@sjcrh/proteinpaint-server 2.142.0 → 2.143.0

package/routes/termdb.DE.js

@@ -28,8 +28,7 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const genome = genomes[q.genome];
-      if (!genome)
-        throw "invalid genome";
+      if (!genome) throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
       let term_results = [];
       if (q.tw) {
@@ -42,8 +41,7 @@ function init({ genomes }) {
           },
           ds
         );
-        if (term_results.error)
-          throw term_results.error;
+        if (term_results.error) throw term_results.error;
       }
       let term_results2 = [];
       if (q.tw2) {
@@ -56,44 +54,33 @@ function init({ genomes }) {
           },
           ds
         );
-        if (term_results2.error)
-          throw term_results2.error;
+        if (term_results2.error) throw term_results2.error;
       }
       const results = await run_DE(req.query, ds, term_results, term_results2);
-      if (!results || !results.data)
-        throw "No data [termdb.DE.ts init()]";
+      if (!results || !results.data) throw "No data [termdb.DE.ts init()]";
       res.send(results);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
-      if (e instanceof Error && e.stack)
-        console.log(e);
+      if (e instanceof Error && e.stack) console.log(e);
     }
   };
 }
 async function run_DE(param, ds, term_results, term_results2) {
-  if (param.samplelst?.groups?.length != 2)
-    throw ".samplelst.groups.length!=2";
-  if (param.samplelst.groups[0].values?.length < 1)
-    throw "samplelst.groups[0].values.length<1";
-  if (param.samplelst.groups[1].values?.length < 1)
-    throw "samplelst.groups[1].values.length<1";
+  if (param.samplelst?.groups?.length != 2) throw ".samplelst.groups.length!=2";
+  if (param.samplelst.groups[0].values?.length < 1) throw "samplelst.groups[0].values.length<1";
+  if (param.samplelst.groups[1].values?.length < 1) throw "samplelst.groups[1].values.length<1";
   const q = ds.queries.rnaseqGeneCount;
-  if (!q)
-    return;
-  if (!q.file)
-    throw "unknown data type for rnaseqGeneCount";
-  if (!q.storage_type)
-    throw "storage_type is not defined";
+  if (!q) return;
+  if (!q.file) throw "unknown data type for rnaseqGeneCount";
+  if (!q.storage_type) throw "storage_type is not defined";
   param.storage_type = q.storage_type;
   const group1names = [];
   const conf1_group1 = [];
   const conf2_group1 = [];
   for (const s of param.samplelst.groups[0].values) {
-    if (!Number.isInteger(s.sampleId))
-      continue;
+    if (!Number.isInteger(s.sampleId)) continue;
     const n = ds.cohort.termdb.q.id2sampleName(s.sampleId);
-    if (!n)
-      continue;
+    if (!n) continue;
     if (q.allSampleSet.has(n)) {
       if (param.tw && !param.tw2) {
         if (term_results.samples[s.sampleId]) {
@@ -136,11 +123,9 @@ async function run_DE(param, ds, term_results, term_results2) {
   const conf1_group2 = [];
   const conf2_group2 = [];
   for (const s of param.samplelst.groups[1].values) {
-    if (!Number.isInteger(s.sampleId))
-      continue;
+    if (!Number.isInteger(s.sampleId)) continue;
     const n = ds.cohort.termdb.q.id2sampleName(s.sampleId);
-    if (!n)
-      continue;
+    if (!n) continue;
     if (q.allSampleSet.has(n)) {
       if (param.tw && !param.tw2) {
         if (term_results.samples[s.sampleId]) {
@@ -181,10 +166,8 @@ async function run_DE(param, ds, term_results, term_results2) {
   }
   const sample_size1 = group1names.length;
   const sample_size2 = group2names.length;
-  if (sample_size1 < 1)
-    throw "sample size of group1 < 1";
-  if (sample_size2 < 1)
-    throw "sample size of group2 < 1";
