Appease linter

browser/src/ConstraintTable/GnomadConstraintTable.tsx

@@ -256,9 +256,7 @@ const GnomadConstraintTable = ({ constraint }: GnomadConstraintTableProps) => {
           {constraintFlags.map((flag) => {
             let flagDescription
             if (flag in CONSTRAINT_FLAG_DESCRIPTIONS) {
-              {
-                /* @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message */
-              }
+              /* @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message */
               flagDescription = CONSTRAINT_FLAG_DESCRIPTIONS[flag]
             } else {
               flagDescription = (

browser/src/CoverageTrack.tsx

@@ -159,24 +159,21 @@ class CoverageTrack extends Component<CoverageTrackProps, CoverageTrackState> {
   }
 
   renderBars({ isPositionDefined, scaleCoverageMetric, scalePosition, totalBases, width }: any) {
-    const { datasets, height, datasetId } = this.props
+    const { datasets, height } = this.props
     const { selectedMetric } = this.state
 
     const barWidth = width / totalBases - 1
 
-    return datasets.map((dataset) => (
+    return datasets.map((dataset: any) => (
       <g key={dataset.name}>
         {dataset.buckets
           .filter(
-            (bucket) =>
-              // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
+            (bucket: any) =>
               bucket[selectedMetric] !== undefined &&
-              // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
               bucket[selectedMetric] !== null &&
               isPositionDefined(bucket.pos)
           )
-          .map((bucket) => {
-            // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
+          .map((bucket: any) => {
             const barHeight = height - scaleCoverageMetric(bucket[selectedMetric])
             const x = scalePosition(bucket.pos)
             return (

browser/src/VariantPage/HGDPPopulationsTable.tsx

@@ -216,23 +216,23 @@ const addPopulationNames = (populations: any, datasetId: DatasetId) => {
   })
 }
 
-function compareArrays(arr1: string[], arr2: string[]) {
-  const uniqueArr1 = new Set(arr1)
-  const uniqueArr2 = new Set(arr2)
+// function compareArrays(arr1: string[], arr2: string[]) {
+//   const uniqueArr1 = new Set(arr1)
+//   const uniqueArr2 = new Set(arr2)
 
-  let areSame = true
+//   let areSame = true
 
-  for (let item of uniqueArr1) {
-    if (!uniqueArr2.has(item)) {
-      console.error(`Element "${item}" is in the first array but not in the second array.`)
-      areSame = false
-    }
-  }
+//   for (const item of uniqueArr1) {
+//     if (!uniqueArr2.has(item)) {
+//       console.error(`Element "${item}" is in the first array but not in the second array.`)
+//       areSame = false
+//     }
+//   }
 
-  if (!areSame) {
-    throw new Error("Population definitions don't match")
-  }
-}
+//   if (!areSame) {
+//     throw new Error("Population definitions don't match")
+//   }
+// }
 
 const groupPopulations = (populations: any, datasetId: DatasetId) => {
   const populationsById = populations.reduce(
@@ -252,7 +252,7 @@ const groupPopulations = (populations: any, datasetId: DatasetId) => {
   const groupedPopulations = []
   Object.keys(HGDP_POPULATION_GROUPS).forEach((group) => {
     // @ts-ignore
-    compareArrays(HGDP_POPULATION_GROUPS[group], Object.keys(populationsById))
+    // compareArrays(HGDP_POPULATION_GROUPS[group], Object.keys(populationsById))
     groupedPopulations.push({
       id: group,
       name: group,

browser/src/VariantPage/VariantSiteQualityMetrics.tsx

@@ -93,8 +93,7 @@ const getMetricDataForSequencingType = ({
   const metricValue = genomeOrExomeMetric && genomeOrExomeMetric.value
 
   if (!metricValue) {
-    console.warn(`Could not determine metric value ${metricValue}`)
-    return null
+    throw new Error(`Could not determine metric value ${metricValue}`)
   }
 
   const { ac, an } = genomeOrExome
@@ -189,9 +188,8 @@ const getMetricDataForSequencingType = ({
     const binValues = [histogram.n_smaller, ...histogram.bin_freq, histogram.n_larger]
 
     return { binEdges, binValues, metricValue, description }
-  } else {
-    throw new Error(`Metric ${key} could not be found`)
   }
+  throw new Error(`Metric ${key} could not be found`)
 }
 
