gOS Case Report (prebuilt)

This repository now ships prebuilt bundles via GitHub Releases and publishes the latest build to GitHub Pages. You can run the app locally without rebuilding, explore the demo data baked into shared/, or develop from source with the usual React tooling.

Quick start (no build required)

Prereqs: python3, curl, and tar. Optionally set GITHUB_TOKEN to avoid GitHub API rate limits.

./setup.sh
open http://localhost:3001

What happens:

• Fetches the latest stable GitHub Release for mskilab/case-report (override with REPO=owner/repo, TAG=v1.2.3, or --channel edge).
• Downloads build-<sha>.tar.gz, its checksum, and the LATEST metadata, verifies the checksum, and unpacks into out/build-<sha>/.
• Copies the shared/ data into the unpacked build.
• Serves the static app on PORT (default 3001). Set SKIP_SERVER=1 to skip launching the server.

Developing from source

yarn install --frozen-lockfile
CI=false yarn start   # dev server on http://localhost:3000
yarn test             # interactive tests
CI=false yarn build   # production build into ./build

Shared data bundle

The shared/ directory contains the minimum data/config the UI expects:

• shared/datasets.json – datasets the UI lists in the sidebar.
• shared/datafiles.json – maps dataset identifiers to files on disk.
• shared/settings.json – defaults for theme, landing dataset, feature toggles.
• shared/data/, shared/common/, shared/genes/, etc. – sample payloads that back the demo experience.

Add your own case report data by mirroring the structure above and updating the JSON manifests accordingly.

Configuring datasets

The datasets.json file defines available datasets and their configuration. Each dataset entry supports:

{
  "id": "my-dataset",
  "title": "My Dataset",
  "datafilesPath": "datafiles.json",
  "commonPath": "common/",
  "dataPath": "data/",
  "reference": "hg19",
  "optionalFilteredEventsColumns": [
    {
      "id": "custom-col",
      "title": "Custom Column",
      "dataIndex": "customField",
      "viewType": "gene-link"
    }
  ],
  "schema": [
    {
      "id": "sample_type",
      "title": "Sample Type",
      "type": "string"
    }
  ]
}

Filtered Events Columns: Extend the filtered events list columns using optionalFilteredEventsColumns. Supports partial column definitions that merge with defaults. Available viewType renderers:

• "gene-link" – renders gene names as clickable links
• "tier-badge" – renders tier/category badges
• "formatted-number" – renders formatted numeric values
• "string-basic" – renders plain text (default)
• "location-link" – renders genomic locations as links
• "class-icon" – renders class with icon

Cohort Filters: Define dataset-specific filters for the cohort-level view using schema. When provided, this overrides the default schema from settings. Each filter must include id, title, and type.

Deployments

• Edge channel (latest main): .github/workflows/build-artifacts.yml builds on every push to main and publishes a GitHub prerelease. This is intended for an “edge” instance that should always track the newest commit on main.
• Stable channel (promoted builds): Use .github/workflows/promote-stable.yml to promote a specific build-* prerelease to a stable (non-prerelease) release. The GitHub .../releases/latest endpoint will then point at the promoted release.
• GitHub Pages: The build workflow also deploys to the github-pages environment, so the live Pages site tracks the edge channel.

Picking what to deploy

• Edge instance: deploy the most recent release (including prereleases). In GitHub API terms, call GET /repos/:owner/:repo/releases and pick the first entry.
• Staging instance: deploy only stable releases via GET /repos/:owner/:repo/releases/latest (this endpoint ignores prereleases).

Running locally

• Stable (default): ./setup.sh
• Edge: ./setup.sh --channel edge

The legacy deploy-builds branch is no longer used; artifacts now live solely on GitHub Releases.

Troubleshooting

• If downloads fail, set GITHUB_TOKEN (PAT or Actions token) to raise the GitHub API limit.
• If the checksum mismatches, rerun ./setup.sh to redownload the assets.
• Ensure python3 is on your PATH; it powers the local HTTP server.