pull through metadata template fields

loculus-project · Dec 23, 2024 · e61a0e0 · e61a0e0
1 parent da8a87e
commit e61a0e0
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Showing 7 changed files with 22 additions and 10 deletions.
diff --git a/website/src/components/Submission/DataUploadForm.tsx b/website/src/components/Submission/DataUploadForm.tsx
@@ -35,6 +35,7 @@ type DataUploadFormProps = {
     action: UploadAction;
     group: Group;
     referenceGenomeSequenceNames: ReferenceGenomesSequenceNames;
+    metadataTemplateFields: string[];
     onSuccess: () => void;
     onError: (message: string) => void;
 };
@@ -131,6 +132,7 @@ const InnerDataUploadForm = ({
     onError,
     group,
     referenceGenomeSequenceNames,
+    metadataTemplateFields,
 }: DataUploadFormProps) => {
     const [metadataFile, setMetadataFile] = useState<File | null>(null);
     // can be null; if null -> don't apply mapping.
@@ -302,7 +304,7 @@ const InnerDataUploadForm = ({
                                         inputFile={metadataFile}
                                         columnMapping={columnMapping}
                                         setColumnMapping={setColumnMapping}
-                                        possibleTargetColumns={['foo', 'bar']} // TODO
+                                        possibleTargetColumns={metadataTemplateFields}
                                     />
                                 )}
                             </div>

diff --git a/website/src/components/Submission/RevisionForm.tsx b/website/src/components/Submission/RevisionForm.tsx
@@ -13,6 +13,7 @@ type RevisionFormProps = {
     clientConfig: ClientConfig;
     group: Group;
     referenceGenomeSequenceNames: ReferenceGenomesSequenceNames;
+    metadataTemplateFields: string[];
 };
 
 export const RevisionForm: FC<RevisionFormProps> = ({
@@ -21,13 +22,15 @@ export const RevisionForm: FC<RevisionFormProps> = ({
     clientConfig,
     group,
     referenceGenomeSequenceNames,
+    metadataTemplateFields,
 }) => {
     return (
         <div className='flex flex-col items-center'>
             <DataUploadForm
                 accessToken={accessToken}
                 organism={organism}
                 referenceGenomeSequenceNames={referenceGenomeSequenceNames}
+                metadataTemplateFields={metadataTemplateFields}
                 clientConfig={clientConfig}
                 action='revise'
                 onError={(message) => toast.error(message, { position: 'top-center', autoClose: false })}

diff --git a/website/src/components/Submission/SubmissionForm.tsx b/website/src/components/Submission/SubmissionForm.tsx
@@ -13,6 +13,7 @@ type SubmissionFormProps = {
     clientConfig: ClientConfig;
     group: Group;
     referenceGenomeSequenceNames: ReferenceGenomesSequenceNames;
+    metadataTemplateFields: string[];
 };
 
 export const SubmissionForm: FC<SubmissionFormProps> = ({
@@ -21,13 +22,15 @@ export const SubmissionForm: FC<SubmissionFormProps> = ({
     clientConfig,
     group,
     referenceGenomeSequenceNames,
+    metadataTemplateFields,
 }) => {
     return (
         <div className='flex flex-col items-center'>
             <DataUploadForm
                 accessToken={accessToken}
                 organism={organism}
                 referenceGenomeSequenceNames={referenceGenomeSequenceNames}
+                metadataTemplateFields={metadataTemplateFields}
                 clientConfig={clientConfig}
                 action='submit'
                 onError={(message) => toast.error(message, { position: 'top-center', autoClose: false })}

diff --git a/website/src/config.ts b/website/src/config.ts
@@ -3,6 +3,7 @@ import path from 'path';
 
 import type { z, ZodError } from 'zod';
 
+import { ACCESSION_FIELD, SUBMISSION_ID_FIELD } from './settings.ts';
 import { type InstanceConfig, type Schema, type WebsiteConfig, websiteConfig } from './types/config.ts';
 import { type ReferenceGenomes } from './types/referencesGenomes.ts';
 import { runtimeConfig, type RuntimeConfig, type ServiceUrls } from './types/runtimeConfig.ts';
@@ -92,12 +93,14 @@ export function getSchema(organism: string): Schema {
     return getConfig(organism).schema;
 }
 
-export function getMetadataTemplateFields(organism: string): string[] {
+export function getMetadataTemplateFields(organism: string, action: 'submit' | 'revise'): string[] {
     const schema = getConfig(organism).schema;
     if (schema.metadataTemplate !== undefined) {
         return schema.metadataTemplate;
     }
-    return getConfig(organism).schema.inputFields.map((field) => field.name);
+    const baseFields = getConfig(organism).schema.inputFields.map((field) => field.name);
+    const extraFields = action === 'submit' ? [SUBMISSION_ID_FIELD] : [ACCESSION_FIELD, SUBMISSION_ID_FIELD];
+    return [...extraFields, ...baseFields];
 }
 
