@sjcrh/proteinpaint-server 2.142.0 → 2.143.0

package/routes/termdb.config.js

@@ -23,16 +23,13 @@ function init({ genomes }) {
     mayCopyFromCookie(q, req.cookies);
     try {
       const genome = genomes[q.genome];
-      if (!genome)
-        throw "invalid genome";
+      if (!genome) throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
       return make(q, req, res, ds, genome);
     } catch (e) {
       res.send({ error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
-      else
-        console.log(e);
+      if (e.stack) console.log(e.stack);
+      else console.log(e);
     }
   };
 }
@@ -64,34 +61,20 @@ function make(q, req, res, ds, genome) {
     defaultTw4correlationPlot: tdb.defaultTw4correlationPlot,
     authFilter: req.query.filter
   };
-  if (tdb.plotConfigByCohort)
-    c.plotConfigByCohort = tdb.plotConfigByCohort;
-  if (tdb.multipleTestingCorrection)
-    c.multipleTestingCorrection = tdb.multipleTestingCorrection;
-  if (tdb.helpPages)
-    c.helpPages = tdb.helpPages;
-  if (tdb.minTimeSinceDx)
-    c.minTimeSinceDx = tdb.minTimeSinceDx;
-  if (tdb.timeUnit)
-    c.timeUnit = tdb.timeUnit;
-  if (tdb.cohortStartTimeMsg)
-    c.cohortStartTimeMsg = tdb.cohortStartTimeMsg;
-  if (tdb.hasAncestry)
-    c.hasAncestry = tdb.hasAncestry;
-  if (tdb.logscaleBase2)
-    c.logscaleBase2 = tdb.logscaleBase2;
-  if (tdb.useCasesExcluded)
-    c.useCasesExcluded = tdb.useCasesExcluded;
-  if (tdb.excludedTermtypeByTarget)
-    c.excludedTermtypeByTarget = tdb.excludedTermtypeByTarget;
-  if (tdb.survival)
-    c.survival = tdb.survival;
-  if (tdb.regression)
-    c.regression = tdb.regression;
-  if (ds.assayAvailability)
-    c.assayAvailability = ds.assayAvailability;
-  if (ds.cohort.correlationVolcano)
-    c.correlationVolcano = ds.cohort.correlationVolcano;
+  if (tdb.plotConfigByCohort) c.plotConfigByCohort = tdb.plotConfigByCohort;
+  if (tdb.multipleTestingCorrection) c.multipleTestingCorrection = tdb.multipleTestingCorrection;
+  if (tdb.helpPages) c.helpPages = tdb.helpPages;
+  if (tdb.minTimeSinceDx) c.minTimeSinceDx = tdb.minTimeSinceDx;
+  if (tdb.timeUnit) c.timeUnit = tdb.timeUnit;
+  if (tdb.cohortStartTimeMsg) c.cohortStartTimeMsg = tdb.cohortStartTimeMsg;
+  if (tdb.hasAncestry) c.hasAncestry = tdb.hasAncestry;
+  if (tdb.logscaleBase2) c.logscaleBase2 = tdb.logscaleBase2;
+  if (tdb.useCasesExcluded) c.useCasesExcluded = tdb.useCasesExcluded;
+  if (tdb.excludedTermtypeByTarget) c.excludedTermtypeByTarget = tdb.excludedTermtypeByTarget;
+  if (tdb.survival) c.survival = tdb.survival;
+  if (tdb.regression) c.regression = tdb.regression;
+  if (ds.assayAvailability) c.assayAvailability = ds.assayAvailability;
+  if (ds.cohort.correlationVolcano) c.correlationVolcano = ds.cohort.correlationVolcano;
   addRestrictAncestries(c, tdb);
   addScatterplots(c, ds);
   addMatrixplots(c, ds);
@@ -99,21 +82,18 @@ function make(q, req, res, ds, genome) {
   c.requiredAuth = authApi.getRequiredCredForDsEmbedder(q.dslabel, q.embedder);
   const info = authApi.getNonsensitiveInfo(req);
   c.clientAuthResult = info?.clientAuthResult || {};
-  if (tdb.displaySampleIds)
-    c.displaySampleIds = tdb.displaySampleIds(c.clientAuthResult);
+  if (tdb.displaySampleIds) c.displaySampleIds = tdb.displaySampleIds(c.clientAuthResult);
   c.authFilter = req.query.filter;
   res.send({ termdbConfig: c });
 }
 function addRestrictAncestries(c, tdb) {
-  if (!tdb.restrictAncestries)
