@sjcrh/proteinpaint-server 2.142.0 → 2.143.0

package/routes/termdb.singlecellSamples.js

@@ -28,17 +28,13 @@ 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.samples.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
@@ -49,16 +45,13 @@ function init({ genomes }) {
 }
 async function validate_query_singleCell(ds, genome) {
   const q = ds.queries.singleCell;
-  if (!q)
-    return;
-  if (typeof q.samples != "object")
-    throw "singleCell.samples{} not object";
+  if (!q) return;
+  if (typeof q.samples != "object") throw "singleCell.samples{} not object";
   if (typeof q.samples.get == "function") {
   } else {
     await validateSamplesNative(q.samples, q.data, ds);
   }
-  if (typeof q.data != "object")
-    throw "singleCell.data{} not object";
+  if (typeof q.data != "object") throw "singleCell.data{} not object";
   if (q.data.src == "gdcapi") {
     gdc_validate_query_singleCell_data(ds, genome);
   } else if (q.data.src == "native") {
@@ -67,8 +60,7 @@ async function validate_query_singleCell(ds, genome) {
     throw "unknown singleCell.data.src";
   }
   if (q.geneExpression) {
-    if (typeof q.geneExpression != "object")
-      throw "singleCell.geneExpression not object";
+    if (typeof q.geneExpression != "object") throw "singleCell.geneExpression not object";
     if (q.geneExpression.src == "native") {
       validateGeneExpressionNative(q.geneExpression);
     } else if (q.geneExpression.src == "gdcapi") {
@@ -78,23 +70,18 @@ async function validate_query_singleCell(ds, genome) {
     }
   }
   if (q.DEgenes) {
-    if (typeof q.DEgenes != "object")
-      throw "singleCell.DEgenes not object";
+    if (typeof q.DEgenes != "object") throw "singleCell.DEgenes not object";
     validate_query_singleCell_DEgenes(ds);
   }
   if (q.images) {
-    if (typeof q.images != "object")
-      throw "singleCell.images not object";
+    if (typeof q.images != "object") throw "singleCell.images not object";
     validateImages(q.images);
   }
 }
 function validateImages(images) {
-  if (!images.folder)
-    throw "images.folder missing";
-  if (!images.label)
-    images.label = "Images";
-  if (!images.fileName)
-    throw "images.fileName missing";
+  if (!images.folder) throw "images.folder missing";
+  if (!images.label) images.label = "Images";
+  if (!images.fileName) throw "images.fileName missing";
 }
 async function validateSamplesNative(S, D, ds) {
   const samples = /* @__PURE__ */ new Map();
@@ -106,23 +93,19 @@ async function validateSamplesNative(S, D, ds) {
           throw `singlecell.sample file name ${fn} does not end with required suffix ${plot.fileSuffix}`;
         sampleName = fn.split(plot.fileSuffix)[0];
       }
-      if (!sampleName)
-        throw `singlecell.sample: cannot derive sample name from file name ${fn}`;
+      if (!sampleName) throw `singlecell.sample: cannot derive sample name from file name ${fn}`;
       const sid = ds.cohort.termdb.q.sampleName2id(sampleName);
-      if (sid == void 0)
-        throw `singlecell.sample: unknown sample name ${sampleName}`;
+      if (sid == void 0) throw `singlecell.sample: unknown sample name ${sampleName}`;
       samples.set(sid, { sample: sampleName });
     }
   }
   if (S.sampleColumns) {
     for (const { termid } of S.sampleColumns) {
       const term = ds.cohort.termdb.q.termjsonByOneid(termid);
-      if (!term)
-        throw "unknown termid from singlecell.samples.sampleColumns[]";
+      if (!term) throw "unknown termid from singlecell.samples.sampleColumns[]";
       const s2v = ds.cohort.termdb.q.getAllValues4term(termid);
       for (const [sid, v] of s2v.entries()) {
-        if (!samples.has(sid))
-          continue;
+        if (!samples.has(sid)) continue;
         samples.get(sid)[termid] = term.values?.[v]?.label || v;
       }
     }