+  if (sample_size1 < 1) throw "sample size of group1 < 1";
+  if (sample_size2 < 1) throw "sample size of group2 < 1";
   const commonnames = group1names.filter((element) => group2names.includes(element));
   if (commonnames.length > 0) {
     throw "Common elements found between both groups:" + commonnames.map((i) => i).join(",");
@@ -233,8 +216,7 @@ async function run_DE(param, ds, term_results, term_results2) {
       await readFileAndDelete(mds_imagePath, "mds_image", result2);
     }
     const images = [result2.ql_image];
-    if (result2.mds_image)
-      images.push(result2.mds_image);
+    if (result2.mds_image) images.push(result2.mds_image);
     return {
       data: result2.gene_data,
       sample_size1,
@@ -259,16 +241,13 @@ async function readFileAndDelete(file, key, response) {
   };
   response[key] = obj;
   fs.unlink(file, (err) => {
-    if (err)
-      throw err;
+    if (err) throw err;
   });
 }
 async function validate_query_rnaseqGeneCount(ds) {
   const q = ds.queries.rnaseqGeneCount;
-  if (!q)
-    return;
-  if (!q.file)
-    throw "unknown data type for rnaseqGeneCount";
+  if (!q) return;
+  if (!q.file) throw "unknown data type for rnaseqGeneCount";
   q.file = path.join(serverconfig.tpmasterdir, q.file);
   {
     let samples = [];
@@ -284,13 +263,11 @@ async function validate_query_rnaseqGeneCount(ds) {
       const time2 = (/* @__PURE__ */ new Date()).valueOf();
       mayLog("Time taken to query gene expression:", time2 - time1, "ms");
       samples = result.split(",");
-    } else
-      throw "unknown storage type:" + ds.queries.rnaseqGeneCount.storage_type;
+    } else throw "unknown storage type:" + ds.queries.rnaseqGeneCount.storage_type;
     q.allSampleSet = new Set(samples);
     const unknownSamples = [];
     for (const n of q.allSampleSet) {
-      if (!ds.cohort.termdb.q.sampleName2id(n))
-        unknownSamples.push(n);
+      if (!ds.cohort.termdb.q.sampleName2id(n)) unknownSamples.push(n);
     }
     console.log(q.allSampleSet.size, `rnaseqGeneCount samples from ${ds.label}`);
   }

package/routes/termdb.boxplot.js

@@ -1,7 +1,7 @@
 import { boxplotPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 import { boxplot_getvalue } from "../src/utils.js";
-import { sortKey2values } from "./termdb.violin.ts";
+import { sortPlot2Values } from "./termdb.violin.ts";
 import { roundValueAuto } from "#shared/roundValue.js";
 import { getMean, getVariance } from "#shared/descriptive.stats.js";
 const minSampleSize = 5;
@@ -23,103 +23,99 @@ function init({ genomes }) {
     const q = req.query;
     try {
       const genome = genomes[q.genome];
-      if (!genome)
-        throw "invalid genome name";
+      if (!genome) throw "invalid genome name";
       const ds = genome.datasets?.[q.dslabel];
-      if (!ds)
-        throw "invalid ds";
+      if (!ds) throw "invalid ds";
       const terms = [q.tw];
-      if (q.overlayTw)
-        terms.push(q.overlayTw);
+      if (q.overlayTw) terms.push(q.overlayTw);
+      if (q.divideTw) terms.push(q.divideTw);
       const data = await getData({ filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__ }, ds);
-      if (data.error)
-        throw data.error;
+      if (data.error) throw data.error;
       const sampleType = `All ${data.sampleType?.plural_name || "samples"}`;
       const overlayTerm = q.overlayTw;
-      const { absMin, absMax, key2values, uncomputableValues } = parseValues(
+      const divideTerm = q.divideTw;
+      const { absMin, absMax, chart2plot2values, uncomputableValues } = parseValues(
         q,
         data,
         sampleType,
         q.isLogScale,
-        overlayTerm
