Use genome details and genome slug explain endpoints (#1047)

Switched to using: - The url explainer endpoint of the metadata api, which receives a string that can be either a genome tag or genome uuid, and returns brief information about the genome that tells the client all it needs to know for further api requests - The genome details endpoint to dynamically fetch data that is displayed in right-hand sidebar on the species page.
Ensembl · Nov 7, 2023 · 3305bc9 · 3305bc9
1 parent bf6e83b
commit 3305bc9
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Showing 23 changed files with 373 additions and 648 deletions.
diff --git a/config.ts b/config.ts
@@ -71,7 +71,9 @@ const getBaseApiUrls = (): BaseApiUrls => {
     variationApiUrl:
       process.env.SSR_VARIATION_GRAPHQL_API_URL ??
       `${defaultServerHost}${defaultApiUrls.variationApiUrl}`,
-    metadataApiBaseUrl: defaultApiUrls.metadataApiBaseUrl, // irrelevant for server-side rendering
+    metadataApiBaseUrl:
+      process.env.SSR_METADATA_API_URL ??
+      `${defaultServerHost}${defaultApiUrls.metadataApiBaseUrl}`,
     genomeBrowserBackendBaseUrl: defaultApiUrls.genomeBrowserBackendBaseUrl, // irrelevant for server-side rendering
     refgetBaseUrl: defaultApiUrls.refgetBaseUrl, // irrelevant for server-side rendering
     tracksApiBaseUrl: defaultApiUrls.tracksApiBaseUrl, // irrelevant for server-side rendering

diff --git a/gitlab-ci-templates/.setup-review-template.yaml b/gitlab-ci-templates/.setup-review-template.yaml
@@ -61,6 +61,8 @@
     - sed -i "s#<DEPLOYMENT_ENV>#${TOOLS_API_SERVICE_SLUG}#g" ensembl_tools_api_service.yaml
     - sed -i "s#<DEPLOYMENT_ENV>#${TOOLS_API_SERVICE_SLUG}#g" ensembl_tools_api_ingress.yaml
     - sed -i "s#<SUB_DOMAIN>#${CI_COMMIT_REF_SLUG}#g" ensembl_tools_api_ingress.yaml
+    # ensembl-search-api
+    - sed -i "s#<SUB_DOMAIN>#${CI_COMMIT_REF_SLUG}#g" ensembl_search_hub_ingress.yaml
     # metadata api
     - sed -i "s#<SUB_DOMAIN>#${CI_COMMIT_REF_SLUG}#g" metadata_api_ingress.yaml
   script:
@@ -93,5 +95,7 @@
     - kubectl apply -f ensembl_client_node_service.yaml
     - kubectl apply -f ensembl_client_node_ingress.yaml
     - kubectl apply -f ensembl_client_node_cm.yaml
+    # ensembl searchapi ingress
+    - kubectl apply -f ensembl_search_hub_ingress.yaml
     # metadata api ingress
     - kubectl apply -f metadata_api_ingress.yaml
diff --git a/src/content/app/entity-viewer/EntityViewerPage.tsx b/src/content/app/entity-viewer/EntityViewerPage.tsx
@@ -25,7 +25,7 @@ import { getPathParameters } from 'src/shared/hooks/useUrlParams';
 import useHasMounted from 'src/shared/hooks/useHasMounted';
 
 import {
-  fetchGenomeInfo,
+  fetchGenomeSummary,
   isGenomeNotFoundError
 } from 'src/shared/state/genome/genomeApiSlice';
 import { updatePageMeta } from 'src/shared/state/page-meta/pageMetaSlice';
@@ -92,7 +92,7 @@ export const serverFetch: ServerFetch = async (params) => {
   }
 
   const genomeInfoResponsePromise = dispatch(
-    fetchGenomeInfo.initiate(genomeIdFromUrl)
+    fetchGenomeSummary.initiate(genomeIdFromUrl)
   );
   const { data: genomeInfoData, error: genomeInfoError } =
     await genomeInfoResponsePromise;
@@ -103,7 +103,7 @@ export const serverFetch: ServerFetch = async (params) => {
     };
   }
 
-  const genomeId = genomeInfoData?.genomeId as string; // by this point, genomeId clearly exists
+  const genomeId = genomeInfoData?.genome_id as string; // by this point, genomeId clearly exists
 
