Merge pull request #688 from ProteinsWebTeam/reorganization_interpro_…

…scan Reorganization of the InterPro Scan Search results section
ProteinsWebTeam · Feb 3, 2025 · f3bc74e · f3bc74e
2 parents 6fc9a93 + 75357e8
commit f3bc74e
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Showing 9 changed files with 380 additions and 263 deletions.
diff --git a/patches/@nightingale-elements+nightingale-interpro-track+5.0.0.patch b/patches/@nightingale-elements+nightingale-interpro-track+5.0.0.patch
@@ -1,5 +1,5 @@
 diff --git a/node_modules/@nightingale-elements/nightingale-interpro-track/src/InterproEntryLayout.ts b/node_modules/@nightingale-elements/nightingale-interpro-track/src/InterproEntryLayout.ts
-index 8302fc6..ac45de6 100644
+index 8302fc6..7f604b1 100644
 --- a/node_modules/@nightingale-elements/nightingale-interpro-track/src/InterproEntryLayout.ts
 +++ b/node_modules/@nightingale-elements/nightingale-interpro-track/src/InterproEntryLayout.ts
 @@ -39,24 +39,30 @@ export default class InterproEntryLayout extends DefaultLayout {
@@ -11,7 +11,7 @@ index 8302fc6..ac45de6 100644
    constructor({
      expanded,
      padding,
-+    samesize,
++    samesize, 
      ...otherOptions
 -  }: LayoutOptions & { expanded: boolean; padding: number }) {
 +  }: LayoutOptions & { expanded: boolean; padding: number, samesize?: boolean }) {
@@ -77,7 +77,7 @@ index 8302fc6..ac45de6 100644
    ) {
 +
 +    let childHeight = this.samesize ? EXPANDED_HEIGHT : CHILD_HEIGHT
-+
++    
      for (let i = 0; i < residues.length; i++) {
        const resGroup = residues[i];
        InterproEntryLayout.filterOutResidueFragmentsOutOfLocation(

diff --git a/src/components/IPScan/EntrySubPage/index.tsx b/src/components/IPScan/EntrySubPage/index.tsx
@@ -18,6 +18,7 @@ const flatMatchesFromIPScanPayload = function* (
       yield {
         accession: match.signature.entry.accession,
         name: match.signature.entry.description,
+        short_name: match.signature.entry.name,
         source_database: 'InterPro',
         matches: [
           {

diff --git a/src/components/IPScan/Summary/serializers.ts b/src/components/IPScan/Summary/serializers.ts
@@ -1,8 +1,12 @@
 import { NOT_MEMBER_DBS } from 'menuConfig';
 import { iproscan2urlDB } from 'utils/url-patterns';
+import {
+  proteinViewerReorganization,
+  sectionsReorganization,
+} from 'components/Related/DomainsOnProtein';
 
-const OTHER_FEATURES_DBS = ['funfam'];
-const OTHER_RESIDUES_DBS = ['pirsr'];
+const OTHER_FEATURES_DBS = [''];
+const OTHER_RESIDUES_DBS = [''];
 
 type IpScanEntry = {
   accession: string;
@@ -54,7 +58,7 @@ const integrateSignature = (
 const match2residues = (match: Iprscan5Match | IpScanMatch) => {
   return match.locations
     .map(({ sites }) =>
-      sites
+      sites?.length && sites?.length > 0
         ? {
             accession: match?.signature?.accession || match?.accession,
             locations: sites.map((site) => ({
@@ -176,6 +180,7 @@ export const mergeData = (
     };
 
     const residues = match2residues(match);
+
     if (
       residues.length > 0 &&
       !OTHER_RESIDUES_DBS.includes(residues?.[0]?.source_database || '')

diff --git a/src/components/Matches/index.tsx b/src/components/Matches/index.tsx
@@ -406,8 +406,9 @@ const Matches = ({
           name: string,
           {
             accession,
+            short_name,
             source_database: sourceDatabase,
-          }: { accession: string; source_database: string },
+          }: { short_name: string; accession: string; source_database: string },
         ) => (
           <Link
             to={
@@ -420,7 +421,10 @@ const Matches = ({
             }
           >
             <HighlightedText
-              text={name}
+              // If name is != ∅, short_name in the counter was found (Protein page case)
+              // If name is ∅, it means that the short name from the counters was not found (InterProScan results page case), so display short_name from renderer
+              // If short_name from renderer is null, then leave the cell blank
+              text={name == '∅' ? (short_name ? short_name : '') : name}
               textToHighlight={search?.search as string}
             />
           </Link>

diff --git a/src/components/ProteinViewer/Popup/Entry/index.tsx b/src/components/ProteinViewer/Popup/Entry/index.tsx
@@ -18,7 +18,7 @@ export type EntryDetail = {
     type: string;
     entry: string;
     protein?: string;
-    parent?: { protein?: string };
+    parent?: { protein?: string; accession: string };
     locations: Array<ProtVistaLocation>;
     confidence?: string;
   };
@@ -55,7 +55,8 @@ const ProtVistaEntryPopup = ({
     confidence,
   } = detail?.feature || {};
   const isInterPro = sourceDatabase.toLowerCase() === 'interpro';
-  const integrated = detail.feature?.integrated;
+  const integrated =
+    detail.feature?.integrated || detail.feature?.parent?.accession;
 
   // To include the type of fragment of the secondary structure
   let type = originalType;

diff --git a/src/components/ProteinViewer/index.tsx b/src/components/ProteinViewer/index.tsx
@@ -365,7 +365,6 @@ export const ProteinViewer = ({
                 {children}
               </Options>
               {protein.accession &&
-                !protein.accession.startsWith('iprscan') &&
                 mainTracks.length !== Object.entries(hideCategories).length && (
                   <ShowMoreTracks
                     showMore={showMore}
@@ -418,8 +417,16 @@ export const ProteinViewer = ({
                   const sectionName = typeNameToSectionName[type];
 
                   // Show only the main tracks unless button "Show more" is clicked
+
+                  // TEMPORARY: The second condition in OR is for the special case of families in the Interpro Scan result section: hide the div
+                  // insummary view because representative families are not available, so it'd be empty.
                   let hideDiv: string = '';
-                  if (!showMore && !mainTracks.includes(type)) {
+                  if (
+                    (!showMore && !mainTracks.includes(type)) ||
+                    (type === 'families' &&
+                      !showMore &&
+                      protein.accession.includes('iprscan'))
+                  ) {
                     hideDiv = 'none';
                   }