Move seq pages so they aren't within organism/ (#1319)

loculus-project · Mar 11, 2024 · d511087 · d511087
1 parent 41c6fff
commit d511087
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Showing 18 changed files with 199 additions and 156 deletions.
diff --git a/website/src/components/Navigation/OrganismSelector.astro b/website/src/components/Navigation/OrganismSelector.astro
@@ -4,7 +4,10 @@ import { type Organism } from '../../config';
 import { routes } from '../../routes';
 import IwwaArrowDown from '~icons/iwwa/arrow-down';
 
-const { knownOrganisms, organism } = cleanOrganism(Astro.params.organism);
+const { knownOrganisms, organism: originalOrganism } = cleanOrganism(Astro.params.organism);
+const { implicitOrganism } = Astro.props;
+const foundimplicitOrganism = knownOrganisms.find((knownOrganism: Organism) => knownOrganism.key === implicitOrganism);
+const organism = foundimplicitOrganism || originalOrganism;
 
 const label = organism === undefined ? 'Organisms' : organism.displayName;
 const firstBitOfUrl = Astro.url.pathname.split('/')[1];

diff --git a/website/src/components/SearchPage/Table.tsx b/website/src/components/SearchPage/Table.tsx
@@ -117,7 +117,7 @@ export const Table: FC<TableProps> = ({
                         {data.map((row, index) => (
                             <tr key={index}>
                                 <td>
-                                    <a href={routes.sequencesDetailsPage(organism, row[primaryKey] as string)}>
+                                    <a href={routes.sequencesDetailsPage(row[primaryKey] as string)}>
                                         {row[primaryKey]}
                                     </a>
                                 </td>

diff --git a/website/src/components/SequenceDetailsPage/SequencesBanner.astro b/website/src/components/SequenceDetailsPage/SequencesBanner.astro
@@ -7,10 +7,9 @@ import { getAccessionVersionString } from '../../utils/extractAccessionVersion';
 interface Props {
     sequenceEntryHistory: SequenceEntryHistory;
     accessionVersion: string;
-    organism: string;
 }
 
-const { sequenceEntryHistory, accessionVersion, organism } = Astro.props;
+const { sequenceEntryHistory, accessionVersion } = Astro.props;
 
 const ownHistoryEntry = sequenceEntryHistory.find((entry) => entry.accessionVersion === accessionVersion);
 
@@ -29,10 +28,7 @@ const isLatestVersion = ownHistoryEntry?.versionStatus === siloVersionStatuses.l
                 {latestAccessionVersion !== undefined && (
                     <p>
                         Go to the latest version:
-                        <a
-                            href={routes.sequencesDetailsPage(organism, latestAccessionVersion)}
-                            class='font-bold underline mx-3'
-                        >
+                        <a href={routes.sequencesDetailsPage(latestAccessionVersion)} class='font-bold underline mx-3'>
                             {getAccessionVersionString(latestAccessionVersion)}
                         </a>
                     </p>

diff --git a/website/src/components/SequenceDetailsPage/SequencesDataTableTitle.astro b/website/src/components/SequenceDetailsPage/SequencesDataTableTitle.astro
@@ -13,7 +13,7 @@ interface Props {
     accessionVersion: string;
 }
 
-const { sequenceEntryHistory, organism, accessionVersion } = Astro.props;
+const { sequenceEntryHistory, accessionVersion } = Astro.props;
 ---
 
 <div class='flex justify-between flex-wrap'>
@@ -25,7 +25,7 @@ const { sequenceEntryHistory, organism, accessionVersion } = Astro.props;
         sequenceEntryHistory !== undefined && sequenceEntryHistory.length > 1 && (
             <div class='dropdown dropdown-hover'>
                 <label tabindex='0' class='btn btn-sm btn-outline py-1'>
-                    <a href={routes.versionPage(organism, accessionVersion)} class='text-sm'>
+                    <a href={routes.versionPage(accessionVersion)} class='text-sm'>
                         All versions
                     </a>
                     <Arrow />
@@ -36,7 +36,7 @@ const { sequenceEntryHistory, organism, accessionVersion } = Astro.props;
                 >
                     {sequenceEntryHistory.map((version) => (
                         <li>
-                            <a href={routes.sequencesDetailsPage(organism, getAccessionVersionString({ ...version }))}>
+                            <a href={routes.sequencesDetailsPage(getAccessionVersionString({ ...version }))}>
                                 {getAccessionVersionString({ ...version })}
 
