Linkout wip

kubernetes/loculus/templates/_common-metadata.tpl

@@ -168,6 +168,13 @@ organisms:
     schema:
       {{- with ($instance.schema | include "loculus.patchMetadataSchema" | fromYaml) }}
       organismName: {{ quote .organismName }}
+      {{ if .linkOuts }}
+      linkOuts:
+        {{- range $linkOut := .linkOuts }}
+        - name: {{ quote $linkOut.name }}
+          url: {{ quote $linkOut.url }}
+        {{- end }}
+      {{ end }}
       loadSequencesAutomatically: {{ .loadSequencesAutomatically | default false }}
       {{- $nucleotideSequences := .nucleotideSequences | default (list "main")}}
       {{ if .image }}

kubernetes/loculus/values.yaml

@@ -33,6 +33,21 @@ defaultOrganismConfig: &defaultOrganismConfig
     loadSequencesAutomatically: true
     organismName: "Ebola Sudan"
     image: "/images/organisms/ebolasudan_small.jpg"
+    linkOuts:
+      - name: "Nextclade simple"
+        url: "https://clades.nextstrain.org/?input-fasta={{[unalignedNucleotideSequences|fasta]}}&dataset-name=nextstrain/ebola/sudan&dataset-server={{https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output}}"
+      - name: "Make a renamed fasta"
+        url: "https://metadata-sequence-combiner.vercel.app/api/combine?sequencesUrl={{[unalignedNucleotideSequences|json]}}&metadataUrl={{[metadata|json]}}&fields=displayName"
+      - name: "Nextclade renamed fasta"
+        url: "https://clades.nextstrain.org/?input-fasta={{https://metadata-sequence-combiner.vercel.app/api/combine?sequencesUrl={{[unalignedNucleotideSequences|json]}}&metadataUrl={{[metadata|json]}}&fields=displayName}}&dataset-name=nextstrain/ebola/sudan&dataset-server={{https://raw.githubusercontent.com/nextstrain/nextclade_data/ebola/data_output}}"
+      - name: "Make a renamed fasta with dates"
+        url: "https://metadata-sequence-combiner.vercel.app/api/combine?sequencesUrl={{[alignedNucleotideSequences|json]}}&metadataUrl={{[metadata|json]}}&fields=displayName,sampleCollectionDate"
+      - name: "Analyse with Delphy (not working for some reason)"
+        url: "https://delphy.fathom.info/?https://metadata-sequence-combiner.vercel.app/api/combine?sequencesUrl={{[alignedNucleotideSequences|json]}}&metadataUrl={{[metadata|json]}}&fields=displayName,sampleCollectionDate&filterForValidDateString=sampleCollectionDate"
+      - name: "Analyse with Delphy (use proxy, better but still not working)"
+        url: "https://delphy.fathom.info/?https://delphy.fathom.info/proxy/metadata-sequence-combiner.vercel.app/api/combine?sequencesUrl={{[alignedNucleotideSequences|json]}}&metadataUrl={{[metadata|json]}}&fields=displayName,sampleCollectionDate&filterForValidDateString=sampleCollectionDate"
+
+
     earliestReleaseDate:
       enabled: true
       externalFields:

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

@@ -12,6 +12,7 @@ export type DownloadOption = {
     includeRestricted: boolean;
     dataType: DownloadDataType;
     compression: Compression;
+    dataFormat: string | undefined;
 };
 
 /**
@@ -45,13 +46,20 @@ export class DownloadUrlGenerator {
         if (!option.includeRestricted) {
             params.set('dataUseTerms', 'OPEN');
         }
-        if (option.dataType.type === 'metadata') {
+        if (option.dataType.type === 'metadata' ) {
             params.set('dataFormat', metadataDefaultDownloadDataFormat);
+        } else {
+            params.set('dataFormat', 'fasta');
         }
         if (option.compression !== undefined) {
             params.set('compression', option.compression);
         }
 
