@sjcrh/proteinpaint-server 2.67.1 → 2.68.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.67.1",
+  "version": "2.68.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",

package/routes/snp.js

@@ -97,6 +97,8 @@ function snp2hit(snp) {
     chromEnd: Number(fields[2]),
     name: fields[3],
     observed,
+    ref,
+    alt: alts,
     alleles: [ref, ...alts]
   };
   return hit;

package/routes/termdb.categories.js

@@ -1,6 +1,5 @@
 import { getOrderedLabels } from "#src/termdb.barchart.js";
 import { getData } from "#src/termdb.matrix.js";
-import { TermTypes } from "#shared/terms.js";
 const api = {
   endpoint: "termdb/categories",
   methods: {
@@ -19,7 +18,6 @@ const api = {
               genome: "hg38-test",
               dslabel: "TermdbTest",
               embedder: "localhost",
-              getcategories: 1,
               term: { id: "diaggrp" },
               filter: {
                 type: "tvslst",
@@ -79,6 +77,8 @@ function init({ genomes }) {
   };
 }
 async function trigger_getcategories(q, res, tdb, ds, genome) {
+  if (!q.tw.$id)
+    q.tw.$id = "_";
   const $id = q.tw.$id;
   const arg = {
     filter: q.filter,
@@ -92,7 +92,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
   if (data.error)
     throw data.error;
   const lst = [];
-  if (q.tw.term.type == "geneVariant" && !q.tw.q.groupsetting.inuse) {
+  if (q.tw.term.type == "geneVariant" && !q.tw.q.groupsetting?.inuse) {
     const samples = data.samples;
     const dtClassMap = /* @__PURE__ */ new Map();
     if (ds.assayAvailability?.byDt) {
@@ -103,7 +103,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
       }
     }
     const sampleCountedFor = /* @__PURE__ */ new Set();
-    for (const [sampleId, sampleData] of Object.entries(samples)) {
+    for (const sampleData of Object.values(samples)) {
       const key = $id;
       const values = sampleData[key].values;
       sampleCountedFor.clear();
@@ -171,34 +171,6 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
     orderedLabels
   });
 }
-function getDefaultQ(term, q) {
-  if (term.type == "categorical")
-    return {};
-  if (term.type == "survival")
-    return {};
-  if (term.type == "integer" || term.type == "float")
-    return term.bins.default;
-  if (term.type == "condition") {
-    return {
-      mode: q.mode,
-      breaks: q.breaks,
-      bar_by_grade: q.bar_by_grade,
-      /*Leave this here until bug with term1_q not passing to getCategories is figured out.
-      Commented out b/c tvs condition tests fail.*/
-      //bar_by_children: term.subconditions || q.bar_by_children,
-      bar_by_children: q.bar_by_children,
-      value_by_max_grade: q.value_by_max_grade,
-      value_by_most_recent: q.value_by_most_recent,
-      //value_by_computable_grade: term.subconditions || q.value_by_computable_grade
-      value_by_computable_grade: q.value_by_computable_grade
-    };
-  }
-  if (term.type == "geneVariant")
-    return {};
-  if (term.type == TermTypes.SINGLECELL_CELLTYPE)
-    return {};
-  throw "unknown term type";
-}
 export {
   api
 };

package/routes/termdb.config.js

@@ -76,6 +76,8 @@ function make(q, res, ds, genome) {
     c.hasAncestry = tdb.hasAncestry;
   if (tdb.logscaleBase2)
     c.logscaleBase2 = tdb.logscaleBase2;
+  if (tdb.useCasesExcluded)
+    c.useCasesExcluded = tdb.useCasesExcluded;
   if (ds.assayAvailability)
     c.assayAvailability = ds.assayAvailability;
   if (ds.customTwQByType)

package/routes/termdb.getdescrstats.js

@@ -18,7 +18,7 @@ const api = {
               genome: "hg38-test",
               dslabel: "TermdbTest",
               embedder: "localhost",
-              tid: "hrtavg",
+              tw: { term: { id: "hrtavg" }, q: { mode: "continuous" } },
               filter: {
                 type: "tvslst",
                 in: true,
@@ -54,45 +54,45 @@ const api = {
 function init({ genomes }) {
   return async (req, res) => {
     const q = req.query;
+    let result;
     try {
-      const g = genomes[req.query.genome];
-      if (!g)
+      const genome = genomes[req.query.genome];
+      if (!genome)
         throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
+      const ds = genome.datasets[req.query.dslabel];
       if (!ds)
         throw "invalid dataset name";
       const tdb = ds.cohort.termdb;
       if (!tdb)
         throw "invalid termdb object";
-      await trigger_getdescrstats(q, res, ds, g);
+      if (!q.tw.$id)
+        q.tw.$id = "_";
+      const data = await getData({ filter: q.filter, filter0: q.filter0, terms: [q.tw] }, ds, genome);
+      if (data.error)
+        throw data.error;
+      const values = [];
+      for (const key in data.samples) {
+        const sample = data.samples[key];
+        const value = sample[q.tw.$id].value;
+        if (q.tw.q.hiddenValues?.[value]) {
+          continue;
+        }
+        if (q.logScale) {
+          if (value === 0) {
+            continue;
+          }
+        }
+        values.push(Number(value));
+      }
+      result = Summarystats(values);
     } catch (e) {
-      res.send({ error: e?.message || e });
       if (e instanceof Error && e.stack)
         console.log(e);
+      result = { error: e?.message || e };
     }
+    res.send(result);
   };
 }
-async function trigger_getdescrstats(q, res, ds, genome) {
-  const terms = [q.tw];
-  const data = await getData({ filter: q.filter, terms }, ds, genome);
-  if (data.error)
-    throw data.error;
-  const values = [];
-  for (const key in data.samples) {
-    const sample = data.samples[key];
-    const value = sample[q.tw.$id].value;
-    if (q.tw.q.hiddenValues?.[value]) {
-      continue;
-    }
-    if (q.settings?.violin?.unit === "log") {
-      if (value === 0) {
-        continue;
-      }
-    }
-    values.push(parseFloat(value));
-  }
-  res.send(Summarystats(values));
-}
 export {
   api
 };