-    return;
+  if (!tdb.restrictAncestries) return;
   c.restrictAncestries = tdb.restrictAncestries.map((i) => {
     return { name: i.name, tvs: i.tvs, PCcount: i.PCcount };
   });
 }
 function addScatterplots(c, ds) {
-  if (!ds.cohort.scatterplots)
-    return;
+  if (!ds.cohort.scatterplots) return;
   c.scatterplots = ds.cohort.scatterplots.plots.map((p) => {
     return {
       name: p.name,
@@ -130,16 +110,14 @@ function addScatterplots(c, ds) {
   });
 }
 function addMatrixplots(c, ds) {
-  if (!ds.cohort.matrixplots)
-    return;
+  if (!ds.cohort.matrixplots) return;
   c.matrixplots = ds.cohort.matrixplots.plots.map((p) => {
     return { name: p.name };
   });
 }
 function addNonDictionaryQueries(c, ds, genome) {
   const q = ds.queries;
-  if (!q)
-    return;
+  if (!q) return;
   c.queries = {
     defaultCoord: q.defaultCoord || genome.defaultcoord,
     gbRestrictMode: q.gbRestrictMode
@@ -154,8 +132,7 @@ function addNonDictionaryQueries(c, ds, genome) {
       details: q.snvindel.details,
       populations: q.snvindel.populations
     };
-    if (q.snvindel.byisoform?.processTwsInOneQuery)
-      q2.snvindel.byisoform = { processTwsInOneQuery: true };
+    if (q.snvindel.byisoform?.processTwsInOneQuery) q2.snvindel.byisoform = { processTwsInOneQuery: true };
   }
   if (q.trackLst) {
     q2.trackLst = q.trackLst;
@@ -177,16 +154,13 @@ function addNonDictionaryQueries(c, ds, genome) {
       "gainColor",
       "lossColor"
     ]) {
-      if (k in q.cnv)
-        q2.cnv[k] = q.cnv[k];
+      if (k in q.cnv) q2.cnv[k] = q.cnv[k];
     }
   }
   if (q.geneCnv) {
   }
-  if (q.topMutatedGenes)
-    q2.topMutatedGenes = q.topMutatedGenes;
-  if (q.topVariablyExpressedGenes)
-    q2.topVariablyExpressedGenes = q.topVariablyExpressedGenes;
+  if (q.topMutatedGenes) q2.topMutatedGenes = q.topMutatedGenes;
+  if (q.topVariablyExpressedGenes) q2.topVariablyExpressedGenes = q.topVariablyExpressedGenes;
   if (q.singleSampleMutation) {
     q2.singleSampleMutation = {
       sample_id_key: q.singleSampleMutation.sample_id_key,
@@ -260,24 +234,18 @@ function addNonDictionaryQueries(c, ds, genome) {
 function getAllowedTermTypes(ds) {
   const typeSet = /* @__PURE__ */ new Set();
   for (const r of ds.cohort.termdb.termtypeByCohort) {
-    if (r.termType)
-      typeSet.add(r.termType);
+    if (r.termType) typeSet.add(r.termType);
   }
   if (ds.cohort.termdb.allowedTermTypes) {
-    for (const t of ds.cohort.termdb.allowedTermTypes)
-      typeSet.add(t);
+    for (const t of ds.cohort.termdb.allowedTermTypes) typeSet.add(t);
   }
-  if (ds.queries?.geneExpression)
-    typeSet.add(TermTypes.GENE_EXPRESSION);
-  if (ds.queries?.metaboliteIntensity)
-    typeSet.add(TermTypes.METABOLITE_INTENSITY);
-  if (ds.queries?.ssGSEA)
-    typeSet.add(TermTypes.SSGSEA);
+  if (ds.queries?.geneExpression) typeSet.add(TermTypes.GENE_EXPRESSION);
+  if (ds.queries?.metaboliteIntensity) typeSet.add(TermTypes.METABOLITE_INTENSITY);
+  if (ds.queries?.ssGSEA) typeSet.add(TermTypes.SSGSEA);
   return [...typeSet];
 }
 function getSelectCohort(ds, req) {
-  if (!ds.cohort.termdb.selectCohort)
-    return;
+  if (!ds.cohort.termdb.selectCohort) return;
   const copy = Object.assign({}, ds.cohort.termdb.selectCohort);
   if (ds.cohort.termdb.selectCohort.descriptionByUser) {
     copy.description = ds.cohort.termdb.selectCohort.descriptionByUser(authApi.getNonsensitiveInfo(req));

