Merge branch 'main' into label-meta-with-displaynamesj

loculus-project · Nov 12, 2024 · 2718a66 · 2718a66
2 parents 90d8c41 + e83bce3
commit 2718a66
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diff --git a/docs/package-lock.json b/docs/package-lock.json
diff --git a/docs/package.json b/docs/package.json
@@ -12,10 +12,10 @@
     },
     "dependencies": {
         "@astrojs/check": "^0.9.4",
-        "@astrojs/starlight": "^0.28.6",
+        "@astrojs/starlight": "^0.29.0",
         "@astrojs/starlight-tailwind": "^2.0.3",
         "@astrojs/tailwind": "^5.1.2",
-        "astro": "^4.16.9",
+        "astro": "^4.16.10",
         "prettier": "^3.3.3",
         "prettier-plugin-astro": "^0.14.1",
         "prettier-plugin-tailwindcss": "^0.6.8",

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1106,27 +1106,27 @@ defaultOrganismConfig: &defaultOrganismConfig
   referenceGenomes:
     nucleotideSequences:
       - name: "main"
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/reference.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/reference.fasta]]"
         insdcAccessionFull: NC_002549.1
     genes:
       - name: NP
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/NP.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/NP.fasta]]"
       - name: VP35
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/VP35.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/VP35.fasta]]"
       - name: VP40
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/VP40.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/VP40.fasta]]"
       - name: GP
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/GP.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/GP.fasta]]"
       - name: ssGP
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/ssGP.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/ssGP.fasta]]"
       - name: sGP
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/sGP.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/sGP.fasta]]"
       - name: VP30
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/VP30.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/VP30.fasta]]"
       - name: VP24
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/VP24.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/VP24.fasta]]"
       - name: L
-        sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/ebola-zaire/L.fasta]]"
+        sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-zaire/L.fasta]]"
 defaultOrganisms:
   ebola-zaire:
     <<: *defaultOrganismConfig
@@ -1194,31 +1194,31 @@ defaultOrganisms:
     referenceGenomes:
       nucleotideSequences:
         - name: main
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/reference.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/reference.fasta]]"
           insdcAccessionFull: NC_009942.1
       genes:
         - name: 2K
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/2K.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/2K.fasta]]"
         - name: NS1
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS1.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS1.fasta]]"
         - name: NS2A
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS2A.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS2A.fasta]]"
         - name: NS2B
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS2B.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS2B.fasta]]"
         - name: NS3
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS3.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS3.fasta]]"
         - name: NS4A
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS4A.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS4A.fasta]]"
         - name: NS4B
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS4B.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS4B.fasta]]"
         - name: NS5
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/NS5.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/NS5.fasta]]"
         - name: capsid
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/capsid.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/capsid.fasta]]"
         - name: env
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/env.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/env.fasta]]"
         - name: prM
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/west-nile/prM.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/west-nile/prM.fasta]]"
   dummy-organism:
     schema:
       image: "https://www.un.org/sites/un2.un.org/files/field/image/1583952355.1997.jpg"
@@ -1277,32 +1277,32 @@ defaultOrganisms:
     referenceGenomes:
       nucleotideSequences:
         - name: "main"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/reference.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/reference.fasta]]"
       genes:
         - name: "E"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/E.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/E.fasta]]"
         - name: "M"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/M.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/M.fasta]]"
         - name: "N"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/N.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/N.fasta]]"
         - name: "ORF1a"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF1a.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF1a.fasta]]"
         - name: "ORF1b"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF1b.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF1b.fasta]]"
         - name: "ORF3a"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF3a.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF3a.fasta]]"
         - name: "ORF6"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF6.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF6.fasta]]"
         - name: "ORF7a"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF7a.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF7a.fasta]]"
         - name: "ORF7b"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF7b.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF7b.fasta]]"
         - name: "ORF8"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF8.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF8.fasta]]"
         - name: "ORF9b"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/ORF9b.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/ORF9b.fasta]]"
         - name: "S"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/S.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/S.fasta]]"
   not-aligned-organism:
     schema:
       image: "https://cdn.who.int/media/images/default-source/mca/mca-covid-19/coronavirus-2.tmb-1920v.jpg?sfvrsn=4dba955c_19"
@@ -1361,7 +1361,7 @@ defaultOrganisms:
     referenceGenomes:
       nucleotideSequences:
         - name: "main"
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/sars-cov-2/reference.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/sars-cov-2/reference.fasta]]"
       genes: []
   cchf:
     <<: *defaultOrganismConfig
@@ -1426,21 +1426,21 @@ defaultOrganisms:
     referenceGenomes:
       nucleotideSequences:
         - name: L
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_L.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_L.fasta]]"
           insdcAccessionFull: NC_005301.3
         - name: M
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_M.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_M.fasta]]"
           insdcAccessionFull: NC_005300.2
         - name: S
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/reference_S.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_S.fasta]]"
           insdcAccessionFull: NC_005302.1
       genes:
         - name: RdRp
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/RdRp.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/RdRp.fasta]]"
         - name: GPC
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/GPC.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/GPC.fasta]]"
         - name: NP
-          sequence: "[[URL:https://raw.githubusercontent.com/corneliusroemer/seqs/main/artefacts/cchf/NP.fasta]]"
+          sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/NP.fasta]]"
 auth:
   smtp:
     host: "in-v3.mailjet.com"
@@ -1459,8 +1459,8 @@ insecureCookies: false
 bannerMessage: "This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly."
 additionalHeadHTML: ""
 images:
-  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.3.1"
-  lapis: "ghcr.io/genspectrum/lapis:0.3.7"
+  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.3.2"
+  lapis: "ghcr.io/genspectrum/lapis:0.3.8"
 secrets:
   smtp-password:
     type: raw

