[do not merge] Bisect PR to locate bug

backend/src/main/kotlin/org/loculus/backend/config/Config.kt

@@ -54,9 +54,6 @@ enum class MetadataType {
     @JsonProperty("boolean")
     BOOLEAN,
 
-    @JsonProperty("authors")
-    AUTHORS,
-
     ;
 
     override fun toString(): String = lowerCase(name)

backend/src/main/kotlin/org/loculus/backend/service/submission/ProcessedSequenceEntryValidator.kt

@@ -166,7 +166,7 @@ class ProcessedSequenceEntryValidator(
         }
 
         val isOfCorrectPrimitiveType = when (metadata.type) {
-            MetadataType.STRING, MetadataType.AUTHORS -> fieldValue.isTextual
+            MetadataType.STRING -> fieldValue.isTextual
             MetadataType.INTEGER -> fieldValue.isInt
             MetadataType.FLOAT -> fieldValue.isFloatingPointNumber
             MetadataType.NUMBER -> fieldValue.isNumber

deploy.py

@@ -18,11 +18,11 @@
 HELM_CHART_DIR = ROOT_DIR / 'kubernetes' / 'loculus'
 HELM_VALUES_FILE = HELM_CHART_DIR / 'values.yaml'
 
-WEBSITE_PORT_MAPPING = '-p 127.0.0.1:3000:30081@agent:0'
-BACKEND_PORT_MAPPING = '-p 127.0.0.1:8079:30082@agent:0'
-LAPIS_PORT_MAPPING = '-p 127.0.0.1:8080:80@loadbalancer'
-DATABASE_PORT_MAPPING = '-p 127.0.0.1:5432:30432@agent:0'
-KEYCLOAK_PORT_MAPPING = '-p 127.0.0.1:8083:30083@agent:0'
+WEBSITE_PORT_MAPPING = '-p 3000:30081@agent:0'
+BACKEND_PORT_MAPPING = '-p 8079:30082@agent:0'
+LAPIS_PORT_MAPPING = '-p 8080:80@loadbalancer'
+DATABASE_PORT_MAPPING = '-p 5432:30432@agent:0'
+KEYCLOAK_PORT_MAPPING = '-p 8083:30083@agent:0'
 
 PORTS = [WEBSITE_PORT_MAPPING, BACKEND_PORT_MAPPING, LAPIS_PORT_MAPPING, DATABASE_PORT_MAPPING, KEYCLOAK_PORT_MAPPING]
 

kubernetes/loculus/templates/_config-processor.tpl

@@ -40,11 +40,6 @@
         secretKeyRef:
           name: backend-keycloak-client-secret
           key: backendKeycloakClientSecret
-    - name: LOCULUSSUB_orcidSecret
-      valueFrom:
-        secretKeyRef:
-          name: orcid
-          key: orcidSecret
 {{- end }}
 
 

kubernetes/loculus/templates/keycloak-config-map.yaml

@@ -29,7 +29,7 @@ data:
       "accessTokenLifespan": 36000,
       "ssoSessionIdleTimeout": 36000,
       "users": [
-        {{ if $.Values.createTestAccounts }}
+        {{ if $.Values.devMode }}
           {{- $browsers := list "firefox" "webkit" "chromium"}}
           {{- range $_, $browser := $browsers }}
             {{- range $index, $_ := until 20}}
@@ -332,7 +332,7 @@ data:
         "linkOnly" : false,
         "firstBrokerLoginFlowAlias" : "first broker login",
         "config" : {
-          "clientSecret" : "[[orcidSecret]]",
+          "clientSecret" : "65897b89-a888-427d-8828-1f1dd97bf6c1",
           "clientId" : "APP-P1P7N7T9YVBHQ4EH"
         }
       } ],

kubernetes/loculus/templates/lapis-silo-database-config.yaml

@@ -16,7 +16,7 @@ data:
       metadata:
       {{- range (concat $commonMetadata .metadata) }}
         - name: {{ .name }}
-          type: {{ (.type | eq "timestamp") | ternary "int" ((.type | eq "authors") | ternary "string" .type) }}
+          type: {{ (.type | eq "timestamp") | ternary "int" .type }}
           {{- if .generateIndex }}
           generateIndex: {{ .generateIndex }}
           {{- end }}

