Use biotype from Thoas replacing all so_terms(#529)

src/ensembl/src/content/app/browser/drawer/drawer-views/gene-summary/GeneSummary.tsx

@@ -17,7 +17,7 @@
 import React, { useState } from 'react';
 import { useSelector } from 'react-redux';
 import { gql, useQuery } from '@apollo/client';
-import { Pick3 } from 'ts-multipick';
+import { Pick2, Pick3 } from 'ts-multipick';
 import classNames from 'classnames';
 
 import * as urlFor from 'src/shared/helpers/urlHelper';
@@ -47,7 +47,6 @@ const GENE_QUERY = gql`
       stable_id
       unversioned_stable_id
       symbol
-      so_term
       transcripts {
         stable_id
       }
@@ -59,6 +58,12 @@ const GENE_QUERY = gql`
           length
         }
       }
+      metadata {
+        biotype {
+          label
+          value
+        }
+      }
     }
   }
 `;
@@ -70,8 +75,8 @@ type Gene = Pick<
   | 'symbol'
   | 'name'
   | 'alternative_symbols'
-  | 'so_term'
 > &
+  Pick2<FullGene, 'metadata', 'biotype'> &
   Pick3<FullGene, 'slice', 'strand', 'code'> &
   Pick3<FullGene, 'slice', 'location', 'length'> & {
     transcripts: { stable_id: string }[];
@@ -122,7 +127,7 @@ const GeneSummary = () => {
               <span className={styles.featureSymbol}>{gene.symbol}</span>
             )}
             <span className={styles.stableId}>{stableId}</span>
-            <div>{gene.so_term.toLowerCase()}</div>
+            <div>{gene.metadata.biotype.label}</div>
             <div>{getStrandDisplayName(gene.slice.strand.code)}</div>
             <div>{getFormattedLocation(ensObjectGene.location)}</div>
           </div>
@@ -161,7 +166,10 @@ const GeneSummary = () => {
             <div className={styles.downloadWrapper}>
               <InstantDownloadGene
                 genomeId={ensObjectGene.genome_id}
-                gene={{ id: gene.stable_id, so_term: gene.so_term }}
+                gene={{
+                  id: gene.stable_id,
+                  biotype: gene.metadata.biotype.value
+                }}
               />
               <CloseButton
                 className={styles.closeButton}

src/ensembl/src/content/app/browser/drawer/drawer-views/transcript-summary/TranscriptSummary.scss

@@ -13,6 +13,12 @@
     font-size: 12px;
   }
 
+  .questionButton {
+    padding-left: 10px;
+    position: relative;
+    top: 2px;
+  }
+
   .value {
     grid-column: value;
 
@@ -48,8 +54,11 @@
   flex-wrap: nowrap;
   overflow: hidden;
 
-  & > span:not(:first-child) {
-    margin-left: 30px;
+  & > span:not(:nth-child(1)) {
+    margin-left: 40px;
+  }
+  & > span:nth-child(2) {
+    margin-left: 10px;
   }
 }
 

src/ensembl/src/content/app/browser/drawer/drawer-views/transcript-summary/TranscriptSummary.tsx

@@ -39,27 +39,30 @@ import { InstantDownloadTranscript } from 'src/shared/components/instant-downloa
 import ViewInApp from 'src/shared/components/view-in-app/ViewInApp';
 import ExternalReference from 'src/shared/components/external-reference/ExternalReference';
 import CloseButton from 'src/shared/components/close-button/CloseButton';
+import QuestionButton from 'ensemblRoot/src/shared/components/question-button/QuestionButton';
 
 import { EnsObjectGene } from 'src/shared/state/ens-object/ensObjectTypes';
 import { FullTranscript } from 'src/shared/types/thoas/transcript';
 import { FullGene } from 'src/shared/types/thoas/gene';
 
 import styles from './TranscriptSummary.scss';
+import { TranscriptQualityLabel } from 'ensemblRoot/src/content/app/entity-viewer/shared/components/default-transcript-label/TranscriptQualityLabel';
 
