fix(lapis2-docs): use relative links so that they work when deployed …

…behind a proxy #725

lapis2-docs/README.md

@@ -8,7 +8,7 @@ This documentation is a website built with
 | Command                   | Action                                           |
 |:--------------------------|:-------------------------------------------------|
 | `npm install`             | Installs dependencies                            |
-| `npm run dev`             | Starts local dev server at `localhost:3000`      |
+| `npm run dev`             | Starts local dev server at `localhost:4321`      |
 | `npm run build`           | Build your production site to `./dist/`          |
 | `npm run preview`         | Preview your build locally, before deploying     |
 | `npm run astro ...`       | Run CLI commands like `astro add`, `astro check` |

lapis2-docs/astro.config.mjs

@@ -36,35 +36,35 @@ export default defineConfig({
                     items: [
                         {
                             label: 'Introduction',
-                            link: '/references/introduction/',
+                            link: '/references/introduction',
                         },
                         {
                             label: 'Fields',
-                            link: '/references/fields/',
+                            link: '/references/fields',
                         },
                         {
                             label: 'Filters',
-                            link: '/references/filters/',
+                            link: '/references/filters',
                         },
                         {
                             label: 'Additional Request Properties',
-                            link: '/references/additional-request-properties/',
+                            link: '/references/additional-request-properties',
                         },
                         {
                             label: 'Open API / Swagger',
-                            link: '/references/open-api-definition/',
+                            link: '/references/open-api-definition',
                         },
                         {
                             label: 'Database Config',
-                            link: '/references/database-config/',
+                            link: '/references/database-config',
                         },
                         {
                             label: 'Reference Genomes',
-                            link: '/references/reference-genomes/',
+                            link: '/references/reference-genomes',
                         },
                         {
                             label: 'Nucleotide And Amino Acid Symbols',
-                            link: '/references/nucleotide-and-amino-acid-symbols/',
+                            link: '/references/nucleotide-and-amino-acid-symbols',
                         },
                     ],
                 },
@@ -73,37 +73,37 @@ export default defineConfig({
                     items: filterAvailableConcepts([
                         {
                             label: 'Data versions',
-                            link: '/concepts/data-versions/',
+                            link: '/concepts/data-versions',
                         },
                         {
                             label: 'Mutation filters',
-                            link: '/concepts/mutation-filters/',
+                            link: '/concepts/mutation-filters',
                         },
                         {
                             label: 'Ambiguous symbols',
-                            link: '/concepts/ambiguous-symbols/',
+                            link: '/concepts/ambiguous-symbols',
                         },
                         {
                             label: 'Pango lineage query',
-                            link: '/concepts/pango-lineage-query/',
+                            link: '/concepts/pango-lineage-query',
                             onlyIfFeature: 'sarsCoV2VariantQuery',
                         },
                         {
                             label: 'Request methods: GET and POST',
-                            link: '/concepts/request-methods/',
+                            link: '/concepts/request-methods',
                         },
                         {
                             label: 'Response format',
-                            link: '/concepts/response-format/',
+                            link: '/concepts/response-format',
                         },
                         {
                             label: 'Variant query',
-                            link: '/concepts/variant-query/',
+                            link: '/concepts/variant-query',
                             onlyIfFeature: 'sarsCoV2VariantQuery',
                         },
                         {
                             label: 'Request Id',
-                            link: '/concepts/request-id/',
+                            link: '/concepts/request-id',
                         },
                     ]),
                 },

lapis2-docs/src/components/Configuration/MetadataTypesList.astro

@@ -1,6 +1,7 @@
 ---
 import { OnlyIf } from '../OnlyIf.tsx';
 import { getConfig } from '../../config.ts';
+import BaseAwareLink from '../BaseAwareLink.astro';
 ---
 
 SILO currently supports the following metadata types:
@@ -13,7 +14,7 @@ SILO currently supports the following metadata types:
         <code>pango_lineage</code>: Systematic classification of lineage with inheritance structure that can be computed
         for some pathogens.
         <OnlyIf condition={!!getConfig().schema.metadata.find((m) => m.type === 'pango_lineage')}>
-            Also see <a href='/concepts/pango-lineage-query'>here</a>.
+            Also see <BaseAwareLink href='/concepts/pango-lineage-query'>here</BaseAwareLink>.
         </OnlyIf>
     </li>
     <li><code>date</code>: Values must be valid dates in the form <code>YYYY-MM-DD</code>.</li>

lapis2-docs/src/content/docs/concepts/ambiguous-symbols.mdx

@@ -3,7 +3,7 @@ title: Ambiguous symbols
 description: Explanation how ambiguous reads are handled in the data
 ---
 