+        overlayTerm,
+        divideTerm
       );
-      const plots = [];
-      for (const [key, values] of sortKey2values(data, key2values, overlayTerm)) {
-        const sortedValues = values.sort((a, b) => a - b);
-        const vs = sortedValues.map((v) => {
-          const value = { value: v };
-          return value;
-        });
-        const boxplot = boxplot_getvalue(vs);
-        if (!boxplot)
-          throw "boxplot_getvalue failed [termdb.boxplot init()]";
-        const descrStats = setDescrStats(boxplot, sortedValues);
-        const _plot = {
-          boxplot,
-          descrStats
-        };
-        if (overlayTerm) {
-          const _key = overlayTerm?.term?.values?.[key]?.label || key;
-          const plotLabel = `${_key}, n=${values.length}`;
-          const overlayBins = numericBins(overlayTerm, data);
-          const plot = Object.assign(_plot, {
-            color: overlayTerm?.term?.values?.[key]?.color || null,
-            key: _key,
-            overlayBins: overlayBins.has(key) ? overlayBins.get(key) : null,
-            seriesId: key
+      if (!absMin && absMin !== 0) throw "absMin is undefined [termdb.boxplot init()]";
+      if (!absMax && absMax !== 0) throw "absMax is undefined [termdb.boxplot init()]";
+      const charts = {};
+      for (const [chart, plot2values] of chart2plot2values) {
+        const plots = [];
+        for (const [key, values] of sortPlot2Values(data, plot2values, overlayTerm)) {
+          const sortedValues = values.sort((a, b) => a - b);
+          const vs = sortedValues.map((v) => {
+            const value = { value: v };
+            return value;
           });
-          plot.boxplot.label = plotLabel;
-          plots.push(plot);
-        } else {
-          const plotLabel = `${sampleType}, n=${values.length}`;
-          const plot = Object.assign(_plot, {
-            key: sampleType
-          });
-          plot.boxplot.label = plotLabel;
-          plots.push(plot);
+          const boxplot = boxplot_getvalue(vs);
+          if (!boxplot) throw "boxplot_getvalue failed [termdb.boxplot init()]";
+          const descrStats = setDescrStats(boxplot, sortedValues);
+          const _plot = {
+            boxplot,
+            descrStats
+          };
+          if (overlayTerm) {
+            const _key = overlayTerm?.term?.values?.[key]?.label || key;
+            const plotLabel = `${_key}, n=${values.length}`;
+            const overlayBins = numericBins(overlayTerm, data);
+            const plot = Object.assign(_plot, {
+              color: overlayTerm?.term?.values?.[key]?.color || null,
+              key: _key,
+              overlayBins: overlayBins.has(key) ? overlayBins.get(key) : null,
+              seriesId: key
+            });
+            plot.boxplot.label = plotLabel;
+            plots.push(plot);
+          } else {
+            const plotLabel = `${sampleType}, n=${values.length}`;
+            const plot = Object.assign(_plot, {
+              key: sampleType
+            });
+            plot.boxplot.label = plotLabel;
+            plots.push(plot);
+          }
         }
-      }
-      if (absMin == null || absMax == null)
-        throw "absMin or absMax is null [termdb.boxplot init()]";
-      if (q.tw.term?.values)
-        setHiddenPlots(q.tw, plots);
-      if (overlayTerm && overlayTerm.term?.values)
-        setHiddenPlots(overlayTerm, plots);
-      if (q.orderByMedian == true) {
-        plots.sort((a, b) => a.boxplot.p50 - b.boxplot.p50);
+        if (q.tw.term?.values) setHiddenPlots(q.tw, plots);
+        if (overlayTerm && overlayTerm.term?.values) setHiddenPlots(overlayTerm, plots);
