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04. Common Workflows

End-to-end walkthroughs for creating a project, launching analysis (pipeline), and reviewing results. Each step includes route patterns and code references.

1) Create a Project

  • Go to / or /projects → Projects panel is visible alongside Files.
  • Click “Add Project”, fill Name and Description, submit.
  • Creates via projectsActions.createProject → src/components/Projects/index.jsx:38-45,62-73
  • Open project by clicking its Name link → navigates to /projects/:projectId.

Refs: - Projects panel → src/components/ProjectFiles.js:6-14 - Create/Update/Delete flows → src/redux/modules/projects/index.js:25-84

2) Upload Files (optional)

  • On the same page, use the file picker to upload data.
  • Upload triggers filesActions.uploadFile(file); Files list shows project-related files when inside a project route.

Refs: - Files UI → src/components/Files/index.jsx:1 - Upload/Delete/Check actions → src/components/Files/index.jsx:31-40,43-61,97-127

3) Open Analysis (Pipelines/Processes)

  • Navigate to the project: /projects/:projectId.
  • Click sidebar “Analysis” to go to /projects/:projectId/processes.
  • Select a process from the header selector to navigate to /projects/:projectId/processes/:processId.

Refs: - Sidebar nav → src/components/Project/index.jsx:147-176 - Header selectors drive history.push(...) → src/components/Layout/index.jsx:93,103,106 - Route mapping for processes → src/routes/PrivateRoutes.jsx:49-57

4) Configure And Start Pipeline

  • In the Process view, the graph renders jobs. Configure block settings as needed.
  • Click “Start ▶” to enqueue/trigger execution for the current process.
  • This dispatches jobsActions.startProcess(processId) which updates jobs and refreshes the pipeline.

Refs: - Start button handler → src/components/Project/Process/index.jsx:739-747,892-905 - Saga for start → src/redux/modules/jobs/index.js:262-287

Deep links: - Base: /projects/:projectId/processes/:processId - With tab: /projects/:projectId/processes/:processId/:tabName - Review tab: /projects/:projectId/processes/:processId/review/:tabReview

5) Review Results

  • From sidebar, click “Results” → /projects/:projectId/results.
  • The Results view shows pipeline graph and allows exploring outputs, including Vitessce visualization for supported tasks.
  • Task selection and variable channels load via tasks selectors/actions.

Refs: - Results route mapping → src/routes/PrivateRoutes.jsx:56 - Results component → src/components/Project/Results/index.jsx:1 - Vitessce/task loading hooks → src/components/Project/Results/index.jsx:86-121,149-170

6) Download Outputs (when available)

  • Some jobs expose downloads (e.g., AnnData). Downloads are handled via jobsActions.downloadJob.

Refs: - Download saga → src/redux/modules/jobs/index.js:382-416

Notes & Tips

  • Path names constants → src/models/PathNames.js
  • Cross-tab auth logout → src/routes/PrivateRoutes.jsx:17-24
  • Use “Refresh” on the Process view if job statuses lag.