-[The symbols page](/references/nucleotide-and-amino-acid-symbols)
+[The symbols page](../references/nucleotide-and-amino-acid-symbols)
 lists all symbols that the underlying sequence files in `.FASTA` format can contain.
 The ambiguous symbols arise from imperfect reads in the sequencer.
 

lapis2-docs/src/content/docs/concepts/mutation-filters.mdx

@@ -23,6 +23,6 @@ i.e. has the same base as the reference genome at the specified position.
 
 :::note
 Both, nucleotide and amino acid mutation filter, also support `Maybe` queries.
-Read more in [ambiguous symbols](/concepts/ambiguous-symbols).
+Read more in [ambiguous symbols](../concepts/ambiguous-symbols).
 **Example:** <MaybeAminoAcidMutationExample/>.
 :::

lapis2-docs/src/content/docs/concepts/pango-lineage-query.mdx

@@ -4,18 +4,19 @@ description: Pango lineage query
 ---
 
 import { OnlyIf } from '../../../components/OnlyIf.tsx';
-import { getConfig } from '../../../config.ts';
+import { getConfig, hasFeature } from '../../../config.ts';
 
 <OnlyIf condition={!!getConfig().schema.metadata.find(m => m.type === 'pango_lineage')}>
 
 Pango lineage names inherit the hierarchical nature of genetic lineages. For example, B.1.1 is a sub-lineage of B.1.
 More information about the pango nomenclature can be found on the website of the
 [Pango network](https://www.pango.network/).
 
-With the pangoLineage filter and in [variant queries](/concepts/variant-query/), it is possible to not only filter for a very
-specific lineage but also to include its sub-lineages. To include sub-lineages, add a `*` at the end. For example,
-writing B.1.351 will only give samples of B.1.351. Writing B.1.351* or B.1.351.* (there is no difference between these
-two options) will return B.1.351, B.1.351.1, B.1.351.2, etc.
+With the pangoLineage filter<OnlyIf condition={hasFeature('sarsCoV2VariantQuery')}> and in [variant queries](../concepts/variant-query/)</OnlyIf>,
+it is possible to not only filter for a very specific lineage but also to include its sub-lineages.
+To include sub-lineages, add a `*` at the end.
+For example, writing B.1.351 will only give samples of B.1.351.
+Writing B.1.351* or B.1.351.* (there is no difference between these two options) will return B.1.351, B.1.351.1, B.1.351.2, etc.
 
 An official pango lineage name can only have at most three number components. A sub-lineage of a lineage with a
 maximal-length name (e.g., B.1.617.2) will get an alias. A list of aliases can be found

lapis2-docs/src/content/docs/concepts/request-id.mdx

@@ -13,7 +13,7 @@ This will greatly simplify identifying the problem in our log files.
 
 You can provide a request id in the request as an HTTP header `X-Request-Id`.
 This is useful if you want to correlate requests in your own log files with the LAPIS log files
-to track problems across systems.
+to track problems across systems, e.g. if your own API calls LAPIS.
 
 :::caution
 If you use the `X-Request-Id` header, make sure that the value is unique.

lapis2-docs/src/content/docs/concepts/request-methods.mdx

@@ -53,9 +53,7 @@ example code for doing it with curl and from R and Python:
   </Tab>
 </TabsBox>
 
-{/* prettier-ignore */}
 :::note
-This is a general example and will only work on instances that have the fields `region`,
-`country`, and `date`. Check out the [fields](../../references/fields/) and [filters](../../references/filters/) page to
-see information about this instance. {/* prettier-ignore */}
+This is a general example and will only work on instances that have the fields `region`, `country`, and `date`.
+Check out the [fields](../references/fields/) and [filters](../references/filters/) page to see information about this instance.
 :::

lapis2-docs/src/content/docs/concepts/response-format.mdx

@@ -4,7 +4,7 @@ description: Response format
 ---
 
 The response format is tailored to each specific endpoint.
-To view the response format for a particular endpoint, please visit our [Swagger UI](/references/open-api-definition/).
+To view the response format for a particular endpoint, please visit our [Swagger UI](../references/open-api-definition/).
 Once there, select the endpoint of interest and scroll down to the "Responses" section.
 A '200' response code indicates a successful request, while any other code signifies an error.
 