+        if (q.orderByMedian == true) {
+          plots.sort((a, b) => a.boxplot.p50 - b.boxplot.p50);
+        }
+        charts[chart] = { chartId: chart, plots };
       }
       const returnData = {
         absMin,
         absMax,
-        plots,
+        charts,
         uncomputableValues: setUncomputableValues(uncomputableValues)
       };
       res.send(returnData);
     } catch (e) {
       res.send({ error: e?.message || e });
-      if (e instanceof Error && e.stack)
-        console.error(e);
+      if (e instanceof Error && e.stack) console.error(e);
     }
   };
 }
 function setHiddenPlots(term, plots) {
   for (const v of Object.values(term.term?.values)) {
     const plot = plots.find((p) => p.key === v.label);
-    if (plot)
-      plot.isHidden = v?.uncomputable;
+    if (plot) plot.isHidden = v?.uncomputable;
   }
   if (term.q?.hiddenValues) {
     for (const key of Object.keys(term.q.hiddenValues)) {
       const plot = plots.find((p) => p.key === key);
-      if (plot)
-        plot.isHidden = true;
+      if (plot) plot.isHidden = true;
     }
   }
   return plots;
 }
 function setDescrStats(boxplot, sortedValues) {
-  if (sortedValues.length < minSampleSize)
-    return [{ id: "total", label: "Total", value: sortedValues.length }];
+  if (sortedValues.length < minSampleSize) return [{ id: "total", label: "Total", value: sortedValues.length }];
   const mean = getMean(sortedValues);
   const variance = getVariance(sortedValues);
   const sd = Math.sqrt(variance);
@@ -139,46 +135,50 @@ function setDescrStats(boxplot, sortedValues) {
 function setUncomputableValues(values) {
   if (Object.entries(values)?.length) {
     return Object.entries(values).map(([label, v]) => ({ label, value: v }));
-  } else
-    return null;
+  } else return null;
 }
-function parseValues(q, data, sampleType, isLog, overlayTerm) {
-  const key2values = /* @__PURE__ */ new Map();
+function parseValues(q, data, sampleType, isLog, overlayTerm, divideTerm) {
+  const chart2plot2values = /* @__PURE__ */ new Map();
   const uncomputableValues = {};
   let absMin = null, absMax = null;
   for (const val of Object.values(data.samples)) {
     const value = val[q.tw.$id];
-    if (!Number.isFinite(value?.value))
-      continue;
+    if (!Number.isFinite(value?.value)) continue;
     if (q.tw.term.values?.[value.value]?.uncomputable) {
       const label = q.tw.term.values[value.value].label;
       uncomputableValues[label] = (uncomputableValues[label] || 0) + 1;
       continue;
     }
-    if (isLog && value.value <= 0)
-      continue;
+    if (isLog && value.value <= 0) continue;
+    let chart = "";
+    let plot = sampleType;
+    if (divideTerm) {
+      if (!val[divideTerm?.$id]) continue;
+      const value0 = val[divideTerm.$id];
+      if (divideTerm.term?.values?.[value0.key]?.uncomputable) {
+        const label = divideTerm.term.values[value0?.key]?.label;
+        uncomputableValues[label] = (uncomputableValues[label] || 0) + 1;
+      }
+      chart = value0.key;
+    }
     if (overlayTerm) {
-      if (!val[overlayTerm?.$id])
-        continue;
+      if (!val[overlayTerm?.$id]) continue;
       const value2 = val[overlayTerm.$id];
       if (overlayTerm.term?.values?.[value2.key]?.uncomputable) {
         const label = overlayTerm.term.values[value2?.key]?.label;
         uncomputableValues[label] = (uncomputableValues[label] || 0) + 1;
       }
-      if (!key2values.has(value2.key))
-        key2values.set(value2.key, []);
-      key2values.get(value2.key).push(value.value);
-    } else {
-      if (!key2values.has(sampleType))
-        key2values.set(sampleType, []);