 // TODO: narrow down the types for spliced exons and product-generating_contexts
 type Transcript = Pick<
   FullTranscript,
   | 'stable_id'
   | 'unversioned_stable_id'
-  | 'so_term'
   | 'external_references'
   | 'slice'
   | 'spliced_exons'
   | 'product_generating_contexts'
+  | 'metadata'
 >;
 
 // TODO: narrow down the type and use it in the Transcript type
-type ProductGeneratingContext = Transcript['product_generating_contexts'][number];
+type ProductGeneratingContext =
+  Transcript['product_generating_contexts'][number];
 
 type Gene = Pick<
   FullGene,
@@ -77,7 +80,6 @@ const GENE_AND_TRANSCRIPT_QUERY = gql`
     transcript(byId: { genome_id: $genomeId, stable_id: $transcriptId }) {
       stable_id
       unversioned_stable_id
-      so_term
       external_references {
         accession_id
         url
@@ -131,6 +133,23 @@ const GENE_AND_TRANSCRIPT_QUERY = gql`
           length
         }
       }
+      metadata {
+        biotype {
+          label
+          value
+          definition
+        }
+        canonical {
+          value
+          label
+          definition
+        }
+        mane {
+          value
+          label
+          definition
+        }
+      }
     }
   }
 `;
@@ -163,9 +182,12 @@ const TranscriptSummary = () => {
   }
 
   const { gene, transcript } = data;
-  const defaultProductGeneratingContext = transcript.product_generating_contexts.find(
-    (entry) => entry.default
-  ) as ProductGeneratingContext;
+  const metadata = transcript.metadata;
+
+  const defaultProductGeneratingContext =
+    transcript.product_generating_contexts.find(
+      (entry) => entry.default
+    ) as ProductGeneratingContext;
 
   const product = defaultProductGeneratingContext.product;
   const stableId = getDisplayStableId(transcript);
@@ -203,8 +225,16 @@ const TranscriptSummary = () => {
         <div className={styles.value}>
           <div className={styles.featureDetails}>
             <span className={styles.featureSymbol}>{stableId}</span>
-            {transcript.so_term && (
-              <span>{transcript.so_term.toLowerCase()}</span>
+            <span className={styles.label}>
+              <TranscriptQualityLabel metadata={metadata} />
+            </span>
+            {metadata.biotype && (
+              <>
+                <span>{metadata.biotype.label}</span>
+                <div className={styles.questionButton}>
+                  <QuestionButton helpText={metadata.biotype.definition} />
+                </div>
+              </>
             )}
             {transcript.slice.strand.code && (
               <span>{getStrandDisplayName(transcript.slice.strand.code)}</span>
@@ -240,7 +270,7 @@ const TranscriptSummary = () => {
         </div>
       </div>
 
-      {transcript.so_term === 'protein_coding' && (
+      {metadata.biotype.value === 'protein_coding' && (
         <div className={styles.row}>
           <div className={styles.label}>Protein</div>
           <div className={styles.value}>
@@ -289,7 +319,7 @@ const TranscriptSummary = () => {
                 genomeId={ensObjectGene.genome_id}
                 transcript={{
                   id: transcript.unversioned_stable_id,
-                  so_term: transcript.so_term
+                  biotype: metadata.biotype.value
                 }}
                 gene={{ id: gene.unversioned_stable_id }}
                 theme="light"
@@ -307,7 +337,9 @@ const TranscriptSummary = () => {
         <div className={styles.label}>Gene</div>
         <div className={styles.value}>
           <div>
-            {gene.symbol && <span className={styles.geneSymbol}>{gene.symbol}</span>}
+            {gene.symbol && (
+              <span className={styles.geneSymbol}>{gene.symbol}</span>
+            )}
             {gene.symbol !== stableId && <span>{gene.stable_id}</span>}
           </div>
         </div>