package/routes/termdb.topVariablyExpressedGenes.js

@@ -20,6 +20,7 @@ const api = {
 };
 function init({ genomes }) {
   return async (req, res) => {
+    let result;
     try {
       const q = req.query;
       const genome = genomes[q.genome];
@@ -31,13 +32,15 @@ function init({ genomes }) {
       if (!ds.queries?.topVariablyExpressedGenes)
         throw "not supported on dataset";
       const t = Date.now();
-      const genes = await ds.queries.topVariablyExpressedGenes.getGenes(q);
+      result = {
+        genes: await ds.queries.topVariablyExpressedGenes.getGenes(q)
+      };
       if (serverconfig.debugmode)
         console.log("topVariablyExpressedGenes", Date.now() - t, "ms");
-      res.send({ genes });
     } catch (e) {
-      res.send({ status: "error", error: e.message || e });
+      result = { status: e.status || 400, error: e.message || e };
     }
+    res.send(result);
   };
 }
 function validate_query_TopVariablyExpressedGenes(ds, genome) {
@@ -87,7 +90,7 @@ async function computeGenes4nativeDs(q, ds, matrixFile, samples) {
     input_file: matrixFile,
     samples: samples.join(","),
     filter_extreme_values: true,
-    num_genes: Number(q.maxGenes),
+    num_genes: q.maxGenes,
     param: "var"
   };
   const rust_output = await run_rust("topGeneByExpressionVariance", JSON.stringify(input_json));
@@ -146,24 +149,45 @@ function gdcValidateQuery(ds, genome) {
     const arg = {
       // add any to avoid tsc err
       case_filters: makeFilter(q),
-      selection_size: Number(q.maxGenes)
+      selection_size: q.maxGenes,
+      min_median_log2_uqfpkm: q.min_median_log2_uqfpkm
     };
-    arg.gene_ids = tempGetCGCgenes(genome);
+    if (q.geneSet) {
+      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";
+        arg.gene_ids = map2ensg(q.geneSet.geneList, genome);
+        if (arg.gene_ids.length == 0)
+          throw "no valid genes from custom gene set";
+      } else {
+        throw "unknown q.geneSet.type";
+      }
+    } else {
+      arg.gene_type = "protein_coding";
+    }
     return arg;
   }
 }
-function tempGetCGCgenes(genome) {
-  const lst = [];
-  for (const s of genome.geneset[0].lst) {
-    const a = genome.genedb.getAliasByName.all(s);
-    if (a) {
-      for (const b of a) {
-        if (b.alias.startsWith("ENSG"))
-          lst.push(b.alias);
+function map2ensg(lst, genome) {
+  const ensg = [];
+  for (const name of lst) {
+    if (name.startsWith("ENSG") && name.length == 15) {
+      ensg.push(name);
+      continue;
+    }
+    const tmp = genome.genedb.getAliasByName.all(name);
+    if (Array.isArray(tmp)) {
+      for (const a of tmp) {
+        if (a.alias.startsWith("ENSG")) {
+          ensg.push(a.alias);
+          break;
+        }
       }
     }
   }
-  return lst;
+  return ensg;
 }
 export {
   api,

package/routes/termdb.violin.js

@@ -2,7 +2,7 @@ import { trigger_getViolinPlotData } from "#src/termdb.violin.js";
 const api = {
   endpoint: "termdb/violin",
   methods: {
-    get: {
+    all: {
       init,
       request: {
         typeId: "getViolinRequest"
@@ -48,28 +48,27 @@ const api = {
           }
         }
       ]
-    },
-    post: {
-      alternativeFor: "get",
-      init
     }
   }
 };
 function init({ genomes }) {
   return async (req, res) => {
     const q = req.query;
+    let data;
     try {
-      const g = genomes[req.query.genome];
-      const ds = g.datasets[req.query.dslabel];
+      const g = genomes[q.genome];
       if (!g)
         throw "invalid genome name";
-      const data = await trigger_getViolinPlotData(req.query, null, ds, g);
-      res.send(data);
+      const ds = g.datasets?.[q.dslabel];
+      if (!ds)
+        throw "invalid ds";
+      data = await trigger_getViolinPlotData(q, null, ds, g);
     } catch (e) {
-      res.send({ error: e?.message || e });
+      data = { error: e?.message || e };
       if (e instanceof Error && e.stack)
         console.log(e);
     }
+    res.send(data);
   };
 }
 export {