package/routes/termdb.descrstats.js

@@ -20,22 +20,17 @@ function init({ genomes }) {
     let result;
     try {
       const genome = genomes[req.query.genome];
-      if (!genome)
-        throw "invalid genome name";
+      if (!genome) throw "invalid genome name";
       const ds = genome.datasets[req.query.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
+      if (!ds) throw "invalid dataset name";
       const tdb = ds.cohort.termdb;
-      if (!tdb)
-        throw "invalid termdb object";
-      if (!q.tw.$id)
-        q.tw.$id = "_";
+      if (!tdb) throw "invalid termdb object";
+      if (!q.tw.$id) q.tw.$id = "_";
       const data = await getData(
         { filter: q.filter, filter0: q.filter0, terms: [q.tw], __protected__: q.__protected__ },
         ds
       );
-      if (data.error)
-        throw data.error;
+      if (data.error) throw data.error;
       const values = [];
       for (const key in data.samples) {
         const sample = data.samples[key];
@@ -60,8 +55,7 @@ function init({ genomes }) {
         result = {};
       }
     } catch (e) {
-      if (e instanceof Error && e.stack)
-        console.log(e);
+      if (e instanceof Error && e.stack) console.log(e);
       result = { error: e?.message || e };
     }
     res.send(result);

package/routes/termdb.filterTermValues.js

@@ -18,20 +18,17 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets?.[req.query.dslabel];
       res.send(await getFilters(req.query, ds));
     } catch (e) {
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
       res.send({ status: "error", error: e.message || e });
     }
   };
 }
 async function getFilters(query, ds) {
-  if (!query.filterByUserSites)
-    authApi.mayAdjustFilter(query, ds, query.terms);
+  if (!query.filterByUserSites) authApi.mayAdjustFilter(query, ds, query.terms);
   const samplesPerFilter = await getSamplesPerFilter(query, ds);
   const filtersData = await getData(
     {
@@ -60,8 +57,7 @@ function getList(samplesPerFilter, filtersData, tw, showAll) {
   for (const value of values) {
     const label = value.label.replace(/["']/g, "");
     const disabled = !sampleValues.includes(value.key || value.label);
-    if (!showAll && disabled)
-      continue;
+    if (!showAll && disabled) continue;
     filteredValues.push({ value: value.key || value.label, label, disabled });
   }
   filteredValues.unshift({ label: "", value: "" });

package/routes/termdb.numericcategories.js

@@ -18,26 +18,21 @@ function init({ genomes }) {
     const q = req.query;
     try {
       const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets[req.query.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
+      if (!ds) throw "invalid dataset name";
       const tdb = ds.cohort.termdb;
-      if (!tdb)
-        throw "invalid termdb object";
+      if (!tdb) throw "invalid termdb object";
       const result = await trigger_getnumericcategories(q, tdb, ds);
       res.send(result);
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack)
-        console.log(e);
+      if (e instanceof Error && e.stack) console.log(e);
     }
   };
 }
 async function trigger_getnumericcategories(q, tdb, ds) {
-  if (!q.tid)
-    throw ".tid missing";
+  if (!q.tid) throw ".tid missing";
   const arg = {
     ds,
     term_id: q.tid,