   // If the url is just /entity-viewer/:genomeId, update page meta and exit
   if (!entityId) {

diff --git a/...t/app/entity-viewer/contexts/entity-viewer-ids-context/EntityViewerIdsContextProvider.tsx b/...t/app/entity-viewer/contexts/entity-viewer-ids-context/EntityViewerIdsContextProvider.tsx
@@ -26,7 +26,7 @@ import {
 import { useAppSelector } from 'src/store';
 import usePrevious from 'src/shared/hooks/usePrevious';
 import { useUrlParams } from 'src/shared/hooks/useUrlParams';
-import { useGenomeInfoQuery } from 'src/shared/state/genome/genomeApiSlice';
+import { useGenomeSummaryByGenomeSlugQuery } from 'src/shared/state/genome/genomeApiSlice';
 
 import {
   getEntityViewerActiveGenomeId,
@@ -59,18 +59,16 @@ const EntityViewerIdsContextProvider = (props: {
   ]);
   const { genomeId: genomeIdInUrl, entityId: entityIdInUrl } = params;
 
-  const { currentData: genomeInfo, error } = useGenomeInfoQuery(
-    genomeIdInUrl ?? '',
-    {
+  const { currentData: genomeSummary, error } =
+    useGenomeSummaryByGenomeSlugQuery(genomeIdInUrl ?? '', {
       skip: !genomeIdInUrl
-    }
-  );
+    });
 
-  const genomeId = genomeInfo?.genomeId;
+  const genomeId = genomeSummary?.genome_id;
   const genomeIdForUrl =
     genomeIdInUrl ??
-    genomeInfo?.genomeTag ??
-    genomeInfo?.genomeId ??
+    genomeSummary?.genome_tag ??
+    genomeSummary?.genome_id ??
     savedGenomeInfo?.genome_tag ??
     savedGenomeInfo?.genome_id;
 

diff --git a/...ntent/app/genome-browser/contexts/genome-browser-ids-context/useParsedGenomeBrowserUrl.ts b/...ntent/app/genome-browser/contexts/genome-browser-ids-context/useParsedGenomeBrowserUrl.ts
@@ -26,7 +26,7 @@ import { useUrlParams } from 'src/shared/hooks/useUrlParams';
 
 import {
   isGenomeNotFoundError,
-  useGenomeInfoQuery
+  useGenomeSummaryByGenomeSlugQuery
 } from 'src/shared/state/genome/genomeApiSlice';
 
 const useParsedGenomeBrowserUrl = () => {
@@ -39,14 +39,14 @@ const useParsedGenomeBrowserUrl = () => {
   const locationInUrl = urlSearchParams.get('location');
 
   const {
-    currentData: genomeInfo,
+    currentData: genomeSummary,
     isFetching,
     isError,
     error
-  } = useGenomeInfoQuery(genomeIdInUrl ?? '', {
+  } = useGenomeSummaryByGenomeSlugQuery(genomeIdInUrl ?? '', {
     skip: !genomeIdInUrl
   });
-  const genomeId = genomeInfo?.genomeId;
+  const genomeId = genomeSummary?.genome_id;
   const isMissingGenomeId = isError && isGenomeNotFoundError(error);
 
   let focusObjectId;

diff --git a/src/content/app/genome-browser/hooks/useBrowserRouting.test.tsx b/src/content/app/genome-browser/hooks/useBrowserRouting.test.tsx
@@ -39,12 +39,10 @@ import { GenomeBrowserIdsProvider } from '../contexts/genome-browser-ids-context
 const mockChangeFocusObject = jest.fn();
 const mockChangeBrowserLocation = jest.fn();
 
-const mockGenomeSearchApiBaseUrl = 'http://genome-search-api';
 const mockMetadataApiBaseUrl = 'http://metadata-api';
 const mockGenomeBrowserObj = {};
 
 jest.mock('config', () => ({
-  genomeSearchBaseUrl: 'http://genome-search-api',
   metadataApiBaseUrl: 'http://metadata-api',
   coreApiUrl: 'http://graphql-api'
 }));
@@ -66,19 +64,17 @@ jest.mock(
 );
 
 const humanGenomeInfo = {
-  assembly_name: 'GRCh38.p13',
-  common_name: 'Human',
   genome_id: 'homo_sapiens_GCA_000001405_28',
-  scientific_name: 'Homo sapiens',
-  genome_tag: 'grch38'
+  genome_tag: 'grch38',
+  common_name: 'Human',
+  scientific_name: 'Homo sapiens'
 };
 
 const wheatGenomeInfo = {
-  assembly_name: 'IWGSC',
-  common_name: null,
   genome_id: 'triticum_aestivum_GCA_900519105_1',
-  scientific_name: 'Triticum aestivum',
-  genome_tag: 'iwgsc'
+  genome_tag: 'iwgsc',
+  common_name: null,
+  scientific_name: 'Triticum aestivum'
 };
 
