clarify sequency entry route naming

loculus-project · Oct 17, 2024 · 4650614 · 4650614
1 parent 7f34c6f
commit 4650614
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Showing 11 changed files with 23 additions and 20 deletions.
diff --git a/website/src/components/SearchPage/SeqPreviewModal.tsx b/website/src/components/SearchPage/SeqPreviewModal.tsx
@@ -102,7 +102,7 @@ export const SeqPreviewModal: React.FC<SeqPreviewModalProps> = ({
                     )}
                 </button>
                 <DownloadButton seqId={seqId} />
-                <a href={routes.sequencesDetailsPage(seqId)} title='Open in full window' className={BUTTONCLASS}>
+                <a href={routes.sequenceEntryDetailsPage(seqId)} title='Open in full window' className={BUTTONCLASS}>
                     <OouiNewWindowLtr className='w-6 h-6' />
                 </a>
                 <button type='button' className={BUTTONCLASS} onClick={onClose} title='Close'>
@@ -146,12 +146,12 @@ const DownloadButton: React.FC<DownloadButtonProps> = ({ seqId }: { seqId: strin
             </button>
             <ul className='dropdown-content z-20 menu p-1 shadow bg-base-100 rounded-btn absolute top-full -left-4'>
                 <li>
-                    <a href={routes.sequencesFastaPage(seqId, true)} className='block px-4 py-2 hover:bg-gray-100'>
+                    <a href={routes.sequenceEntryFastaPage(seqId, true)} className='block px-4 py-2 hover:bg-gray-100'>
                         FASTA
                     </a>
                 </li>
                 <li>
-                    <a href={routes.sequencesTsvPage(seqId, true)} className='block px-4 py-2 hover:bg-gray-100'>
+                    <a href={routes.sequenceEntryTsvPage(seqId, true)} className='block px-4 py-2 hover:bg-gray-100'>
                         Metadata TSV
                     </a>
                 </li>

diff --git a/website/src/components/SearchPage/Table.tsx b/website/src/components/SearchPage/Table.tsx
@@ -94,10 +94,10 @@ export const Table: FC<TableProps> = ({
                 e.preventDefault();
                 setPreviewedSeqId(seqId);
             } else {
-                window.open(routes.sequencesDetailsPage(seqId));
+                window.open(routes.sequenceEntryDetailsPage(seqId));
             }
         } else if (e.button === 1) {
-            window.open(routes.sequencesDetailsPage(seqId));
+            window.open(routes.sequenceEntryDetailsPage(seqId));
         }
     };
 
@@ -186,7 +186,7 @@ export const Table: FC<TableProps> = ({
                                     aria-label='SearchResult'
                                 >
                                     <a
-                                        href={routes.sequencesDetailsPage(row[primaryKey] as string)}
+                                        href={routes.sequenceEntryDetailsPage(row[primaryKey] as string)}
                                         className='text-primary-900 hover:text-primary-800 hover:no-underline'
                                         onClick={(e) => e.preventDefault()}
                                         onAuxClick={(e) => e.preventDefault()}

diff --git a/website/src/components/SequenceDetailsPage/SequenceEntryHistoryMenu.tsx b/website/src/components/SequenceDetailsPage/SequenceEntryHistoryMenu.tsx
@@ -34,7 +34,7 @@ export const SequenceEntryHistoryMenu: React.FC<Props> = ({
                     {sequenceEntryHistory.map((version) => (
                         <li key={version.accessionVersion}>
                             <a
-                                href={routes.sequencesDetailsPage(version.accessionVersion)}
+                                href={routes.sequenceEntryDetailsPage(version.accessionVersion)}
                                 onClick={(e) => {
                                     if (setPreviewedSeqId) {
                                         setPreviewedSeqId(version.accessionVersion);

diff --git a/website/src/components/SequenceDetailsPage/SequencesBanner.astro b/website/src/components/SequenceDetailsPage/SequencesBanner.astro
@@ -28,7 +28,10 @@ const isLatestVersion = ownHistoryEntry?.versionStatus === versionStatuses.lates
                 {latestAccessionVersion !== undefined && (
                     <p>
                         The latest version is:
-                        <a href={routes.sequencesDetailsPage(latestAccessionVersion)} class='font-bold underline mx-1'>
+                        <a
+                            href={routes.sequenceEntryDetailsPage(latestAccessionVersion)}
+                            class='font-bold underline mx-1'
+                        >
                             {getAccessionVersionString(latestAccessionVersion)}
                         </a>
                     </p>

diff --git a/website/src/components/SequenceDetailsPage/SequencesDataTableTitle.astro b/website/src/components/SequenceDetailsPage/SequencesDataTableTitle.astro
@@ -40,15 +40,15 @@ const { sequenceEntryHistory, accessionVersion, showDownload } = Astro.props;
                     <ul class='dropdown-content z-20 menu p-1 shadow bg-base-100 rounded-btn top-full -left-22 w-35'>
                         <li>
                             <a
-                                href={routes.sequencesFastaPage(accessionVersion, true)}
+                                href={routes.sequenceEntryFastaPage(accessionVersion, true)}
                                 class='block px-4 py-2 outlineButtonDropdownItem'
                             >
                                 FASTA
                             </a>
                         </li>
                         <li>
                             <a
-                                href={routes.sequencesTsvPage(accessionVersion, true)}
+                                href={routes.sequenceEntryTsvPage(accessionVersion, true)}
                                 class='block px-4 py-2 outlineButtonDropdownItem'
                             >
                                 Metadata TSV

