@sjcrh/proteinpaint-server 2.138.0 → 2.138.2

package/dataset/termdb.test.js

@@ -4,7 +4,8 @@ function termdb_test_default() {
     isSupportedChartOverride: {
       runChart: () => true,
       frequencyChart: () => true,
-      report: () => true
+      report: () => true,
+      summarizeMutationDiagnosis: () => true
     },
     cohort: {
       massNav: {
@@ -175,6 +176,9 @@ function termdb_test_default() {
               ]
             }
           }
+        },
+        defaultTw4correlationPlot: {
+          disease: { id: "diaggrp", q: {} }
         }
       },
       scatterplots: {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.138.0",
+  "version": "2.138.2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -64,7 +64,7 @@
     "@sjcrh/proteinpaint-r": "2.137.2-0",
     "@sjcrh/proteinpaint-rust": "2.137.2-0",
     "@sjcrh/proteinpaint-shared": "2.137.3",
-    "@sjcrh/proteinpaint-types": "2.138.0",
+    "@sjcrh/proteinpaint-types": "2.138.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/brainImaging.js

@@ -62,7 +62,7 @@ async function getBrainImage(query, genomes, plane, index) {
     if (overlayTW)
       terms.push(overlayTW);
     const selectedSampleNames = query.selectedSampleFileNames.map((s) => s.split(".nii")[0]);
-    const data = await getData({ terms }, ds, q.genome);
+    const data = await getData({ terms }, ds);
     const divideByCat = {};
     const uniqueOverlayTwCats = /* @__PURE__ */ new Set();
     for (const sampleName of selectedSampleNames) {

package/routes/correlationVolcano.js

@@ -29,7 +29,7 @@ function init({ genomes }) {
       const ds = genome.datasets?.[q.dslabel];
       if (!ds)
         throw "invalid ds";
-      const result = await compute(q, ds, genome);
+      const result = await compute(q, ds);
       res.send(result);
     } catch (e) {
       res.send({ error: e?.message || e });
@@ -38,16 +38,16 @@ function init({ genomes }) {
     }
   };
 }
-async function compute(q, ds, genome) {
+async function compute(q, ds) {
   const terms = [q.featureTw, ...q.variableTwLst];
   const data = await getData(
     {
       filter: q.filter,
       filter0: q.filter0,
-      terms
+      terms,
+      __protected__: q.__protected__
     },
-    ds,
-    genome
+    ds
   );
   if (data.error)
     throw data.error;

package/routes/filterTermValues.js

@@ -21,34 +21,14 @@ function init({ genomes }) {
       if (!g)
         throw "invalid genome name";
       const ds = g.datasets?.[req.query.dslabel];
-      getFilters(req.query, ds, g, res);
+      getFilters(req.query, ds, res);
     } catch (e) {
       console.log(e);
       res.send({ status: "error", error: e.message || e });
     }
   };
 }
-function getList(samplesPerFilter, filtersData, tw) {
-  const values = Object.values(tw.term.values);
-  values.sort((v1, v2) => v1.label.localeCompare(v2.label));
-  const twSamples = samplesPerFilter[tw.term.id];
-  const data = [];
-  for (const sample of twSamples) {
-    data.push(filtersData.samples[sample]);
-  }
-  const annotations = data.filter((s) => s != void 0).map((sample) => sample[tw.$id]?.value);
-  const sampleValues = Array.from(new Set(annotations));
-  const filteredValues = [];
-  for (const value of values) {
-    const label = value.label.replace(/["']/g, "");
-    const disabled = !sampleValues.includes(value.key || value.label);
-    filteredValues.push({ value: value.key || value.label, label, disabled });
-  }
-  filteredValues.unshift({ label: "", value: "" });
-  filteredValues.sort((a, b) => a.label.localeCompare(b.label));
-  return filteredValues;
-}
-async function getFilters(query, ds, genome, res) {
+async function getFilters(query, ds, res) {
   if (!query.filterByUserSites)
     authApi.mayAdjustFilter(query, ds, query.terms);
   try {
@@ -58,12 +38,11 @@ async function getFilters(query, ds, genome, res) {
         terms: query.terms,
         __protected__: query.__protected__
       },
-      ds,
-      genome
+      ds
     );
     const tw2List = {};
     for (const tw of query.terms) {
-      tw2List[tw.term.id] = getList(samplesPerFilter, filtersData, tw);
+      tw2List[tw.term.id] = getList(samplesPerFilter, filtersData, tw, query.showAll);
     }
     res.send({ ...tw2List });
   } catch (e) {
@@ -71,6 +50,28 @@ async function getFilters(query, ds, genome, res) {
     res.send({ error: e.message || e });
   }
 }
+function getList(samplesPerFilter, filtersData, tw, showAll) {
+  const values = Object.values(tw.term.values);
+  values.sort((v1, v2) => v1.label.localeCompare(v2.label));
+  const twSamples = samplesPerFilter[tw.term.id];
+  const data = [];
+  for (const sample of twSamples) {
+    data.push(filtersData.samples[sample]);
+  }
+  const annotations = data.filter((s) => s != void 0).map((sample) => sample[tw.$id]?.value);
+  const sampleValues = Array.from(new Set(annotations));
+  const filteredValues = [];
+  for (const value of values) {
+    const label = value.label.replace(/["']/g, "");
+    const disabled = !sampleValues.includes(value.key || value.label);
+    if (!showAll && disabled)
+      continue;
+    filteredValues.push({ value: value.key || value.label, label, disabled });
+  }
+  filteredValues.unshift({ label: "", value: "" });
+  filteredValues.sort((a, b) => a.label.localeCompare(b.label));
+  return filteredValues;
+}
 export {
   api
 };