+        if(option.dataFormat!==undefined){
+            params.delete('dataFormat');
+            params.set('dataFormat', option.dataFormat);
+        }
+
         downloadParameters.toUrlSearchParams().forEach(([name, value]) => {
             params.append(name, value);
         });

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

@@ -0,0 +1,105 @@
+import { type FC, useState } from 'react';
+import { Menu } from '@headlessui/react';
+import IwwaArrowDown from '~icons/iwwa/arrow-down';
+import DashiconsExternal from '~icons/dashicons/external';
+import { type DownloadUrlGenerator, type DownloadOption } from './DownloadUrlGenerator';
+import { type SequenceFilter } from './SequenceFilters';
+import { type ReferenceGenomesSequenceNames } from '../../../types/referencesGenomes';
+import { processTemplate } from '../../../utils/templateProcessor';
+
+const DATA_TYPES = ["unalignedNucleotideSequences", "metadata", "alignedNucleotideSequences"] as const;
+
+type LinkOut = {
+    name: string;
+    url: string;
+};
+
+type LinkOutMenuProps = {
+    downloadUrlGenerator: DownloadUrlGenerator;
+    sequenceFilter: SequenceFilter;
+    referenceGenomesSequenceNames: ReferenceGenomesSequenceNames;
+    linkOuts: LinkOut[];
+};
+
+export const LinkOutMenu: FC<LinkOutMenuProps> = ({
+    downloadUrlGenerator,
+    sequenceFilter,
+    referenceGenomesSequenceNames,
+    linkOuts,
+}) => {
+    const [isOpen, setIsOpen] = useState(false);
+
+    const generateLinkOutUrl = (linkOut: LinkOut) => {
+        // Find all placeholders in the template that match [type] or [type|format]
+        const placeholderRegex = /\[([\w]+)(?:\|([\w]+))?\]/g;
+        const placeholders = Array.from(linkOut.url.matchAll(placeholderRegex));
+
+        // Generate URLs for all found placeholders
+        const urlMap = placeholders.reduce((acc, match) => {
+            const [fullMatch, dataType, dataFormat] = match;
+
+            // Skip if not a valid data type
+            if (!DATA_TYPES.includes(dataType as any)) {
+                return acc;
+            }
+
+            const downloadOption: DownloadOption = {
+                includeOldData: false,
+                includeRestricted: false,
+                dataType: {
+                    type: dataType,
+                    segment: undefined,
+                },
+                compression: undefined,
+                dataFormat: dataFormat,
+            };
+
+            const { url } = downloadUrlGenerator.generateDownloadUrl(sequenceFilter, downloadOption);
+
+            // Use the full match (including format if present) as the key
+            // This ensures we replace exactly what was in the template
+            return {
+                ...acc,
+                [fullMatch.slice(1, -1)]: url, // Remove the [] brackets
+            };
+        }, {} as Record<string, string>);
+
+        // Process template with all URLs
+        return processTemplate(linkOut.url, urlMap);
+    };
+
+    return (
+        <Menu as="div" className="ml-2 relative inline-block text-left">
+            <Menu.Button 
+                className="outlineButton flex items-center"
+                onClick={() => setIsOpen(!isOpen)}
+            >
+                Tools
+                <IwwaArrowDown className="ml-2 h-5 w-5" aria-hidden="true" />
+            </Menu.Button>
+
+            <Menu.Items className="absolute right-0 mt-2 w-56 origin-top-right rounded-md bg-white shadow-lg ring-1 ring-black ring-opacity-5 focus:outline-none">
+                <div className="py-1">
+                    {linkOuts.map((linkOut) => (
+                        <Menu.Item key={linkOut.name}>
+                            {({ active }) => (
+                                <a
+                                    href={generateLinkOutUrl(linkOut)}
+                                    target="_blank"
+                                    rel="noopener noreferrer"
+                                    className={`
+                                        ${active ? 'bg-gray-100 text-gray-900' : 'text-gray-700'}
+                                        flex items-center justify-between px-4 py-2 text-sm
+                                    `}
+                                >
+                                    {linkOut.name}
+                                    <DashiconsExternal className="h-4 w-4 ml-2" />
+                                </a>
+                            )}
+                        </Menu.Item>
+                    ))}
+                </div>
+            </Menu.Items>
+        </Menu>
+    );
+};

