refactor: format

Author: ivan-aksamentov

packages/nextclade-web/.prettierignore

@@ -1,11 +1,13 @@
-/\.build
-/\.cache
+/\.build/
+/\.cache/
 /\.editorconfig
 /\.env
-/\.git
+/\.git/
 /\.gitignore
-/\.idea
-/\.ignore
+/\.idea/
+/\.ignore/
 /\.prettierignore
 /\.vscode*
-/node_modules
+/node_modules/
+/src/gen/
+/vendor/

packages/nextclade-web/src/components/Common/Multitoggle.tsx

@@ -73,6 +73,7 @@ export const Switch = styled.fieldset<{ $width: number }>`
   width: ${(props) => props.$width}px;
   background-color: ${(props) => props.theme.gray300};
   border-radius: 3px;
+  /* prettier-ignore */
   box-shadow: inset 0 1px 3px rgba(0, 0, 0, 0.3), 0 1px rgba(255, 255, 255, 0.1);
   pointer-events: initial;
 `

packages/nextclade-web/src/components/Layout/UpdateNotification.tsx

@@ -142,7 +142,7 @@ const Toast = styled(ToastBase)`
 const ToastBody = styled(ToastBodyBase)`
   min-width: ${TOAST_WIDTH};
   opacity: 1 !important;
-  background: ${(props) => props.theme.bodyBg}; ;
+  background: ${(props) => props.theme.bodyBg};
 `
 
 const ToastHeader = styled(ToastHeaderBase)`

packages/nextclade-web/src/components/Loading/Loading.tsx

@@ -32,6 +32,7 @@ const BrandLogo = styled(BrandLogoBase)<{ $size: number }>`
   box-shadow: 0 0 0 0 rgba(0, 0, 0, 1);
 `
 
+// prettier-ignore
 const SpinnerAnimation = styled.div<{ $size: number }>`
   margin: auto;
   display: flex;

packages/nextclade-web/src/components/Main/SuggestionPanel.tsx

@@ -67,10 +67,10 @@ export function ButtonSuggest() {
       title: isRunning
         ? t('Running')
         : !canRun
-        ? t('Please provide sequence data for the algorithm')
-        : hasAutodetectResults
-        ? t('Re-launch suggestions engine!')
-        : t('Launch suggestions engine!'),
+          ? t('Please provide sequence data for the algorithm')
+          : hasAutodetectResults
+            ? t('Re-launch suggestions engine!')
+            : t('Launch suggestions engine!'),
     }
   }, [autodetectRunState, hasAutodetectResults, hasRequiredInputs, t])
 

packages/nextclade-web/src/components/Results/ResultsTableUnknownDataset.tsx

@@ -50,10 +50,18 @@ export function ResultsTableUnknownDataset() {
 
   // TODO: we could use a map (object) and refer to filters by name,
   // in order to reduce code duplication in the state, callbacks and components being rendered
-  const sortByIndexAsc = useSetAtom(sortAnalysisResultsAtom({ category: SortCategory.index, direction: SortDirection.asc }))
-  const sortByIndexDesc = useSetAtom(sortAnalysisResultsAtom({ category: SortCategory.index, direction: SortDirection.desc }))
-  const sortByNameAsc = useSetAtom(sortAnalysisResultsAtom({ category: SortCategory.seqName, direction: SortDirection.asc }))
-  const sortByNameDesc = useSetAtom(sortAnalysisResultsAtom({ category: SortCategory.seqName, direction: SortDirection.desc }))
+  const sortByIndexAsc = useSetAtom(
+    sortAnalysisResultsAtom({ category: SortCategory.index, direction: SortDirection.asc }),
+  )
+  const sortByIndexDesc = useSetAtom(
+    sortAnalysisResultsAtom({ category: SortCategory.index, direction: SortDirection.desc }),
+  )
+  const sortByNameAsc = useSetAtom(
+    sortAnalysisResultsAtom({ category: SortCategory.seqName, direction: SortDirection.asc }),
+  )
+  const sortByNameDesc = useSetAtom(
+    sortAnalysisResultsAtom({ category: SortCategory.seqName, direction: SortDirection.desc }),
+  )
 
   return (
     <Table rounded={false}>

packages/nextclade-web/src/components/SequenceView/SequenceSelector.tsx

@@ -240,15 +240,15 @@ function prepareOptions(genes: Gene[]) {
         isDisabled: true,
       })
 
