Use Refget and thoas for instant download (#437)

src/ensembl/src/content/app/browser/zmenu/Zmenu.test.tsx

@@ -24,12 +24,11 @@ import ZmenuContent from './ZmenuContent';
 import { createZmenuContent } from 'tests/fixtures/browser';
 
 jest.mock('./ZmenuContent', () => () => <div>ZmenuContent</div>);
+jest.mock('./ZmenuInstantDownload', () => () => (
+  <div>ZmenuInstantDownload</div>
+));
 
 describe('<Zmenu />', () => {
-  afterEach(() => {
-    jest.resetAllMocks();
-  });
-
   const defaultProps: ZmenuProps = {
     anchor_coordinates: {
       x: 490,
@@ -47,6 +46,8 @@ describe('<Zmenu />', () => {
   let wrapper: any;
 
   beforeEach(() => {
+    jest.resetAllMocks();
+
     wrapper = mount(<Zmenu {...defaultProps} />);
   });
 

src/ensembl/src/content/app/browser/zmenu/ZmenuInstantDownload.tsx

@@ -31,6 +31,7 @@ type Props = {
 };
 
 const ZmenuInstantDownload = (props: Props) => {
+  const genomeId = getGenomeId(props.id);
   const transcriptId = getStableId(props.id);
   const params = {
     endpoint: `/lookup/id/${transcriptId}?content-type=application/json;expand=1`,
@@ -58,6 +59,7 @@ const ZmenuInstantDownload = (props: Props) => {
 
   return (
     <InstantDownloadTranscript
+      genomeId={genomeId}
       {...preparePayload(data as TranscriptInResponse)}
       layout="vertical"
     />
@@ -65,6 +67,7 @@ const ZmenuInstantDownload = (props: Props) => {
 };
 
 // TODO: we may want to move this to a common helper file that deals with messaging with Genome Browser
+const getGenomeId = (id: string) => id.split(':').shift();
 const getStableId = (id: string) => id.split(':').pop();
 
 const preparePayload = (transcript: TranscriptInResponse) => {

src/ensembl/src/content/app/entity-viewer/EntityViewer.tsx

@@ -15,12 +15,12 @@
  */
 
 import React, { useEffect } from 'react';
-import { ApolloClient, InMemoryCache, ApolloProvider } from '@apollo/client';
-import { connect } from 'react-redux';
-import { replace, Replace } from 'connected-react-router';
+import { ApolloProvider } from '@apollo/client';
+import { useSelector, useDispatch } from 'react-redux';
+import { replace } from 'connected-react-router';
 import { useParams } from 'react-router-dom';
 
-import { BreakpointWidth } from 'src/global/globalConfig';
+import { client } from 'src/gql-client';
 import * as urlFor from 'src/shared/helpers/urlHelper';
 import { buildFocusIdForUrl } from 'src/shared/state/ens-object/ensObjectHelpers';
 
@@ -43,46 +43,24 @@ import GeneView from './gene-view/GeneView';
 import GeneViewSideBar from './gene-view/components/gene-view-sidebar/GeneViewSideBar';
 import GeneViewSidebarTabs from './gene-view/components/gene-view-sidebar-tabs/GeneViewSidebarTabs';
 
-import { RootState } from 'src/store';
-import { SidebarStatus } from 'src/content/app/entity-viewer/state/sidebar/entityViewerSidebarState';
-
 import styles from './EntityViewer.scss';
 
-type Props = {
-  isSidebarOpen: boolean;
-  activeGenomeId: string | null;
-  activeEntityId: string | null;
-  viewportWidth: BreakpointWidth;
-  replace: Replace;
-  setDataFromUrl: (params: EntityViewerParams) => void;
-  toggleSidebar: (status?: SidebarStatus) => void;
-};
-
 export type EntityViewerParams = {
   genomeId?: string;
   entityId?: string;
 };
 