                                 <p class={`font-bold ${getVersionStatusColor(version.versionStatus)}`}>

diff --git a/website/src/components/SequenceDetailsPage/SequencesDetailsPage.astro b/website/src/components/SequenceDetailsPage/SequencesDetailsPage.astro
@@ -46,7 +46,7 @@ const isMyGroup =
 <div>
     <a
         class='mt-4 inline-block text-blue-600 hover:text-blue-800'
-        href={routes.sequencesFastaPage(organism, accessionVersion) + '?download'}
+        href={routes.sequencesFastaPage(accessionVersion) + '?download'}
     >
         Download FASTA
     </a>

diff --git a/website/src/layouts/BaseLayout.astro b/website/src/layouts/BaseLayout.astro
@@ -13,9 +13,10 @@ const { name: websiteName, logo } = websiteConfig;
 
 interface Props {
     title: string;
+    implicitOrganism?: string;
 }
 
-const { title } = Astro.props;
+const { title, implicitOrganism } = Astro.props;
 ---
 
 <html lang='en'>
@@ -47,7 +48,7 @@ const { title } = Astro.props;
                                 >
                                 <a href='/' class='fancytitle mr-4'>{websiteName}</a>
                             </div>
-                            <OrganismSelector />
+                            <OrganismSelector implicitOrganism={implicitOrganism} />
                         </div>
                     </div>
                     <Navigation />

diff --git a/website/src/pages/404.astro b/website/src/pages/404.astro
@@ -5,9 +5,6 @@ import BaseLayout from '../layouts/BaseLayout.astro';
 <BaseLayout title='Not Found'>
     <div class='bc'>
         <h1 class='title'>Page not found</h1>
-        <p>
-            The page you are looking for does not exist.
-            <a href='/'>Go to start page.</a>
-        </p>
+        <p>The page you are looking for does not exist.</p>
     </div>
 </BaseLayout>
diff --git a/website/src/pages/500.astro b/website/src/pages/500.astro
@@ -5,8 +5,5 @@ import BaseLayout from '../layouts/BaseLayout.astro';
 <BaseLayout title='Internal Server Error'>
     <div class='bc'>
         <h1 class='title'>An Error occurred</h1>
-        <p>
-            <a href='/'>Go to start page.</a>
-        </p>
     </div>
 </BaseLayout>
diff --git a/website/src/pages/[organism]/seq/[accessionVersion]/index.astro b/website/src/pages/[organism]/seq/[accessionVersion]/index.astro
diff --git a/...anism]/seq/[accessionVersion].fa/index.ts → .../pages/seq/[accessionVersion].fa/index.ts b/...anism]/seq/[accessionVersion].fa/index.ts → .../pages/seq/[accessionVersion].fa/index.ts
@@ -1,20 +1,20 @@
 import type { APIRoute } from 'astro';
 import { err, type Result } from 'neverthrow';
 
-import { getReferenceGenomes } from '../../../../config.ts';
-import { routes } from '../../../../routes.ts';
-import { LapisClient } from '../../../../services/lapisClient.ts';
-import type { ProblemDetail } from '../../../../types/backend.ts';
-import { parseAccessionVersionFromString } from '../../../../utils/extractAccessionVersion.ts';
-import { fastaEntryToString, parseFasta } from '../../../../utils/parseFasta.ts';
+import { getConfiguredOrganisms } from '../../../config';
+import { getReferenceGenomes } from '../../../config.ts';
+import { routes } from '../../../routes.ts';
+import { LapisClient } from '../../../services/lapisClient.ts';
+import { type ProblemDetail } from '../../../types/backend.ts';
+import { parseAccessionVersionFromString } from '../../../utils/extractAccessionVersion.ts';
+import { fastaEntryToString, parseFasta } from '../../../utils/parseFasta.ts';
 
 export const GET: APIRoute = async ({ params, redirect, request }) => {
     const accessionVersion = params.accessionVersion!;
-    const organism = params.organism!;
 
     const isDownload = new URL(request.url).searchParams.has('download');
 