 const committedHuman = {
@@ -177,29 +173,24 @@ const renderComponent = ({
 };
 
 const server = setupServer(
-  rest.get(`${mockGenomeSearchApiBaseUrl}/genome/info`, (req, res, ctx) => {
-    const genomeId = req.url.searchParams.get('genome_id');
-
-    if (
-      genomeId === humanGenomeInfo.genome_id ||
-      genomeId === humanGenomeInfo.genome_tag
-    ) {
-      return res(
-        ctx.json({
-          genome_info: [humanGenomeInfo]
-        })
-      );
-    } else if (
-      genomeId === wheatGenomeInfo.genome_id ||
-      genomeId === wheatGenomeInfo.genome_tag
-    ) {
-      return res(
-        ctx.json({
-          genome_info: [wheatGenomeInfo]
-        })
-      );
+  rest.get(
+    `${mockMetadataApiBaseUrl}/genome/:slug/explain`,
+    (req, res, ctx) => {
+      const { slug } = req.params;
+
+      if (
+        slug === humanGenomeInfo.genome_id ||
+        slug === humanGenomeInfo.genome_tag
+      ) {
+        return res(ctx.json(humanGenomeInfo));
+      } else if (
+        slug === wheatGenomeInfo.genome_id ||
+        slug === wheatGenomeInfo.genome_tag
+      ) {
+        return res(ctx.json(wheatGenomeInfo));
+      }
     }
-  }),
+  ),
   rest.get(`${mockMetadataApiBaseUrl}/validate_location`, (req, res, ctx) => {
     const location = req.url.searchParams.get('location');
 

diff --git a/src/content/app/genome-browser/state/focus-object/focusObjectSlice.ts b/src/content/app/genome-browser/state/focus-object/focusObjectSlice.ts
@@ -14,17 +14,11 @@
  * limitations under the License.
  */
 
-import {
-  createAsyncThunk,
-  createSlice,
-  type Action,
-  type ThunkAction
-} from '@reduxjs/toolkit';
+import { createAsyncThunk, createSlice } from '@reduxjs/toolkit';
 
 import isGeneFocusObject from './isGeneFocusObject';
 import * as focusObjectStorageService from 'src/content/app/genome-browser/services/focus-objects/focusObjectStorageService';
 
-import { fetchGenomeInfo } from 'src/shared/state/genome/genomeApiSlice';
 import { getTrackPanelGene } from 'src/content/app/genome-browser/state/api/genomeBrowserApiSlice';
 
 import { shouldFetch } from 'src/shared/helpers/fetchHelper';
@@ -147,28 +141,6 @@ const buildFocusVariantObject = (payload: {
   };
 };
 
-export const fetchExampleFocusObjects =
-  (genomeId: string): ThunkAction<void, RootState, void, Action<string>> =>
-  async (dispatch) => {
-    const genomeInfoResponsePromise = dispatch(
-      fetchGenomeInfo.initiate(genomeId)
-    );
-    const { data: genomeInfoResponse } = await genomeInfoResponsePromise;
-    genomeInfoResponsePromise.unsubscribe();
-
-    if (!genomeInfoResponse) {
-      // failed network request; nothing to do
-      return;
-    }
-
-    const { genomeInfo } = genomeInfoResponse;
-    const exampleFocusObjects = genomeInfo.example_objects;
-
-    exampleFocusObjects.forEach(({ id, type }) => {
-      dispatch(fetchFocusObject({ genomeId, type, objectId: id }));
-    });
-  };
-
 export const fetchFocusObject = createAsyncThunk(
   'genome-browser/fetch-focus-object',
   async (payload: string | FocusObjectIdConstituents, thunkAPI) => {

diff --git a/src/content/app/new-species-selector/types/speciesSearchMatch.ts b/src/content/app/new-species-selector/types/speciesSearchMatch.ts
@@ -14,21 +14,21 @@
  * limitations under the License.
  */
 
