@sjcrh/proteinpaint-server 2.142.0 → 2.143.0

package/routes/correlationVolcano.js

@@ -22,23 +22,19 @@ 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 result = await compute(q, ds);
       res.send(result);
     } 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);
     }
   };
 }
 async function compute(q, ds) {
-  if (!q.featureTw.$id)
-    throw "featureTw.$id missing";
+  if (!q.featureTw.$id) throw "featureTw.$id missing";
   if (!ds.cohort.correlationVolcano.feature.termTypes.includes(q.featureTw?.term.type))
     throw "unsupported featureTw.term.type";
   const data = await getData(
@@ -50,22 +46,18 @@ async function compute(q, ds) {
     },
     ds
   );
-  if (data.error)
-    throw data.error;
+  if (data.error) throw data.error;
   const vtid2array = /* @__PURE__ */ new Map();
   for (const tw of q.variableTwLst) {
     vtid2array.set(tw.$id, { id: tw.$id, v1: [], v2: [] });
   }
   for (const sid in data.samples) {
     const featureValue = data.samples[sid][q.featureTw.$id]?.value;
-    if (!Number.isFinite(featureValue))
-      continue;
+    if (!Number.isFinite(featureValue)) continue;
     for (const tw of q.variableTwLst) {
-      if (!tw.$id)
-        throw "variableTwLst[].$id missing";
+      if (!tw.$id) throw "variableTwLst[].$id missing";
       const variableValue = data.samples[sid][tw.$id]?.value;
-      if (!Number.isFinite(variableValue))
-        continue;
+      if (!Number.isFinite(variableValue)) continue;
       vtid2array.get(tw.$id).v1.push(featureValue);
       vtid2array.get(tw.$id).v2.push(variableValue);
     }
@@ -79,8 +71,7 @@ async function compute(q, ds) {
     acceptedVariables.push(v);
   }
   const result = { skippedVariables, variableItems: [] };
-  if (!acceptedVariables.length)
-    return result;
+  if (!acceptedVariables.length) return result;
   const input = {
     method: q.correlationMethod || "pearson",
     terms: acceptedVariables
@@ -105,34 +96,25 @@ async function compute(q, ds) {
 }
 function validate_correlationVolcano(ds) {
   const cv = ds.cohort.correlationVolcano;
-  if (!cv)
-    return;
-  if (typeof cv.feature != "object")
-    throw "cv.feature not obj";
-  if (!Array.isArray(cv.feature.termTypes))
-    throw "cv.feature.termTypes[] not array";
+  if (!cv) return;
+  if (typeof cv.feature != "object") throw "cv.feature not obj";
+  if (!Array.isArray(cv.feature.termTypes)) throw "cv.feature.termTypes[] not array";
   for (const t of cv.feature.termTypes) {
     if (t == "geneExpression") {
-      if (!ds.queries?.geneExpression)
-        throw "geneExpression cv.feature is not supported";
+      if (!ds.queries?.geneExpression) throw "geneExpression cv.feature is not supported";
     } else if (t == "ssGSEA") {
-      if (!ds.queries?.ssGSEA)
-        throw "ssGSEA cv.feature is not supported";
+      if (!ds.queries?.ssGSEA) throw "ssGSEA cv.feature is not supported";
     } else {
       throw "unknown cv.feature.termType";
     }
   }
-  if (typeof cv.variables != "object")
-    throw "cv.variables not obj";
+  if (typeof cv.variables != "object") throw "cv.variables not obj";
   if (cv.variables.type == "dictionaryTerm") {
-    if (!Array.isArray(cv.variables.termIds))
-      throw "cv.variables.termIds not array when type=dictionaryTerm";
+    if (!Array.isArray(cv.variables.termIds)) throw "cv.variables.termIds not array when type=dictionaryTerm";
     for (const id of cv.variables.termIds) {
       const t = ds.cohort.termdb.q.termjsonByOneid(id);
-      if (!t)
-        throw "cv.variables.termIds: unknown id: " + id;
-      if (t.type != "integer" && t.type != "float")
-        throw "cv.variables.termIds: not integer/float: " + id;
+      if (!t) throw "cv.variables.termIds: unknown id: " + id;
+      if (t.type != "integer" && t.type != "float") throw "cv.variables.termIds: not integer/float: " + id;
     }
   } else {
     throw "unknown cv.variables.type";

