Temporal fix for UniprotID missing

EyeSeeTea · Jan 29, 2024 · b7cab48 · b7cab48
1 parent f98c2d1
commit b7cab48
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Showing 13 changed files with 93 additions and 62 deletions.
diff --git a/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/ApiPdbRepository.ts b/app/assets/javascripts/3dbio_viewer/src/data/repositories/protvista/ApiPdbRepository.ts
@@ -81,7 +81,7 @@ interface Data {
 type DataRequests = { [K in keyof Data]-?: Future<RequestError, Data[K] | undefined> };
 
 interface Options {
-    proteinId: string;
+    proteinId: Maybe<string>;
     pdbId: Maybe<string>;
     chainId: string;
 }
@@ -103,34 +103,33 @@ export class ApiPdbRepository implements PdbRepository {
         debugVariable({ apiData: data });
         const { proteinId } = options;
 
-        const variants = getVariants(
-            data.ebiVariation,
-            data.mutagenesis,
-            data.genomicVariantsCNCB,
-            proteinId
-        );
+        const variants = proteinId
+            ? getVariants(data.ebiVariation, data.mutagenesis, data.genomicVariantsCNCB, proteinId)
+            : undefined;
 
         // prettier-ignore
         const fragmentsList = {
-            featureFragments: on(data.features, features => getFeatureFragments(options.proteinId, features)),
-            pfamDomainFragments: on(data.pfamAnnotations, pfamAnnotations => getPfamDomainFragments(pfamAnnotations, proteinId)),
-            smartDomainFragments: on(data.smartAnnotations, smartAnnotations => getSmartDomainFragments(smartAnnotations, proteinId)),
-            interproFragments: on(data.interproAnnotations, interproAnnotations => getInterproDomainFragments(interproAnnotations, proteinId)),
-            elmdbFragments: on(data.elmdbUniprot, elmdbUniprot => getElmdbUniprotFragments(elmdbUniprot, proteinId)),
-            functionalMappingFragments: on(data.cv19Tracks, getFunctionalMappingFragments),
             structureCoverageFragments: on(data.coverage, coverage => getStructureCoverageFragments(coverage, options.chainId)),
-            emValidationFragments: on(data.pdbAnnotations, pdbAnnotations => getEmValidationFragments(pdbAnnotations, options.chainId)),
-            mobiFragments: on(data.mobiUniprot, mobiUniprot => getMobiUniprotFragments(mobiUniprot, proteinId)),
-            proteomicsFragments: on(data.proteomics, proteomics => getProteomicsFragments(proteomics, proteinId)),
-            pdbRedoFragments: on(data.pdbRedo, pdbRedo => getPdbRedoFragments(pdbRedo, options.chainId)),
-            epitomesFragments: on(data.iedb, getEpitomesFragments),
-            phosphiteFragments: on(data.phosphositeUniprot, phosphositeUniprot => getPhosphiteFragments(phosphositeUniprot, proteinId)),
-            dbPtmFragments: on(data.dbPtm, dbPtm => getDbPtmFragments(dbPtm, proteinId)),
-            molprobityFragments: on(data.molprobity, molprobity => getMolprobityFragments(molprobity, options.chainId)),
-            antigenFragments: on(data.antigenic, antigenic => getAntigenicFragments(antigenic, proteinId)),
+            // emValidationFragments: on(data.pdbAnnotations, pdbAnnotations => getEmValidationFragments(pdbAnnotations, options.chainId)),
+            // pdbRedoFragments: on(data.pdbRedo, pdbRedo => getPdbRedoFragments(pdbRedo, options.chainId)),
+            // molprobityFragments: on(data.molprobity, molprobity => getMolprobityFragments(molprobity, options.chainId)),
+            // ...(proteinId ? {
+            //     featureFragments: on(data.features, features => getFeatureFragments(proteinId, features)),
+            //     functionalMappingFragments: on(data.cv19Tracks, getFunctionalMappingFragments),
+            //     epitomesFragments: on(data.iedb, getEpitomesFragments),
+            //     pfamDomainFragments: on(data.pfamAnnotations, pfamAnnotations => getPfamDomainFragments(pfamAnnotations, proteinId)),
+            //     smartDomainFragments: on(data.smartAnnotations, smartAnnotations => getSmartDomainFragments(smartAnnotations, proteinId)),
+            //     interproFragments: on(data.interproAnnotations, interproAnnotations => getInterproDomainFragments(interproAnnotations, proteinId)),
+            //     elmdbFragments: on(data.elmdbUniprot, elmdbUniprot => getElmdbUniprotFragments(elmdbUniprot, proteinId)),
+            //     mobiFragments: on(data.mobiUniprot, mobiUniprot => getMobiUniprotFragments(mobiUniprot, proteinId)),
+            //     proteomicsFragments: on(data.proteomics, proteomics => getProteomicsFragments(proteomics, proteinId)),
+            //     phosphiteFragments: on(data.phosphositeUniprot, phosphositeUniprot => getPhosphiteFragments(phosphositeUniprot, proteinId)),
+            //     dbPtmFragments: on(data.dbPtm, dbPtm => getDbPtmFragments(dbPtm, proteinId)),
+            //     antigenFragments: on(data.antigenic, antigenic => getAntigenicFragments(antigenic, proteinId))
+            // } : {}),
         };
 