-      key2values.get(sampleType).push(value.value);
+      plot = value2.key;
     }
-    if (absMin === null || value.value < absMin)
-      absMin = value.value;
-    if (absMax === null || value.value > absMax)
-      absMax = value.value;
+    if (!chart2plot2values.has(chart)) chart2plot2values.set(chart, /* @__PURE__ */ new Map());
+    const plot2values = chart2plot2values.get(chart);
+    if (!plot2values.has(plot)) plot2values.set(plot, []);
+    const values = plot2values.get(plot);
+    values.push(value.value);
+    if (absMin === null || value.value < absMin) absMin = value.value;
+    if (absMax === null || value.value > absMax) absMax = value.value;
   }
-  return { absMax, absMin, key2values, uncomputableValues };
+  return { absMax, absMin, chart2plot2values, uncomputableValues };
 }
 function numericBins(overlayTerm, data) {
   const overlayBins = data.refs.byTermId[overlayTerm?.$id]?.bins ?? [];

package/routes/termdb.categories.js

@@ -19,25 +19,20 @@ 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";
       await trigger_getcategories(q, res, tdb, ds);
     } catch (e) {
       res.send({ 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_getcategories(q, res, tdb, ds) {
-  if (!q.tw.$id)
-    q.tw.$id = "_";
+  if (!q.tw.$id) q.tw.$id = "_";
   const $id = q.tw.$id;
   const arg = {
     filter: q.filter,
@@ -50,8 +45,7 @@ async function trigger_getcategories(q, res, tdb, ds) {
     __protected__: q.__protected__
   };
   const data = await getData(arg, ds);
-  if (data.error)
-    throw data.error;
+  if (data.error) throw data.error;
   const [lst, orderedLabels] = getCategories(data, q, ds, $id);
   res.send({
     lst,
@@ -74,8 +68,7 @@ function getCategories(data, q, ds, $id) {
     const sampleCountedFor = /* @__PURE__ */ new Set();
     for (const sampleData of Object.values(samples)) {
       const key = $id;
-      if (!Object.keys(sampleData).includes(key))
-        continue;
+      if (!Object.keys(sampleData).includes(key)) continue;
       const values = sampleData[key].values;
       sampleCountedFor.clear();
       for (const value of values) {
@@ -114,10 +107,8 @@ function getCategories(data, q, ds, $id) {
     const key2count = /* @__PURE__ */ new Map();
     for (const sid in data.samples) {
       const v = data.samples[sid][$id];
-      if (!v)
-        continue;
-      if (!("key" in v))
-        continue;
+      if (!v) continue;
+      if (!("key" in v)) continue;
       key2count.set(v.key, 1 + (key2count.get(v.key) || 0));
     }
     for (const [key, count] of key2count) {

package/routes/termdb.cluster.js

@@ -31,20 +31,16 @@ 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) throw "invalid dataset name";
       if (ds.label === "GDC" && !ds.__gdc?.doneCaching)
         throw "The server has not finished caching the case IDs: try again in about 2 minutes.";
       if ([TermTypes.GENE_EXPRESSION, TermTypes.METABOLITE_INTENSITY, NUMERIC_DICTIONARY_TERM].includes(q.dataType)) {
         if (!ds.queries?.[q.dataType] && q.dataType !== NUMERIC_DICTIONARY_TERM)
           throw `no ${q.dataType} data on this dataset`;
-        if (!q.terms)
-          throw `missing gene list`;
-        if (!Array.isArray(q.terms))
-          throw `gene list is not an array`;
+        if (!q.terms) throw `missing gene list`;
+        if (!Array.isArray(q.terms)) throw `gene list is not an array`;
         if (q.terms.length < 3)
           throw `A minimum of three genes is required for clustering. Please refresh this page to clear this error.`;
         result = await getResult(q, ds);
@@ -52,8 +48,7 @@ function init({ genomes }) {
         throw "unknown q.dataType " + q.dataType;
