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plugin for Apollo 3","maintainers":[{"name":"shashankbrgowda","email":"shashank.b.r.gowda45587@gmail.com"}],"readme":"# Havana Apollo Plugin\n\nThe Havana Apollo Plugin is a JBrowse 2 plugin designed for Apollo 3. It adds\nHavana-specific annotation controls to Apollo's transcript details and provides\na workflow for sending annotated genes to the Havana integration service.\n\nThe plugin uses Apollo's change system for annotation edits. Saving to Havana is\na separate action that sends selected Apollo gene IDs to the Havana integration\nAPI.\n\n## Functionality\n\n### Gene and transcript biotypes\n\nThe plugin provides curated Havana biotype menus for both genes and transcripts.\n\n- Gene biotype selections update the gene's `biotype` attribute.\n- Transcript biotype selections update both the `biotype` attribute and the\n  Apollo feature type when required.\n- Changing a transcript to a non-coding transcript type removes its CDS.\n- Changing a transcript to an mRNA creates a CDS spanning the transcript's exon\n  boundaries when a CDS does not already exist.\n- All edits are submitted through Apollo's change manager and remain part of the\n  normal Apollo editing history.\n\n### Havana annotation attributes\n\nAdditional Havana fields are displayed in Apollo's transcript details:\n\n- CDS start and end completeness, stored using the `mRNA_start_NF` and\n  `mRNA_end_NF` attributes.\n- Controlled remarks for genes and transcripts. These values are selected from\n  the Havana remark menus and are exported to GFF3.\n- Hidden remarks for genes and transcripts. These are free-text, multi-value\n  internal notes that are not exported to GFF3.\n- Gene symbol editing, which keeps the `gene_name` and `name` attributes in\n  sync.\n- Gene description editing, stored as a single `description` value.\n- Gene biotype editing alongside the selected transcript's Havana attributes.\n\nThe gene section also shows the external gene identifier, Apollo gene\nidentifier, and selected Apollo transcript identifier to make it clear which\nfeatures are being edited.\n\n### Saving annotations to Havana\n\nThe fixed **Save to Havana** button opens a dialog with four workflows:\n\n#### Selected feature\n\n- Loads the complete top-level gene for the selected transcript.\n- Previews the gene and its transcripts, including identifiers, type, biotype,\n  location, strand, remarks, and hidden remarks.\n- Warns when the gene already appears to be synchronized with Havana.\n- Sends the selected gene to the Havana integration API.\n\n#### Bulk save\n\n- Finds recent Apollo changes made by the current user.\n- Resolves transcript and child-feature changes to their top-level genes.\n- Deduplicates the results so each affected gene is shown once, using its most\n  recent change.\n- Shows whether each gene is `Pending` or `Done` based on its Apollo update and\n  Havana save timestamps.\n- Supports one-day, one-week, and one-month date ranges, text filtering,\n  pagination, feature previews, and selection of multiple genes.\n\n#### Deleted genes\n\n- Finds recent gene deletions made by the current user.\n- Deduplicates deleted genes and provides the same date-range, filtering,\n  pagination, preview, and selection controls as bulk save.\n- Sends selected genes to the Havana delete workflow together with the current\n  assembly identifier.\n\n#### Failed saves\n\n- Displays failures reported by the Havana integration service for the current\n  assembly.\n- Shows the feature, failure type, error message, submitting user, status, retry\n  count, and creation time.\n- Supports date-range filtering, text search, and pagination.\n\nThe dialog reports API errors through Apollo notifications. After a successful\nsave that contains changes, the page is refreshed so Apollo displays the latest\nsynchronization state.\n\n## Integration flow\n\n1. Havana-specific edits are recorded as standard Apollo changes.\n2. The plugin uses the authenticated Apollo internet account token for Apollo\n   and Havana API requests.\n3. Apollo supplies top-level feature data and the current user's recent change\n   history.\n4. The Havana integration API processes selected save or delete requests and\n   exposes failed-save information.\n\nThe plugin therefore requires a configured Apollo API, a reachable Havana\nintegration API, and an authenticated `ApolloInternetAccount`.\n\n## Development\n\nTo develop against JBrowse Web and Apollo3:\n\n- Start a development version of JBrowse Web (see\n  [here](https://github.com/GMOD/jbrowse-components/blob/master/CONTRIBUTING.md))\n- Start a development version of Apollo3\n- Install dependencies with `pnpm install`\n- In this project, run `pnpm dev`\n- Add the following to your Apollo3 config:\n\n```javascript\nplugins: [\n  {\n    name: 'HavanaApolloPlugin',\n    url: 'http://localhost:9001/dist/havana-apollo-plugin.umd.development.js',\n  },\n]\n```\n\n- When you make changes to your plugin, it will automatically be re-built. You\n  can then refresh JBrowse Web to see the changes.\n\nBefore submitting a change, run the relevant checks:\n\n```sh\npnpm lint\npnpm test\npnpm build\n```\n\nSee [CONTRIBUTING.md](CONTRIBUTING.md) for the contribution, commit, and pull\nrequest guidelines.\n\n## Publishing to npm\n\n### Why versioning depends on Git\n\n`pnpm version` creates a Git commit and tag for the npm release, so it requires\na clean working tree. The tag identifies the source used for that package\nversion.\n\nRun the version command only after committing every change intended for the\nrelease:\n\n```sh\npnpm version patch\n```\n\nUse `minor` or `major` instead of `patch` when appropriate. The command updates\n`package.json`, and the version lifecycle script synchronizes `src/version.ts`.\nThe current `postversion` script then pushes the version commit and tag.\n\nDo not update `package.json` and `src/version.ts` separately. If another change\nis committed after the version tag, run the appropriate version command again\nbefore publishing so the new release tag includes that change.\n\n### Release workflow\n\n1. Complete and commit all release changes on a non-`main` branch.\n2. Run the relevant tests, lint, and build checks.\n3. Confirm the working tree is clean with `git status --short`.\n4. Run `pnpm version patch`, `minor`, or `major`.\n5. Merge the branch into `main` through a pull request.\n6. Switch to `main`, pull the merged changes, and run `pnpm publish`.\n\n`pnpm publish` is restricted to `main` or `master`. If pnpm asks whether to\npublish from another branch, answer **No**, merge the pull request, and publish\nfrom the updated `main` branch.\n\nPublish the new version with:\n\n```sh\ngit switch main\ngit pull --ff-only\npnpm publish\n```\n\nPublishing automatically runs:\n\n- `pnpm test` and `pnpm lint` through `prepublishOnly`.\n- `pnpm build` through `prepack`.\n- `pnpm clean` through the build's `prebuild` step.\n\nYou do not need to run `pnpm clean` or `pnpm build` again immediately before\npublishing. Run `pnpm install` only when dependencies changed, the lockfile\nchanged, or `node_modules` is unavailable.\n","readmeFilename":"README.md","license":"Apache-2.0"}