@@ -15,7 +15,7 @@ Genomic sequences (such as those from `unalignedNucleotideSequences`, `alignedAm
 
 ## Example
 
-To understand the response from the `nucleotideMutation` endpoint, refer to the relevant section in the Swagger UI:
+To understand the response of the `nucleotideMutation` endpoint, refer to the relevant section in the Swagger UI:
 
 ![Example nucleotide mutation response](../../../images/concepts/example_nucleotide_mutation_response_200.png)
 
@@ -30,5 +30,5 @@ Fields marked with an asterisk (\*) are always included in the response; unmarke
 
 :::note
 Every response, regardless of format, includes the data version as it is crucial information. For more details, visit the
-[data versions page](/concepts/data-versions/).
+[data versions page](../concepts/data-versions/).
 :::

lapis2-docs/src/content/docs/concepts/variant-query.mdx

@@ -48,14 +48,14 @@ Get the sequences that fulfill exactly 2 out of 4 conditions:
 [exactly-2-of: 123A & 234T, !234T, S:345- | S:346-, [2-of: 222T, 333G, 444A, 555C]]
 ```
 
-For SARS-CoV-2, it is also possible to use [Pango lineage queries](/concepts/pango-lineage-query/) (either called by pangolin
+For SARS-CoV-2, it is also possible to use [Pango lineage queries](../concepts/pango-lineage-query/) (either called by pangolin
 or by Nextclade) and filter by Nextstrain clades:
 
 ```
 BA.5* | nextcladePangoLineage:BA.5* | nextstrainClade:22B
 ```
 
-LAPIS supports a ternary logic to query [ambiguous nucleotide symbols](/concepts/ambiguous-symbols/).
+LAPIS supports a ternary logic to query [ambiguous nucleotide symbols](../concepts/ambiguous-symbols/).
 
 ```
 MAYBE(123W)

lapis2-docs/src/content/docs/getting-started/introduction.mdx

@@ -20,7 +20,7 @@ to answer genomic epidemiological questions. Main features include:
     engine.
 
 :::tip
-To get started, you can use our [**interactive wizard**](/getting-started/generate-your-request/) to generate your query.
+To get started, you can use our [**interactive wizard**](./generate-your-request/) to generate your query.
 We provide code examples for Python and R.
 :::
 
@@ -43,5 +43,5 @@ If you have any trouble, feel free to reach out to us.
 
 :::note
 This documentation also includes a section about how to set up your own instance of LAPIS.
-Refer to [this tutorial](/maintainer-docs/tutorials/start-lapis-and-silo/) for a quick start guide.
+Refer to [this tutorial](../maintainer-docs/tutorials/start-lapis-and-silo/) for a quick start guide.
 :::

lapis2-docs/src/content/docs/maintainer-docs/references/database-configuration.mdx

@@ -9,8 +9,8 @@ import { hasFeature } from '../../../../config.ts';
 
 LAPIS and SILO need a `database_config.yaml`.
 It's main purpose is to define the database schema for the sequence metadata.
-See the [tutorial](/maintainer-docs/tutorials/start-lapis-and-silo#writing-configuration) for an example,
-or use our [config generator](/maintainer-docs/tutorials/generate-your-config) to generate your own config.
+See the [tutorial](../tutorials/start-lapis-and-silo#writing-configuration) for an example,
+or use our [config generator](../tutorials/generate-your-config) to generate your own config.
 More examples can be found in our tests.
 
 The database config is considered static configuration that doesn't change with data updates.
@@ -46,11 +46,11 @@ it will be beneficial to set `dateToSortBy` to that column.
 
 The metadata object permits the following fields:
 
-| Key           | Type    | Required | Description                                                                                         |
-| ------------- | ------- | -------- | --------------------------------------------------------------------------------------------------- |
-| name          | string  | true     | The name of the feature.                                                                            |
-| type          | enum    | true     | The [type of the metadata](#metadata-types).                                                        |
-| generateIndex | boolean | false    | Some [metadata types](#metadata-types) permit generating an index for faster queries on the column. |
+| Key           | Type    | Required | Description                                           |
+| ------------- | ------- | -------- | ----------------------------------------------------- |
+| name          | string  | true     | The name of the feature.                              |
+| type          | enum    | true     | The [type of the metadata](#metadata-types).          |
+| generateIndex | boolean | false    | See [Generating an index](#generating-an-index) below |
 
 ### Metadata Types
 
@@ -78,4 +78,4 @@ The feature object permits the following fields:
 Currently, there is only one available feature: `sarsCoV2VariantQuery`.
 This enables a specialized query language for SARS-CoV-2 instances.
 
