feat(docs): generate correct URLs for nucleotide sequences endpoints …

…in multi-segmented case #521

lapis2-docs/.env.example

@@ -1,3 +1,4 @@
 # Create a .env file with this input might NOT work. You might need to properly set CONFIG_FILE as an
 # environment variable.
-CONFIG_FILE=../lapis2/src/test/resources/config/testDatabaseConfig.yaml
+CONFIG_FILE=../siloLapisTests/testData/testDatabaseConfig.yaml
+REFERENCE_GENOMES_FILE=../siloLapisTests/testData/reference_genomes.json

lapis2-docs/Dockerfile

@@ -6,6 +6,7 @@ RUN apk update && apk add curl
 
 COPY . .
 ENV CONFIG_FILE=/config/database_config.yaml
+ENV REFERENCE_GENOMES_FILE=/config/reference_genomes.json
 
 EXPOSE 3000
 VOLUME /config

lapis2-docs/README.md

@@ -17,7 +17,7 @@ This documentation is a website built with
 For running and building the website, the environment variables `LAPIS_URL` and `CONFIG_FILE` must be set, e.g.:
 
 ```shell
-CONFIG_FILE=../siloLapisTests/testData/testDatabaseConfig.yaml LAPIS_URL=http://localhost:8080 npm run dev
+CONFIG_FILE=../siloLapisTests/testData/testDatabaseConfig.yaml REFERENCE_GENOMES_FILE=../siloLapisTests/testData/reference_genomes.json LAPIS_URL=http://localhost:8080 npm run dev
 ```
 
 ## Deploying

lapis2-docs/package.json

@@ -27,7 +27,8 @@
         "swagger-ui": "^5.10.5",
         "swagger-ui-react": "^5.10.5",
         "tailwindcss": "^3.3.7",
-        "yaml": "^2.3.4"
+        "yaml": "^2.3.4",
+        "zod": "^3.22.4"
     },
     "devDependencies": {
         "@astrojs/check": "^0.3.2",

lapis2-docs/src/components/QueryGenerator/QueryGenerator.tsx

@@ -5,15 +5,17 @@ import { Result } from './Result';
 import { type Config } from '../../config';
 import { type OrderByLimitOffset, OrderLimitOffsetSelection } from './OrderLimitOffsetSelection.tsx';
 import { getInitialQueryState, type QueryTypeSelectionState } from './QueryTypeSelectionState.ts';
+import { type ReferenceGenomes } from '../../reference_genomes.ts';
 
 type Props = {
     config: Config;
+    referenceGenomes: ReferenceGenomes;
     lapisUrl: string;
 };
 
-export const QueryGenerator = ({ config, lapisUrl }: Props) => {
+export const QueryGenerator = ({ config, referenceGenomes, lapisUrl }: Props) => {
     const [step, setStep] = useState(0);
-    const [queryType, setQueryType] = useState<QueryTypeSelectionState>(getInitialQueryState());
+    const [queryType, setQueryType] = useState<QueryTypeSelectionState>(getInitialQueryState(referenceGenomes));
     const [filters, setFilters] = useState<Filters>(new Map());
     const [orderByLimitOffset, setOrderByLimitOffset] = useState<OrderByLimitOffset>({
         orderBy: [],
@@ -33,7 +35,14 @@ export const QueryGenerator = ({ config, lapisUrl }: Props) => {
             </div>
 
             <div className='mt-8'>
-                {step === 0 && <QueryTypeSelection config={config} state={queryType} onStateChange={setQueryType} />}
+                {step === 0 && (
+                    <QueryTypeSelection
+                        config={config}
+                        referenceGenomes={referenceGenomes}
+                        state={queryType}
+                        onStateChange={setQueryType}
+                    />
+                )}
                 {step === 1 && <FiltersSelection config={config} filters={filters} onFiltersChange={setFilters} />}
                 {step === 2 && (
                     <OrderLimitOffsetSelection

