feat: add opt-in rich fasta headers with metadata

kubernetes/loculus/templates/_common-metadata.tpl

@@ -176,6 +176,9 @@ organisms:
       {{ if .description }}
       description: {{ quote .description }}
       {{ end }}
+      {{ if .richFastaHeaderFields}}
+      richFastaHeaderFields: {{ toJson .richFastaHeaderFields }}
+      {{ end }}
       primaryKey: accessionVersion
       inputFields: {{- include "loculus.inputFields" . | nindent 8 }}
         - name: versionComment

kubernetes/loculus/values.yaml

@@ -37,6 +37,7 @@ defaultOrganismConfig: &defaultOrganismConfig
       enabled: true
       externalFields:
         - ncbiReleaseDate
+    richFastaHeaderFields: ["displayName"]
     ### Field list
     ## General fields
     # name: Key used across app to refer to this field (required)

website/src/components/SearchPage/DownloadDialog/DownloadDataType.ts

@@ -1,6 +1,10 @@
 export type DownloadDataType =
     | { type: 'metadata' }
-    | { type: 'unalignedNucleotideSequences'; segment?: string }
+    | {
+          type: 'unalignedNucleotideSequences';
+          segment?: string;
+          includeRichFastaHeaders?: boolean;
+      }
     | { type: 'alignedNucleotideSequences'; segment?: string }
     | { type: 'alignedAminoAcidSequences'; gene: string };
 
@@ -20,21 +24,3 @@ export const dataTypeForFilename = (dataType: DownloadDataType): string => {
             return `aligned-aa-${dataType.gene}`;
     }
 };
-
-/**
- * Get the LAPIS endpoint where to download this data type from.
- */
-export const getEndpoint = (dataType: DownloadDataType) => {
-    const segmentPath = (segment?: string) => (segment !== undefined ? `/${segment}` : '');
-
-    switch (dataType.type) {
-        case 'metadata':
-            return '/sample/details';
-        case 'unalignedNucleotideSequences':
-            return '/sample/unalignedNucleotideSequences' + segmentPath(dataType.segment);
-        case 'alignedNucleotideSequences':
-            return '/sample/alignedNucleotideSequences' + segmentPath(dataType.segment);
-        case 'alignedAminoAcidSequences':
-            return `/sample/alignedAminoAcidSequences/${dataType.gene}`;
-    }
-};

website/src/components/SearchPage/DownloadDialog/DownloadForm.tsx

@@ -19,6 +19,7 @@ export const DownloadForm: FC<DownloadFormProps> = ({ referenceGenomesSequenceNa
     const [unalignedNucleotideSequence, setUnalignedNucleotideSequence] = useState(0);
     const [alignedNucleotideSequence, setAlignedNucleotideSequence] = useState(0);
     const [alignedAminoAcidSequence, setAlignedAminoAcidSequence] = useState(0);
+    const [includeRichFastaHeaders, setIncludeRichFastaHeaders] = useState(0);
 
     const isMultiSegmented = referenceGenomesSequenceNames.nucleotideSequences.length > 1;
 