kubernetes/loculus/templates/loculus-website-config.yaml

@@ -20,7 +20,7 @@ data:
   runtime_config.json: |
     {
         "name" : "{{ $.Values.name }}",
-        "insecureCookies": {{ $.Values.insecureCookies }},
+        "devMode": {{ $.Values.devMode }},
         "serverSide": {
             {{- if .Values.usePublicRuntimeConfigAsServerSide }}
             {{- template "loculus.publicRuntimeConfig" dict "Values" .Values "externalLapisUrlConfig" $externalLapisUrlConfig -}}

kubernetes/loculus/values.yaml

@@ -287,7 +287,7 @@ defaultOrganisms:
           header: Authors
         - name: authors
           displayName: Authors
-          type: authors
+          type: string
           header: Authors
         - name: submitter_country
           displayName: Submitter country
@@ -876,7 +876,7 @@ auth:
     envelopeFrom: "[email protected]"
   verifyEmail: true
   resetPasswordAllowed: true
-insecureCookies: false
+devMode: true # TODO https://github.com/loculus-project/loculus/issues/1568: remove this from default Values
 bannerMessage: "This is a development environment. Data will not be persisted."
 additionalHeadHTML: '<script defer data-domain="main.loculus.org" src="https://plausible.io/js/script.js"></script>'
 imageTags:
@@ -922,10 +922,6 @@ secrets:
     type: raw
     data:
       initialAdminPassword: "admin"
-  orcid:
-    type: raw
-    data:
-      orcidSecret: "dummy"
 enableCrossRefCredentials: true
 runDevelopmentKeycloakDatabase: true
 runDevelopmentMainDatabase: true

kubernetes/loculus/values_e2e_and_dev.yaml

@@ -5,5 +5,4 @@ secrets:
         insdcIngestUserPassword: "insdc_ingest"
         dummyPreprocessingPipelinePassword: "preprocessing_pipeline"
         siloImportJobPassword: "silo_import_job"
-        backendUserPassword: "backend"
-createTestAccounts: true
+        backendUserPassword: "backend"

kubernetes/loculus/values_preview_server.yaml

@@ -1,12 +1,6 @@
-createTestAccounts: true
 secrets:
   smtp-password:
     type: sealedsecret
     clusterWide: "true"
     data:
       secretKey: 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
-  orcid:
-    type: sealedsecret
-    clusterWide: "true"
-    data:
-      orcidSecret: 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

website/src/components/ReviewPage/ReviewPage.tsx

@@ -20,7 +20,7 @@ import {
 } from '../../types/backend.ts';
 import { type ClientConfig } from '../../types/runtimeConfig.ts';
 import { displayConfirmationDialog } from '../ConfirmationDialog.tsx';
-import { getLastApprovalTimeKey } from '../SearchPage/RecentSequencesBanner.tsx';
+import { LAST_APPROVAL_TIME_LOCAL_STORAGE_KEY } from '../SearchPage/RecentSequencesBanner.tsx';
 import { ManagedErrorFeedback, useErrorFeedbackState } from '../common/ManagedErrorFeedback.tsx';
 import { withQueryProvider } from '../common/withQueryProvider.tsx';
 import BiTrash from '~icons/bi/trash';
@@ -284,7 +284,7 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, group, a
                                     scope: approveAllDataScope.value,
                                 });
 
-                                storeLastApprovalTime(organism);
+                                storeLastApprovalTime();
                             },
                         })
                     }
@@ -310,7 +310,7 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, group, a
                                     groupIdsFilter: [group.groupId],
                                     scope: approveAllDataScope.value,
                                 });
-                                storeLastApprovalTime(organism);
+                                storeLastApprovalTime();
                             }}
                             deleteAccessionVersion={() =>
                                 hooks.deleteSequenceEntries({
@@ -355,9 +355,9 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, group, a
     );
 };
 