-const client = new ApolloClient({
-  uri: '/thoas',
-  cache: new InMemoryCache({
-    typePolicies: {
-      Gene: {
-        keyFields: ['stable_id'],
-        fields: {
-          slice: {
-            merge: false
-          }
-        }
-      }
-    }
-  })
-});
+const EntityViewer = () => {
+  const activeGenomeId = useSelector(getEntityViewerActiveGenomeId);
+  const activeEntityId = useSelector(getEntityViewerActiveEntityId);
+  const isSidebarOpen = useSelector(isEntityViewerSidebarOpen);
+  const viewportWidth = useSelector(getBreakpointWidth);
+
+  const dispatch = useDispatch();
+  const onSidebarToggle = () => dispatch(toggleSidebar());
 
-const EntityViewer = (props: Props) => {
   const params: EntityViewerParams = useParams(); // NOTE: will likely cause a problem when server-side rendering
   const { genomeId, entityId } = params;
-  const { activeGenomeId, activeEntityId } = props;
 
   useEffect(() => {
     if (activeGenomeId && activeEntityId && !entityId) {
@@ -91,9 +69,11 @@ const EntityViewer = (props: Props) => {
         genomeId: activeGenomeId,
         entityId: entityIdForUrl
       });
-      props.replace(replacementUrl);
+
+      dispatch(replace(replacementUrl));
     }
-    props.setDataFromUrl(params);
+
+    dispatch(setDataFromUrl(params));
   }, [params.genomeId, params.entityId]);
 
   return (
@@ -109,10 +89,10 @@ const EntityViewer = (props: Props) => {
             sidebarContent={<GeneViewSideBar />}
             sidebarNavigation={<GeneViewSidebarTabs />}
             sidebarToolstripContent={<EntityViewerSidebarToolstrip />}
-            isSidebarOpen={props.isSidebarOpen}
-            onSidebarToggle={props.toggleSidebar}
+            isSidebarOpen={isSidebarOpen}
+            onSidebarToggle={onSidebarToggle}
             isDrawerOpen={false}
-            viewportWidth={props.viewportWidth}
+            viewportWidth={viewportWidth}
           />
         ) : (
           <ExampleLinks />
@@ -122,19 +102,4 @@ const EntityViewer = (props: Props) => {
   );
 };
 
-const mapStateToProps = (state: RootState) => {
-  return {
-    activeGenomeId: getEntityViewerActiveGenomeId(state),
-    activeEntityId: getEntityViewerActiveEntityId(state),
-    isSidebarOpen: isEntityViewerSidebarOpen(state),
-    viewportWidth: getBreakpointWidth(state)
-  };
-};
-
-const mapDispatchToProps = {
-  replace,
-  setDataFromUrl,
-  toggleSidebar
-};
-
-export default connect(mapStateToProps, mapDispatchToProps)(EntityViewer);
+export default EntityViewer;

src/ensembl/src/content/app/entity-viewer/gene-view/components/default-transcripts-list/transcripts-list-item-info/TranscriptsListItemInfo.test.tsx

@@ -28,10 +28,22 @@ import ViewInApp from 'src/shared/components/view-in-app/ViewInApp';
 import { createGene } from 'tests/fixtures/entity-viewer/gene';
 import { createTranscript } from 'tests/fixtures/entity-viewer/transcript';
 
+jest.mock('@apollo/client', () => ({
+  gql: jest.fn(),
+  useQuery: jest.fn(() => ({
+    data: null,
+    loading: true
+  }))
+}));
+
 jest.mock('src/shared/components/view-in-app/ViewInApp', () => () => (
   <div>ViewInApp</div>
 ));
 
+jest.mock('src/shared/components/instant-download', () => ({
+  InstantDownloadTranscript: () => <div>InstantDownloadTranscript</div>
+}));
+
 const transcript = createTranscript();
 const gene = createGene({ transcripts: [transcript] });
 const expandDownload = false;

src/ensembl/src/content/app/entity-viewer/gene-view/components/default-transcripts-list/transcripts-list-item-info/TranscriptsListItemInfo.tsx