-        const protein = getProtein(proteinId, data.uniprot);
+        const protein = proteinId ? getProtein(proteinId, data.uniprot) : undefined;
         const experiment = on(data.pdbExperiment, pdbExperiment =>
             options.pdbId ? getExperiment(options.pdbId, pdbExperiment) : undefined
         );
@@ -227,31 +226,35 @@ function getData(options: Options): FutureData<Partial<Data>> {
 
     // Move URLS to each track module?
     //prettier-ignore
-    const data$: DataRequests = {
-        uniprot: getXML(`${routes.uniprot}/uniprotkb/${proteinId}.xml`),
-        pdbEmdbsEmValidations,
-        features: getJSON(`${ebiProteinsApiUrl}/features/${proteinId}`),
-        cv19Tracks: getJSON(`${bioUrl}/cv19_annotations/${proteinId}_annotations.json`),
+    const data$: Partial<DataRequests> = {
+        //PDBID
+        pdbSummary: onF(pdbId, pdbId => getJSON(`${ebiBaseUrl}/pdbe/api/pdb/entry/summary/${pdbId}`)),
         pdbAnnotations: onF(pdbId, pdbId => getJSON(`${pdbAnnotUrl}/all/${pdbId}/${chainId}/?format=json`)),
         pdbPublications,
         coverage: onF(pdbId, pdbId => getJSON(`${bioUrl}/api/alignments/Coverage/${pdbId}${chainId}`)),
-        pdbSummary: onF(pdbId, pdbId => getJSON(`${ebiBaseUrl}/pdbe/api/pdb/entry/summary/${pdbId}`)),
-        ebiVariation: getJSON(`${ebiProteinsApiUrl}/variation/${proteinId}`),
-        mobiUniprot: getJSON(`${bioUrl}/api/annotations/mobi/Uniprot/${proteinId}`),
-        phosphositeUniprot: getJSON(`${bioUrl}/api/annotations/Phosphosite/Uniprot/${proteinId}`),
-        dbPtm: getJSON(`${bioUrl}/api/annotations/dbptm/Uniprot/${proteinId}`),
-        pfamAnnotations: getJSON(`${bioUrl}/api/annotations/Pfam/Uniprot/${proteinId}`),
-        smartAnnotations: getJSON(`${bioUrl}/api/annotations/SMART/Uniprot/${proteinId}`),
-        interproAnnotations: getJSON(`${bioUrl}/api/annotations/interpro/Uniprot/${proteinId}`),
-        proteomics: getJSON(`${ebiProteinsApiUrl}/proteomics/${proteinId}`),
         pdbRedo: onF(pdbId, pdbId => getJSON(`${bioUrl}/api/annotations/PDB_REDO/${pdbId}`)),
-        iedb: getJSON(`${bioUrl}/api/annotations/IEDB/Uniprot/${proteinId}`),
         pdbExperiment: onF(pdbId, pdbId => getJSON(`${ebiBaseUrl}/pdbe/api/pdb/entry/experiment/${pdbId}`)),
-        elmdbUniprot: getJSON(`${bioUrl}/api/annotations/elmdb/Uniprot/${proteinId}`),
         molprobity: onF(pdbId, pdbId => getJSON(`${bioUrl}/compute/molprobity/${pdbId}`)),
-        antigenic: getJSON(`${ebiProteinsApiUrl}/antigen/${proteinId}`),
-        mutagenesis: getJSON(`${bioUrl}/api/annotations/biomuta/Uniprot/${proteinId}`),
-        genomicVariantsCNCB: getJSON(`${bioUrl}/ws/lrs/features/variants/Genomic_Variants_CNCB/${proteinId}/`),
+        //UNIPROT
+        ...(proteinId ? {
+            uniprot: getXML(`${routes.uniprot}/uniprotkb/${proteinId}.xml`),
+            pdbEmdbsEmValidations,