package/routes/termdb.percentile.js

@@ -20,29 +20,23 @@ function init({ genomes }) {
     const q = req.query;
     try {
       const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets[req.query.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
+      if (!ds) throw "invalid dataset name";
       await trigger_getpercentile(q, res, ds);
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack)
-        console.log(e);
+      if (e instanceof Error && e.stack) console.log(e);
     }
   };
 }
 async function trigger_getpercentile(q, res, ds) {
   const term = q.term;
-  if (!term)
-    throw "term is missing";
-  if (!isNumericTerm(term))
-    throw "not numeric term";
+  if (!term) throw "term is missing";
+  if (!isNumericTerm(term)) throw "not numeric term";
   const tw = { $id: "_", term, q: { mode: "continuous" } };
   const data = await getData({ filter: q.filter, filter0: q.filter0, terms: [tw], __protected__: q.__protected__ }, ds);
-  if (data.error)
-    throw data.error;
+  if (data.error) throw data.error;
   const values = [];
   for (const key in data.samples) {
     const sample = data.samples[key];

package/routes/termdb.profileFormScores.js

@@ -17,8 +17,7 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets?.[req.query.dslabel];
       const result = await getScoresDict(req.query, ds);
       res.send(result);
@@ -29,11 +28,9 @@ function init({ genomes }) {
   };
 }
 async function getScoresDict(query, ds) {
-  if (!query.filterByUserSites)
-    query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
+  if (!query.filterByUserSites) query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
   const terms = [...query.scoreTerms, query.facilityTW];
-  if (query.scScoreTerms)
-    terms.push(...query.scScoreTerms);
+  if (query.scScoreTerms) terms.push(...query.scScoreTerms);
   const data = await getData(
     {
       terms,
@@ -60,16 +57,12 @@ async function getScoresDict(query, ds) {
     }
   }
   let sitesSelected = [];
-  if (query.site)
-    sitesSelected = [query.site];
-  else if (!query.isAggregate)
-    sitesSelected = [sites[0].value];
-  else
-    sitesSelected = query.sites;
+  if (query.site) sitesSelected = [query.site];
+  else if (!query.isAggregate) sitesSelected = [sites[0].value];
+  else sitesSelected = query.sites;
   const sampleData = sitesSelected?.length == 1 ? data.samples[sitesSelected[0]] : null;
   let samples = sampleData ? [sampleData] : Object.values(data.samples);
-  if (sitesSelected?.length > 0)
-    samples = samples.filter((s) => sitesSelected.includes(s.sample));
+  if (sitesSelected?.length > 0) samples = samples.filter((s) => sitesSelected.includes(s.sample));
   const term2Score = {};
   for (const d of query.scoreTerms) {
     const getDictFunc = (sample) => getDict(d.$id, sample);
@@ -87,8 +80,7 @@ async function getScoresDict(query, ds) {
   return { term2Score, sites, hospital, n: sampleData ? 1 : samples.length };
 }
 function getDict(key, sample) {
-  if (!sample[key])
-    return null;
+  if (!sample[key]) return null;
   const termData = sample[key].value;
   return JSON.parse(termData);
 }
@@ -96,26 +88,22 @@ function getPercentsDict(getDictFunc, samples) {
   const percentageDict = {};
   for (const sample of samples) {
     const percents = getDictFunc(sample);
-    if (!percents)
-      continue;
+    if (!percents) continue;
     for (const key in percents) {
       const value = percents[key];
-      if (!percentageDict[key])
-        percentageDict[key] = 0;
+      if (!percentageDict[key]) percentageDict[key] = 0;
       percentageDict[key] += value;
     }
   }
   return percentageDict;
 }
 function getSCPercentsDict(tw, samples) {
-  if (!tw)
-    throw "tw not defined";
+  if (!tw) throw "tw not defined";
   const percentageDict = {};
   for (const sample of samples) {
     const twData = sample[tw.$id];
     const key = twData?.value;
-    if (!percentageDict[key])
-      percentageDict[key] = 0;
+    if (!percentageDict[key]) percentageDict[key] = 0;
     percentageDict[key] += 1;
   }
   return percentageDict;