package/routes/dataset.js

@@ -20,10 +20,8 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const genome = genomes[q.genome];
-      if (!genome)
-        throw "unknown genome";
-      if (!genome.datasets)
-        throw "genomeobj.datasets{} missing";
+      if (!genome) throw "unknown genome";
+      if (!genome.datasets) throw "genomeobj.datasets{} missing";
       let ds;
       for (const k in genome.datasets) {
         if (k.toLowerCase() == q.dsname.toLowerCase()) {
@@ -31,8 +29,7 @@ function init({ genomes }) {
           break;
         }
       }
-      if (!ds)
-        throw "invalid dsname";
+      if (!ds) throw "invalid dsname";
       const copy = ds.isMds3 ? mds3_init.client_copy(ds) : ds.isMds ? mds_clientcopy(ds) : copy_legacyDataset(ds);
       return res.send({ ds: copy });
     } catch (e) {
@@ -72,8 +69,7 @@ function mds_clientcopy(ds) {
     const toclient = {};
     for (const k in ds.cohort.sampleAttribute.attributes) {
       const a = ds.cohort.sampleAttribute.attributes[k];
-      if (!a.clientnoshow)
-        toclient[k] = a;
+      if (!a.clientnoshow) toclient[k] = a;
     }
     ds2.sampleAttribute = { attributes: toclient };
   }
@@ -168,8 +164,7 @@ function mds_clientcopy(ds) {
             const lst = [];
             if (e.boxplotbysamplegroup.attributes)
               lst.push(e.boxplotbysamplegroup.attributes.map((i) => i.label).join(", "));
-            for (const i of e.boxplotbysamplegroup.additionals)
-              lst.push(i.label);
+            for (const i of e.boxplotbysamplegroup.additionals) lst.push(i.label);
             clientquery.checkexpressionrank.boxplotgroupers = lst;
           }
         }
@@ -222,8 +217,7 @@ function copy_legacyDataset(ds) {
           rep.lst = [];
           for (const e of at.lst) {
             const rep2 = {};
-            for (const k2 in e)
-              rep2[k2] = e[k2];
+            for (const k2 in e) rep2[k2] = e[k2];
             rep.lst.push(rep2);
           }
         } else {

package/routes/deleteWSIAnnotation.js

@@ -0,0 +1,75 @@
+import { deleteWSIAnnotationPayload } from "#types/checkers";
+import { getDbConnection } from "#src/aiHistoDBConnection.ts";
+import { runSQL } from "#src/runSQLHelpers.ts";
+const api = {
+  endpoint: `deleteWSIAnnotation`,
+  methods: {
+    delete: {
+      ...deleteWSIAnnotationPayload,
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const query = req.query;
+      if (!query.genome) throw new Error(".genome is required for deleteWSIAnnotation request.");
+      if (!query.dslabel) throw new Error(".dslabel is required for deleteWSIAnnotation request.");
+      if (!query.annotation) throw new Error(".annotation:{} is required for deleteWSIAnnotation request.");
+      if (!query.projectId) throw new Error(".projectId is required for deleteWSIAnnotation request.");
+      if (!query.wsimage) throw new Error(".wsimage is required for deleteWSIAnnotation request.");
+      const g = genomes[query.genome];
+      if (!g) throw new Error("invalid genome name");
+      const ds = g.datasets[query.dslabel];
+      if (!ds) throw new Error("invalid dataset name");
+      if (typeof ds.queries?.WSImages?.deleteAnnotation === "function") {
+        const result = await ds.queries.WSImages.deleteAnnotation(query);
+        if (result?.status === "error") {
+          return res.status(500).send(result);
+        }
+      }
+      res.status(200).send({ status: `Annotation = ${query.annotation.zoomCoordinates} deleted.` });
+    } catch (e) {
+      console.warn(e);
+      res.status(500).send({
+        status: "error",
+        error: e?.message || String(e)
+      });
+    }
+  };
+}
+async function validate_query_deleteWSIAnnotation(ds) {
+  if (!ds.queries?.WSImages?.db) return;
+  const connection = getDbConnection(ds);
+  if (!connection) {
+    return;
+  }
+  validateQuery(ds, connection);
+}
+function validateQuery(ds, connection) {
+  ds.queries.WSImages.deleteAnnotation = async (query) => {
+    const sql = `
+        DELETE FROM project_annotations
+        WHERE project_id = ?
+          AND coordinates = ?
+          AND image_id = (
+            SELECT id FROM project_images
+            WHERE project_id = ?
+              AND image_path = ?
+        )
+    `;
+    const params = [
+      query.projectId,
+      JSON.stringify(query.annotation.zoomCoordinates),
+      query.projectId,
+      query.wsimage
+      // this is the image_path
+    ];
+    return runSQL(connection, sql, params, "delete annotation");
+  };
+}
+export {
+  api,
+  validate_query_deleteWSIAnnotation
+};