diff --git a/website/src/components/ReviewPage/ReviewCard.tsx b/website/src/components/ReviewPage/ReviewCard.tsx
@@ -130,7 +130,7 @@ const ButtonBar: FC<ButtonBarProps> = ({
             >
                 <WpfPaperPlane />
             </button>
-            <Tooltip
+            <CustomTooltip
                 id={'approve-tooltip' + sequenceEntryStatus.accession}
                 content={
                     approvable
@@ -152,7 +152,7 @@ const ButtonBar: FC<ButtonBarProps> = ({
                     <ClarityNoteEditLine />
                 </button>
             )}
-            <Tooltip
+            <CustomTooltip
                 id={'edit-tooltip' + sequenceEntryStatus.accession}
                 content={notProcessed ? 'Processing...' : 'Edit this sequence entry'}
             />
@@ -166,7 +166,7 @@ const ButtonBar: FC<ButtonBarProps> = ({
             >
                 <BiTrash />
             </button>
-            <Tooltip
+            <CustomTooltip
                 id={'delete-tooltip' + sequenceEntryStatus.accession}
                 content={notProcessed ? 'Cannot discard. Wait for preprocessing.' : 'Discard this sequence entry'}
             />
@@ -217,7 +217,7 @@ const Errors: FC<ErrorsProps> = ({ errors, accession }) => {
                             >
                                 {error.message}
                             </p>
-                            <Tooltip
+                            <CustomTooltip
                                 id={'error-tooltip-' + accession + '-' + uniqueKey}
                                 content='You must fix this error before releasing this sequence entry'
                             />
@@ -266,7 +266,7 @@ const DataUseTermsIcon: FC<DataUseTermsIconProps> = ({ dataUseTerms, accession }
             <div data-tooltip-id={'dataUseTerm-tooltip-' + accession}>
                 {dataUseTerms.type === restrictedDataUseTermsType ? <Locked /> : <Unlocked />}
             </div>
-            <Tooltip id={'dataUseTerm-tooltip-' + accession} content={hintText} />
+            <CustomTooltip id={'dataUseTerm-tooltip-' + accession} content={hintText} />
         </>
     );
 };
@@ -289,7 +289,7 @@ const StatusIcon: FC<StatusIconProps> = ({ status, dataUseTerms, accession, hasW
                 >
                     <EmptyCircle className='text-gray-500' />
                 </div>
-                <Tooltip id={'awaitingProcessing-tooltip-' + accession} content='Awaiting processing' />
+                <CustomTooltip id={'awaitingProcessing-tooltip-' + accession} content='Awaiting processing' />
                 <DataUseTermsIcon dataUseTerms={dataUseTerms} accession={accession} />
             </div>
         );
@@ -300,7 +300,7 @@ const StatusIcon: FC<StatusIconProps> = ({ status, dataUseTerms, accession, hasW
                 <div data-tooltip-id={`error-tooltip-` + accession} key={'error-tooltip-' + accession}>
                     <QuestionMark className='text-red-600' />
                 </div>
-                <Tooltip id={`error-tooltip-` + accession} content='Error detected' />
+                <CustomTooltip id={`error-tooltip-` + accession} content='Error detected' />
                 <DataUseTermsIcon dataUseTerms={dataUseTerms} accession={accession} />
             </div>
         );
@@ -311,21 +311,20 @@ const StatusIcon: FC<StatusIconProps> = ({ status, dataUseTerms, accession, hasW
                 <div data-tooltip-id={'inProcessing-tooltip-' + accession} key={'inProcessing-tooltip-' + accession}>
                     <span className='loading loading-spinner loading-sm' />
                 </div>
-                <Tooltip id={'inProcessing-tooltip-' + accession} content='In processing' />
+                <CustomTooltip id={'inProcessing-tooltip-' + accession} content='In processing' />
                 <DataUseTermsIcon dataUseTerms={dataUseTerms} accession={accession} />
             </div>
         );
     }
     if (status === processedStatus && !hasErrors) {
         return (
-            // TODO(#702): When queries are implemented, this should be a yellow tick with a warning note if there are warnings
             <div className='p-2 flex flex-col justify-between'>
                 <div data-tooltip-id={'awaitingApproval-tooltip-' + accession}>
-                    <TickOutline className={hasWarnings === true ? 'text-yellow-400' : `text-green-500`} />
+                    <TickOutline className={hasWarnings ? 'text-yellow-400' : `text-green-500`} />
                 </div>
-                <Tooltip
+                <CustomTooltip
                     id={'awaitingApproval-tooltip-' + accession}
-                    content='Passed QC [TODO: sometimes (with warnings)]'
+                    content={hasWarnings ? 'Passed QC with warnings' : 'Passed QC'}
                 />
                 <DataUseTermsIcon dataUseTerms={dataUseTerms} accession={accession} />
             </div>
@@ -365,15 +364,15 @@ const KeyValueComponent: FC<KeyValueComponentProps> = ({
                     {value}
                 </span>
                 {primaryMessages !== undefined && (
-                    <Tooltip
+                    <CustomTooltip
                         id={textTooltipId}
                         content={primaryMessages.map((annotation) => annotation.message).join(', ')}
                     />
                 )}
                 {secondaryMessages !== undefined && (
                     <>
                         <Note className='text-yellow-500 inline-block' data-tooltip-id={noteTooltipId} />
-                        <Tooltip
+                        <CustomTooltip
                             id={noteTooltipId}
                             content={secondaryMessages.map((annotation) => annotation.message).join(', ')}
                         />
@@ -384,6 +383,11 @@ const KeyValueComponent: FC<KeyValueComponentProps> = ({
     );
 };
 