package/routes/termdb.profileScores.js

@@ -17,8 +17,7 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets?.[req.query.dslabel];
       const result = await getScores(req.query, ds);
       res.send(result);
@@ -29,8 +28,7 @@ function init({ genomes }) {
   };
 }
 async function getScores(query, ds) {
-  if (!query.filterByUserSites)
-    query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
+  if (!query.filterByUserSites) query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
   const terms = [query.facilityTW];
   for (const term of query.scoreTerms) {
     terms.push(term.score);
@@ -61,16 +59,12 @@ async function getScores(query, ds) {
     }
   }
   let sitesSelected = [];
-  if (query.site)
-    sitesSelected = [query.site];
-  else if (!query.isAggregate)
-    sitesSelected = [sites[0].value];
-  else
-    sitesSelected = query.sites;
+  if (query.site) sitesSelected = [query.site];
+  else if (!query.isAggregate) sitesSelected = [sites[0].value];
+  else sitesSelected = query.sites;
   const sampleData = sitesSelected?.length == 1 ? data.samples[sitesSelected[0]] : null;
   let samples = Object.values(data.samples);
-  if (sitesSelected?.length > 0)
-    samples = samples.filter((s) => sitesSelected.includes(s.sample));
+  if (sitesSelected?.length > 0) samples = samples.filter((s) => sitesSelected.includes(s.sample));
   const term2Score = {};
   for (const d of query.scoreTerms) {
     term2Score[d.score.term.id] = getPercentage(d, samples, sampleData);
@@ -81,8 +75,7 @@ async function getScores(query, ds) {
   return { term2Score, sites, hospital, n: sampleData ? 1 : samples.length };
 }
 function getPercentage(d, samples, sampleData) {
-  if (!d)
-    return null;
+  if (!d) return null;
   const isAggregate = sampleData == null;
   if (isAggregate) {
     const scores = samples.filter((sample) => sample[d.score.$id]?.value).map((sample) => sample[d.score.$id].value / (sample[d.maxScore.$id]?.value || d.maxScore) * 100);

package/routes/termdb.rootterm.js

@@ -18,18 +18,14 @@ function init({ genomes }) {
     const q = req.query;
     try {
       const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const [ds, tdb] = get_ds_tdb(g, q);
-      if (!ds)
-        throw "invalid dataset name";
-      if (!tdb)
-        throw "invalid termdb object";
+      if (!ds) throw "invalid dataset name";
+      if (!tdb) throw "invalid termdb object";
       await trigger_rootterm(req, q, res, tdb);
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack)
-        console.log(e);
+      if (e instanceof Error && e.stack) console.log(e);
     }
   };
 }

package/routes/termdb.sampleImages.js

@@ -21,11 +21,9 @@ function init({ genomes }) {
       const q = req.query;
       const sampleId = q.sampleId;
       const genome = genomes[q.genome];
-      if (!genome)
-        throw "invalid genome";
+      if (!genome) throw "invalid genome";
       const ds = genome.datasets?.[q.dslabel];
-      if (!ds)
-        throw "invalid dslabel";
+      if (!ds) throw "invalid dslabel";
       const images = await ds.queries.images.getSampleImages({ sampleId });
       res.send({ images });
     } catch (e) {
@@ -35,8 +33,7 @@ function init({ genomes }) {
 }
 function validate_query_getSampleImages(ds) {
   const q = ds.queries.images;
-  if (!q)
-    return;
+  if (!q) return;
   nativeValidateQuery(ds);
 }
 function nativeValidateQuery(ds) {
@@ -52,8 +49,7 @@ async function getSampleImages(ds, folder, sampleId) {
   const images = [];
   for (const row of rows) {
     const file = path.join(serverconfig.tpmasterdir, folder, row.fileName);
-    if (!fs.existsSync(file))
-      throw new Error(`File ${row.fileName} does not exist`);
+    if (!fs.existsSync(file)) throw new Error(`File ${row.fileName} does not exist`);
     const data = await fs.promises.readFile(file);
     images.push({
       src: "data:image/jpeg;base64," + Buffer.from(data).toString("base64")