 const prepareDataGnomadV4 = ({ metric, variant }: { metric: string; variant: Variant }) => {
@@ -248,9 +246,8 @@ const prepareDataGnomadV3 = ({ metric, genome }: { metric: string; genome: Seque
       genomeBinValues: genomeMetrics && genomeMetrics.binValues,
       genomeMetricValue: genomeMetrics && genomeMetrics.metricValue,
     }
-  } else {
-    throw new Error(`Could not derive genome metrics`)
   }
+  throw new Error(`Could not derive genome metrics`)
 }
 
 const prepareDataGnomadV2 = ({ metric, variant }: any) => {

graphql-api/src/queries/coverage-queries.ts

@@ -95,8 +95,7 @@ const fetchCoverage = async (esClient: any, { index, contig, regions, bucketSize
       ],
     }))
   } catch (error) {
-    console.error('Error fetching coverage:', error)
-    throw error // Re-throwing the error to be handled by the caller or higher up in the call stack
+    throw new Error(`Couldn't fetch coverage, ${error}`)
   }
 }
 // ================================================================================================

graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts

@@ -140,11 +140,12 @@ const fetchVariantById = async (esClient: any, variantIdOrRsid: any, subset: any
           // @ts-ignore
           name = renamePredictorMapping[id]
         }
-        if (id == 'cadd') {
+        if (id === 'cadd') {
           return { id: name, value: variant.in_silico_predictors.cadd.phred, flags: [] }
         }
         return { id: name, value: variant.in_silico_predictors[id].toPrecision(3), flags: [] }
       }
+      throw new Error('In silico predictor not found in variant')
     })
     .filter((item) => item)
 
@@ -312,18 +313,10 @@ const shapeVariantSummary = (subset: any, context: any) => {
 // Gene query
 // ================================================================================================
 
-const fetchVariantsByGene = async (esClient: any, gene: any, subset: any) => {
-  subset = 'all'
-
-  let exomeSubset = 'all'
-  let genomeSubset = 'all'
-
-  if (subset === 'tgp' || subset === 'hgdp') {
-    genomeSubset = subset
-  }
-  if (subset === 'non_ukb') {
-    exomeSubset = 'non_ukb'
-  }
+const fetchVariantsByGene = async (esClient: any, gene: any, _subset: any) => {
+  const subset = 'all'
+  const exomeSubset = 'all'
+  const genomeSubset = 'all'
 
   try {
     const filteredRegions = gene.exons.filter((exon: any) => exon.feature_type === 'CDS')
@@ -385,25 +378,18 @@ const fetchVariantsByGene = async (esClient: any, gene: any, subset: any) => {
 
     return shapedHits
   } catch (error) {
-    console.error('Error fetching variants by gene:', error)
-    throw error // You can re-throw the error if needed or handle it accordingly.
+    throw new Error(`'Error fetching variants by gene:', ${error}`)
   }
 }
 
 // ================================================================================================
 // Region query
 // ================================================================================================
 
-const fetchVariantsByRegion = async (esClient: any, region: any, subset: any) => {
-  let exomeSubset = 'all'
-  let genomeSubset = 'all'
-
-  if (subset === 'tgp' || subset === 'hgdp') {
-    genomeSubset = subset
-  }
-  if (subset === 'non_ukb') {
-    exomeSubset = 'non_ukb'
-  }
+const fetchVariantsByRegion = async (esClient: any, region: any, _subset: any) => {
+  const subset = 'all'
+  const exomeSubset = 'all'
+  const genomeSubset = 'all'
 
   const hits = await fetchAllSearchResults(esClient, {
     index: GNOMAD_V4_VARIANT_INDEX,
@@ -452,18 +438,11 @@ const fetchVariantsByRegion = async (esClient: any, region: any, subset: any) =>
 // Transcript query
 // ================================================================================================
 
-const fetchVariantsByTranscript = async (esClient: any, transcript: any, subset: any) => {
-  subset = 'all'
-
-  let exomeSubset = 'all'
-  let genomeSubset = 'all'
+const fetchVariantsByTranscript = async (esClient: any, transcript: any, _subset: any) => {
+  const subset = 'all'
+  const exomeSubset = 'all'
+  const genomeSubset = 'all'
 
-  if (subset === 'tgp' || subset === 'hgdp') {
-    genomeSubset = subset
-  }
-  if (subset === 'non_ukb') {
-    exomeSubset = 'non_ukb'
-  }
   const filteredRegions = transcript.exons.filter((exon: any) => exon.feature_type === 'CDS')
   const sortedRegions = filteredRegions.sort((r1: any, r2: any) => r1.xstart - r2.xstart)
   const padding = 75