-const storeLastApprovalTime = (organism: string) => {
+const storeLastApprovalTime = () => {
     const lastApprovalTime = Math.floor(Date.now() / 1000);
-    localStorage.setItem(getLastApprovalTimeKey(organism), lastApprovalTime.toString());
+    localStorage.setItem(LAST_APPROVAL_TIME_LOCAL_STORAGE_KEY, lastApprovalTime.toString());
 };
 
 export const ReviewPage = withQueryProvider(InnerReviewPage);

website/src/components/SearchPage/RecentSequencesBanner.tsx

@@ -1,17 +1,13 @@
 import React, { useEffect, useState } from 'react';
 
-export const getLastApprovalTimeKey = (organism: string) => organism + 'lastApprovalTime';
+export const LAST_APPROVAL_TIME_LOCAL_STORAGE_KEY = 'lastApprovalTime';
 
-interface RecentSequencesBannerProps {
-    organism: string;
-}
-
-export const RecentSequencesBanner: React.FC<RecentSequencesBannerProps> = ({ organism }) => {
+export const RecentSequencesBanner: React.FC = () => {
     const [showBanner, setShowBanner] = useState(false);
 
     useEffect(() => {
         const checkApprovalTime = () => {
-            const lastApproveTimeString = localStorage.getItem(getLastApprovalTimeKey(organism));
+            const lastApproveTimeString = localStorage.getItem(LAST_APPROVAL_TIME_LOCAL_STORAGE_KEY);
             if (lastApproveTimeString === null) {
                 setShowBanner(false);
                 return;
@@ -28,7 +24,7 @@ export const RecentSequencesBanner: React.FC<RecentSequencesBannerProps> = ({ or
 
         // Clear the interval on component unmount
         return () => clearInterval(intervalId);
-    }, [organism]);
+    }, []);
     if (!showBanner) {
         return null;
     }

website/src/components/SearchPage/SearchFullUI.tsx

@@ -74,7 +74,7 @@ export const SearchFullUI = ({
                 />
             </div>
             <div className='flex-1'>
-                <RecentSequencesBanner organism={organism} />
+                <RecentSequencesBanner />
                 <div className=' text-sm text-gray-800 mb-6 justify-between flex px-6 items-baseline'>
                     <div className='mt-auto'>
                         Search returned {data.totalCount.toLocaleString()} sequence{data.totalCount === 1 ? '' : 's'}
@@ -101,6 +101,7 @@ export const SearchFullUI = ({
                     orderBy={orderBy}
                     classOfSearchPage={SEARCH}
                 />
+
                 <div className='mt-4 flex justify-center'>
                     <SearchPagination
                         count={Math.ceil(data.totalCount / pageSize)}

website/src/components/SequenceDetailsPage/DataTable.astro

@@ -1,9 +1,7 @@
 ---
-import { AuthorList } from './AuthorList';
 import { DataUseTermsHistoryModal } from './DataUseTermsHistoryModal';
 import { SubstitutionsContainer } from './MutationBadge';
-import { getDataTableData } from './getDataTableData';
-import { type TableDataEntry } from './getTableData';
+import { toHeaderMap, type TableDataEntry } from './getTableData';
 import { type DataUseTermsHistoryEntry } from '../../types/backend';
 
 interface Props {
@@ -12,25 +10,18 @@ interface Props {
 }
 
 const { tableData, dataUseTermsHistory } = Astro.props;
-const data = getDataTableData(tableData);
+const headerMap = toHeaderMap(tableData);
 ---
 
-<div>
-    {
-        data.topmatter.authors !== undefined && data.topmatter.authors.length > 0 && (
-            <div class='px-6 mb-4'>
-                <AuthorList authors={data.topmatter.authors} client:load />
-            </div>
-        )
-    }
+<div class='mt-2'>
     <div>
         {
-            data.table.map(({ header, rows }) => (
+            Object.entries(headerMap).map(([header, names]) => (
                 <div class='pb-8'>
                     {header !== '' && <h1 class='py-2 font-medium text-primary-600'>{header}</h1>}
                     <table class='table-auto'>
                         <tbody class='bg-white'>
-                            {rows.map(({ label, value, customDisplay }) => (
+                            {names.map(({ label, value, customDisplay }) => (
                                 <tr>
                                     <td class='py-1 w-44 text-sm font-medium text-gray-900 text-right'>{label}</td>
                                     <td class='px-4 py-1 text-sm text-gray-600'>