@@ -134,11 +117,9 @@ async function validateSamplesNative(S, D, ds) {
 function validateDataNative(D, ds) {
   const nameSet = /* @__PURE__ */ new Set();
   for (const plot of D.plots) {
-    if (nameSet.has(plot.name))
-      throw "duplicate plot.name";
+    if (nameSet.has(plot.name)) throw "duplicate plot.name";
     nameSet.add(plot.name);
-    if (!plot.folder)
-      throw "plot.folder missing";
+    if (!plot.folder) throw "plot.folder missing";
   }
   const file2Lines = {};
   D.get = async (q) => {
@@ -148,8 +129,7 @@ function validateDataNative(D, ds) {
       geneExpMap = await ds.queries.singleCell.geneExpression.get({ sample: q.sample, gene: q.gene });
     }
     for (const plot of D.plots) {
-      if (!q.plots.includes(plot.name))
-        continue;
+      if (!q.plots.includes(plot.name)) continue;
       const tsvfile = path.join(serverconfig.tpmasterdir, plot.folder, (q.sample.eID || q.sample.sID) + plot.fileSuffix);
       if (!file2Lines[tsvfile]) {
         await file_is_readable(tsvfile);
@@ -172,10 +152,8 @@ function validateDataNative(D, ds) {
       for (const l of file2Lines[tsvfile]) {
         const cellId = l[0], x = Number(l[plot.coordsColumns.x]), y = Number(l[plot.coordsColumns.y]);
         const category = l[colorColumn?.index] || "";
-        if (!cellId)
-          throw "cell id missing";
-        if (!Number.isFinite(x) || !Number.isFinite(y))
-          throw "x/y not number";
+        if (!cellId) throw "cell id missing";
+        if (!Number.isFinite(x) || !Number.isFinite(y)) throw "x/y not number";
         const cell = { cellId, x, y, category };
         if (geneExpMap) {
           if (geneExpMap[cellId] !== void 0) {
@@ -184,8 +162,7 @@ function validateDataNative(D, ds) {
           } else {
             noExpCells.push(cell);
           }
-        } else
-          noExpCells.push(cell);
+        } else noExpCells.push(cell);
       }
       plots.push({
         name: plot.name,
@@ -223,8 +200,7 @@ function validateGeneExpressionNative(G) {
     } catch (e) {
       if (typeof e == "string") {
         const geneNotFound = `Gene '${q.gene}' not found in the HDF5 file`;
-        if (e.includes(geneNotFound))
-          throw "No expression data for this gene";
+        if (e.includes(geneNotFound)) throw "No expression data for this gene";
       }
       console.log(e);
       throw "error reading h5 file: " + e;
@@ -241,12 +217,10 @@ function gdc_validateGeneExpression(G, ds, genome) {
         throw "GDC scRNA file mapping is not cached";
       }
       const hdf5id = ds.__gdc.scrnaAnalysis2hdf5.get(fileid);
-      if (!hdf5id)
-        throw "cannot map eID to hdf5 id";
+      if (!hdf5id) throw "cannot map eID to hdf5 id";
       const aliasLst = genome.genedb.getAliasByName.all(q.gene);
       const gencodeId = aliasLst.find((a) => a?.alias.toUpperCase().startsWith("ENSG"))?.alias;
-      if (!gencodeId)
-        throw "cannot map gene symbol to GENCODE";
+      if (!gencodeId) throw "cannot map gene symbol to GENCODE";
       const body = {
         gene_ids: [gencodeId],
         file_id: hdf5id
@@ -254,8 +228,7 @@ function gdc_validateGeneExpression(G, ds, genome) {
       const { host } = ds.getHostHeaders(q);
       const t = Date.now();
       const response = await ky.post(joinUrl(host.rest, "scrna_seq/gene_expression"), { 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 out = await response.json();
       mayLog("gdc scrna gene exp", q.gene, Date.now() - t);
       const result = out.data[0].cells;
@@ -265,8 +238,7 @@ function gdc_validateGeneExpression(G, ds, genome) {
       }
       return data;
     } catch (e) {
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
       return { error: "GDC scRNAseq gene expression request failed with error: " + (e.message || e) };
     }
   };