@@ -34,9 +34,10 @@ import { buildFocusIdForUrl } from 'src/shared/state/ens-object/ensObjectHelpers
 
 import { InstantDownloadTranscript } from 'src/shared/components/instant-download';
 import ViewInApp from 'src/shared/components/view-in-app/ViewInApp';
+import CloseButton from 'src/shared/components/close-button/CloseButton';
+
 import { toggleTranscriptDownload } from 'src/content/app/entity-viewer/state/gene-view/transcripts/geneViewTranscriptsSlice';
 import { clearExpandedProteins } from 'src/content/app/entity-viewer/state/gene-view/proteins/geneViewProteinsSlice';
-import CloseButton from 'src/shared/components/close-button/CloseButton';
 
 import { Gene } from 'src/content/app/entity-viewer/types/gene';
 import { Transcript } from 'src/content/app/entity-viewer/types/transcript';
@@ -151,7 +152,7 @@ export const TranscriptsListItemInfo = (
             </span>
           )}
         </div>
-        {props.expandDownload && renderInstantDownload(props)}
+        {props.expandDownload && renderInstantDownload({ ...props, genomeId })}
       </div>
       <div className={transcriptsListStyles.right}>
         <div className={styles.transcriptName}>
@@ -166,12 +167,16 @@ export const TranscriptsListItemInfo = (
 };
 
 const renderInstantDownload = ({
+  transcript,
   gene,
-  transcript
-}: TranscriptsListItemInfoProps) => {
+  genomeId
+}: TranscriptsListItemInfoProps & {
+  genomeId: string;
+}) => {
   return (
     <div className={styles.download}>
       <InstantDownloadTranscript
+        genomeId={genomeId}
         transcript={{
           id: transcript.unversioned_stable_id,
           so_term: transcript.so_term

src/ensembl/src/content/app/entity-viewer/gene-view/components/proteins-list/proteins-list-item-info/ProteinsListItemInfo.tsx

@@ -15,6 +15,7 @@
  */
 
 import React, { useEffect, useState } from 'react';
+import { useParams } from 'react-router-dom';
 import set from 'lodash/fp/set';
 
 import { CircleLoader } from 'src/shared/components/loader/Loader';
@@ -64,6 +65,9 @@ const addProteinDomains = (
 
 const ProteinsListItemInfo = (props: Props) => {
   const { transcript, trackLength } = props;
+  const params: { [key: string]: string } = useParams();
+  const { genomeId } = params;
+
   const [
     transcriptWithProteinDomains,
     setTranscriptWithProteinDomains
@@ -199,6 +203,7 @@ const ProteinsListItemInfo = (props: Props) => {
             )}
             <div className={styles.downloadWrapper}>
               <InstantDownloadProtein
+                genomeId={genomeId}
                 transcriptId={transcript.unversioned_stable_id}
               />
             </div>

src/ensembl/src/content/app/entity-viewer/types/cdna.ts

@@ -18,4 +18,5 @@ export type CDNA = {
   start: number;
   end: number;
   length: number;
+  sequence_checksum?: string;
 };

src/ensembl/src/content/app/entity-viewer/types/cds.ts

@@ -21,4 +21,5 @@ export type CDS = {
   relative_end: number;
   protein_length: number;
   nucleotide_length: number;
+  sequence_checksum?: string;
 };

src/ensembl/src/content/app/entity-viewer/types/product.ts

@@ -53,6 +53,7 @@ export type Product = {
   length: number;
   protein_domains: ProteinDomain[];
   external_references: ExternalReference[];
+  sequence_checksum?: string;
 };
 
 export type ProteinDomain = {

src/ensembl/src/gql-client.ts

+/**
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { ApolloClient, InMemoryCache } from '@apollo/client';
+
+export const client = new ApolloClient({
+  uri: '/thoas',
+  cache: new InMemoryCache({
+    typePolicies: {
+      Gene: {
+        keyFields: ['stable_id'],
+        fields: {
+          slice: {
+            merge: false
+          }
+        }
+      }
+    }
+  })
+});

src/ensembl/src/shared/components/instant-download/instant-download-fetch/fetchForProtein.ts