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

@@ -37,9 +37,8 @@ const ZmenuInstantDownload = (props: Props) => {
     endpoint: `/lookup/id/${transcriptId}?content-type=application/json;expand=1`,
     host: 'https://rest.ensembl.org'
   };
-  const { loadingState, data, error } = useApiService<TranscriptInResponse>(
-    params
-  );
+  const { loadingState, data, error } =
+    useApiService<TranscriptInResponse>(params);
 
   if (
     loadingState === LoadingState.NOT_REQUESTED ||
@@ -73,12 +72,12 @@ const getStableId = (id: string) => id.split(':').pop();
 const preparePayload = (transcript: TranscriptInResponse) => {
   const geneId = transcript.Parent;
   const transcriptId = transcript.id;
-  const so_term = transcript.biotype;
+  const biotype = transcript.biotype;
 
   return {
     transcript: {
       id: transcriptId,
-      so_term
+      biotype
     },
     gene: {
       id: geneId

src/ensembl/src/content/app/entity-viewer/gene-view/GeneView.tsx

@@ -92,7 +92,6 @@ const QUERY = gql`
       transcripts {
         stable_id
         unversioned_stable_id
-        so_term
         slice {
           location {
             start
@@ -164,6 +163,19 @@ const QUERY = gql`
           }
         }
         metadata {
+          biotype {
+            label
+            value
+            definition
+          }
+          tsl {
+            label
+            value
+          }
+          appris {
+            label
+            value
+          }
           canonical {
             value
             label
@@ -173,6 +185,10 @@ const QUERY = gql`
             value
             label
             definition
+            ncbi_transcript {
+              id
+              url
+            }
           }
           gencode_basic {
             label
@@ -237,7 +253,8 @@ const GeneViewWithData = (props: GeneViewWithDataProps) => {
   const gbUrl = urlFor.browser({ genomeId, focus: focusId });
 
   const shouldShowFilterIndicator =
-    sortingRule !== SortingRule.DEFAULT || Object.values(filters).some(Boolean);
+    sortingRule !== SortingRule.DEFAULT ||
+    Object.values(filters).some((filter) => filter.selected);
 
   const filterLabel = (
     <span

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

@@ -19,9 +19,9 @@ import { useSelector, useDispatch } from 'react-redux';
 import { Pick2, Pick3 } from 'ts-multipick';
 
 import { getFeatureCoordinates } from 'src/content/app/entity-viewer/shared/helpers/entity-helpers';
-import { transcriptSortingFunctions } from 'src/content/app/entity-viewer/shared/helpers/transcripts-sorter';
+import { getTranscriptSortingFunction } from 'src/content/app/entity-viewer/shared/helpers/transcripts-sorter';
 
-import { filterTranscriptsBySOTerm } from 'src/content/app/entity-viewer/shared/helpers/transcripts-filter';
+import { filterTranscripts } from 'src/content/app/entity-viewer/shared/helpers/transcripts-filter';
 
 import {
   getExpandedTranscriptIds,
@@ -51,7 +51,6 @@ type ProductGeneratingContext = {
   cds: Pick<FullCDS, 'relative_start' | 'relative_end'>;
 };
 type Transcript = DefaultTranscriptListItemProps['transcript'] & {
-  so_term: FullTranscript['so_term'];
   product_generating_contexts: ProductGeneratingContext[];
 } & {
   spliced_exons: Array<Pick3<SplicedExon, 'exon', 'slice', 'location'>>;
@@ -82,18 +81,17 @@ const DefaultTranscriptslist = (props: Props) => {
 
   const { gene } = props;
 
-  const sortingFunction = transcriptSortingFunctions[sortingRule];
-  const sortedTranscripts = sortingFunction(gene.transcripts) as Transcript[];
-  const filteredTranscripts = Object.values(filters).some(Boolean)
-    ? (filterTranscriptsBySOTerm(sortedTranscripts, filters) as Transcript[])
-    : sortedTranscripts;
+  const filteredTranscripts = filterTranscripts(gene.transcripts, filters);
+
+  const sortingFunction = getTranscriptSortingFunction<Transcript>(sortingRule);
+  const sortedTranscripts = sortingFunction(filteredTranscripts);
 
   useEffect(() => {
     const hasExpandedTranscripts = !!expandedTranscriptIds.length;
 