-          for (const cds of gene.cdses) {
+      for (const cds of gene.cdses) {
         const option: Option = {
           value: `cds-${cds.name}`,
           cds,
         }
         defaultOption = option
         options.push(option)
 
-              for (const protein of cds.proteins) {
+        for (const protein of cds.proteins) {
           options.push({
             value: `protein-${protein.name}`,
             protein,

packages/nextclade-web/src/hooks/useExportResults.ts

@@ -92,7 +92,7 @@ function useResultsExport(exportFn: ExportFunction) {
           setIsRunning(false)
         })
     },
-    [exportFn, setGlobalError]
+    [exportFn, setGlobalError],
   )
 
   return { isRunning, isDone, fn }
@@ -121,9 +121,7 @@ function mapAllErrors<T>(results: NextcladeResult[], mapFn: (result: AnalysisErr
 }
 
 function mapGoodResults<T>(results: NextcladeResult[], datasetName: string, mapFn: (result: AnalysisOutput) => T): T[] {
-  const filteredResults = results.filter(
-    (result) => result.result?.analysisResult.datasetName === datasetName
-  )
+  const filteredResults = results.filter((result) => result.result?.analysisResult.datasetName === datasetName)
 
   return filteredResults
     .filter((result) => notUndefinedOrNull(result.result))
@@ -136,9 +134,7 @@ function mapGoodResults<T>(results: NextcladeResult[], datasetName: string, mapF
 }
 
 function mapErrors<T>(results: NextcladeResult[], datasetName: string, mapFn: (result: AnalysisError) => T): T[] {
-  const filteredResults = results.filter(
-    (result) => result.result?.analysisResult.datasetName === datasetName
-  )
+  const filteredResults = results.filter((result) => result.result?.analysisResult.datasetName === datasetName)
 
   return filteredResults
     .filter((result) => notUndefinedOrNull(result.error))
@@ -159,7 +155,7 @@ async function prepareCsvData(
   aaMotifsDescs: AaMotifsDesc[] | undefined,
   csvColumnConfig: CsvColumnConfig,
   delimiter: string,
-  worker: ExportWorker
+  worker: ExportWorker,
 ): Promise<string> {
   return worker.serializeResultsCsv(
     results,
@@ -169,7 +165,7 @@ async function prepareCsvData(
     refNodes ?? {},
     aaMotifsDescs ?? [],
     delimiter,
-    csvColumnConfig
+    csvColumnConfig,
   )
 }
 
@@ -179,23 +175,23 @@ async function prepareJsonData(
   cladeNodeAttrDescs: CladeNodeAttrDesc[] | undefined,
   phenotypeAttrDescs: PhenotypeAttrDesc[] | undefined,
   refNodes: AuspiceRefNodesDesc | undefined,
-  worker: ExportWorker
+  worker: ExportWorker,
 ): Promise<string> {
   return worker.serializeResultsJson(
     results,
     errors,
     cladeNodeAttrDescs ?? [],
     phenotypeAttrDescs ?? [],
     refNodes ?? {},
-    PACKAGE_VERSION
+    PACKAGE_VERSION,
   )
 }
 
 function prepareFastaData(analysisResults: NextcladeResult[], datasetName: string): string {
   const fastaEntries = mapGoodResults(
     analysisResults,
     datasetName,
-    (result) => `>${result.analysisResult.seqName}\n${result.query}`
+    (result) => `>${result.analysisResult.seqName}\n${result.query}`,
   )
   return `${fastaEntries.join('\n')}\n`
 }
@@ -225,10 +221,7 @@ function preparePeptideFiles(analysisResults: NextcladeResult[], datasetName: st
   return Array.from(peptideFilesMap.values())
 }
 
-export const useExportFasta = createSimpleExportHook(
-  prepareFastaData,
-  'application/x-fasta;charset=utf-8'
-)
+export const useExportFasta = createSimpleExportHook(prepareFastaData, 'application/x-fasta;charset=utf-8')
 
 export const useExportCsv = createCsvExportHook(';', 'text/csv;charset=utf-8')
 