       }
     } 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
@@ -94,8 +89,7 @@ async function getResult(q, ds) {
   if (skippedSexChrGenes?.length) {
     removedHierClusterTerms.push({ text: "Skipped sex chromosome genes", lst: skippedSexChrGenes });
   }
-  if (term2sample2value.size == 0)
-    throw "no data";
+  if (term2sample2value.size == 0) throw "no data";
   if (term2sample2value.size == 1) {
     const g = Array.from(term2sample2value.keys())[0];
     return { term: { gene: g, type: TermTypes.GENE_EXPRESSION }, data: term2sample2value.get(g) };
@@ -104,8 +98,7 @@ async function getResult(q, ds) {
   const clustering = await doClustering(term2sample2value, q, Object.keys(bySampleId).length);
   mayLog("clustering done:", formatElapsedTime(Date.now() - t));
   const result = { clustering, byTermId, bySampleId };
-  if (removedHierClusterTerms.length)
-    result.removedHierClusterTerms = removedHierClusterTerms;
+  if (removedHierClusterTerms.length) result.removedHierClusterTerms = removedHierClusterTerms;
   return result;
 }
 async function getNumericDictTermAnnotation(q, ds) {
@@ -149,10 +142,8 @@ async function doClustering(data, q, numCases = 1e3) {
     throw `termdb.cluster: There are no overlapping tested samples shared across the selected ${termType2label(
       q.dataType
     )}`;
-  if (!clusterMethodLst.find((i) => i.value == q.clusterMethod))
-    throw "Invalid cluster method";
-  if (!distanceMethodLst.find((i) => i.value == q.distanceMethod))
-    throw "Invalid distance method";
+  if (!clusterMethodLst.find((i) => i.value == q.clusterMethod)) throw "Invalid cluster method";
+  if (!distanceMethodLst.find((i) => i.value == q.distanceMethod)) throw "Invalid distance method";
   const inputData = {
     matrix: [],
     row_names: [],
@@ -172,8 +163,7 @@ async function doClustering(data, q, numCases = 1e3) {
     }
     inputData.matrix.push(q.zScoreTransformation ? getZscore(row) : row);
   }
-  if (inputData.matrix.length == 0)
-    throw "Clustering matrix is empty";
+  if (inputData.matrix.length == 0) throw "Clustering matrix is empty";
   const Routput = JSON.parse(await run_R("hclust.R", JSON.stringify(inputData)));
   const row_names_index = Routput.RowOrder.map((row) => inputData.row_names.indexOf(row.name));
   const col_names_index = Routput.ColOrder.map((col) => inputData.col_names.indexOf(col.name));
@@ -211,8 +201,7 @@ function getZscore(l) {
 }
 async function validate_query_geneExpression(ds, genome) {
   const q = ds.queries.geneExpression;
-  if (!q)
-    return;
+  if (!q) return;
   q.geneExpression2bins = {};
   if (q.src == "gdcapi") {
     gdc_validate_query_geneExpression(ds, genome);
@@ -268,25 +257,20 @@ async function validateNative(q, ds) {
       tmp = await run_rust("validateHDF5", JSON.stringify({ hdf5_file: q.file }));
     }
     const vr = JSON.parse(tmp);
-    if (vr.status !== "success")
-      throw vr.message;
+    if (vr.status !== "success") throw vr.message;
     if (q.newformat) {
-      if (!vr.samples?.length)
-        throw "HDF5 file has no samples, please check file.";
+      if (!vr.samples?.length) throw "HDF5 file has no samples, please check file.";
       for (const sn of vr.samples) {
         const si = ds.cohort.termdb.q.sampleName2id(sn);
-        if (si == void 0)
-          throw `unknown sample ${sn} from HDF5 ${q.file}`;
+        if (si == void 0) throw `unknown sample ${sn} from HDF5 ${q.file}`;
         q.samples.push(si);
       }
       console.log(`${ds.label}: geneExpression HDF5 file validated. Format: ${vr.format}, Samples:`, vr.samples.length);
     } else {
-      if (!vr.sampleNames?.length)
