels, { depth: 5 });
-    console.log(JSON.stringify([sample1Id]));
-    expect(outputs2.sampleLabels[JSON.stringify([sample1Id])]).toBeDefined();
+    // console.dir(outputs2.sampleLabels, { depth: 5 });
+    // console.log(JSON.stringify([sample1Id]));
+    expect(outputs2.sampleLabels[sample1Id]).toBeDefined();
 
     await project.runBlock(clonotypingBlockId);
     const clonotypingStableState3 = (await helpers.awaitBlockDoneAndGetStableBlockState(
@@ -155,7 +155,7 @@ blockTest(
       ).toString('utf8')
     );
 
-    console.dir(alignJsonReport, { depth: 5 });
+    // console.dir(alignJsonReport, { depth: 5 });
     expect(alignJsonReport.aligned).toBeDefined();
     expect(alignJsonReport.aligned).greaterThan(2);
 
@@ -165,7 +165,7 @@ blockTest(
 
     const clonesPfColumnList = await ml.driverKit.pFrameDriver.listColumns(clonesPfHandle);
 
-    console.log(clonesPfColumnList);
+    // console.log(clonesPfColumnList);
     expect(clonesPfColumnList).length.to.greaterThanOrEqual(1);
 
     // console.dir(clonotypingStableState3, { depth: 8 });