diff --git a/website/src/pages/seq/[accessionVersion].fa/index.ts b/website/src/pages/seq/[accessionVersion].fa/index.ts
@@ -9,7 +9,7 @@ import { createDownloadAPIRoute } from '../sequenceDownload.ts';
 export const GET: APIRoute = createDownloadAPIRoute(
     'text/x-fasta',
     'fa',
-    routes.sequencesFastaPage,
+    routes.sequenceEntryFastaPage,
     async (accessionVersion: string, organism: string) => {
         const lapisClient = LapisClient.createForOrganism(organism);
         const referenceGenomes = getReferenceGenomes(organism);

diff --git a/website/src/pages/seq/[accessionVersion].tsv/index.ts b/website/src/pages/seq/[accessionVersion].tsv/index.ts
@@ -7,7 +7,7 @@ import { createDownloadAPIRoute } from '../sequenceDownload';
 export const GET: APIRoute = createDownloadAPIRoute(
     'text/tab-separated-values',
     'tsv',
-    routes.sequencesTsvPage,
+    routes.sequenceEntryTsvPage,
     (accessionVersion: string, organism: string) => {
         const lapisClient = LapisClient.createForOrganism(organism);
         return lapisClient.getSequenceEntryVersionDetailsTsv(accessionVersion);

diff --git a/website/src/pages/seq/[accessionVersion]/getSequenceDetailsTableData.ts b/website/src/pages/seq/[accessionVersion]/getSequenceDetailsTableData.ts
@@ -44,7 +44,7 @@ export const getSequenceDetailsTableData = async (
         const latestVersionResult = await lapisClient.getLatestAccessionVersion(accession);
         return latestVersionResult.map((latestVersion) => ({
             type: SequenceDetailsTableResultType.REDIRECT,
-            redirectUrl: routes.sequencesDetailsPage(latestVersion),
+            redirectUrl: routes.sequenceEntryDetailsPage(latestVersion),
         }));
     }
 

diff --git a/website/src/pages/seq/[accessionVersion]/versions.astro b/website/src/pages/seq/[accessionVersion]/versions.astro
@@ -32,7 +32,7 @@ const { organism, versionListResult } = await getVersionsData(accession);
                                 <div class='font-semibold'>{version.submittedAtTimestamp}</div>
                                 <div class='flex flex-row gap-3 justify-start'>
                                     <a
-                                        href={routes.sequencesDetailsPage(
+                                        href={routes.sequenceEntryDetailsPage(
                                             getAccessionVersionString(extractAccessionVersion(version)),
                                         )}
                                         class='underline'

diff --git a/website/src/routes/routes.ts b/website/src/routes/routes.ts
@@ -24,13 +24,13 @@ export const routes = {
             groupId,
             searchParams: new URLSearchParams({}),
         }),
-    sequencesDetailsPage: (accessionVersion: AccessionVersion | string) =>
+    sequenceEntryDetailsPage: (accessionVersion: AccessionVersion | string) =>
         `/seq/${getAccessionVersionString(accessionVersion)}`,
-    sequencesVersionsPage: (accessionVersion: AccessionVersion | string) =>
+    sequenceEntryVersionsPage: (accessionVersion: AccessionVersion | string) =>
         `/seq/${getAccessionVersionString(accessionVersion)}/versions`,
-    sequencesFastaPage: (accessionVersion: AccessionVersion | string, download = false) =>
+    sequenceEntryFastaPage: (accessionVersion: AccessionVersion | string, download = false) =>
         sequenceEntryDownloadUrl(accessionVersion, FileType.FASTA, download),
-    sequencesTsvPage: (accessionVersion: AccessionVersion | string, download = false) =>
+    sequenceEntryTsvPage: (accessionVersion: AccessionVersion | string, download = false) =>
         sequenceEntryDownloadUrl(accessionVersion, FileType.TSV, download),
     createGroup: () => '/user/createGroup',
     submissionPageWithoutGroup: (organism: string) => withOrganism(organism, '/submission'),
@@ -67,7 +67,7 @@ function withOrganism(organism: string, path: `/${string}`) {
 }
 
 function sequenceEntryDownloadUrl(accessionVersion: AccessionVersion | string, fileType: FileType, download = false) {
-    let url = `${routes.sequencesDetailsPage(accessionVersion)}.${fileType}`;
+    let url = `${routes.sequenceEntryDetailsPage(accessionVersion)}.${fileType}`;
     if (download) {
         url += '?download';
     }

diff --git a/website/src/utils/shouldMiddlewareEnforceLogin.spec.ts b/website/src/utils/shouldMiddlewareEnforceLogin.spec.ts
@@ -25,7 +25,7 @@ describe('shouldMiddlewareEnforceLogin', () => {
         expectNoLogin(`/${testOrganism}/search`);
         expectNoLogin(`/`);
         expectNoLogin(`/${testOrganism}`);
-        expectNoLogin(routes.sequencesDetailsPage('id_002156'));
+        expectNoLogin(routes.sequenceEntryDetailsPage('id_002156'));
     });
 
     function expectForceLogin(path: string) {