-<OnlyIf condition={hasFeature('sarsCoV2VariantQuery')}>See [variant queries](/concepts/variant-query).</OnlyIf>
+<OnlyIf condition={hasFeature('sarsCoV2VariantQuery')}>See [variant queries](../../concepts/variant-query).</OnlyIf>

lapis2-docs/src/content/docs/maintainer-docs/references/preprocessing.mdx

@@ -70,7 +70,7 @@ All filenames are relative to the `inputDirectory`.
     The file with Pango lineage definitions, relative to the inputDirectory.
     See the section on the [Pango Lineage Definition File below](#the-pango-lineage-definition-file) for details.
 -   `referenceGenomeFilename`:
-    The file with [reference genomes](/maintainer-docs/references/reference-genomes), relative to the inputDirectory.
+    The file with [reference genomes](../references/reference-genomes), relative to the inputDirectory.
 
 ## `NDJSON` Format
 
@@ -90,7 +90,7 @@ Each line in the NDJSON file must be a JSON object with the following keys:
 
 :::note
 You must configure two metadata columns for insertions in the
-[database configuration](/maintainer-docs/references/database-configuration)
+[database configuration](../references/database-configuration)
 with the exact names and types as in this snippet:
 
 ```yaml
@@ -109,20 +109,20 @@ Otherwise, SILO will not recognize insertions in the NDJSON format.
 
 The sequences object contains sequences for each segment or gene.
 It must include all `nucleotideSequences` (or `genes`, respectively) specified in the
-[reference genomes](/maintainer-docs/references/reference-genomes)
+[reference genomes](../references/reference-genomes)
 as keys.
 Its values are the sequences as strings of
-[valid symbols](/references/nucleotide-and-amino-acid-symbols)
+[valid symbols](../../references/nucleotide-and-amino-acid-symbols)
 or `null`.
 
 #### Insertions Object
 
 The insertions object contains a list of insertions for each segment or gene.
 It must include all `nucleotideSequences` (or `genes`, respectively) specified in the
-[reference genomes](/maintainer-docs/references/reference-genomes)
+[reference genomes](../references/reference-genomes)
 as keys.
 Its values are arrays of strings in the format `<position>:<insertion>`.
-The insertions must consist of [valid symbols](/references/nucleotide-and-amino-acid-symbols).
+The insertions must consist of [valid symbols](../../references/nucleotide-and-amino-acid-symbols).
 
 #### Example of the Schema
 
@@ -184,7 +184,7 @@ SILO expects the following files in the `inputDirectory`:
 ### Metadata File
 
 The metadata file must be a TSV (tab-separated values) file.
-Its columns must correspond to the metadata fields specified in the [database configuration](/maintainer-docs/references/database-configuration).
+Its columns must correspond to the metadata fields specified in the [database configuration](../references/database-configuration).
 Empty values will be interpreted as `null`.
 
 #### Example
@@ -228,7 +228,7 @@ The filenames must follow this pattern:
     The `gene_` prefix is configurable in the preprocessing configuration via `genePrefix`.
 
 There must be one corresponding file for every segment and gene defined in the
-[reference genomes](/maintainer-docs/references/reference-genomes).
+[reference genomes](../references/reference-genomes).
 
 The header in the FASTA files must match the `primaryKey` column in the metadata file.
 There must be a one-to-one correspondence between entries in the metadata file and sequences in the FASTA files.

lapis2-docs/src/content/docs/maintainer-docs/references/reference-genomes.mdx

@@ -39,7 +39,7 @@ The file must contain a JSON object with two keys:
 
 A reference sequence is a JSON object that permits the following keys:
 
-| Key      | Type   | Required | Description                                                                                     |
-| -------- | ------ | -------- | ----------------------------------------------------------------------------------------------- |
-| name     | string | true     | The name of the sequence. Must be unique.                                                       |
-| sequence | string | true     | The sequence. See [here for allowed characters](/references/nucleotide-and-amino-acid-symbols). |
+| Key      | Type   | Required | Description                                                                                          |
+| -------- | ------ | -------- | ---------------------------------------------------------------------------------------------------- |
+| name     | string | true     | The name of the sequence. Must be unique.                                                            |
+| sequence | string | true     | The sequence. See [here for allowed characters](../../references/nucleotide-and-amino-acid-symbols). |