package/routes/profileFormScores.js

@@ -20,7 +20,7 @@ function init({ genomes }) {
       if (!g)
         throw "invalid genome name";
       const ds = g.datasets?.[req.query.dslabel];
-      const result = await getScoresDict(req.query, ds, g);
+      const result = await getScoresDict(req.query, ds);
       res.send(result);
     } catch (e) {
       console.log(e);
@@ -28,7 +28,7 @@ function init({ genomes }) {
     }
   };
 }
-async function getScoresDict(query, ds, genome) {
+async function getScoresDict(query, ds) {
   if (!query.filterByUserSites)
     query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
   const terms = [...query.scoreTerms, query.facilityTW];
@@ -41,8 +41,7 @@ async function getScoresDict(query, ds, genome) {
       //if isRadarFacility and site is specified, do not apply the filter
       __protected__: query.__protected__
     },
-    ds,
-    genome
+    ds
   );
   const lst = Object.values(data.samples);
   let sites = lst.map((s) => {

package/routes/profileScores.js

@@ -20,7 +20,7 @@ function init({ genomes }) {
       if (!g)
         throw "invalid genome name";
       const ds = g.datasets?.[req.query.dslabel];
-      const result = await getScores(req.query, ds, g);
+      const result = await getScores(req.query, ds);
       res.send(result);
     } catch (e) {
       console.log(e);
@@ -28,7 +28,7 @@ function init({ genomes }) {
     }
   };
 }
-async function getScores(query, ds, genome) {
+async function getScores(query, ds) {
   if (!query.filterByUserSites)
     query.__protected__.ignoredTermIds.push(query.facilityTW.term.id);
   const terms = [query.facilityTW];
@@ -45,8 +45,7 @@ async function getScores(query, ds, genome) {
       //if site is specified, do not apply the filter that is for the aggregation
       __protected__: query.__protected__
     },
-    ds,
-    genome
+    ds
   );
   const lst = Object.values(data.samples);
   let sites = lst.map((s) => {

package/routes/termdb.DE.js

@@ -40,8 +40,7 @@ function init({ genomes }) {
             filter0: q.filter0,
             terms
           },
-          ds,
-          genome
+          ds
         );
         if (term_results.error)
           throw term_results.error;
@@ -55,8 +54,7 @@ function init({ genomes }) {
             filter0: q.filter0,
             terms: terms2
           },
-          ds,
-          genome
+          ds
         );
         if (term_results2.error)
           throw term_results2.error;

package/routes/termdb.boxplot.js

@@ -31,15 +31,7 @@ function init({ genomes }) {
       const terms = [q.tw];
       if (q.overlayTw)
         terms.push(q.overlayTw);
-      const data = await getData(
-        {
-          filter: q.filter,
-          filter0: q.filter0,
-          terms
-        },
-        ds,
-        genome
-      );
+      const data = await getData({ filter: q.filter, filter0: q.filter0, terms, __protected__: q.__protected__ }, ds);
       if (data.error)
         throw data.error;
       const sampleType = `All ${data.sampleType?.plural_name || "samples"}`;

