Merge branch 'cell-level-upload-details' of github.com:biomage-org/ap…

…i into cell-level-upload-details Signed-off-by: stefanbabukov <[email protected]>
biomage-org · Nov 7, 2023 · a888309 · a888309
2 parents 446e847 + 653f098
commit a888309
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diff --git a/src/api.v2/helpers/s3/patchCellSetsObject.js b/src/api.v2/helpers/s3/patchCellSetsObject.js
@@ -6,13 +6,28 @@ const putObject = require('./putObject');
 
 const validateRequest = require('../../../utils/schema-validator');
 
+function removeElementsWithTypeCLM(data) {
+  // Filter out cell-level metadata cell sets
+  return data.filter((item) => item.type !== 'CLM' && item.type !== 'CLMPerSample');
+}
+
+const containsTypeCLM = (data) => data.some((item) => {
+  const appendObject = item.$append;
+  return appendObject && (appendObject.type === 'CLM' || appendObject.type === 'CLMPerSample');
+});
+
 const patchCellSetsObject = async (experimentId, patch) => {
   const currentCellSet = await getObject({
     Bucket: bucketNames.CELL_SETS,
     Key: experimentId,
   });
 
-  const { cellSets: prePatchCellSets } = JSON.parse(currentCellSet);
+  let { cellSets: prePatchCellSets } = JSON.parse(currentCellSet);
+
+  // If the patch contains a cell-level metadata we need to clear them before to avoid duplications
+  if (containsTypeCLM(patch)) {
+    prePatchCellSets = removeElementsWithTypeCLM(prePatchCellSets);
+  }
 
   /**
    * The $remove operation will replace the element in the array with an
@@ -26,7 +41,6 @@ const patchCellSetsObject = async (experimentId, patch) => {
   );
 
   const patchedCellSets = { cellSets: patchedCellSetslist };
-
   await validateRequest(patchedCellSets, 'cell-sets-bodies/CellSets.v2.yaml');
 
   await putObject({

diff --git a/tests/api.v2/helpers/s3/__snapshots__/patchCellSetsObject.test.js.snap b/tests/api.v2/helpers/s3/__snapshots__/patchCellSetsObject.test.js.snap
@@ -1,5 +1,22 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
+exports[`patchCellSetsObject Patch with CLM elements replaces old CLM cell sets 1`] = `
+Array [
+  Object {
+    "children": Array [],
+    "key": "sample2",
+    "name": "Sample 2",
+    "type": "notCLM",
+  },
+  Object {
+    "children": Array [],
+    "key": "New",
+    "name": "New CLM",
+    "type": "CLM",
+  },
+]
+`;
+
 exports[`patchCellSetsObject Works correctly 1`] = `
 Object {
   "Body": "{\\"cellSets\\":[{\\"key\\":\\"louvain\\",\\"name\\":\\"louvain clusters\\",\\"rootNode\\":true,\\"type\\":\\"cellSets\\",\\"children\\":[{\\"key\\":\\"louvain-0\\",\\"name\\":\\"Cluster 0\\",\\"rootNode\\":false,\\"type\\":\\"cellSets\\",\\"color\\":\\"#77aadd\\",\\"cellIds\\":[0,1,2,3]},{\\"key\\":\\"new-cluster-1\\",\\"name\\":\\"New Cluster 1\\",\\"rootNode\\":false,\\"color\\":\\"#3957ff\\",\\"type\\":\\"cellSets\\",\\"cellIds\\":[4,5,6]}]}]}",

diff --git a/tests/api.v2/helpers/s3/patchCellSetsObject.test.js b/tests/api.v2/helpers/s3/patchCellSetsObject.test.js
@@ -56,10 +56,16 @@ const mockPatch = [
   },
 ];
 
-getObject.mockReturnValue(mockCellSets);
 
 describe('patchCellSetsObject', () => {
+  beforeEach(() => {
+    jest.resetAllMocks(); // This resets the state of all mocks
+  });
+
+
   it('Works correctly', async () => {
+    getObject.mockReturnValue(mockCellSets);
+
     const result = await patchCellSetsObject(mockExperimentId, mockPatch);
 
     // Put a modified object
@@ -102,4 +108,53 @@ describe('patchCellSetsObject', () => {
 
     await expect(patchCellSetsObject(mockExperimentId, malformedPatch)).rejects.toThrow();
   });
+
+  it('Patch with CLM elements replaces old CLM cell sets', async () => {
+    // Mock cellSets with CLM types
+    const mockCellSetsWithCLM = JSON.stringify({
+      cellSets: [
+        {
+          key: 'sample1',
+          name: 'To remove 1',
+          type: 'CLM',
+          children: [],
+        },
+        // This should stay since it's not CLM type
+        {
+          key: 'sample2',
+          name: 'Sample 2',
+          type: 'notCLM',
+          children: [],
+        },
+        {
+          key: 'sample3',
+          name: 'To Remove 2',
+          type: 'CLMPerSample',
+          children: [],
+        },
+      ],
+    });
+
+    const mockPatchThatContainsCLM = [
+      {
+        $append: {
+          key: 'New',
+          name: 'New CLM',
+          type: 'CLM',
+          children: [],
+        },
+      },
+    ];
+
+    getObject.mockReturnValueOnce(mockCellSetsWithCLM);
+
+    await patchCellSetsObject(mockExperimentId, mockPatchThatContainsCLM);
+
+    // Put a modified object without CLM types
+    const putParams = putObject.mock.calls[0][0];
+    const modifiedCellSets = JSON.parse(putParams.Body).cellSets;
+
+    // Check that the elements with CLM types have been removed
+    expect(modifiedCellSets).toMatchSnapshot();
+  });
 });