wip: now tests should pass in CI

platforma-open · Sep 6, 2024 · a85c181 · a85c181
1 parent d0910f2
commit a85c181
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Showing 10 changed files with 109 additions and 123 deletions.
diff --git a/package.json b/package.json
@@ -60,13 +60,12 @@
         "@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",
-        "@milaboratory/sdk-test": "file:/Volumes/Data/Projects/MiLaboratory/platforma/ts-sdk-test"
+        "@milaboratory/sdk-test": "file:/Volumes/Data/Projects/MiLaboratory/platforma/ts-sdk-test",
+        "@milaboratory/milaboratories.samples-and-data.workflow": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/block-samples-and-data/workflow"
       }
     }
   },
   "pnpm": {
-    "overrides": {
-      "@milaboratory/milaboratories.samples-and-data.workflow": "file:/Volumes/Data/Projects/MiLaboratory/blocks-beta/block-samples-and-data/workflow"
-    }
+    "overrides": {}
   }
 }
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml
@@ -13,14 +13,17 @@ catalog:
   '@milaboratory/sdk-ui': ^0.12.21
   '@milaboratory/sdk-test': ^1.5.5
 
-  '@milaboratory/tengo-sdk': ~1.1.8
+  '@milaboratory/tengo-sdk': ^1.2.1
+  '@milaboratory/pframes-conv': ^0.4.25
 
-  '@milaboratory/platforma-uikit': ^1.1.0
-  '@milaboratory/sdk-vue': ^1.0.42
+  '@milaboratory/mixcr': 4.7.0-68-develop
+
+  '@milaboratory/platforma-uikit': ^1.1.2
+  '@milaboratory/sdk-vue': ^1.1.1
   '@milaboratory/helpers': ^1.5.3
 
   'vue': ^3.4.38
-  'vue-tsc': ^2.1.4
+  'vue-tsc': ^2.1.6
 
   'zod': ^3.23.8
   'utility-types': ^3.11.0
@@ -40,8 +43,8 @@ catalog:
   '@ag-grid-community/styles': ^32.1.0
 
   '@changesets/cli': ^2.27.8
-  
+
   # other blocks used in tests
 
-  '@milaboratory/milaboratories.samples-and-data': 1.1.5
+  '@milaboratory/milaboratories.samples-and-data': 1.1.6
   '@milaboratory/milaboratories.samples-and-data.model': 1.1.1
diff --git a/test/src/wf.test.ts b/test/src/wf.test.ts
@@ -18,11 +18,7 @@ blockTest('empty imputs', { timeout: 10000 }, async ({ rawPrj: project, ml, help
     5000
   )) as InferBlockState<typeof platforma>;
   expect(stableState.outputs).toMatchObject({ inputOptions: { ok: true, value: [] } });
-  const presetsOutput = wrapOutputs(stableState.outputs).presets;
-  const presetsStr = Buffer.from(
-    await ml.driverKit.blobDriver.getContent(presetsOutput!.handle)
-  ).toString();
-  const presets = JSON.parse(presetsStr);
+  const presets = wrapOutputs(stableState.outputs).presets;
   expect(presets).length.gt(10);
 });
 
@@ -36,15 +32,16 @@ blockTest(
     } satisfies BlockArgs);
     const stableState = (await awaitStableState(
       project.getBlockState(blockId),
-      5000
+      10000
     )) as InferBlockState<typeof platforma>;
-    expect(stableState.outputs).toMatchObject({ preset: { ok: true } });
+    const preset = wrapOutputs(stableState.outputs).preset;
+    expect(preset).toBeTypeOf('object');
   }
 );
 
 blockTest(
   'simple project',
-  { timeout: 25000 },
+  { timeout: 30000 },
   async ({ rawPrj: project, ml, helpers, expect }) => {
     const sndBlockId = await project.addBlock('Samples & Data', samplesAndDataBlockSpec);
     const clonotypingBlockId = await project.addBlock('MiXCR Clonotyping', myBlockSpec);
@@ -101,7 +98,7 @@ blockTest(
 
     const clonotypingStableState1 = (await awaitStableState(
       clonotypingBlockState,
-      5000
+      15000
     )) as InferBlockState<typeof platforma>;
 
     expect(clonotypingStableState1.outputs).toMatchObject({
@@ -127,7 +124,7 @@ blockTest(
 
     const clonotypingStableState2 = (await awaitStableState(
       project.getBlockState(clonotypingBlockId),
-      10000
+      15000
     )) as InferBlockState<typeof platforma>;
 
     const outputs2 = wrapOutputs<BlockOutputs>(clonotypingStableState2.outputs);
@@ -138,7 +135,7 @@ blockTest(
     await project.runBlock(clonotypingBlockId);
     const clonotypingStableState3 = (await helpers.awaitBlockDoneAndGetStableBlockState(
       clonotypingBlockId,
-      10000
+      15000
     )) as InferBlockState<typeof platforma>;
     const outputs3 = wrapOutputs<BlockOutputs>(clonotypingStableState3.outputs);
 