website/src/components/SearchPage/SearchFullUI.tsx

@@ -21,6 +21,8 @@
 import type { ReferenceGenomesSequenceNames } from '../../types/referencesGenomes.ts';
 import type { ClientConfig } from '../../types/runtimeConfig.ts';
 import { formatNumberWithDefaultLocale } from '../../utils/formatNumber.tsx';
+import { LinkOutMenu } from './DownloadDialog/LinkOutMenu.tsx';
+import type { LinkOut } from '../../types/config.ts';
 import {
     getFieldValuesFromQuery,
     getColumnVisibilitiesFromQuery,
@@ -46,6 +48,7 @@
     initialCount: number;
     initialQueryDict: QueryState;
     showEditDataUseTermsControls?: boolean;
+    linkOuts: LinkOut[] | undefined;
 }
 interface QueryState {
     [key: string]: string;
@@ -71,6 +74,7 @@
     initialData,
     initialCount,
     initialQueryDict,
+    linkOuts,   
     showEditDataUseTermsControls = false,
 }: InnerSearchFullUIProps) => {
     if (!hiddenFieldValues) {
@@ -377,6 +381,15 @@
                                 sequenceFilter={sequencesFilter}
                                 referenceGenomesSequenceNames={referenceGenomesSequenceNames}
                             />
+                            {linkOuts!==undefined && linkOuts.length > 0 && (
+                            <LinkOutMenu
+                                downloadUrlGenerator={downloadUrlGenerator}
+                                sequenceFilter={sequencesFilter}
+                                referenceGenomesSequenceNames={referenceGenomesSequenceNames}
+                                linkOuts={linkOuts}
+                                />
+                            )
+                            }
                         </div>
                     </div>
 

website/src/pages/[organism]/search/index.astro

@@ -57,5 +57,6 @@ const { data, totalCount } = await performLapisSearchQueries(
         initialData={data}
         initialCount={totalCount}
         initialQueryDict={initialQueryDict}
+        linkOuts={schema.linkOuts}
     />
 </BaseLayout>

website/src/types/config.ts

@@ -89,6 +89,12 @@ export type GroupedMetadataFilter = {
     notSearchable?: boolean;
     initiallyVisible?: boolean;
 };
+export const linkOut = z.object({
+    name: z.string(),
+    url: z.string(),
+});
+
+export type LinkOut = z.infer<typeof linkOut>;
 
 const schema = z.object({
     organismName: z.string(),
@@ -102,6 +108,7 @@ const schema = z.object({
     defaultOrderBy: z.string(),
     defaultOrder: orderByType,
     loadSequencesAutomatically: z.boolean().optional(),
+    linkOuts: z.array(linkOut).optional(),
 });
 export type Schema = z.infer<typeof schema>;
 

website/src/utils/templateProcessor.ts

@@ -0,0 +1,32 @@
+/**
+ * Process a URL template by replacing placeholders with values
+ */
+export function processTemplate(template: string, params: Record<string, string>) {
+    // Helper function to recursively process {{ }} expressions
+    function processNestedBraces(str: string): string {
+        // Regex to find innermost {{ }} pairs that don't contain other {{ }}
+        const regex = /{{([^{}]+)}}/g;
+
+        // If no more {{ }} found, return the string
+        if (!str.match(regex)) {
+            return str;
+        }
+
+        // Replace all innermost {{ }} with their URL encoded content
+        const processed = str.replace(regex, (match, content) => {
+            return encodeURIComponent(content.trim());
+        });
+
+        // Recursively process any remaining {{ }}
+        return processNestedBraces(processed);
+    }
+
+    // Replace special placeholders with their values
+    let result = template;
+    Object.entries(params).forEach(([key, value]) => {
+        result = result.replace(`[${key}]`, value || '');
+    });
+
+    // Process all {{ }} expressions recursively
+    return processNestedBraces(result);
+}