 export function getRuntimeConfig(): RuntimeConfig {

diff --git a/website/src/pages/[organism]/submission/[groupId]/revise.astro b/website/src/pages/[organism]/submission/[groupId]/revise.astro
@@ -2,7 +2,7 @@
 import { cleanOrganism } from '../../../../components/Navigation/cleanOrganism';
 import { RevisionForm } from '../../../../components/Submission/RevisionForm';
 import SubmissionPageWrapper from '../../../../components/Submission/SubmissionPageWrapper.astro';
-import { getRuntimeConfig } from '../../../../config';
+import { getMetadataTemplateFields, getRuntimeConfig } from '../../../../config';
 import { getAccessToken } from '../../../../utils/getAccessToken';
 import { getReferenceGenomesSequenceNames } from '../../../../utils/search';
 import { getGroupsAndCurrentGroup } from '../../../../utils/submissionPages';
@@ -17,6 +17,7 @@ if (!cleanedOrganism) {
     };
 }
 const referenceGenomeSequenceNames = getReferenceGenomesSequenceNames(cleanedOrganism.key);
+const metadataTemplateFields = getMetadataTemplateFields(cleanedOrganism.key, 'revise');
 const groupsResult = await getGroupsAndCurrentGroup(Astro.params, Astro.locals.session);
 
 const clientConfig = getRuntimeConfig().public;
@@ -30,6 +31,7 @@ const clientConfig = getRuntimeConfig().public;
                     accessToken={getAccessToken(Astro.locals.session)!}
                     organism={organism}
                     referenceGenomeSequenceNames={referenceGenomeSequenceNames}
+                    metadataTemplateFields={metadataTemplateFields}
                     clientConfig={clientConfig}
                     group={group}
                     client:load

diff --git a/website/src/pages/[organism]/submission/[groupId]/submit.astro b/website/src/pages/[organism]/submission/[groupId]/submit.astro
@@ -2,7 +2,7 @@
 import { cleanOrganism } from '../../../../components/Navigation/cleanOrganism';
 import { SubmissionForm } from '../../../../components/Submission/SubmissionForm';
 import SubmissionPageWrapper from '../../../../components/Submission/SubmissionPageWrapper.astro';
-import { getRuntimeConfig } from '../../../../config';
+import { getMetadataTemplateFields, getRuntimeConfig } from '../../../../config';
 import { getAccessToken } from '../../../../utils/getAccessToken';
 import { getReferenceGenomesSequenceNames } from '../../../../utils/search';
 import { getGroupsAndCurrentGroup } from '../../../../utils/submissionPages';
@@ -18,6 +18,7 @@ if (!cleanedOrganism) {
     };
 }
 const referenceGenomeSequenceNames = getReferenceGenomesSequenceNames(cleanedOrganism.key);
+const metadataTemplateFields = getMetadataTemplateFields(cleanedOrganism.key, 'submit');
 
 const groupsResult = await getGroupsAndCurrentGroup(Astro.params, Astro.locals.session);
 
@@ -36,6 +37,7 @@ Astro.response.headers.append('Expires', '0');
                 <SubmissionForm
                     accessToken={getAccessToken(Astro.locals.session)!}
                     referenceGenomeSequenceNames={referenceGenomeSequenceNames}
+                    metadataTemplateFields={metadataTemplateFields}
                     organism={organism}
                     clientConfig={clientConfig}
                     group={group}

diff --git a/website/src/pages/[organism]/submission/template/index.ts b/website/src/pages/[organism]/submission/template/index.ts
@@ -3,7 +3,6 @@ import type { APIRoute } from 'astro';
 import { cleanOrganism } from '../../../../components/Navigation/cleanOrganism';
 import type { UploadAction } from '../../../../components/Submission/DataUploadForm.tsx';
 import { getMetadataTemplateFields } from '../../../../config';
-import { ACCESSION_FIELD, SUBMISSION_ID_FIELD } from '../../../../settings.ts';
 
 /** The TSV template file that users can download from the submission page. */
 export const GET: APIRoute = ({ params, request }) => {
@@ -16,7 +15,8 @@ export const GET: APIRoute = ({ params, request }) => {
     }
 
     const action: UploadAction = new URL(request.url).searchParams.get('format') === 'revise' ? 'revise' : 'submit';
-    const extraFields = action === 'submit' ? [SUBMISSION_ID_FIELD] : [ACCESSION_FIELD, SUBMISSION_ID_FIELD];
+    const fieldNames = getMetadataTemplateFields(organism.key, action);
+    const tsvTemplate = fieldNames.join('\t') + '\n';
 
     const headers: Record<string, string> = {
         'Content-Type': 'text/tsv', // eslint-disable-line @typescript-eslint/naming-convention
@@ -25,9 +25,6 @@ export const GET: APIRoute = ({ params, request }) => {
     const filename = `${organism.displayName.replaceAll(' ', '_')}_metadata_${action === 'revise' ? 'revision_' : ''}template.tsv`;
     headers['Content-Disposition'] = `attachment; filename="${filename}"`;
 
-    const fieldNames = getMetadataTemplateFields(organism.key);
-    const tsvTemplate = [...extraFields, ...fieldNames].join('\t') + '\n';
-
     return new Response(tsvTemplate, {
         headers,
     });