Init cassia

.github/workflows/ci.yaml

@@ -280,8 +280,10 @@ jobs:
           tags: ${{ format('{0}/{1}:{2}', steps.login-ecr.outputs.registry, steps.ref.outputs.repo-name, steps.ref.outputs.image-tag) }}
           push: true
           provenance: false
-          cache-from: type=gha,scope=${{ github.workflow }}
-          cache-to: type=gha,mode=max,scope=${{ github.workflow }},ignore-error=true
+          # GHA cache (type=gha) disabled: restoring the mode=max cache fills the
+          # runner disk and the build fails with "no space left on device" during
+          # COPY. Restore via registry cache (type=registry to a dedicated mutable
+          # ECR repo) if build times become a problem.
 
   deploy:
     name: Deploy to Kubernetes

src/__test__/components/data-exploration/cell-sets-tool/AnnotateClustersTool.test.jsx

@@ -0,0 +1,71 @@
+import React from 'react';
+import { render, screen, waitFor } from '@testing-library/react';
+import { Provider } from 'react-redux';
+import userEvent from '@testing-library/user-event';
+
+import { makeStore } from 'redux/store';
+import AnnotateClustersTool from 'components/data-exploration/cell-sets-tool/AnnotateClustersTool';
+import { runCassiaAnnotation } from 'redux/actions/cellSets';
+import createTestComponentFactory from '__test__/test-utils/testComponentFactory';
+import fake from '__test__/test-utils/constants';
+
+jest.mock('redux/actions/cellSets', () => ({
+  __esModule: true,
+  runCellSetsAnnotation: jest.fn(() => () => {}),
+  runCassiaAnnotation: jest.fn(() => () => {}),
+}));
+
+const experimentId = fake.EXPERIMENT_ID;
+const AnnotateClustersToolFactory = createTestComponentFactory(
+  AnnotateClustersTool,
+  { experimentId, onRunAnnotation: jest.fn() },
+);
+
+const renderTool = () => render(
+  <Provider store={makeStore()}>
+    {AnnotateClustersToolFactory()}
+  </Provider>,
+);
+
+describe('AnnotateClustersTool', () => {
+  beforeEach(() => {
+    jest.clearAllMocks();
+  });
+
+  it('defaults to CASSIA and shows the additional-context input', () => {
+    renderTool();
+
+    expect(screen.getByRole('radio', { name: 'CASSIA' })).toBeChecked();
+    expect(screen.getByRole('radio', { name: 'ScType' })).not.toBeChecked();
+    // CASSIA-only free-text context box is present
+    expect(screen.getByText(/Additional context/i)).toBeInTheDocument();
+  });
+
+  it('sends the entered context to runCassiaAnnotation on confirm', async () => {
+    renderTool();
+
+    userEvent.type(screen.getByPlaceholderText(/Large Intestine/i), 'Large Intestine');
+    userEvent.type(screen.getByPlaceholderText(/e\.g\. Human/i), 'Human');
+    userEvent.type(
+      screen.getByPlaceholderText(/colorectal tumor/i),
+      '3 tumor, 2 normal',
+    );
+
+    userEvent.click(screen.getByRole('button', { name: /Compute/i }));
+
+    // Confirmation modal opens; it names Amazon Bedrock (appears in both the
+    // alert title and body, so assert the unique modal title).
+    await waitFor(() => {
+      expect(screen.getByText(/Confirm CASSIA annotation/i)).toBeInTheDocument();
+    });
+    expect(screen.getAllByText(/Amazon Bedrock/i).length).toBeGreaterThan(0);
+
+    userEvent.click(screen.getByRole('button', { name: /Continue/i }));
+
+    await waitFor(() => {
+      expect(runCassiaAnnotation).toHaveBeenCalledWith(
+        experimentId, 'Human', 'Large Intestine', '3 tumor, 2 normal',
+      );
+    });
+  });
+});

src/__test__/components/data-exploration/cell-sets-tool/CellSetsTool.test.jsx

@@ -723,14 +723,13 @@ describe('CellSetsTool', () => {
       userEvent.click(deleteAnnotatedCellClassButton);
     });
 
-    // get all the cell set groups
-    const numCellGroupsAfterDelete = screen.getAllByRole('img', { name: 'down' }).length;
-
     await waitFor(() => {
-      // This test used to assert that "Annotated cell set" text is not found in "screen"
-      // in order to verify that deletion was successful.
-      // 4 Cell groups: louvain, custom cell sets, sample, Track_1 (metadata)
-      expect(numCellGroupsAfterDelete).toEqual(4);
+      // Deletion is optimistic, so the annotated cell class is gone immediately.
+      // Count the expand carets: of the remaining groups (louvain, custom cell
+      // sets, sample, Track_1) only the three non-empty ones show a "down" caret
+      // - the empty "Custom cell sets" group shows none.
+      const numCellGroupsAfterDelete = screen.getAllByRole('img', { name: 'down' }).length;
+      expect(numCellGroupsAfterDelete).toEqual(3);
 
       expect(screen.queryByText('Annotated cell class')).toBeNull();
 