lapis2-docs/src/components/QueryGenerator/QueryTypeSelection.tsx

@@ -1,20 +1,23 @@
-import type { ReactNode } from 'react';
+import type { Dispatch, ReactNode, SetStateAction } from 'react';
 import type { Config } from '../../config';
 import { CheckBoxesWrapper, ContainerWrapper, LabeledCheckBox, LabelWrapper } from './styled-components';
 import {
     type AlignmentType,
     alignmentTypes,
     type DetailsType,
+    MULTI_SEGMENTED,
     type QueryTypeSelectionState,
     type Selection,
     type SequenceType,
     sequenceTypes,
 } from './QueryTypeSelectionState.ts';
+import { type ReferenceGenomes } from '../../reference_genomes.ts';
 
 type Props = {
     config: Config;
+    referenceGenomes: ReferenceGenomes;
     state: QueryTypeSelectionState;
-    onStateChange: (state: QueryTypeSelectionState) => void;
+    onStateChange: Dispatch<SetStateAction<QueryTypeSelectionState>>;
 };
 
 export const QueryTypeSelection = (props: Props) => {
@@ -274,14 +277,26 @@ const Insertions = ({ state, onStateChange }: Props) => {
     );
 };
 
-const NucleotideSequences = ({ state, onStateChange }: Props) => {
+const NucleotideSequences = ({ referenceGenomes, state, onStateChange }: Props) => {
     const changeType = (type: AlignmentType) => {
         onStateChange({
             ...state,
             nucleotideSequences: { ...state.nucleotideSequences, type },
         });
     };
 
+    const changeSegment = (segmentName: string) =>
+        onStateChange((prev) => ({
+            ...prev,
+            nucleotideSequences: {
+                ...prev.nucleotideSequences,
+                segment: {
+                    type: MULTI_SEGMENTED,
+                    segmentName,
+                },
+            },
+        }));
+
     return (
         <ContainerWrapper>
             <div>
@@ -299,12 +314,29 @@ const NucleotideSequences = ({ state, onStateChange }: Props) => {
                         />
                     ))}
                 </CheckBoxesWrapper>
+                {state.nucleotideSequences.segment.type === MULTI_SEGMENTED && (
+                    <>
+                        <LabelWrapper>Which segments are you interested in?</LabelWrapper>
+                        <select
+                            className='input input-bordered w-full max-w-xs'
+                            disabled={state.selection !== 'nucleotideSequences'}
+                            value={state.nucleotideSequences.segment.segmentName}
+                            onChange={(e) => changeSegment(e.target.value)}
+                        >
+                            {referenceGenomes.nucleotideSequences.map((segment) => (
+                                <option value={segment.name} key={segment.name}>
+                                    {segment.name}
+                                </option>
+                            ))}
+                        </select>
+                    </>
+                )}
             </div>
         </ContainerWrapper>
     );
 };
 
-const AminoAcidSequences = ({ state, onStateChange }: Props) => {
+const AminoAcidSequences = ({ referenceGenomes, state, onStateChange }: Props) => {
     const changeGene = (gene: string) => {
         onStateChange({
             ...state,
@@ -316,13 +348,18 @@ const AminoAcidSequences = ({ state, onStateChange }: Props) => {
         <ContainerWrapper>
             <div>
                 <LabelWrapper>Which gene/reading frame are you interested in?</LabelWrapper>
-                <input
-                    type='text'
+                <select
                     className='input input-bordered w-full max-w-xs'
                     disabled={state.selection !== 'aminoAcidSequences'}
                     value={state.aminoAcidSequences.gene}
                     onChange={(e) => changeGene(e.target.value)}
-                />
+                >
+                    {referenceGenomes.genes.map((gene) => (
+                        <option value={gene.name} key={gene.name}>
+                            {gene.name}
+                        </option>
+                    ))}
+                </select>
             </div>
         </ContainerWrapper>
     );

lapis2-docs/src/components/QueryGenerator/QueryTypeSelectionState.ts

@@ -1,5 +1,6 @@
 import type { Config, MetadataType } from '../../config.ts';
 import type { ResultField, ResultFieldType } from '../../utils/code-generators/types.ts';
+import { isMultiSegmented, type ReferenceGenomes } from '../../reference_genomes.ts';
 
 export type Selection = keyof Omit<QueryTypeSelectionState, 'selection'>;
 
@@ -9,6 +10,9 @@ export type DetailsType = 'all' | 'selected';
 export const alignmentTypes = ['unaligned', 'aligned'] as const;
 export type AlignmentType = (typeof alignmentTypes)[number];
 