package/routes/dsdata.js

@@ -24,13 +24,10 @@ function init({ genomes }) {
   return async function handle_dsdata(req, res) {
     try {
       const q = req.query;
-      if (!genomes[q.genome])
-        throw "invalid genome";
-      if (!q.dsname)
-        throw ".dsname missing";
+      if (!genomes[q.genome]) throw "invalid genome";
+      if (!q.dsname) throw ".dsname missing";
       const ds = genomes[q.genome].datasets[q.dsname];
-      if (!ds)
-        throw "invalid dsname";
+      if (!ds) throw "invalid dsname";
       const data = [];
       for (const query of ds.queries) {
         if (q.expressiononly && !query.isgeneexpression) {
@@ -56,16 +53,14 @@ function init({ genomes }) {
       }
       res.send({ data });
     } catch (e) {
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
       res.send({ error: e.message || e });
     }
   };
 }
 function handle_dsdata_makequery(ds, query, req, genomes) {
   if (req.query.isoform) {
-    if (genomes[req.query.genome].genomicNameRegexp.test(req.query.isoform))
-      return;
+    if (genomes[req.query.genome].genomicNameRegexp.test(req.query.isoform)) return;
   }
   const [sqlstr, values] = query.makequery(req.query);
   if (!sqlstr) {
@@ -84,8 +79,7 @@ function handle_dsdata_makequery(ds, query, req, genomes) {
     result.isgeneexpression = true;
     result.config = query.config;
     for (const q2 of ds.queries) {
-      if (!q2.dsblocktracklst)
-        continue;
+      if (!q2.dsblocktracklst) continue;
       for (const tk of q2.dsblocktracklst) {
         if (tk.type == common.tkt.junction) {
           result.config.dsjunctiontk = tk;
@@ -109,8 +103,7 @@ function handle_dsdata_vcf(query, req) {
     ps.stderr.on("data", (i) => out2.push(i));
     ps.on("close", () => {
       const e = out2.join("").trim();
-      if (e != "")
-        reject("error querying vcf file");
+      if (e != "") reject("error querying vcf file");
       const tmp = out.join("").trim();
       resolve({
         lines: tmp == "" ? [] : tmp.split("\n"),

package/routes/dzimages.js

@@ -20,16 +20,12 @@ function init({ genomes }) {
     try {
       const q = req.query;
       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";
       const sampleId = q.sampleId;
-      if (!sampleId)
-        throw "invalid sampleId";
-      if (illegalpath(req.query.file))
-        throw `illegalpath filepath`;
+      if (!sampleId) throw "invalid sampleId";
+      if (illegalpath(req.query.file)) throw `illegalpath filepath`;
       const filename = path.basename(q.file);
       const allowedExtensions = [".dzi", ".jpeg", ".png"];
       const extension = path.extname(filename);