package/routes/termdb.singleSampleMutation.js

@@ -17,17 +17,13 @@ function init({ genomes }) {
     let result;
     try {
       const g = genomes[q.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets[q.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
-      if (!ds.queries?.singleSampleMutation)
-        throw "not supported on this dataset";
+      if (!ds) throw "invalid dataset name";
+      if (!ds.queries?.singleSampleMutation) throw "not supported on this dataset";
       result = await ds.queries.singleSampleMutation.get(q);
     } catch (e) {
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
       result = {
         status: e.status || 400,
         error: e.message || e
@@ -38,8 +34,7 @@ function init({ genomes }) {
 }
 async function validate_query_singleSampleMutation(ds, genome) {
   const _q = ds.queries.singleSampleMutation;
-  if (!_q)
-    return;
+  if (!_q) return;
   if (_q.src == "gdcapi") {
     gdcValidate_query_singleSampleMutation(ds, genome);
   } else if (_q.src == "native") {
@@ -48,8 +43,7 @@ async function validate_query_singleSampleMutation(ds, genome) {
       {
         const vt = typeof q.sample;
         if (vt == "string") {
-          if (q.sample == "")
-            throw "sample is blank string";
+          if (q.sample == "") throw "sample is blank string";
           sample = q.sample;
         } else if (vt == "number") {
           sample = q.sample.toString();
@@ -57,18 +51,15 @@ async function validate_query_singleSampleMutation(ds, genome) {
           throw "sample value is not string or number";
         }
       }
-      if (illegalpath(sample))
-        throw "invalid sample name";
+      if (illegalpath(sample)) throw "invalid sample name";
       const tmp = fileurl({
         query: {
           file: path.join(_q.folder, sample)
         }
       });
-      if (tmp[0])
-        throw tmp[0];
+      if (tmp[0]) throw tmp[0];
       const file = tmp[1];
-      if (!file)
-        throw "no file returned";
+      if (!file) throw "no file returned";
       await file_is_readable(file);
       const data = await read_file(file);
       return { mlst: JSON.parse(data) };

package/routes/termdb.singlecellDEgenes.js

@@ -19,13 +19,10 @@ function init({ genomes }) {
     let result;
     try {
       const g = genomes[q.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets[q.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
-      if (!ds.queries?.singleCell?.DEgenes)
-        throw "not supported on this dataset";
+      if (!ds) throw "invalid dataset name";
+      if (!ds.queries?.singleCell?.DEgenes) throw "not supported on this dataset";
       result = await ds.queries.singleCell.DEgenes.get(q);
       if (!result || !result.genes || !result?.genes?.length) {
         result = {
@@ -34,8 +31,7 @@ function init({ genomes }) {
         };
       }
     } catch (e) {
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
       result = {
         status: e.status || 400,
         error: e.message || e

package/routes/termdb.singlecellData.js

@@ -18,17 +18,13 @@ function init({ genomes }) {
     let result;
     try {
       const g = genomes[q.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets[q.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
-      if (!ds.queries?.singleCell)
-        throw "no singlecell data on this dataset";
+      if (!ds) throw "invalid dataset name";
+      if (!ds.queries?.singleCell) throw "no singlecell data on this dataset";
       result = await ds.queries.singleCell.data.get(q);
     } catch (e) {
-      if (e.stack)
-        console.log(e);
+      if (e.stack) console.log(e);
       result = {
         status: e.status || 400,
         error: e.message || e