+export const SINGLE_SEGMENTED = 'singleSegmented' as const;
+export const MULTI_SEGMENTED = 'multiSegmented' as const;
+
 export type QueryTypeSelectionState = {
     selection: Selection;
     aggregatedAll: {};
@@ -28,13 +32,21 @@ export type QueryTypeSelectionState = {
     };
     nucleotideSequences: {
         type: AlignmentType;
+        segment:
+            | {
+                  type: typeof SINGLE_SEGMENTED;
+              }
+            | {
+                  type: typeof MULTI_SEGMENTED;
+                  segmentName: string;
+              };
     };
     aminoAcidSequences: {
         gene: string;
     };
 };
 
-export function getInitialQueryState(): QueryTypeSelectionState {
+export function getInitialQueryState(referenceGenomes: ReferenceGenomes): QueryTypeSelectionState {
     return {
         selection: 'aggregatedAll',
         aggregatedAll: {},
@@ -54,9 +66,12 @@ export function getInitialQueryState(): QueryTypeSelectionState {
         },
         nucleotideSequences: {
             type: 'unaligned',
+            segment: isMultiSegmented(referenceGenomes)
+                ? { type: MULTI_SEGMENTED, segmentName: referenceGenomes.nucleotideSequences[0].name }
+                : { type: SINGLE_SEGMENTED },
         },
         aminoAcidSequences: {
-            gene: '',
+            gene: referenceGenomes.genes[0].name,
         },
     };
 }
@@ -93,9 +108,7 @@ function getFieldsThatAreAlwaysPresent(selection: Selection): ResultField[] {
                 { name: 'count', type: 'integer', nullable: false },
             ];
         case 'details':
-            return [];
         case 'nucleotideSequences':
-            return [];
         case 'aminoAcidSequences':
             return [];
     }

lapis2-docs/src/components/QueryGenerator/Result.tsx

@@ -8,7 +8,7 @@ import type { Config } from '../../config';
 import { useState } from 'react';
 import type { ResultField } from '../../utils/code-generators/types';
 import { ContainerWrapper, LabelWrapper } from './styled-components';
-import { getResultFields, type QueryTypeSelectionState } from './QueryTypeSelectionState.ts';
+import { getResultFields, MULTI_SEGMENTED, type QueryTypeSelectionState } from './QueryTypeSelectionState.ts';
 import type { OrderByLimitOffset } from './OrderLimitOffsetSelection.tsx';
 
 type Props = {
@@ -125,11 +125,11 @@ function constructPostQuery({ queryType, filters, config, lapisUrl, orderByLimit
             }
             break;
         case 'mutations':
-            endpoint += queryType.mutations.type === 'nucleotide' ? 'nuc-mutations' : 'aa-mutations';
+            endpoint += queryType.mutations.type === 'nucleotide' ? 'nucleotideMutations' : 'aminoAcidMutations';
             body.minProportion = queryType.mutations.minProportion;
             break;
         case 'insertions':
-            endpoint += queryType.insertions.type === 'nucleotide' ? 'nuc-insertions' : 'aa-insertions';
+            endpoint += queryType.insertions.type === 'nucleotide' ? 'nucleotideInsertions' : 'aminoAcidInsertions';
             break;
         case 'details':
             endpoint += 'details';
@@ -139,11 +139,16 @@ function constructPostQuery({ queryType, filters, config, lapisUrl, orderByLimit
             }
             break;
         case 'nucleotideSequences':
-            // TODO(#521): multi segment case
-            endpoint += queryType.nucleotideSequences.type === 'unaligned' ? 'nuc-sequences' : 'nuc-sequences-aligned';
+            endpoint +=
+                queryType.nucleotideSequences.type === 'unaligned'
+                    ? 'nucleotideSequences'
+                    : 'alignedNucleotideSequences';
+            if (queryType.nucleotideSequences.segment.type === MULTI_SEGMENTED) {
+                endpoint += `/${queryType.nucleotideSequences.segment.segmentName}`;
+            }
             break;
         case 'aminoAcidSequences':
-            endpoint += `aa-sequences-aligned/${queryType.aminoAcidSequences.gene}`;
+            endpoint += `alignedAminoAcidSequences/${queryType.aminoAcidSequences.gene}`;
             break;
     }
     for (let [name, value] of filters) {

lapis2-docs/src/content/docs/getting-started/generate-your-request.mdx

@@ -5,7 +5,7 @@ description: A step-by-step wizard to help you generate a request
 
 import { getConfig } from '../../../config.ts';
 import { getLapisUrl } from '../../../lapisUrl.js';
-
+import { getReferenceGenomes } from "../../../reference_genomes.js";
 import { QueryGenerator } from '../../../components/QueryGenerator/QueryGenerator.tsx';
 