diff --git a/workflow/package.json b/workflow/package.json
@@ -11,6 +11,8 @@
   "devDependencies": {
     "@milaboratory/tengo-template-builder": "catalog:",
     "@milaboratory/tengo-sdk": "catalog:",
+    "@milaboratory/pframes-conv": "catalog:",
+    "@milaboratory/mixcr": "catalog:",
     "@milaboratory/sdk-test": "catalog:",
     "vitest": "catalog:",
     "typescript": "catalog:"

diff --git a/workflow/src/get-preset.tpl.tengo b/workflow/src/get-preset.tpl.tengo
@@ -3,6 +3,7 @@
 self := import("@milaboratory/tengo-sdk:tpl")
 ll := import("@milaboratory/tengo-sdk:ll")
 exec := import("@milaboratory/tengo-sdk:exec")
+assets := import("@milaboratory/tengo-sdk:assets")
 
 self.validateInputs({
 	"__options__,closed": "",
@@ -13,15 +14,17 @@ self.validateInputs({
 	}
 })
 
+mixcrSw := assets.importSoftware("@milaboratory/mixcr:main")
+
 self.defineOutputs("preset")
 
 self.body(func(inputs) {
 	presetName := inputs.request.presetName
 	species := inputs.request.species
 
 	mixcrCmdBuilder := exec.builder().
+						software(mixcrSw).
 						printErrStreamToStdout().
-						cmd("mixcr").
 						arg("exportPreset").
 						arg("--preset-name").
 						arg(presetName)

diff --git a/workflow/src/list-presets.tpl.tengo b/workflow/src/list-presets.tpl.tengo
@@ -4,12 +4,15 @@ self := import("@milaboratory/tengo-sdk:tpl")
 ll := import("@milaboratory/tengo-sdk:ll")
 exec := import("@milaboratory/tengo-sdk:exec")
 file := import("@milaboratory/tengo-sdk:file")
+assets := import("@milaboratory/tengo-sdk:assets")
 
 self.defineOutputs("presets")
 
+mixcrSw := assets.importSoftware("@milaboratory/mixcr:main")
+
 self.body(func(inputs) {
 	listPresets := exec.builder().
-						cmd("mixcr").
+						software(mixcrSw).
 						arg("listPresetSpecificationsForUI").
 						arg("presets.json").
 						inUiQueue().

diff --git a/workflow/src/mixcr-analyze.tpl.tengo b/workflow/src/mixcr-analyze.tpl.tengo
@@ -10,10 +10,11 @@ render := import("@milaboratory/tengo-sdk:render")
 
 json := import("json")
 
-exportClonesTpl := assets.importTemplate(":export-clones")
-
 self.defineOutputs("qc", "reports", "clones", "log")
 
+exportClonesTpl := assets.importTemplate(":export-clones")
+mixcrSw := assets.importSoftware("@milaboratory/mixcr:main")
+
 progressPrefix := "[==PROGRESS==]"
 
 self.body(func(inputs) {
@@ -42,7 +43,7 @@ self.body(func(inputs) {
 		mixcrCmdBuilder := exec.builder().
 							printErrStreamToStdout().
 							env("MI_PROGRESS_PREFIX", progressPrefix).
-							cmd("mixcr").
+							software(mixcrSw).
 							arg("analyze")
 
 		if !is_undefined(species) {

diff --git a/workflow/src/prerun.tpl.tengo b/workflow/src/prerun.tpl.tengo
@@ -17,7 +17,10 @@ wf.body(func(args) {
 
 	if !is_undefined(args.preset) {
 		getPreset := render.create(getPresetTpl, {
-			preset: args.preset
+			request: {
+				presetName: args.preset,
+				species: args.species
+			}
 		})
 		outputs.preset = getPreset.output("preset", 24 * 60 * 60 * 1000)
 	}

diff --git a/workflow/src/test/columns.test.ts b/workflow/src/test/columns.test.ts
@@ -32,7 +32,7 @@ const testCases: TestCase[] = [
 
 tplTest.for(testCases)(
   'checking preset for $presetName',
-  { timeout: 10000 },
+  { timeout: 20000 },
   async ({ presetName, species, check }, { helper, expect }) => {
     const resultC = (
       await helper.renderTemplate(true, 'test.columns.test', ['conf'], (tx) => {
@@ -44,7 +44,7 @@ tplTest.for(testCases)(
         };
       })
     ).computeOutput('conf', (c) => c?.getDataAsJson());
-    const result = await awaitStableState(resultC, 10000);
+    const result = await awaitStableState(resultC, 15000);
     check(expect, result);
   }
 );