+            features: getJSON(`${ebiProteinsApiUrl}/features/${proteinId}`),
+            cv19Tracks: getJSON(`${bioUrl}/cv19_annotations/${proteinId}_annotations.json`),
+            ebiVariation: getJSON(`${ebiProteinsApiUrl}/variation/${proteinId}`),
+            mobiUniprot: getJSON(`${bioUrl}/api/annotations/mobi/Uniprot/${proteinId}`),
+            phosphositeUniprot: getJSON(`${bioUrl}/api/annotations/Phosphosite/Uniprot/${proteinId}`),
+            dbPtm: getJSON(`${bioUrl}/api/annotations/dbptm/Uniprot/${proteinId}`),
+            pfamAnnotations: getJSON(`${bioUrl}/api/annotations/Pfam/Uniprot/${proteinId}`),
+            smartAnnotations: getJSON(`${bioUrl}/api/annotations/SMART/Uniprot/${proteinId}`),
+            interproAnnotations: getJSON(`${bioUrl}/api/annotations/interpro/Uniprot/${proteinId}`),
+            proteomics: getJSON(`${ebiProteinsApiUrl}/proteomics/${proteinId}`),
+            iedb: getJSON(`${bioUrl}/api/annotations/IEDB/Uniprot/${proteinId}`),
+            elmdbUniprot: getJSON(`${bioUrl}/api/annotations/elmdb/Uniprot/${proteinId}`),
+            antigenic: getJSON(`${ebiProteinsApiUrl}/antigen/${proteinId}`),
+            mutagenesis: getJSON(`${bioUrl}/api/annotations/biomuta/Uniprot/${proteinId}`),
+            genomicVariantsCNCB: getJSON(`${bioUrl}/ws/lrs/features/variants/Genomic_Variants_CNCB/${proteinId}/`)
+        } : {}),
         ligands,
     };
 

diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/entities/Pdb.ts b/app/assets/javascripts/3dbio_viewer/src/domain/entities/Pdb.ts
@@ -15,7 +15,7 @@ export interface Pdb {
     title: Maybe<string>;
     experiment: Maybe<Experiment>;
     emdbs: Emdb[];
-    protein: Protein;
+    protein: Maybe<Protein>;
     chainId: string;
     sequence: string;
     length: number;
@@ -108,10 +108,12 @@ export function getEntityLinks(pdb: Pdb, entity: PdbEntity): Link[] {
             }));
         }
         case "uniprot": {
+            if (!pdb.protein) return [];
             const proteinId = pdb.protein.id.toUpperCase();
             return [{ name: proteinId, url: `https://www.uniprot.org/uniprot/${proteinId}` }];
         }
         case "geneBank": {
+            if (!pdb.protein) return [];
             return pdb.protein.genBank
                 ? pdb.protein.genBank?.map(id => ({
                       name: id ?? "-",

diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/entities/PdbInfo.ts b/app/assets/javascripts/3dbio_viewer/src/domain/entities/PdbInfo.ts
@@ -13,7 +13,7 @@ export interface PdbInfo {
         name: string;
         shortName: string;
         chainId: ChainId;
-        protein: Protein;
+        protein: Maybe<Protein>;
     }>;
     ligands: Ligand[];
 }
@@ -45,6 +45,20 @@ export function buildPdbInfo(options: BuildPdbInfoOptions): PdbInfo {
         .sortBy(obj => obj.chainId)
         .value();
 