@@ -20,42 +20,60 @@ import {
   ProteinOption,
   proteinOptionsOrder
 } from 'src/shared/components/instant-download/instant-download-protein/InstantDownloadProtein';
+import {
+  fetchTranscriptChecksums,
+  TranscriptChecksums
+} from './fetchSequenceChecksums';
 
 type FetchPayload = {
+  genomeId: string;
   transcriptId: string;
   options: ProteinOptions;
 };
 
 export const fetchForProtein = async (payload: FetchPayload) => {
-  const { transcriptId, options } = payload;
-  const urls = buildUrlsForProtein(transcriptId, options);
+  const { genomeId, transcriptId, options } = payload;
+  const productGeneratingContext = await fetchTranscriptChecksums({
+    genomeId,
+    transcriptId
+  });
 
+  const urls = buildUrlsForProtein(productGeneratingContext, options);
   const sequencePromises = urls.map((url) =>
     fetch(url).then((response) => response.text())
   );
 
   const sequences = await Promise.all(sequencePromises);
-  const combinedFasta = sequences.join('\n');
+  const combinedFasta = sequences.join('\n\n');
 
   downloadAsFile(combinedFasta, `${transcriptId}.fasta`, {
     type: 'text/x-fasta'
   });
 };
 
-const buildUrlsForProtein = (id: string, options: ProteinOptions) => {
+const buildUrlsForProtein = (
+  productGeneratingContext: TranscriptChecksums,
+  options: ProteinOptions
+) => {
   return options
     ? proteinOptionsOrder
         .filter((option) => options[option])
-        .map((option) => buildFetchUrl(id, option))
+        .map((option) => buildFetchUrl(productGeneratingContext, option))
     : [];
 };
 
-const buildFetchUrl = (id: string, sequenceType: ProteinOption) => {
-  const sequenceTypeToTypeParam: Record<ProteinOption, string> = {
-    proteinSequence: 'protein',
+const buildFetchUrl = (
+  productGeneratingContext: TranscriptChecksums,
+  sequenceType: ProteinOption
+) => {
+  const sequenceTypeToContextType: Record<ProteinOption, string> = {
+    proteinSequence: 'product',
     cds: 'cds'
   };
-  const typeParam = sequenceTypeToTypeParam[sequenceType];
+  const contextType = sequenceTypeToContextType[
+    sequenceType
+  ] as keyof TranscriptChecksums;
+  const checksum = productGeneratingContext[contextType]?.sequence_checksum;
 
-  return `https://rest.ensembl.org/sequence/id/${id}?content-type=text/x-fasta&type=${typeParam}`;
+  return `/refget/sequence/${checksum}?accept=text/x-fasta`;
 };

src/ensembl/src/shared/components/instant-download/instant-download-fetch/fetchForTranscript.ts

@@ -15,11 +15,16 @@
  */
 
 import downloadAsFile from 'src/shared/helpers/downloadAsFile';
+
 import {
   TranscriptOptions,
   TranscriptOption,
   transcriptOptionsOrder
 } from 'src/shared/components/instant-download/instant-download-transcript/InstantDownloadTranscript';
+import {
+  fetchTranscriptChecksums,
+  TranscriptChecksums
+} from './fetchSequenceChecksums';
 
 type Options = {
   transcript: Partial<TranscriptOptions>;
@@ -29,26 +34,34 @@ type Options = {
 };
 
 type FetchPayload = {
-  transcriptId: string;
+  genomeId: string;
   geneId: string;
+  transcriptId: string;
   options: Options;
 };
 
 export const fetchForTranscript = async (payload: FetchPayload) => {
   const {
+    genomeId,
     geneId,
     transcriptId,
     options: { transcript: transcriptOptions, gene: geneOptions }
   } = payload;
-  const urls = buildUrlsForTranscript(transcriptId, transcriptOptions);
+  const checksums = await fetchTranscriptChecksums({
+    genomeId,
+    transcriptId
+  });
+  const urls = buildUrlsForTranscript({ geneId, checksums }, transcriptOptions);
+
   if (geneOptions.genomicSequence) {
-    urls.push(buildFetchUrl(geneId, 'genomicSequence'));
+    urls.push(buildFetchUrl({ geneId }, 'genomicSequence'));
   }
+
   const sequencePromises = urls.map((url) =>
     fetch(url).then((response) => response.text())
   );
   const sequences = await Promise.all(sequencePromises);
-  const combinedFasta = sequences.join('\n');
+  const combinedFasta = sequences.join('\n\n');
 