package/routes/termdb.termchildren.js

@@ -18,25 +18,20 @@ 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, tdb] = await 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";
       const result = await trigger_children(req, q, tdb);
       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_children(req, q, tdb) {
-  if (!q.tid)
-    throw "no parent term id";
+  if (!q.tid) throw "no parent term id";
   const cohortValues = q.cohortValues ? q.cohortValues : "";
   const treeFilter = q.treeFilter ? q.treeFilter : "";
   const terms = await tdb.q.getTermChildren(req, q.tid, cohortValues, treeFilter);

package/routes/termdb.termsbyids.js

@@ -18,20 +18,16 @@ 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 results = await trigger_gettermsbyid(q, tdb);
       res.send(results);
     } 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.topMutatedGenes.js

@@ -19,31 +19,24 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const g = genomes[q.genome];
-      if (!g)
-        throw "genome missing";
+      if (!g) throw "genome missing";
       const ds = g.datasets?.[q.dslabel];
-      if (!ds)
-        throw "ds missing";
-      if (!ds.queries?.topMutatedGenes)
-        throw "not supported by ds";
+      if (!ds) throw "ds missing";
+      if (!ds.queries?.topMutatedGenes) throw "not supported by ds";
       const genes = await ds.queries.topMutatedGenes.get(q);
       const payload = { genes };
       res.send(payload);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
-      else
-        console.trace(e);
+      if (e.stack) console.log(e.stack);
+      else console.trace(e);
     }
   };
 }
 function validate_query_getTopMutatedGenes(ds) {
   const q = ds.queries?.topMutatedGenes;
-  if (!q)
-    return;
-  if (typeof q.get == "function")
-    return;
+  if (!q) return;
+  if (typeof q.get == "function") return;
   if (!q.arguments) {
     q.arguments = [];
     q.arguments.push({ id: "maxGenes", label: "Gene Count", type: "number", value: 50 });
@@ -94,28 +87,20 @@ function validate_query_getTopMutatedGenes(ds) {
     let sampleStatement = "";
     if (param.filter) {
       const lst = await get_samples(param, ds);
-      if (lst.length == 0)
-        throw "empty sample filter";
+      if (lst.length == 0) throw "empty sample filter";
       sampleStatement = `WHERE sample IN (${lst.map((i) => i.id).join(",")})`;
     }
     const fields = [];
-    if (param.snv_mfndi)
-      fields.push("snv_mfndi");
-    if (param.snv_splice)
-      fields.push("snv_splice");
-    if (param.snv_utr)
-      fields.push("snv_utr");
-    if (param.snv_s)
-      fields.push("snv_s");
-    if (param.sv)
-      fields.push("sv");
-    if (param.fusion)
-      fields.push("fusion");
+    if (param.snv_mfndi) fields.push("snv_mfndi");
+    if (param.snv_splice) fields.push("snv_splice");
+    if (param.snv_utr) fields.push("snv_utr");
+    if (param.snv_s) fields.push("snv_s");
+    if (param.sv) fields.push("sv");
+    if (param.fusion) fields.push("fusion");
     if (param.cnv == 1 && param.cnv_ms?.type && param.cnv_logratio?.type) {
       fields.push(param.cnv_ms.type + param.cnv_logratio.type);
     }
-    if (!fields.length)
-      throw "no fields";
+    if (!fields.length) throw "no fields";
     const query = `WITH
 		filtered AS (
 			SELECT genesymbol, ${fields.join("+")} AS total FROM genesamplemutationcount

package/routes/termdb.topTermsByType.js

@@ -21,13 +21,10 @@ function init({ genomes }) {
       const q = req.query;
       const type = q.type;
       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.queries[type])
-        throw "not supported on dataset";
+      if (!ds) throw "invalid dslabel";
+      if (!ds.queries[type]) throw "not supported on dataset";
       const terms = await ds.queries[type].getTopTerms(q);
       res.send({ terms });
     } catch (e) {
@@ -40,14 +37,10 @@ function validate_query_getTopTermsByType(ds, genome) {
   for (const type of types) {
     if (ds.queries[type]) {
       const q = ds.queries[type];
-      if (!q)
-        return;
-      if (q.src == "gdcapi")
-        gdcValidateQuery(ds, genome, type);
-      else if (q.src == "native")
-        nativeValidateQuery(ds, type);
-      else
-        throw "unknown topVariablyExpressedGenes.src";
+      if (!q) return;
+      if (q.src == "gdcapi") gdcValidateQuery(ds, genome, type);
+      else if (q.src == "native") nativeValidateQuery(ds, type);
+      else throw "unknown topVariablyExpressedGenes.src";
     }
   }
 }
@@ -60,16 +53,14 @@ function nativeValidateQuery(ds, type) {
       for (const i of sidlst) {
         if (typeQuery.samples.includes(i.id)) {
           const n = ds.cohort.termdb.q.id2sampleName(i.id);
-          if (!n)
-            throw "sample id cannot convert to string name";
+          if (!n) throw "sample id cannot convert to string name";
           samples.push(n);
         }
       }
     } else {
       for (const i of typeQuery.samples) {
         const n = ds.cohort.termdb.q.id2sampleName(i.id);
-        if (!n)
-          throw "sample id cannot convert to string name";
+        if (!n) throw "sample id cannot convert to string name";
         samples.push(n);
       }
     }