@@ -256,11 +249,11 @@ export function useExportExcel() {
         allInitialData,
         csvColumnConfig,
         datasetNameToSeqIndices,
-        seqIndicesWithoutDatasetSuggestions
+        seqIndicesWithoutDatasetSuggestions,
       )
       saveBase64File(excelData, filename, 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet')
     },
-    [analysisResults, allInitialData, csvColumnConfig, datasetNameToSeqIndices, seqIndicesWithoutDatasetSuggestions]
+    [analysisResults, allInitialData, csvColumnConfig, datasetNameToSeqIndices, seqIndicesWithoutDatasetSuggestions],
   )
 
   return useResultsExport(exportFn)
@@ -280,15 +273,15 @@ export function useExportJson({ datasetName }: { datasetName: string }) {
       const jsonStr = await prepareJsonData(results, errors, cladeNodeAttrDescs, phenotypeAttrDescs, refNodes, worker)
       saveFile(jsonStr, filename, 'application/json;charset=utf-8')
     },
-    [analysisResults, datasetName, cladeNodeAttrDescs, phenotypeAttrDescs, refNodes]
+    [analysisResults, datasetName, cladeNodeAttrDescs, phenotypeAttrDescs, refNodes],
   )
 
   return useResultsExport(exportFn)
 }
 
 export const useExportNdjson = createResultErrorExportHook(
   (worker, results, errors) => worker.serializeResultsNdjson(results, errors),
-  'application/x-ndjson;charset=utf-8'
+  'application/x-ndjson;charset=utf-8',
 )
 
 export function useExportTree({ datasetName }: { datasetName: string }) {
@@ -302,7 +295,7 @@ export function useExportTree({ datasetName }: { datasetName: string }) {
       const jsonStr = JSON.stringify(tree, null, 2)
       saveFile(jsonStr, filename, 'application/json;charset=utf-8')
     },
-    [tree]
+    [tree],
   )
 
   if (isNil(tree)) {
@@ -322,7 +315,7 @@ export function useExportTreeNwk({ datasetName }: { datasetName: string }) {
       }
       saveFile(treeNwk, filename, 'text/x-nh;charset=utf-8')
     },
-    [treeNwk]
+    [treeNwk],
   )
 
   if (isNil(treeNwk)) {
@@ -343,7 +336,7 @@ export function useExportPeptides({ datasetName }: { datasetName: string }) {
       const files = Array.from(peptides)
       await saveZip({ files, filename })
     },
-    [analysisResults, datasetName]
+    [analysisResults, datasetName],
   )
 
   if (isEmpty(cdses)) {
@@ -355,12 +348,12 @@ export function useExportPeptides({ datasetName }: { datasetName: string }) {
 
 export const useExportGff = createSimpleResultExportHook(
   (worker, results) => worker.serializeResultsGff(results),
-  'text/x-gff3;charset=utf-8'
+  'text/x-gff3;charset=utf-8',
 )
 
 export const useExportTbl = createSimpleResultExportHook(
   (worker, results) => worker.serializeResultsTbl(results),
-  'text/x-tbl;charset=utf-8'
+  'text/x-tbl;charset=utf-8',
 )
 
 async function prepareAllExportData(
@@ -371,7 +364,7 @@ async function prepareAllExportData(
   refNodes: AuspiceRefNodesDesc | undefined,
   aaMotifsDescs: AaMotifsDesc[] | undefined,
   csvColumnConfig: CsvColumnConfig | undefined,
-  worker: ExportWorker
+  worker: ExportWorker,
 ) {
   const results = mapGoodResults(analysisResults, datasetName, (result) => result.analysisResult)
   const errors = mapErrors(analysisResults, datasetName, (err) => err)
@@ -381,8 +374,28 @@ async function prepareAllExportData(
   }
 
   const [csvStr, tsvStr, jsonStr, ndjsonStr, gffStr, tblStr] = await Promise.all([
-    prepareCsvData(results, errors, cladeNodeAttrDescs ?? [], phenotypeAttrDescs ?? [], refNodes, aaMotifsDescs ?? [], csvColumnConfig, ';', worker),
-    prepareCsvData(results, errors, cladeNodeAttrDescs ?? [], phenotypeAttrDescs ?? [], refNodes, aaMotifsDescs ?? [], csvColumnConfig, '\t', worker),
+    prepareCsvData(
+      results,
+      errors,
+      cladeNodeAttrDescs ?? [],
+      phenotypeAttrDescs ?? [],
+      refNodes,
+      aaMotifsDescs ?? [],
+      csvColumnConfig,
+      ';',
+      worker,
+    ),
+    prepareCsvData(
+      results,
+      errors,
+      cladeNodeAttrDescs ?? [],
+      phenotypeAttrDescs ?? [],
+      refNodes,
+      aaMotifsDescs ?? [],
+      csvColumnConfig,
+      '\t',
+      worker,
+    ),
     prepareJsonData(results, errors, cladeNodeAttrDescs ?? [], phenotypeAttrDescs ?? [], refNodes, worker),
     worker.serializeResultsNdjson(results, errors),
     worker.serializeResultsGff(results),
@@ -424,7 +437,7 @@ export function useExportZip({ datasetName }: { datasetName: string }) {
         refNodes,
         aaMotifsDescs,
         csvColumnConfig,
-        worker
+        worker,
       )
 
