Fix a test and add a new one

Signed-off-by: cosa65 <[email protected]>
biomage-org · Nov 9, 2023 · f09b2ac · f09b2ac
1 parent ba52559
commit f09b2ac
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Showing 2 changed files with 119 additions and 3 deletions.
diff --git a/tests/api.v2/helpers/pipeline/pipelineConstruct/__snapshots__/qcHelpers.test.js.snap b/tests/api.v2/helpers/pipeline/pipelineConstruct/__snapshots__/qcHelpers.test.js.snap
@@ -1,5 +1,73 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
+exports[`helper functions for skeletons returns configureEmbedding only if the config has no changes and the previous run failed 1`] = `
+Object {
+  "ConfigureEmbedding": Object {
+    "Next": "EndOfPipeline",
+    "XCatch": Array [
+      Object {
+        "ErrorEquals": Array [
+          "States.ALL",
+        ],
+        "Next": "HandleError",
+        "ResultPath": "$.errorInfo",
+      },
+    ],
+    "XConstructorArgs": Object {
+      "perSample": false,
+      "taskName": "configureEmbedding",
+    },
+    "XStepType": "create-new-step",
+  },
+  "DataIntegration": Object {
+    "Next": "ConfigureEmbedding",
+    "XCatch": Array [
+      Object {
+        "ErrorEquals": Array [
+          "States.ALL",
+        ],
+        "Next": "HandleError",
+        "ResultPath": "$.errorInfo",
+      },
+    ],
+    "XConstructorArgs": Object {
+      "perSample": false,
+      "taskName": "dataIntegration",
+      "uploadCountMatrix": true,
+    },
+    "XStepType": "create-new-step",
+  },
+  "DoubletScoresFilterMap": Object {
+    "Catch": Array [
+      Object {
+        "ErrorEquals": Array [
+          "States.ALL",
+        ],
+        "Next": "HandleError",
+        "ResultPath": "$.errorInfo",
+      },
+    ],
+    "ItemsPath": "$.samples",
+    "Iterator": Object {
+      "StartAt": "DoubletScoresFilter",
+      "States": Object {
+        "DoubletScoresFilter": Object {
+          "End": true,
+          "XConstructorArgs": Object {
+            "perSample": true,
+            "taskName": "doubletScores",
+          },
+          "XStepType": "create-new-step",
+        },
+      },
+    },
+    "Next": "DataIntegration",
+    "ResultPath": null,
+    "Type": "Map",
+  },
+}
+`;
+
 exports[`helper functions for skeletons returns from first not-completed step if the config has changes after that 1`] = `
 Object {
   "CellSizeDistributionFilterMap": Object {
@@ -180,7 +248,7 @@ Object {
 }
 `;
 
-exports[`helper functions for skeletons returns from first not-completed step if the config has no changes 1`] = `
+exports[`helper functions for skeletons returns from first not-completed step if the config has no changes and the previous run failed 1`] = `
 Object {
   "ConfigureEmbedding": Object {
     "Next": "EndOfPipeline",

diff --git a/tests/api.v2/helpers/pipeline/pipelineConstruct/qcHelpers.test.js b/tests/api.v2/helpers/pipeline/pipelineConstruct/qcHelpers.test.js
@@ -3,10 +3,19 @@ const { getQcStepsToRun } = require('../../../../../src/api.v2/helpers/pipeline/
 const { buildQCPipelineSteps } = require('../../../../../src/api.v2/helpers/pipeline/pipelineConstruct/skeletons/qcPipelineSkeleton');
 const fake = require('../../../../test-utils/constants');
 
+const CellLevelMeta = require('../../../../../src/api.v2/model/CellLevelMeta');
+const ExperimentExecution = require('../../../../../src/api.v2/model/ExperimentExecution');
+
 jest.mock('../../../../../src/api.v2/helpers/s3/fileExists', () => ({
   fileExists: jest.fn(() => true),
 }));
 
+jest.mock('../../../../../src/api.v2/model/CellLevelMeta');
+jest.mock('../../../../../src/api.v2/model/ExperimentExecution');
+
+const cellLevelMetaInstance = new CellLevelMeta();
+const experimentExecutionInstance = new ExperimentExecution();
+
 const processingConfig = [
   {
     name: 'numGenesVsNumUmis',
@@ -103,6 +112,18 @@ const processingConfig = [
   },
 ];
 
+const mockCellLevelMetadataCheck = (currentCellLevelMetadataId, previousRunCellLevelMetadataId) => {
+  cellLevelMetaInstance.getMetadataByExperimentIds.mockReturnValueOnce(
+    Promise.resolve([{ id: currentCellLevelMetadataId }]),
+  );
+
+  experimentExecutionInstance.find.mockReturnValueOnce({
+    first: () => Promise.resolve(
+      { lastPipelineParams: { cellMetadataId: previousRunCellLevelMetadataId } },
+    ),
+  });
+};
+
 describe('helper functions for skeletons', () => {
   it('returns the first changed step if it is before all the completed steps', async () => {
     const completedSteps = ['ClassifierFilter'];
@@ -120,17 +141,44 @@ describe('helper functions for skeletons', () => {
     expect(stateMachine).toMatchSnapshot();
   });
 
-  it('returns from first not-completed step if the config has no changes', async () => {
+  it('returns from first not-completed step if the config has no changes and the previous run failed', async () => {
+    const completedSteps = [
+      'ClassifierFilter',
+      'CellSizeDistributionFilter',
+      'MitochondrialContentFilter',
+      'NumGenesVsNumUmisFilter',
+    ];
+
+    const qcSteps = await getQcStepsToRun(fake.EXPERIMENT_ID, [], completedSteps, 'FAILED');
+    expect(qcSteps[0]).toEqual('DoubletScoresFilterMap');
+    const stateMachine = buildQCPipelineSteps(qcSteps);
+    expect(stateMachine).toMatchSnapshot();
+  });
+
+  it('returns configureEmbedding only if the config has no changes and the previous run failed', async () => {
     const completedSteps = [
       'ClassifierFilter',
       'CellSizeDistributionFilter',
       'MitochondrialContentFilter',
       'NumGenesVsNumUmisFilter',
     ];
 
-    const qcSteps = await getQcStepsToRun(fake.EXPERIMENT_ID, [], completedSteps);
+    const qcSteps = await getQcStepsToRun(fake.EXPERIMENT_ID, [], completedSteps, 'FAILED');
     expect(qcSteps[0]).toEqual('DoubletScoresFilterMap');
     const stateMachine = buildQCPipelineSteps(qcSteps);
     expect(stateMachine).toMatchSnapshot();
   });
+
+  it('Throws if the config has no changes', async () => {
+    mockCellLevelMetadataCheck('sameCellLevelId', 'sameCellLevelId');
+
+    const completedSteps = [
+      'ClassifierFilter',
+      'CellSizeDistributionFilter',
+      'MitochondrialContentFilter',
+      'NumGenesVsNumUmisFilter',
+    ];
+
+    expect(async () => await getQcStepsToRun(fake.EXPERIMENT_ID, [], completedSteps, 'SUCCEEDED')).rejects.toThrow();
+  });
 });