-export type SpeciesSearchMatch = {
-  genome_id: string;
-  genome_tag: string | null;
-  common_name: string | null;
-  scientific_name: string;
-  type: {
-    kind: string; // e.g. "population"
-    value: string; // e.g. "European"
-  } | null;
-  is_reference: boolean;
-  assembly: {
-    accession_id: string;
-    name: string;
-    url: string;
-  };
+import type { GenomeInfo } from 'src/shared/state/genome/genomeTypes';
+
+type SearchMatchFieldsFromGenomeInfo =
+  | 'genome_id'
+  | 'genome_tag'
+  | 'common_name'
+  | 'scientific_name'
+  | 'type'
+  | 'is_reference'
+  | 'assembly';
+
+export type SpeciesSearchMatch = Pick<
+  GenomeInfo,
+  SearchMatchFieldsFromGenomeInfo
+> & {
   coding_genes_count: number;
   contig_n50: number | null; // E.coli doesn't have contig n50 in species stats
   has_variation: boolean;

diff --git a/src/content/app/species-selector/state/speciesSelectorEpics.ts b/src/content/app/species-selector/state/speciesSelectorEpics.ts
@@ -36,7 +36,7 @@ import {
   updateCommittedSpecies,
   loadStoredSpecies
 } from 'src/content/app/species-selector/state/speciesSelectorSlice';
-import { fetchGenomeInfo } from 'src/shared/state/genome/genomeApiSlice';
+import { fetchGenomeSummary } from 'src/shared/state/genome/genomeApiSlice';
 
 import type { RootState } from 'src/store';
 import type {
@@ -104,7 +104,7 @@ export const ensureCommittedSpeciesEpic: Epic<Action, Action, RootState> = (
   state$
 ) =>
   action$.pipe(
-    filter(fetchGenomeInfo.matchFulfilled),
+    filter(fetchGenomeSummary.matchFulfilled),
     map((action) => {
       const state = state$.value;
       return {
@@ -114,17 +114,17 @@ export const ensureCommittedSpeciesEpic: Epic<Action, Action, RootState> = (
     }),
     filter(({ action, state }) => {
       // check that the genome is not among committed species
-      const genomeId = action.payload.genomeId;
+      const genomeId = action.payload.genome_id;
       const speciesAlreadyCommitted = getCommittedSpeciesById(state, genomeId);
       return !speciesAlreadyCommitted;
     }),
     map(({ action, state }) => {
-      const { genomeInfo } = action.payload;
+      const genomeInfo = action.payload;
       const newSpecies: CommittedItem = {
         genome_id: genomeInfo.genome_id,
         common_name: genomeInfo.common_name,
         scientific_name: genomeInfo.scientific_name,
-        assembly_name: genomeInfo.assembly_name,
+        assembly_name: genomeInfo.assembly.name,
         genome_tag: genomeInfo.genome_tag,
         isEnabled: true
       };
@@ -180,7 +180,7 @@ export const checkLoadedSpeciesEpic: Epic<Action, Action, RootState> = (
         genome_id: genome.genome_id,
         common_name: genome.common_name,
         scientific_name: genome.scientific_name,
-        assembly_name: genome.assembly_name,
+        assembly_name: genome.assembly.name,
         genome_tag: genome.genome_tag,
         isEnabled: true
       }));

diff --git a/src/content/app/species/SpeciesPage.scss b/src/content/app/species/SpeciesPage.scss
@@ -27,7 +27,3 @@
   font-weight: $bold;
   margin-left: 17px;
 }
-
-.dataForSpecies {
-  color: $medium-dark-grey;
-}
diff --git a/src/content/app/species/SpeciesPage.tsx b/src/content/app/species/SpeciesPage.tsx
@@ -27,7 +27,7 @@ import { updatePageMeta } from 'src/shared/state/page-meta/pageMetaSlice';
 import useHasMounted from 'src/shared/hooks/useHasMounted';
 
 import {
-  fetchGenomeInfo,
+  fetchGenomeSummary,
   isGenomeNotFoundError
 } from 'src/shared/state/genome/genomeApiSlice';
 import { getPathParameters, useUrlParams } from 'src/shared/hooks/useUrlParams';
@@ -79,17 +79,16 @@ export const serverFetch: ServerFetch = async (params) => {
   ) as { genomeId: string };
 
   const genomeInfoResponsePromise = dispatch(
-    fetchGenomeInfo.initiate(genomeIdFromUrl)
+    fetchGenomeSummary.initiate(genomeIdFromUrl)
   );
-  const { data: genomeInfoData, error: genomeInfoError } =
+  const { data: genomeInfo, error: genomeInfoError } =
     await genomeInfoResponsePromise;
 
   if (isGenomeNotFoundError(genomeInfoError)) {
     return {
       status: 404
     };
   } else {
-    const genomeInfo = genomeInfoData?.genomeInfo;
     const title = genomeInfo ? getDisplayName(genomeInfo) : defaultTitle;
     dispatch(
       updatePageMeta({