-        throw "HDF5 file has no samples, please check file.";
+      if (!vr.sampleNames?.length) throw "HDF5 file has no samples, please check file.";
       for (const sn of vr.sampleNames) {
         const si = ds.cohort.termdb.q.sampleName2id(sn);
-        if (si == void 0)
-          throw `unknown sample ${sn} from HDF5 ${q.file}`;
+        if (si == void 0) throw `unknown sample ${sn} from HDF5 ${q.file}`;
         q.samples.push(si);
       }
       console.log(
@@ -335,11 +319,9 @@ async function validateNative(q, ds) {
     mayLog("Time taken to run gene query:", formatElapsedTime(Date.now() - time1));
     if (q.newformat) {
       const genesData = geneData.query_output || {};
-      if (!genesData)
-        throw "No expression data returned from HDF5 query";
+      if (!genesData) throw "No expression data returned from HDF5 query";
       for (const tw of param.terms) {
-        if (!tw.term.gene)
-          continue;
+        if (!tw.term.gene) continue;
         const geneResult = genesData[tw.term.gene];
         if (!geneResult) {
           console.warn(`No data found for gene ${tw.term.gene} in the response`);
@@ -349,10 +331,8 @@ async function validateNative(q, ds) {
         const s2v = {};
         for (const sampleName in samplesData) {
           const sampleId = ds.cohort.termdb.q.sampleName2id(sampleName);
-          if (!sampleId)
-            continue;
-          if (limitSamples && !limitSamples.has(sampleId))
-            continue;
+          if (!sampleId) continue;
+          if (limitSamples && !limitSamples.has(sampleId)) continue;
           s2v[sampleId] = samplesData[sampleName];
         }
         if (Object.keys(s2v).length) {
@@ -365,8 +345,7 @@ async function validateNative(q, ds) {
     } else {
       const genesData = geneData.genes || { [geneNames[0]]: geneData };
       for (const tw of param.terms) {
-        if (!tw.term.gene)
-          continue;
+        if (!tw.term.gene) continue;
         const geneResult = genesData[tw.term.gene];
         if (!geneResult) {
           console.warn(`No data found for gene ${tw.term.gene} in the response`);
@@ -376,10 +355,8 @@ async function validateNative(q, ds) {
         const s2v = {};
         for (const [sampleName, value] of Object.entries(samplesData)) {
           const sampleId = ds.cohort.termdb.q.sampleName2id(sampleName);
-          if (!sampleId)
-            continue;
-          if (limitSamples && !limitSamples.has(sampleId))
-            continue;
+          if (!sampleId) continue;
+          if (limitSamples && !limitSamples.has(sampleId)) continue;
           s2v[sampleId] = value;
         }
         if (Object.keys(s2v).length) {

package/routes/termdb.cohort.summary.js

@@ -16,17 +16,14 @@ 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);
       const count = ds.cohort.termdb.q?.getCohortSampleCount?.(q.cohort) || 1;
       res.send({ count });
     } 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);
     }
   };
 }

package/routes/termdb.cohorts.js

@@ -16,23 +16,19 @@ 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);
       const result = getCohortsData(ds);
       res.send(result);
     } 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);
     }
   };
 }
 function getCohortsData(ds) {
-  if (!ds.cohort.db)
-    return { cohorts: [], features: [], cfeatures: [] };
+  if (!ds.cohort.db) return { cohorts: [], features: [], cfeatures: [] };
   const features = ds.cohort.db.connection.prepare("select * from features").all();
   const cohorts = ds.cohort.db.connection.prepare(
     `select * from cohorts where cohort in (select distinct(cohort) from cohort_features)