docs(lapis): improve landing page, describe lineage queries#1702
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chaoran-chen wants to merge 2 commits into
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docs(lapis): improve landing page, describe lineage queries#1702chaoran-chen wants to merge 2 commits into
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…and customizable FASTA headers
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Pull request overview
Updates LAPIS documentation to improve the landing page and document two additional concepts (lineage queries and customizable FASTA headers), while aligning Playwright navigation tests with the updated “Get started” entry point.
Changes:
- Expanded the docs landing page content and updated the primary CTA from “Introduction” to “Get started”.
- Added new Concept pages: Lineage queries and Customizable FASTA headers, and linked them from existing pages/navigation.
- Updated docs config parsing/helpers (
generateLineageIndex) and adjusted Playwright tests to match the new navigation.
Reviewed changes
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Show a summary per file
| File | Description |
|---|---|
| lapis-docs/tests/queryGenerator.page.ts | Updates navigation click target to “Get started” for query generator flow. |
| lapis-docs/tests/docs.spec.ts | Adds new concept pages to expected navigation list and updates entry click to “Get started”. |
| lapis-docs/tests/configGenerator.page.ts | Updates navigation click target to “Get started” for config generator flow. |
| lapis-docs/src/content/docs/index.mdx | Improves landing page copy, updates CTA labeling, and adds “Known instances” + citation content. |
| lapis-docs/src/content/docs/concepts/response-format.mdx | Adds a pointer to the new customizable FASTA headers documentation. |
| lapis-docs/src/content/docs/concepts/pango-lineage-query.mdx | Clarifies availability note and cross-links to generalized lineage queries. |
| lapis-docs/src/content/docs/concepts/lineage-queries.mdx | New page documenting lineage-index wildcard semantics and advanced query usage. |
| lapis-docs/src/content/docs/concepts/customizable-fasta-headers.mdx | New page documenting fastaHeaderTemplate placeholders and encoding examples. |
| lapis-docs/src/content/docs/concepts/advanced-query.mdx | Fixes an example intro sentence to correctly refer to advanced queries. |
| lapis-docs/src/config.ts | Adjusts generateLineageIndex typing/logic and adds hasLineageFields() helper for conditional docs. |
| lapis-docs/astro.config.mjs | Adds the two new Concept pages to the sidebar navigation. |
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| When requesting sequences as FASTA, you can customize the header line of each record by setting the | ||
| `fastaHeaderTemplate` request property. | ||
| The parameter is ignored if the data format is not FASTA. |
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LAPIS returns an error in this case.
| import { getConfig, hasLineageFields } from '../../../config.ts'; | ||
| import { Code } from '@astrojs/starlight/components'; | ||
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| export const lineageField = 'lineageField'; |
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We usually tried to write the actual field names into the example, since we assume that the docs page runs next to an actual LAPIS instance. We could search the config for a lineage field and only use this hardcoded value as fallback
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This is updating the docs, mainly:
PR Checklist
[ ] All necessary documentation has been adapted.[ ] All necessary changes are explained in thellms.txt.[ ] The implemented feature is covered by an appropriate test.