docs(lapis): fix maintainer docs#1703
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Pages on database configuration and preprocessing were outdated.
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Pull request overview
Updates LAPIS maintainer reference docs to reflect current SILO/LAPIS configuration and preprocessing expectations, replacing older mixed-format and component-driven documentation with a more direct, SILO-referenced spec.
Changes:
- Rewrite preprocessing reference to emphasize SILO-driven preprocessing, NDJSON ingestion, and updated config keys (lineage/phylo/incremental sections).
- Restructure
database_config.yamlreference into explicit top-level/schema/metadata/features sections and remove conditional/component-rendered content. - Remove the docs component previously used to render metadata type documentation (and inline the type list instead).
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| lapis-docs/src/content/docs/maintainer-docs/references/preprocessing.mdx | Rewritten preprocessing reference (NDJSON schema, config keys, lineage/phylo/incremental notes). |
| lapis-docs/src/content/docs/maintainer-docs/references/database-configuration.mdx | Reworked database config reference into a more explicit spec and removed component-based rendering. |
| lapis-docs/src/components/Configuration/MetadataTypesList.astro | Deleted docs component used for listing metadata types (verified no remaining references in repo). |
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| - FASTA files with the sequences | ||
| SILO ingests data in [NDJSON](https://ndjson.org/) format (Newline-Delimited JSON). One JSON object per line | ||
| describes a single sequence record. There is no separate TSV/FASTA input mode. | ||
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| | Key | Type | Required | Description | | ||
| | -------------- | ------ | -------- | ---------------------------------------------------------------------------------------------------------------------------- | | ||
| | `instanceName` | string | true | The name assigned to the instance. Used for display purposes. | | ||
| | `metadata` | array | true | A list of [metadata objects](#the-metadata-object) describing the metadata fields available on the underlying sequence data. | | ||
| | `primaryKey` | string | true | The name of the metadata field that serves as the primary key. The value must match one of the entries in `metadata`. | | ||
| | `features` | array | false | A list of [feature objects](#features) that enable additional query capabilities. Defaults to no features. | |
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| ### Metadata Types | ||
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| <MetadataTypesList /> | ||
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| ##### Generating an Index | ||
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| Columns of type `string` support generating an index. | ||
| For columns of type `pango_lineage`, an index is always generated. | ||
| SILO internally stores precomputed bitmaps for those columns so that a query on that column becomes a trivial lookup. | ||
| LAPIS supports the following metadata types: | ||
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| <ul> | ||
| <li> | ||
| <code>string</code>: Arbitrary text values. | ||
| </li> | ||
| <li> |
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Pages on database configuration and preprocessing were outdated. This updates the pages, mostly relying on Claude. It would be great if someone more familiar with the the setups could review and adapt.
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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.