-    const result = await getSequenceDetailsUnalignedFasta(accessionVersion, organism, isDownload);
+    const result = await getSequenceDetailsUnalignedFasta(accessionVersion, isDownload);
     if (!result.isOk()) {
         return new Response(undefined, {
             status: 404,
@@ -53,7 +53,7 @@ type Redirect = {
     redirectUrl: string;
 };
 
-const getSequenceDetailsUnalignedFasta = async (
+const getSequenceDetailsUnalignedFastaWithOrganism = async (
     accessionVersion: string,
     organism: string,
     isDownload: boolean,
@@ -66,7 +66,7 @@ const getSequenceDetailsUnalignedFasta = async (
         const latestVersionResult = await lapisClient.getLatestAccessionVersion(accession);
         return latestVersionResult.map((latestVersion) => ({
             type: ResultType.REDIRECT,
-            redirectUrl: routes.sequencesFastaPage(organism, latestVersion, isDownload),
+            redirectUrl: routes.sequencesFastaPage(latestVersion, isDownload),
         }));
     }
 
@@ -109,3 +109,17 @@ const getSequenceDetailsUnalignedFasta = async (
         fasta,
     }));
 };
+
+const getSequenceDetailsUnalignedFasta = async (accessionVersion: string, isDownload: boolean) => {
+    const organisms = getConfiguredOrganisms();
+    const results = await Promise.all(
+        organisms.map((organism) =>
+            getSequenceDetailsUnalignedFastaWithOrganism(accessionVersion, organism.key, isDownload),
+        ),
+    );
+    const firstSuccess = results.find((result) => result.isOk());
+    if (firstSuccess) {
+        return firstSuccess;
+    }
+    return results[0];
+};
diff --git a/...onVersion]/getSequenceDetailsTableData.ts → ...onVersion]/getSequenceDetailsTableData.ts b/...onVersion]/getSequenceDetailsTableData.ts → ...onVersion]/getSequenceDetailsTableData.ts
@@ -1,17 +1,18 @@
 import { Result } from 'neverthrow';
 
-import { getTableData, type TableDataEntry } from '../../../../components/SequenceDetailsPage/getTableData.ts';
-import { getSchema } from '../../../../config.ts';
-import { routes } from '../../../../routes.ts';
-import { BackendClient } from '../../../../services/backendClient.ts';
-import { LapisClient } from '../../../../services/lapisClient.ts';
-import type { DataUseTermsHistoryEntry, ProblemDetail } from '../../../../types/backend.ts';
-import type { SequenceEntryHistory } from '../../../../types/lapis.ts';
-import { parseAccessionVersionFromString } from '../../../../utils/extractAccessionVersion.ts';
+import { getTableData, type TableDataEntry } from '../../../components/SequenceDetailsPage/getTableData.ts';
+import { getSchema } from '../../../config.ts';
+import { routes } from '../../../routes.ts';
+import { BackendClient } from '../../../services/backendClient.ts';
+import { LapisClient } from '../../../services/lapisClient.ts';
+import type { DataUseTermsHistoryEntry, ProblemDetail } from '../../../types/backend.ts';
+import type { SequenceEntryHistory } from '../../../types/lapis.ts';
+import { parseAccessionVersionFromString } from '../../../utils/extractAccessionVersion.ts';
 
 export enum SequenceDetailsTableResultType {
     TABLE_DATA = 'tableData',
     REDIRECT = 'redirect',
+    ERROR = 'error',
 }
 
 type TableData = {
@@ -39,7 +40,7 @@ export const getSequenceDetailsTableData = async (
         const latestVersionResult = await lapisClient.getLatestAccessionVersion(accession);
         return latestVersionResult.map((latestVersion) => ({
             type: SequenceDetailsTableResultType.REDIRECT,
-            redirectUrl: routes.sequencesDetailsPage(organism, latestVersion),
+            redirectUrl: routes.sequencesDetailsPage(latestVersion),
         }));
     }