package/routes/gdc.grin2.list.js

@@ -24,11 +24,9 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const g = genomes.hg38;
-      if (!g)
-        throw "hg38 missing";
+      if (!g) throw "hg38 missing";
       const ds = g.datasets?.GDC;
-      if (!ds)
-        throw "hg38 GDC missing";
+      if (!ds) throw "hg38 GDC missing";
       console.log("GRIN2 List Route Received:", JSON.stringify(req.query, null, 2));
       const result = {};
       if (req.query.mafOptions) {
@@ -49,15 +47,13 @@ function init({ genomes }) {
       }
       res.send(result);
     } 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 listMafFiles(q, result, ds) {
-  if (!q.mafOptions)
-    return;
+  if (!q.mafOptions) return;
   if (!result.mafFiles) {
     throw new Error("result.mafFiles must be initialized before calling listMafFiles");
   }
@@ -88,22 +84,17 @@ async function listMafFiles(q, result, ds) {
       "cases.samples.tumor_descriptor"
     ].join(",")
   };
-  if (case_filters.content.length)
-    body.case_filters = case_filters;
+  if (case_filters.content.length) body.case_filters = case_filters;
   const response = await ky.post(joinUrl(host.rest, "files"), { timeout: false, headers, json: body });
-  if (!response.ok)
-    throw `HTTP Error: ${response.status} ${response.statusText}`;
+  if (!response.ok) throw `HTTP Error: ${response.status} ${response.statusText}`;
   const re = await response.json();
-  if (!Number.isInteger(re.data?.pagination?.total))
-    throw "re.data.pagination.total is not int";
-  if (!Array.isArray(re.data?.hits))
-    throw "re.data.hits[] not array";
+  if (!Number.isInteger(re.data?.pagination?.total)) throw "re.data.pagination.total is not int";
+  if (!Array.isArray(re.data?.hits)) throw "re.data.hits[] not array";
   const files = [];
   const filteredFiles = [];
   for (const h of re.data.hits) {
     const c = h.cases?.[0];
-    if (!c)
-      throw "h.cases[0] missing";
+    if (!c) throw "h.cases[0] missing";
     if (h.file_size >= maxFileSizeAllowed) {
       filteredFiles.push({
         fileId: h.id,
@@ -133,8 +124,7 @@ If you want to include it, please increase the maxFileSizeAllowed in the code.`
         }
         file.sample_types.push(tumor_descriptor + " " + tissue_type);
       }
-      if (normalTypeName)
-        file.sample_types.push(normalTypeName);
+      if (normalTypeName) file.sample_types.push(normalTypeName);
     }
     file.sample_types = [...new Set(file.sample_types)];
     files.push(file);
@@ -215,8 +205,7 @@ async function listCnvFiles(q, result, ds) {
       }
     }
   };
-  if (case_filters.content.length)
-    body.case_filters = case_filters;
+  if (case_filters.content.length) body.case_filters = case_filters;
   const { host, headers } = ds.getHostHeaders(q);
   try {
     const re = await ky.post(joinUrl(host.rest, "files"), { timeout: false, headers, json: body }).json();
@@ -232,11 +221,9 @@ async function listCnvFiles(q, result, ds) {
       if (h.data_format != "TXT") {
         continue;
       }
-      if (!h.analysis?.workflow_type)
-        throw "h.analysis.workflow_type missing";
+      if (!h.analysis?.workflow_type) throw "h.analysis.workflow_type missing";
       const c = h.cases?.[0];
-      if (!c)
-        throw "h.cases[0] missing";
+      if (!c) throw "h.cases[0] missing";
       if (h.data_type == "Allele-specific Copy Number Segment") {
       } else if (h.data_type == "Masked Copy Number Segment" || h.data_type == "Copy Number Segment" && h.analysis.workflow_type != "DNACopy") {
         const file = {

package/routes/gdc.grin2.run.js

@@ -34,11 +34,9 @@ function init({ genomes }) {
 }
 async function runGrin2(genomes, req, res) {
   const g = genomes.hg38;
-  if (!g)
-    throw "hg38 missing";
+  if (!g) throw "hg38 missing";
   const ds = g.datasets.GDC;
-  if (!ds)
-    throw "hg38 GDC missing";
+  if (!ds) throw "hg38 GDC missing";
   const parsedRequest = req.query;
   const rustInput = {
     caseFiles: parsedRequest.caseFiles,
@@ -54,8 +52,7 @@ async function runGrin2(genomes, req, res) {
   };
   for (const c in g.majorchr) {
     if (ds.queries.singleSampleMutation?.discoPlot?.skipChrM) {
-      if (c.toLowerCase() == "chrm")
-        continue;
+      if (c.toLowerCase() == "chrm") continue;
     }
     rustInput.chromosomes.push(c);
     pyInput.chromosomelist[c] = g.majorchr[c];