   downloadAsFile(combinedFasta, `${transcriptId}.fasta`, {
     type: 'text/x-fasta'
@@ -56,24 +69,42 @@ export const fetchForTranscript = async (payload: FetchPayload) => {
 };
 
 const buildUrlsForTranscript = (
-  id: string,
+  data: {
+    geneId: string;
+    checksums: TranscriptChecksums;
+  },
   options: Partial<TranscriptOptions>
 ) => {
   return options
     ? transcriptOptionsOrder
         .filter((option) => options[option])
-        .map((option) => buildFetchUrl(id, option))
+        .map((option) => buildFetchUrl(data, option))
     : [];
 };
 
-const buildFetchUrl = (id: string, sequenceType: TranscriptOption) => {
-  const sequenceTypeToTypeParam: Record<TranscriptOption, string> = {
+const buildFetchUrl = (
+  data: {
+    geneId: string;
+    checksums?: TranscriptChecksums;
+  },
+  sequenceType: TranscriptOption
+) => {
+  const sequenceTypeToContextType: Record<TranscriptOption, string> = {
     genomicSequence: 'genomic',
-    proteinSequence: 'protein',
+    proteinSequence: 'product',
     cdna: 'cdna',
     cds: 'cds'
   };
-  const typeParam = sequenceTypeToTypeParam[sequenceType];
 
-  return `https://rest.ensembl.org/sequence/id/${id}?content-type=text/x-fasta&type=${typeParam}`;
+  if (sequenceType === 'genomicSequence') {
+    return `https://rest.ensembl.org/sequence/id/${data.geneId}?content-type=text/x-fasta&type=${sequenceTypeToContextType.genomicSequence}`;
+  } else {
+    const contextType = sequenceTypeToContextType[
+      sequenceType
+    ] as keyof TranscriptChecksums;
+    const checksum =
+      data.checksums && data.checksums[contextType]?.sequence_checksum;
+
+    return `/refget/sequence/${checksum}?accept=text/x-fasta`;
+  }
 };

src/ensembl/src/shared/components/instant-download/instant-download-fetch/fetchSequenceChecksums.ts

+/**
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import { gql } from '@apollo/client';
+
+import { client } from 'src/gql-client';
+
+export type TranscriptChecksums = {
+  cdna: {
+    sequence_checksum: string;
+  };
+  cds: {
+    sequence_checksum: string;
+  };
+  product: {
+    sequence_checksum: string;
+  };
+};
+
+type GeneFragment = {
+  transcript: {
+    product_generating_contexts: TranscriptChecksums[];
+  };
+};
+
+const transcriptChecksumsQuery = gql`
+  query Transcript($genomeId: String!, $transcriptId: String!) {
+    transcript(byId: { genome_id: $genomeId, stable_id: $transcriptId }) {
+      product_generating_contexts {
+        cds {
+          sequence_checksum
+        }
+        cdna {
+          sequence_checksum
+        }
+        product {
+          sequence_checksum
+        }
+      }
+    }
+  }
+`;
+
+type Variables = {
+  genomeId: string;
+  transcriptId: string;
+};
+
+export const fetchTranscriptChecksums = (variables: Variables) =>
+  client
+    .query<GeneFragment>({
+      query: transcriptChecksumsQuery,
+      variables
+    })
+    .then(({ data }) => data.transcript.product_generating_contexts[0]);

src/ensembl/src/shared/components/instant-download/instant-download-protein/InstantDownloadProtein.tsx

@@ -26,6 +26,7 @@ import { TranscriptOptions } from '../instant-download-transcript/InstantDownloa
 import styles from './InstantDownloadProtein.scss';
 
 type InstantDownloadProteinProps = {