package/routes/termdb.topVariablyExpressedGenes.js

@@ -26,13 +26,10 @@ 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 = genome.datasets?.[q.dslabel];
-      if (!ds)
-        throw "invalid dslabel";
-      if (!ds.queries?.topVariablyExpressedGenes)
-        throw "not supported on dataset";
+      if (!ds) throw "invalid dslabel";
+      if (!ds.queries?.topVariablyExpressedGenes) throw "not supported on dataset";
       const t = Date.now();
       result = {
         genes: await ds.queries.topVariablyExpressedGenes.getGenes(q)
@@ -46,8 +43,7 @@ function init({ genomes }) {
 }
 function validate_query_TopVariablyExpressedGenes(ds, genome) {
   const q = ds.queries.topVariablyExpressedGenes;
-  if (!q)
-    return;
+  if (!q) return;
   if (q.src == "gdcapi") {
     gdcValidateQuery(ds, genome);
   } else if (q.src == "native") {
@@ -58,10 +54,8 @@ function validate_query_TopVariablyExpressedGenes(ds, genome) {
 }
 function nativeValidateQuery(ds) {
   const gE = ds.queries.geneExpression;
-  if (!gE)
-    throw "topVariablyExpressedGenes query given but geneExpression missing";
-  if (gE.src != "native")
-    throw "topVariablyExpressedGenes is native but geneExpression.src is not native";
+  if (!gE) throw "topVariablyExpressedGenes query given but geneExpression missing";
+  if (gE.src != "native") throw "topVariablyExpressedGenes is native but geneExpression.src is not native";
   addTopVEarg(ds.queries.topVariablyExpressedGenes);
   ds.queries.topVariablyExpressedGenes.getGenes = async (q) => {
     const samples = [];
@@ -70,16 +64,14 @@ function nativeValidateQuery(ds) {
       for (const i of sidlst) {
         if (gE.samples.includes(i.id)) {
           const n = ds.cohort.termdb.q.id2sampleName(i.id);
-          if (!n)
-            throw "sample id cannot convert to string name";
+          if (!n) throw "sample id cannot convert to string name";
           samples.push(n);
         }
       }
     } else {
       for (const i of gE.samples) {
         const n = ds.cohort.termdb.q.id2sampleName(i.id);
-        if (!n)
-          throw "sample id cannot convert to string name";
+        if (!n) throw "sample id cannot convert to string name";
         samples.push(n);
       }
     }
@@ -135,11 +127,9 @@ function addTopVEarg(q) {
   ];
   if (q.arguments) {
     for (const a of q.arguments) {
-      if (!a.id)
-        throw "missing id of topVE.arguments[]";
+      if (!a.id) throw "missing id of topVE.arguments[]";
       const item = arglst.find((i) => i.id == a.id);
-      if (!item)
-        throw "unknown id of topVE.arguments[]";
+      if (!item) throw "unknown id of topVE.arguments[]";
       Object.assign(item, a);
     }
   }
@@ -209,8 +199,7 @@ function gdcValidateQuery(ds, genome) {
       for (const i of re.gene_selection) {
         if (i.gene_id && typeof i.gene_id == "string") {
           const t = genome.genedb.getNameByAlias.get(i.gene_id);
-          if (t)
-            genes.push(t.name);
+          if (t) genes.push(t.name);
         } else if (i.symbol && typeof i.symbol == "string") {
           genes.push(i.symbol);
         } else {
@@ -234,11 +223,9 @@ function gdcValidateQuery(ds, genome) {
       if (q.geneSet.type == "all") {
         arg.gene_type = "protein_coding";
       } else if (q.geneSet.type == "custom" || q.geneSet.type == "msigdb") {
-        if (!Array.isArray(q.geneSet.geneList))
-          throw "q.geneSet.geneList is not array";
+        if (!Array.isArray(q.geneSet.geneList)) throw "q.geneSet.geneList is not array";
         arg.gene_ids = map2ensg(q.geneSet.geneList, genome);
-        if (arg.gene_ids.length == 0)
-          throw "no valid genes from custom gene set";
+        if (arg.gene_ids.length == 0) throw "no valid genes from custom gene set";
       } else {
         throw "unknown q.geneSet.type";
       }