@@ -34,6 +35,7 @@ export const DownloadForm: FC<DownloadFormProps> = ({ referenceGenomesSequenceNa
                     segment: isMultiSegmented
                         ? referenceGenomesSequenceNames.nucleotideSequences[unalignedNucleotideSequence]
                         : undefined,
+                    includeRichFastaHeaders: includeRichFastaHeaders === 1,
                 };
                 break;
             case 2:
@@ -68,6 +70,7 @@ export const DownloadForm: FC<DownloadFormProps> = ({ referenceGenomesSequenceNa
         unalignedNucleotideSequence,
         alignedNucleotideSequence,
         alignedAminoAcidSequence,
+        includeRichFastaHeaders,
         isMultiSegmented,
         referenceGenomesSequenceNames.nucleotideSequences,
         referenceGenomesSequenceNames.genes,
@@ -114,19 +117,30 @@ export const DownloadForm: FC<DownloadFormProps> = ({ referenceGenomesSequenceNa
                     { label: <>Metadata</> },
                     {
                         label: <>Raw nucleotide sequences</>,
-                        subOptions: isMultiSegmented ? (
+                        subOptions: (
                             <div className='px-8'>
-                                <DropdownOptionBlock
-                                    name='unalignedNucleotideSequences'
-                                    options={referenceGenomesSequenceNames.nucleotideSequences.map((segment) => ({
-                                        label: <>{segment}</>,
-                                    }))}
-                                    selected={unalignedNucleotideSequence}
-                                    onSelect={setUnalignedNucleotideSequence}
+                                {isMultiSegmented ? (
+                                    <DropdownOptionBlock
+                                        name='unalignedNucleotideSequences'
+                                        options={referenceGenomesSequenceNames.nucleotideSequences.map((segment) => ({
+                                            label: <>{segment}</>,
+                                        }))}
+                                        selected={unalignedNucleotideSequence}
+                                        onSelect={setUnalignedNucleotideSequence}
+                                        disabled={dataType !== 1}
+                                    />
+                                ) : undefined}
+                                <RadioOptionBlock
+                                    name='richFastaHeaders'
+                                    title='FASTA header style'
+                                    options={[{ label: <>Accession only</> }, { label: <>Accession and metadata</> }]}
+                                    selected={includeRichFastaHeaders}
+                                    onSelect={setIncludeRichFastaHeaders}
                                     disabled={dataType !== 1}
+                                    variant='nested'
                                 />
                             </div>
-                        ) : undefined,
+                        ),
                     },
                     {
                         label: <>Aligned nucleotide sequences</>,
@@ -170,6 +184,7 @@ export const DownloadForm: FC<DownloadFormProps> = ({ referenceGenomesSequenceNa
                 options={[{ label: <>None</> }, { label: <>Zstandard</> }, { label: <>Gzip</> }]}
                 selected={compression}
                 onSelect={setCompression}
+                disabled={dataType === 1 && includeRichFastaHeaders === 1} // Rich headers don't support compression
             />
         </div>
     );

website/src/components/SearchPage/DownloadDialog/DownloadUrlGenerator.ts

@@ -1,6 +1,6 @@
 import kebabCase from 'just-kebab-case';
 
-import { getEndpoint, dataTypeForFilename, type DownloadDataType } from './DownloadDataType.ts';
+import { dataTypeForFilename, type DownloadDataType } from './DownloadDataType.ts';
 import type { SequenceFilter } from './SequenceFilters.tsx';
 import { IS_REVOCATION_FIELD, metadataDefaultDownloadDataFormat, VERSION_STATUS_FIELD } from '../../../settings.ts';
 import { versionStatuses } from '../../../types/lapis.ts';
@@ -21,19 +21,21 @@ export type DownloadOption = {
 export class DownloadUrlGenerator {
     private readonly organism: string;
     private readonly lapisUrl: string;
+    private readonly richFastaHeaderFields: string[];
 
     /**
      * Create new DownloadUrlGenerator with the given properties.
      * @param organism The organism, will be part of the filename.
      * @param lapisUrl The lapis API URL for downloading.
      */
-    constructor(organism: string, lapisUrl: string) {
+    constructor(organism: string, lapisUrl: string, richFastaHeaderFields: string[] = ['accessionVersion']) {
         this.organism = organism;
         this.lapisUrl = lapisUrl;
+        this.richFastaHeaderFields = richFastaHeaderFields;
     }
 
     public generateDownloadUrl(downloadParameters: SequenceFilter, option: DownloadOption) {
-        const baseUrl = `${this.lapisUrl}${getEndpoint(option.dataType)}`;
+        const baseUrl = this.downloadEndpoint(option.dataType);
         const params = new URLSearchParams();
 
         params.set('downloadAsFile', 'true');
@@ -52,8 +54,20 @@ export class DownloadUrlGenerator {
             params.set('compression', option.compression);
         }
 