package/routes/gdc.maf.js

@@ -22,11 +22,9 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const g = genomes.hg38;
-      if (!g)
-        throw "hg38 missing";
+      if (!g) throw "hg38 missing";
       const ds = g.datasets.GDC;
-      if (!ds)
-        throw "hg38 GDC missing";
+      if (!ds) throw "hg38 GDC missing";
       const payload = await listMafFiles(req.query, ds);
       res.send(payload);
     } catch (e) {
@@ -66,21 +64,16 @@ async function listMafFiles(q, ds) {
       "cases.samples.tumor_descriptor"
     ].join(",")
   };
-  if (case_filters.content.length)
-    body.case_filters = case_filters;
+  if (case_filters.content.length) body.case_filters = case_filters;
   const response = await ky.post(joinUrl(host.rest, "files"), { timeout: false, json: body });
-  if (!response.ok)
-    throw `HTTP Error: ${response.status} ${response.statusText}`;
+  if (!response.ok) throw `HTTP Error: ${response.status} ${response.statusText}`;
   const re = await response.json();
-  if (!Number.isInteger(re.data?.pagination?.total))
-    throw "re.data.pagination.total is not int";
-  if (!Array.isArray(re.data?.hits))
-    throw "re.data.hits[] not array";
+  if (!Number.isInteger(re.data?.pagination?.total)) throw "re.data.pagination.total is not int";
+  if (!Array.isArray(re.data?.hits)) throw "re.data.hits[] not array";
   const files = [];
   for (const h of re.data.hits) {
     const c = h.cases?.[0];
-    if (!c)
-      throw "h.cases[0] missing";
+    if (!c) throw "h.cases[0] missing";
     const file = {
       id: h.id,
       project_id: c.project.project_id,
@@ -98,8 +91,7 @@ async function listMafFiles(q, ds) {
         }
         file.sample_types.push(tumor_descriptor + " " + tissue_type);
       }
-      if (normalTypeName)
-        file.sample_types.push(normalTypeName);
+      if (normalTypeName) file.sample_types.push(normalTypeName);
     }
     file.sample_types = [...new Set(file.sample_types)];
     files.push(file);

package/routes/gdc.mafBuild.js

@@ -22,15 +22,12 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const g = genomes.hg38;
-      if (!g)
-        throw "hg38 missing";
+      if (!g) throw "hg38 missing";
       const ds = g.datasets.GDC;
-      if (!ds)
-        throw "hg38 GDC missing";
+      if (!ds) throw "hg38 GDC missing";
       await buildMaf(q, res, 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 });
     }
   };
@@ -57,8 +54,7 @@ async function buildMaf(q, res, ds) {
     if (streams) {
       const { rustStream, endStream } = streams;
       res.on("close", () => {
-        if (res.writableEnded)
-          return;
+        if (res.writableEnded) return;
         try {
           console.log("\n-- forced res.end() ---\n");
           res.end();
@@ -74,8 +70,7 @@ async function buildMaf(q, res, ds) {
       rustStream.pipe(res, { end: false }).on("error", (e) => {
         console.log("rustStream.pipe().on(error)", e);
       }).on("end", () => {
-        if (res.writableEnded)
-          return;
+        if (res.writableEnded) return;
         console.log("rustStream.on(end), trigger res.end()");
         res.end();
       });
@@ -86,8 +81,7 @@ async function buildMaf(q, res, ds) {
     console.log("error calling stream_rust(gdcmaf)", e);
   }
   function emitJson(data, end = true) {
-    if (res.writableEnded)
-      return;
+    if (res.writableEnded) return;
     if (data) {
       res.write(`\r
 --${boundary}`);
@@ -100,13 +94,11 @@ async function buildMaf(q, res, ds) {
 --${boundary}--\r
 `);
     mayLog("rust gdcmaf", Date.now() - t0);
-    if (end)
-      res.end();
+    if (end) res.end();
   }
 }
 async function getFileLstUnderSizeLimit(lst, host) {
-  if (lst.length == 0)
-    throw "fileIdLst[] not array or blank";
+  if (lst.length == 0) throw "fileIdLst[] not array or blank";
   const body = {
     filters: {
       op: "in",
@@ -116,25 +108,19 @@ async function getFileLstUnderSizeLimit(lst, host) {
     fields: "file_size"
   };
   const response = await ky.post(joinUrl(host.rest, "files"), { timeout: false, json: body });
-  if (!response.ok)
-    throw `HTTP Error: ${response.status} ${response.statusText}`;
+  if (!response.ok) throw `HTTP Error: ${response.status} ${response.statusText}`;
   const re = await response.json();
-  if (!Array.isArray(re.data?.hits))
-    throw "re.data.hits[] not array";
+  if (!Array.isArray(re.data?.hits)) throw "re.data.hits[] not array";
   const out = [];
   let cumsize = 0;
   for (const h of re.data.hits) {
-    if (cumsize >= maxTotalSizeCompressed)
-      break;
-    if (!h.id)
-      throw ".id missing";
-    if (!Number.isInteger(h.file_size))
-      throw ".file_size not integer";
+    if (cumsize >= maxTotalSizeCompressed) break;
+    if (!h.id) throw ".id missing";
+    if (!Number.isInteger(h.file_size)) throw ".file_size not integer";
     cumsize += h.file_size;
     out.push(h.id);
   }
-  if (out.length == 0)
-    throw "no file available";
+  if (out.length == 0) throw "no file available";
   return out;
 }
 export {