+    if (_.isEmpty(chains) && _.isEmpty(options.proteins))
+        return {
+            ...options,
+            chains: [
+                {
+                    id: "A",
+                    name: "A",
+                    shortName: "A",
+                    chainId: "A",
+                    protein: undefined,
+                },
+            ],
+        };
+
     return { ...options, chains };
 }
 

diff --git a/app/assets/javascripts/3dbio_viewer/src/domain/repositories/PdbRepository.ts b/app/assets/javascripts/3dbio_viewer/src/domain/repositories/PdbRepository.ts
@@ -9,7 +9,7 @@ export interface PdbRepository {
 }
 
 export interface PdbOptions {
-    proteinId: ProteinId;
+    proteinId: Maybe<ProteinId>;
     pdbId: Maybe<PdbId>;
-    chainId: ChainId;
+    chainId: Maybe<ChainId>;
 }
diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/BasicInfoViewer.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/BasicInfoViewer.tsx
@@ -81,7 +81,7 @@ function getItems(pdb: Pdb) {
     const resolution = pdb.experiment?.resolution;
 
     const items: Item[] = _.compact([
-        { name: i18n.t("Organism"), value: pdb.protein.organism },
+        pdb.protein ? { name: i18n.t("Organism"), value: pdb.protein.organism } : undefined,
         {
             name: i18n.t("Biological function"),
             isDisabled: true,

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/ChainInfoViewer.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/ChainInfoViewer.tsx
@@ -52,11 +52,17 @@ const Child: React.FC<ChildProps> = props => {
 
 function getItems(pdb: Pdb): Item[] {
     return _.compact([
-        { name: i18n.t("Gene Name"), value: pdb.protein.gen },
-        {
-            name: i18n.t("Gene Bank ID"),
-            value: pdb.protein.genBank ? <Links links={getEntityLinks(pdb, "geneBank")} /> : "-",
-        },
+        pdb.protein ? { name: i18n.t("Gene Name"), value: pdb.protein.gen } : undefined,
+        pdb.protein
+            ? {
+                  name: i18n.t("Gene Bank ID"),
+                  value: pdb.protein.genBank ? (
+                      <Links links={getEntityLinks(pdb, "geneBank")} />
+                  ) : (
+                      "-"
+                  ),
+              }
+            : undefined,
         {
             name: i18n.t("Uniprot ID"),
             value: <Links links={getEntityLinks(pdb, "uniprot")} />,

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/gene-viewer/GeneViewer.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/gene-viewer/GeneViewer.tsx
@@ -13,6 +13,7 @@ interface GeneViewerProps {
 
 export const GeneViewer: React.FC<GeneViewerProps> = props => {
     const { trackDef, pdb } = props;
+    if (!pdb.protein) throw new Error("No UniprotID to show GeneViewer");
     const src = routes.bionotes + `/genomicIFrame?uniprot_acc=${pdb.protein.id.toUpperCase()}`;
     const title = `${trackDef.name}`;
 

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/ppi/ppi-data.ts b/app/assets/javascripts/3dbio_viewer/src/webapp/components/ppi/ppi-data.ts
@@ -67,6 +67,7 @@ export interface InfoAlignmentFromNetwork {
 }
 
 export function getInfoAlignmentFromPdb(pdb: Pdb): Maybe<InfoAlignment> {
+    if (!pdb.protein) return undefined;
     if (pdb.proteinNetwork) {
         return {
             origin: "interactome3d",