+        if (
+            option.dataType.type === 'unalignedNucleotideSequences' &&
+            option.dataType.includeRichFastaHeaders === true
+        ) {
+            // get from config
+            params.set('headerFields', this.richFastaHeaderFields.join(','));
+        }
+
         downloadParameters.toUrlSearchParams().forEach(([name, value]) => {
-            params.append(name, value);
+            // Empty values are not allowed for e.g. aminoAcidInsertion filters
+            // Hence, filter out empty values
+            if (value !== '') {
+                params.append(name, value);
+            }
         });
 
         return {
@@ -69,4 +83,21 @@ export class DownloadUrlGenerator {
         const timestamp = new Date().toISOString().slice(0, 16).replace(':', '');
         return `${organism}_${dataType}_${timestamp}`;
     }
+
+    private readonly downloadEndpoint = (dataType: DownloadDataType) => {
+        const segmentPath = (segment?: string) => (segment !== undefined ? '/' + segment : '');
+
+        switch (dataType.type) {
+            case 'metadata':
+                return this.lapisUrl + '/sample/details';
+            case 'unalignedNucleotideSequences':
+                return dataType.includeRichFastaHeaders === true
+                    ? '/' + this.organism + '/api/sequences' + segmentPath(dataType.segment)
+                    : this.lapisUrl + '/sample/unalignedNucleotideSequences' + segmentPath(dataType.segment);
+            case 'alignedNucleotideSequences':
+                return this.lapisUrl + '/sample/alignedNucleotideSequences' + segmentPath(dataType.segment);
+            case 'alignedAminoAcidSequences':
+                return this.lapisUrl + '/sample/alignedAminoAcidSequences/' + dataType.gene;
+        }
+    };
 }

website/src/components/SearchPage/DownloadDialog/OptionBlock.tsx

@@ -10,6 +10,7 @@ export type OptionBlockProps = {
     selected: number;
     onSelect: (index: number) => void;
     disabled?: boolean;
+    variant?: 'default' | 'nested'; // New prop
 };
 
 export const RadioOptionBlock: FC<OptionBlockProps> = ({
@@ -19,22 +20,30 @@ export const RadioOptionBlock: FC<OptionBlockProps> = ({
     selected,
     onSelect,
     disabled = false,
+    variant = 'default',
 }) => {
     return (
-        <div className='basis-1/2 justify-start'>
-            {title !== undefined && <h4 className='font-bold'>{title}</h4>}
+        // <div className='basis-1/2 justify-start'>
+        <div className={(variant === 'nested' ? 'px-4 mr-10' : '') + ' basis-1/2 justify-start'}>
+            {title !== undefined && (
+                <h4 className={variant === 'nested' ? 'text-sm font-normal' : 'font-bold'}>{title}</h4>
+            )}
             {options.map((option, index) => (
-                <div key={index}>
+                <div key={index} className={disabled ? 'bg-gray-100' : ''}>
                     <label className='label justify-start py-1 items-baseline'>
                         <input
                             type='radio'
                             name={name}
-                            className='mr-4 text-primary-600 focus:ring-primary-600 relative bottom-[-0.2rem]'
+                            className='mr-4 text-primary-600 focus:ring-primary-600 relative bottom-[-0.2rem] disabled:opacity-50'
                             checked={index === selected}
                             onChange={() => onSelect(index)}
                             disabled={disabled}
                         />
-                        <span className='label-text'>{option.label}</span>
+                        <span
+                            className={`label-text ${disabled ? 'text-gray-500' : ''} ${variant === 'nested' ? 'text-sm' : ''}`}
+                        >
+                            {option.label}
+                        </span>
                     </label>
                     {option.subOptions}
                 </div>

website/src/components/SearchPage/SearchFullUI.tsx

@@ -191,7 +191,7 @@ export const InnerSearchFullUI = ({
     };
 
     const lapisUrl = getLapisUrl(clientConfig, organism);
-    const downloadUrlGenerator = new DownloadUrlGenerator(organism, lapisUrl);
+    const downloadUrlGenerator = new DownloadUrlGenerator(organism, lapisUrl, schema.richFastaHeaderFields);
 
     const hooks = lapisClientHooks(lapisUrl).zodiosHooks;
     const aggregatedHook = hooks.useAggregated({}, {});