       const files: ZipFileDescription[] = [
@@ -465,7 +478,7 @@ export function useExportZip({ datasetName }: { datasetName: string }) {
       csvColumnConfig,
       tree,
       treeNwk,
-    ]
+    ],
   )
 
   return useResultsExport(exportFn)
@@ -481,7 +494,7 @@ export function useExportUnknownSeqTsv() {
       const tsvStr = await worker.serializeUnknownCsv(errors, seqIndicesWithoutDatasetSuggestions, '\t')
       saveFile(tsvStr, filename, 'text/tab-separated-values;charset=utf-8')
     },
-    [analysisResults, seqIndicesWithoutDatasetSuggestions]
+    [analysisResults, seqIndicesWithoutDatasetSuggestions],
   )
 
   return useResultsExport(exportFn)
@@ -514,11 +527,11 @@ function createCsvExportHook(delimiter: string, mimeType: string) {
           aaMotifsDescs,
           csvColumnConfig,
           delimiter,
-          worker
+          worker,
         )
         saveFile(csvStr, filename, mimeType)
       },
-      [analysisResults, datasetName, cladeNodeAttrDescs, phenotypeAttrDescs, refNodes, aaMotifsDescs, csvColumnConfig]
+      [analysisResults, datasetName, cladeNodeAttrDescs, phenotypeAttrDescs, refNodes, aaMotifsDescs, csvColumnConfig],
     )
 
     return useResultsExport(exportFn)
@@ -527,7 +540,7 @@ function createCsvExportHook(delimiter: string, mimeType: string) {
 
 function createSimpleResultExportHook(
   workerMethod: (worker: ExportWorker, results: AnalysisResult[]) => Promise<string>,
-  mimeType: string
+  mimeType: string,
 ) {
   return function simpleResultExportHook({ datasetName }: { datasetName: string }) {
     const analysisResults = useAtomValue(analysisResultsAtom)
@@ -538,7 +551,7 @@ function createSimpleResultExportHook(
         const data = await workerMethod(worker, results)
         saveFile(data, filename, mimeType)
       },
-      [analysisResults, datasetName]
+      [analysisResults, datasetName],
     )
 
     return useResultsExport(exportFn)
@@ -547,7 +560,7 @@ function createSimpleResultExportHook(
 
 function createResultErrorExportHook(
   workerMethod: (worker: ExportWorker, results: AnalysisResult[], errors: AnalysisError[]) => Promise<string>,
-  mimeType: string
+  mimeType: string,
 ) {
   return function resultErrorExportHook({ datasetName }: { datasetName: string }) {
     const analysisResults = useAtomValue(analysisResultsAtom)
@@ -559,7 +572,7 @@ function createResultErrorExportHook(
         const data = await workerMethod(worker, results, errors)
         saveFile(data, filename, mimeType)
       },
-      [analysisResults, datasetName]
+      [analysisResults, datasetName],
     )
 
     return useResultsExport(exportFn)
@@ -568,7 +581,7 @@ function createResultErrorExportHook(
 
 function createSimpleExportHook(
   prepareData: (analysisResults: NextcladeResult[], datasetName: string) => string,
-  mimeType: string
+  mimeType: string,
 ) {
   return function simpleExportHook({ datasetName }: { datasetName: string }) {
     const analysisResults = useAtomValue(analysisResultsAtom)
@@ -578,7 +591,7 @@ function createSimpleExportHook(
         const data = prepareData(analysisResults, datasetName)
         saveFile(data, filename, mimeType)
       },
-      [analysisResults, datasetName]
+      [analysisResults, datasetName],
     )
 
     return useResultsExport(exportFn)