     // Expand the first transcript by default
     if (!hasExpandedTranscripts) {
-      dispatch(toggleTranscriptInfo(filteredTranscripts[0].stable_id));
+      dispatch(toggleTranscriptInfo(sortedTranscripts[0].stable_id));
     }
   }, []);
 
@@ -106,7 +104,7 @@ const DefaultTranscriptslist = (props: Props) => {
       </div>
       <div className={styles.content}>
         <StripedBackground {...props} />
-        {filteredTranscripts.map((transcript, index) => {
+        {sortedTranscripts.map((transcript, index) => {
           const expandTranscript = expandedTranscriptIds.includes(
             transcript.stable_id
           );

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

@@ -42,7 +42,6 @@ type Transcript = Pick<
 
 export type DefaultTranscriptListItemProps = {
   gene: TranscriptsListItemInfoProps['gene'];
-  isDefault?: boolean;
   transcript: Transcript;
   rulerTicks: TicksAndScale;
   expandTranscript: boolean;

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

@@ -15,6 +15,7 @@
  */
 
 import React from 'react';
+import faker from 'faker';
 import { render } from '@testing-library/react';
 import userEvent from '@testing-library/user-event';
 import { MemoryRouter } from 'react-router';
@@ -25,7 +26,11 @@ import {
 } from './TranscriptsListItemInfo';
 
 import { createGene } from 'tests/fixtures/entity-viewer/gene';
-import { createTranscript } from 'tests/fixtures/entity-viewer/transcript';
+import {
+  createTranscript,
+  createTranscriptMetadata
+} from 'tests/fixtures/entity-viewer/transcript';
+import { createExternalReference } from 'ensemblRoot/tests/fixtures/entity-viewer/external-reference';
 
 jest.mock('src/shared/components/view-in-app/ViewInApp', () => () => (
   <div data-test-id="viewInApp">ViewInApp</div>
@@ -44,6 +49,50 @@ const gene = createGene({ transcripts: [transcript] });
 const expandDownload = false;
 const expandMoreInfo = false;
 
+const createGencodeBasicTranscript = () => {
+  const metadata = createTranscriptMetadata({
+    gencode_basic: {
+      label: 'gencode basic',
+      value: faker.lorem.word(),
+      definition: faker.lorem.sentence()
+    }
+  });
+
+  const transcript = createTranscript({ metadata });
+  return transcript;
+};
+
+const createMANETranscript = () => {
+  const metadata = createTranscriptMetadata({
+    mane: {
+      label: 'MANE Select',
+      value: 'select',
+      definition: faker.lorem.sentence(),
+      ncbi_transcript: {
+        id: faker.lorem.word(),
+        url: faker.lorem.sentence()
+      }
+    }
+  });
+
+  const transcript = createTranscript({ metadata });
+  return transcript;
+};
+
+const createCCDSXrefTranscript = () => {
+  const xref = {
+    source: {
+      name: 'CCDS',
+      id: faker.datatype.uuid(),
+      url: faker.internet.url()
+    }
+  };
+  const transcript = createTranscript({
+    external_references: [createExternalReference(xref)]
+  });
+  return transcript;
+};
+
 const defaultProps = {
   gene,
   transcript,
@@ -107,4 +156,40 @@ describe('<TranscriptsListItemInfo /', () => {
     userEvent.click(proteinLink);
     expect(defaultProps.onProteinLinkClick).toHaveBeenCalled();
   });
+
+  it('displays metadata when it is available', () => {
+    const { queryByText } = renderComponent({
+      transcript: createGencodeBasicTranscript(),
+      expandMoreInfo: true
+    });
+    const metadataLabel = queryByText('gencode basic');
+    expect(metadataLabel).toBeTruthy();
+  });
+
+  it('displays CCDS when it is available in external references', () => {
+    const { queryByText } = renderComponent({
+      transcript: createCCDSXrefTranscript(),
+      expandMoreInfo: true
+    });
+    const CCDSLabel = queryByText('CCDS');
+    expect(CCDSLabel).toBeTruthy();
+  });
+
+  it('displays the Refseq with a link', () => {
+    const MANETranscript = createMANETranscript();
+    const refseqId = MANETranscript.metadata.mane?.ncbi_transcript?.id;
+    const refseqUrl = MANETranscript.metadata.mane?.ncbi_transcript?.url;
+    const { container, queryByText } = renderComponent({
+      transcript: MANETranscript,
+      expandMoreInfo: true
+    });
+    const refseqLabel = queryByText('RefSeq match');
+    expect(refseqLabel).toBeTruthy();
+
+    const refseqLink = [...container.querySelectorAll('a')].find(
+      (link) => link.textContent === refseqId
+    ) as HTMLElement;
+
+    expect(refseqLink.getAttribute('href')).toBe(refseqUrl);
+  });
 });