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaViewer.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProtvistaViewer.tsx
@@ -51,17 +51,17 @@ export const ProtvistaViewer: React.FC<ProtvistaViewerProps> = props => {
 
     const geneName = React.useMemo(
         () =>
-            pdb.protein.gen
-                ? i18n.t(" encoded by the gene {{geneName}}", { geneName: pdb.protein.gen })
+            pdb.protein?.gen
+                ? i18n.t(" encoded by the gene {{geneName}}", { geneName: pdb.protein?.gen })
                 : undefined,
         [pdb.protein]
     );
 
     const geneBankEntry = React.useMemo(
         () =>
-            !_.isEmpty(pdb.protein.genBank)
+            !_.isEmpty(pdb.protein?.genBank)
                 ? i18n.t(" (GeneBank {{geneBankEntry}})", {
-                      geneBankEntry: pdb.protein.genBank?.join(", "),
+                      geneBankEntry: pdb.protein?.genBank?.join(", "),
                   })
                 : undefined,
         [pdb.protein]
@@ -71,11 +71,11 @@ export const ProtvistaViewer: React.FC<ProtvistaViewerProps> = props => {
         () => ({
             poorQualityRegionMax: _.first(pdb.emdbs)?.emv?.stats?.quartile75,
             poorQualityRegionMin: _.first(pdb.emdbs)?.emv?.stats?.quartile25,
-            proteinName: pdb.protein.name,
+            proteinName: pdb.protein?.name,
             ligandsAndSmallMoleculesCount,
             resolution: _.first(pdb.emdbs)?.emv?.stats?.resolutionMedian,
             chain: pdb.chainId,
-            chainWithProtein: `${pdb.chainId}${pdb.protein.name ? " - " + pdb.protein.name : ""}`,
+            chainWithProtein: `${pdb.chainId}${pdb.protein?.name ? " - " + pdb.protein.name : ""}`,
             uniprotId: getEntityLinks(pdb, "uniprot")
                 .map(link => link.name)
                 .join(", "),

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProvistaGrouped.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ProvistaGrouped.tsx
@@ -22,7 +22,7 @@ export const ProtvistaGrouped: React.FC<ProtvistaGroupedProps> = React.memo(() =
 
     return (
         <ViewerBlock block={block} namespace={namespace}>
-            {i18n.t("Protein")}: {loader.data.protein.id} | {i18n.t("PDB")}: {loader.data.id} |
+            {i18n.t("Protein")}: {loader.data.protein?.id} | {i18n.t("PDB")}: {loader.data.id} |
             {i18n.t("Chain")}: {loader.data.chainId}
             <ProtvistaPdb pdb={loader.data} block={block} showAllTracks={false} />
         </ViewerBlock>

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ToolsButton.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/ToolsButton.tsx
@@ -42,7 +42,7 @@ export const ToolsButton: React.FC<ToolsButtonProps> = props => {
                     return updateLoader(
                         "exportAnnotations",
                         compositionRoot.exportAllAnnotations
-                            .execute({ proteinId: protein.id, pdbId: id, chainId, emdbs })
+                            .execute({ proteinId: protein?.id, pdbId: id, chainId, emdbs })
                             .toPromise()
                     );
             }

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Tooltip.tsx b/app/assets/javascripts/3dbio_viewer/src/webapp/components/protvista/Tooltip.tsx
@@ -74,7 +74,11 @@ const Tools: React.FC<{ pdb: Pdb; subtrack: Subtrack; fragment: FragmentP }> = p
     return (
         <TooltipRow
             title={i18n.t("Tools")}
-            object={getFragmentToolsLink({ protein: pdb.protein.id, subtrack, fragment })}
+            object={
+                pdb.protein
+                    ? getFragmentToolsLink({ protein: pdb.protein.id, subtrack, fragment })
+                    : undefined
+            }
         >
             {link => <Link name={link.name} url={link.url} />}
         </TooltipRow>

diff --git a/app/assets/javascripts/3dbio_viewer/src/webapp/hooks/use-pdb.ts b/app/assets/javascripts/3dbio_viewer/src/webapp/hooks/use-pdb.ts
@@ -52,5 +52,5 @@ export function getPdbOptions(
               .get(chainId, defaultChain)
         : defaultChain;
 
-    return chain ? { pdbId, proteinId: chain.protein.id, chainId: chain.chainId } : undefined;
+    return chain ? { pdbId, proteinId: chain.protein?.id, chainId: chain.chainId } : undefined;
 }