-<QueryGenerator client:load config={getConfig()} lapisUrl={getLapisUrl()} />
+<QueryGenerator client:load config={getConfig()} referenceGenomes={getReferenceGenomes()} lapisUrl={getLapisUrl()} />

lapis2-docs/src/reference_genomes.ts

@@ -0,0 +1,31 @@
+import fs from 'fs';
+import { z } from 'zod';
+
+const referenceSequenceSchema = z.object({
+    name: z.string(),
+    sequence: z.string(),
+});
+
+const referenceGenomesSchema = z.object({
+    nucleotideSequences: z.array(referenceSequenceSchema),
+    genes: z.array(referenceSequenceSchema),
+});
+
+export type ReferenceGenomes = z.infer<typeof referenceGenomesSchema>;
+
+let _referenceGenomes: ReferenceGenomes | null = null;
+
+export function getReferenceGenomes(): ReferenceGenomes {
+    if (_referenceGenomes === null) {
+        const configFilePath = process.env.REFERENCE_GENOMES_FILE;
+        if (configFilePath === undefined) {
+            throw new Error('Please set the environment variable REFERENCE_GENOMES_FILE.');
+        }
+        _referenceGenomes = referenceGenomesSchema.parse(JSON.parse(fs.readFileSync(configFilePath, 'utf8')));
+    }
+    return _referenceGenomes;
+}
+
+export function isMultiSegmented(referenceGenomes: ReferenceGenomes): boolean {
+    return referenceGenomes.nucleotideSequences.length > 1;
+}

lapis2-docs/test-docker-compose.yml

@@ -6,6 +6,7 @@ services:
       - "3000:3000"
     volumes:
       - ../siloLapisTests/testData/testDatabaseConfig.yaml:/config/database_config.yaml
+      - ../siloLapisTests/testData/reference_genomes.json:/config/reference_genomes.json
     environment:
       LAPIS_URL: localhost:8080
       BASE_URL: /docs/

lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt

@@ -20,6 +20,7 @@ import org.genspectrum.lapis.openApi.DataFormat
 import org.genspectrum.lapis.openApi.DetailsFields
 import org.genspectrum.lapis.openApi.DetailsOrderByFields
 import org.genspectrum.lapis.openApi.FieldsToAggregateBy
+import org.genspectrum.lapis.openApi.Gene
 import org.genspectrum.lapis.openApi.INSERTIONS_REQUEST_SCHEMA
 import org.genspectrum.lapis.openApi.InsertionsOrderByFields
 import org.genspectrum.lapis.openApi.LapisAggregatedResponse
@@ -1269,7 +1270,9 @@ class LapisController(
     @GetMapping("$ALIGNED_AMINO_ACID_SEQUENCES_ROUTE/{gene}", produces = ["text/x-fasta"])
     @LapisAlignedAminoAcidSequenceResponse
     fun getAlignedAminoAcidSequence(
-        @PathVariable(name = "gene", required = true) gene: String,
+        @PathVariable(name = "gene", required = true)
+        @Gene
+        gene: String,
         @PrimitiveFieldFilters
         @RequestParam
         sequenceFilters: GetRequestSequenceFilters?,
@@ -1314,7 +1317,9 @@ class LapisController(
     @PostMapping("$ALIGNED_AMINO_ACID_SEQUENCES_ROUTE/{gene}", produces = ["text/x-fasta"])
     @LapisAlignedAminoAcidSequenceResponse
     fun postAlignedAminoAcidSequence(
-        @PathVariable(name = "gene", required = true) gene: String,
+        @PathVariable(name = "gene", required = true)
+        @Gene
+        gene: String,
         @Parameter(schema = Schema(ref = "#/components/schemas/$ALIGNED_AMINO_ACID_SEQUENCE_REQUEST_SCHEMA"))
         @RequestBody
         request: SequenceFiltersRequest,