@@ -765,6 +764,10 @@ describe('AnnotateClustersTool', () => {
 
     // Switch to tab
     userEvent.click(annotateClustersTabTitle);
+
+    // CASSIA is the default method; these tests exercise the ScType select flow
+    // (dropdowns + direct dispatch), so switch to ScType first.
+    userEvent.click(screen.getByRole('radio', { name: 'ScType' }));
   });
 
   it('Renders correctly', async () => {

src/__test__/redux/actions/cellSets/runCassiaAnnotation.test.js

@@ -0,0 +1,57 @@
+import configureMockStore from 'redux-mock-store';
+import thunk from 'redux-thunk';
+
+import runCassiaAnnotation from 'redux/actions/cellSets/runCassiaAnnotation';
+import fake from '__test__/test-utils/constants';
+import fetchWork from 'utils/work/fetchWork';
+
+jest.mock('utils/work/fetchWork', () => jest.fn(() => ({})));
+jest.mock('utils/getTimeoutForWorkerTask', () => jest.fn(() => 100));
+
+const mockStore = configureMockStore([thunk]);
+const experimentId = fake.EXPERIMENT_ID;
+
+const newStore = () => mockStore({
+  cellSets: { error: false, updatingClustering: false, loading: false },
+});
+
+describe('runCassiaAnnotation', () => {
+  beforeEach(() => {
+    jest.clearAllMocks();
+  });
+
+  it('sends name, species, tissue and additionalInfo to the worker', async () => {
+    await newStore().dispatch(
+      runCassiaAnnotation(experimentId, 'Human', 'Large Intestine', '3 tumor, 2 normal'),
+    );
+
+    expect(fetchWork).toHaveBeenCalledTimes(1);
+    const [calledExperimentId, body] = fetchWork.mock.calls[0];
+    expect(calledExperimentId).toEqual(experimentId);
+    expect(body).toEqual({
+      name: 'CASSIAAnnotate',
+      species: 'Human',
+      tissue: 'Large Intestine',
+      additionalInfo: '3 tumor, 2 normal',
+    });
+  });
+
+  it('defaults additionalInfo to an empty string when omitted', async () => {
+    await newStore().dispatch(
+      runCassiaAnnotation(experimentId, 'Human', 'Large Intestine'),
+    );
+
+    const [, body] = fetchWork.mock.calls[0];
+    expect(body.additionalInfo).toBe('');
+  });
+
+  it('does not dispatch a request when cell sets are already updating', async () => {
+    const store = mockStore({
+      cellSets: { error: false, updatingClustering: true, loading: true },
+    });
+
+    await store.dispatch(runCassiaAnnotation(experimentId, 'Human', 'Large Intestine'));
+
+    expect(fetchWork).not.toHaveBeenCalled();
+  });
+});

src/__test__/redux/reducers/componentConfig/cellClassDelete.test.js

@@ -0,0 +1,42 @@
+import cellClassDelete from 'redux/reducers/componentConfig/cellClassDelete';
+import { CELL_CLASS_DELETE } from 'redux/actionTypes/cellSets';
+
+const deleteAction = (key) => ({ type: CELL_CLASS_DELETE, payload: { key } });
+
+describe('cellClassDelete (componentConfig)', () => {
+  it('removes the deleted cell class from heatmap groupedTracks', () => {
+    const state = {
+      interactiveHeatmap: {
+        config: { groupedTracks: ['louvain', 'CASSIA-Gut-Human-1', 'sample'] },
+      },
+    };
+
+    const newState = cellClassDelete(state, deleteAction('CASSIA-Gut-Human-1'));
+
+    expect(newState.interactiveHeatmap.config.groupedTracks).toEqual(['louvain', 'sample']);
+  });
+
+  it('leaves groupedTracks untouched when it does not contain the deleted key', () => {
+    const state = {
+      interactiveHeatmap: { config: { groupedTracks: ['louvain', 'sample'] } },
+    };
+
+    const newState = cellClassDelete(state, deleteAction('CASSIA-Gut-Human-1'));
+
+    expect(newState.interactiveHeatmap.config.groupedTracks).toEqual(['louvain', 'sample']);
+  });
+
+  // Regression: plots whose config has no groupedTracks used to throw
+  // "Cannot read properties of undefined (reading 'includes')".
+  it('does not throw for plot configs without groupedTracks', () => {
+    const state = {
+      embeddingCategoricalMain: { config: { selectedCellSet: 'louvain' } },
+      violinMain: { config: {} },
+      noConfigPlot: {},
+    };
+
+    expect(
+      () => cellClassDelete(state, deleteAction('CASSIA-Gut-Human-1')),
+    ).not.toThrow();
+  });
+});

src/components/Loader.jsx

@@ -1,6 +1,6 @@
 import PropTypes from 'prop-types';
 import { BounceLoader } from 'react-spinners';
-import { Typography, Spin } from 'antd';
+import { Typography, Spin, Progress } from 'antd';
 import useSWR from 'swr';
 import React from 'react';
 import { useSelector } from 'react-redux';
@@ -39,15 +39,21 @@ const slowLoad = () => (
   </>
 );
 
-const fastLoad = (message) => (
+const fastLoad = (message, percent) => (
   <div style={{
     display: 'flex', flexDirection: 'column', alignItems: 'center', justifyContent: 'center',
   }}
   >
     <style>{spinnerStyles}</style>
-    <div style={{ padding: 25 }}>
-      <Spin size='large' className='loader-spinner' />
-    </div>
+    {typeof percent === 'number' ? (
+      <div style={{ width: 300, padding: 25 }}>
+        <Progress percent={percent} status='normal' strokeColor={colors.darkRed} />
+      </div>
+    ) : (
+      <div style={{ padding: 25 }}>
+        <Spin size='large' className='loader-spinner' />
+      </div>
+    )}
     <p style={{ textAlign: 'center' }}>
       <Text>
         {message || "We're getting your data ..."}
@@ -74,10 +80,10 @@ const Loader = ({ experimentId }) => {
   }
 
   if (workerInfo && workerInfo.userMessage) {
-    const { userMessage } = workerInfo;
+    const { userMessage, progressPercent } = workerInfo;
     return (
       <div>
-        {fastLoad(userMessage)}
+        {fastLoad(userMessage, progressPercent)}
       </div>
     );
   }