package/routes/gene2canonicalisoform.js

@@ -20,19 +20,15 @@ const api = {
 function init({ genomes }) {
   return function(req, res) {
     try {
-      if (!req.query.gene)
-        throw ".gene missing";
+      if (!req.query.gene) throw ".gene missing";
       const genome = genomes[req.query.genome];
-      if (!genome)
-        throw "unknown genome";
-      if (!genome.genedb.get_gene2canonicalisoform)
-        throw "gene2canonicalisoform not supported on this genome";
+      if (!genome) throw "unknown genome";
+      if (!genome.genedb.get_gene2canonicalisoform) throw "gene2canonicalisoform not supported on this genome";
       const data = genome.genedb.get_gene2canonicalisoform.get(req.query.gene);
       res.send(data);
     } catch (e) {
       res.send({ error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
     }
   };
 }

package/routes/genelookup.js

@@ -18,14 +18,12 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const g = genomes[q.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const result = getResult(g, q);
       res.send(result);
     } catch (e) {
       res.send({ error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
     }
   };
 }

package/routes/genesetEnrichment.js

@@ -26,13 +26,11 @@ function init({ genomes }) {
       const q = req.query;
       const results = await run_genesetEnrichment_analysis(q, genomes);
       if (!q.geneset_name) {
-        if (typeof results != "object")
-          throw "gsea result is not object";
+        if (typeof results != "object") throw "gsea result is not object";
         res.send(results);
         return;
       }
-      if (typeof results != "string")
-        throw "gsea result is not string";
+      if (typeof results != "string") throw "gsea result is not string";
       res.sendFile(results, (err) => {
         fs.unlink(results, () => {
         });
@@ -42,14 +40,12 @@ function init({ genomes }) {
       });
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
     }
   };
 }
 async function run_genesetEnrichment_analysis(q, genomes) {
-  if (!genomes[q.genome].termdbs)
-    throw "termdb database is not available for " + q.genome;
+  if (!genomes[q.genome].termdbs) throw "termdb database is not available for " + q.genome;
   const genesetenrichment_input = {
     genes: q.genes,
     fold_change: q.fold_change,
@@ -82,11 +78,9 @@ async function run_genesetEnrichment_analysis(q, genomes) {
         mayLog(line);
       }
     }
-    if (data_found)
-      return result;
+    if (data_found) return result;
     const image_file_name = path.join(cachedir_gsea, result.image_file);
-    if (image_found)
-      return image_file_name;
+    if (image_found) return image_file_name;
     throw "data or image not found in gsea output; this should not happen";
   } else if (q.method == "cerno") {
     const time1 = (/* @__PURE__ */ new Date()).valueOf();

package/routes/genesetOverrepresentation.js

@@ -26,8 +26,7 @@ function init({ genomes }) {
   };
 }
 async function run_genesetOverrepresentation_analysis(q, genomes) {
-  if (!genomes[q.genome].termdbs)
-    throw "termdb database is not available for " + q.genome;
+  if (!genomes[q.genome].termdbs) throw "termdb database is not available for " + q.genome;
   const gene_overrepresentation_input_type = {
     sample_genes: q.sample_genes,
     msigdb: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,