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

@@ -56,14 +56,9 @@ import styles from './TranscriptsListItemInfo.scss';
 type Gene = Pick<FullGene, 'unversioned_stable_id' | 'stable_id'>;
 type Transcript = Pick<
   FullTranscript,
-  'stable_id' | 'unversioned_stable_id' | 'so_term' | 'external_references'
+  'stable_id' | 'unversioned_stable_id' | 'external_references' | 'metadata'
 > &
   Pick2<FullTranscript, 'slice', 'location'> &
-  Pick2<
-    FullTranscript,
-    'metadata',
-    'canonical' | 'mane' | 'gencode_basic' | 'appris' | 'tsl'
-  > &
   Pick3<FullTranscript, 'slice', 'region', 'name'> & {
     spliced_exons: Array<
       Pick2<SplicedExon, 'exon', 'stable_id'> &
@@ -126,6 +121,7 @@ export const TranscriptsListItemInfo = (
   const transcriptCCDS = transcript.external_references.find(
     (xref) => xref.source.name === 'CCDS'
   );
+  const transcriptNCBI = transcript.metadata.mane?.ncbi_transcript;
 
   const hasRelevantMetadata = (
     ['gencode_basic', 'tsl', 'appris'] as const
@@ -172,14 +168,24 @@ export const TranscriptsListItemInfo = (
             )}
           </div>
         )}
-        {!!transcriptCCDS && (
+        {(!!transcriptCCDS || !!transcriptNCBI) && (
           <div className={styles.moreInfoColumn}>
-            <ExternalReference
-              classNames={{ label: styles.normalText }}
-              label={'CCDS'}
-              to={transcriptCCDS.url}
-              linkText={transcriptCCDS.accession_id}
-            />
+            {!!transcriptNCBI && (
+              <ExternalReference
+                classNames={{ label: styles.normalText }}
+                label={'RefSeq match'}
+                to={transcriptNCBI.url}
+                linkText={transcriptNCBI.id}
+              />
+            )}
+            {!!transcriptCCDS && (
+              <ExternalReference
+                classNames={{ label: styles.normalText }}
+                label={'CCDS'}
+                to={transcriptCCDS.url}
+                linkText={transcriptCCDS.accession_id}
+              />
+            )}
           </div>
         )}
       </>
@@ -192,7 +198,7 @@ export const TranscriptsListItemInfo = (
       <div className={midStyles}>
         <div className={styles.topLeft}>
           <div>
-            <strong>{transcript.so_term}</strong>
+            <strong>{transcript.metadata.biotype.label}</strong>
           </div>
           <div>{getTranscriptLocation()}</div>
         </div>
@@ -261,7 +267,7 @@ const renderInstantDownload = ({
         genomeId={genomeId}
         transcript={{
           id: transcript.stable_id,
-          so_term: transcript.so_term
+          biotype: transcript.metadata.biotype.value
         }}
         gene={{ id: gene.stable_id }}
       />

src/ensembl/src/content/app/entity-viewer/gene-view/components/gene-view-sidebar/external-references/GeneExternalReferences.tsx

@@ -60,7 +60,6 @@ const QUERY = gql`
       }
       transcripts {
         stable_id
-        so_term
         slice {
           location {
             length
@@ -106,7 +105,6 @@ const QUERY = gql`
 
 type Transcript = {
   stable_id: string;
-  so_term: string;
   slice: Pick2<Slice, 'location', '