+const CustomTooltip: React.FC<React.ComponentProps<typeof Tooltip>> = ({ ...props }) => (
+    // Set positionStrategy and z-index to make the Tooltip float above the ReviewPage toolbar
+    <Tooltip positionStrategy='fixed' className='z-20' place='right' {...props} />
+);
+
 function getTextColorAndMessages(
     errors: ProcessingAnnotation[] | undefined,
     warnings: ProcessingAnnotation[] | undefined,

diff --git a/website/src/components/ReviewPage/ReviewPage.tsx b/website/src/components/ReviewPage/ReviewPage.tsx
@@ -148,6 +148,17 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, group, a
     const noIssuesCount = sequencesData.processingResultCounts[noIssuesProcessingResult];
     const validCount = warningCount + noIssuesCount;
 
+    const selectedCount: number =
+        (showUnprocessed ? unprocessedCount : 0) +
+        (showNoIssues ? noIssuesCount : 0) +
+        (showWarnings ? warningCount : 0) +
+        (showErrors ? errorCount : 0);
+
+    // If we narrowed the selection and the selected page doesn't exist anymore, go to the last existing page instead
+    if ((pageQuery.page - 1) * pageQuery.size > selectedCount) {
+        setPageQuery({ ...pageQuery, page: Math.ceil(selectedCount / pageQuery.size) });
+    }
+
     if (total === 0) {
         return (
             <div className='pt-1 text-gray-600'>
@@ -214,7 +225,7 @@ const InnerReviewPage: FC<ReviewPageProps> = ({ clientConfig, organism, group, a
     const pagination = (
         <div className='flex justify-end align-center gap-3 py-3'>
             <Pagination
-                count={Math.ceil(total / pageQuery.size)}
+                count={Math.ceil(selectedCount / pageQuery.size)}
                 page={pageQuery.page}
                 onChange={(_, newPage) => {
                     setPageQuery({ ...pageQuery, page: newPage });