package/routes/termdb.categories.js

@@ -27,7 +27,7 @@ function init({ genomes }) {
       const tdb = ds.cohort.termdb;
       if (!tdb)
         throw "invalid termdb object";
-      await trigger_getcategories(q, res, tdb, ds, g);
+      await trigger_getcategories(q, res, tdb, ds);
     } catch (e) {
       res.send({ error: e?.message || e });
       if (e instanceof Error && e.stack)
@@ -35,7 +35,7 @@ function init({ genomes }) {
     }
   };
 }
-async function trigger_getcategories(q, res, tdb, ds, genome) {
+async function trigger_getcategories(q, res, tdb, ds) {
   if (!q.tw.$id)
     q.tw.$id = "_";
   const $id = q.tw.$id;
@@ -49,7 +49,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
     // optional, from mds3 mayAddGetCategoryArgs()
     __protected__: q.__protected__
   };
-  const data = await getData(arg, ds, genome);
+  const data = await getData(arg, ds);
   if (data.error)
     throw data.error;
   const [lst, orderedLabels] = getCategories(data, q, ds, $id);

package/routes/termdb.cluster.js

@@ -47,7 +47,7 @@ function init({ genomes }) {
           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, g);
+        result = await getResult(q, ds);
       } else {
         throw "unknown q.dataType " + q.dataType;
       }
@@ -62,7 +62,7 @@ function init({ genomes }) {
     res.send(result);
   };
 }
-async function getResult(q, ds, genome) {
+async function getResult(q, ds) {
   let _q = q;
   if (q.dataType == TermTypes.GENE_EXPRESSION) {
     _q = JSON.parse(JSON.stringify(q));
@@ -71,7 +71,7 @@ async function getResult(q, ds, genome) {
   let term2sample2value, byTermId, bySampleId, skippedSexChrGenes;
   if (q.dataType == NUMERIC_DICTIONARY_TERM) {
     ;
-    ({ term2sample2value, byTermId, bySampleId } = await getNumericDictTermAnnotation(q, ds, genome));
+    ({ term2sample2value, byTermId, bySampleId } = await getNumericDictTermAnnotation(q, ds));
   } else {
     ;
     ({ term2sample2value, byTermId, bySampleId, skippedSexChrGenes } = await ds.queries[q.dataType].get(_q));
@@ -108,12 +108,14 @@ async function getResult(q, ds, genome) {
     result.removedHierClusterTerms = removedHierClusterTerms;
   return result;
 }
-async function getNumericDictTermAnnotation(q, ds, genome) {
+async function getNumericDictTermAnnotation(q, ds) {
   const getDataArgs = {
+    terms: q.terms.map((term) => ({ term, q: { mode: "continuous" } })),
     filter: q.filter,
-    terms: q.terms.map((term) => ({ term, q: { mode: "continuous" } }))
+    filter0: q.filter0,
+    __protected__: q.__protected__
   };
-  const data = await getData(getDataArgs, ds, genome);
+  const data = await getData(getDataArgs, ds);
   const term2sample2value = /* @__PURE__ */ new Map();
   for (const [key, sampleData] of Object.entries(data.samples)) {
     for (const [term, value] of Object.entries(sampleData)) {

package/routes/termdb.descrstats.js

@@ -32,15 +32,18 @@ function init({ genomes }) {
         q.tw.$id = "_";
       const data = await getData(
         { filter: q.filter, filter0: q.filter0, terms: [q.tw], __protected__: q.__protected__ },
-        ds,
-        genome
+        ds
       );
       if (data.error)
         throw data.error;
       const values = [];
       for (const key in data.samples) {
         const sample = data.samples[key];
-        const value = sample[q.tw.$id].value;
+        const v = sample[q.tw.$id];
+        if (!v && v !== 0) {
+          continue;
+        }
+        const value = v.value;
         if (q.tw.q.hiddenValues?.[value]) {
           continue;
         }

package/routes/termdb.violin.js

@@ -32,7 +32,7 @@ function init({ genomes }) {
       const ds = g.datasets?.[q.dslabel];
       if (!ds)
         throw "invalid ds";
-      data = await trigger_getViolinPlotData(q, ds, g);
+      data = await trigger_getViolinPlotData(q, ds);
     } catch (e) {
       data = { error: e?.message || e };
       if (e instanceof Error && e.stack)
@@ -41,7 +41,7 @@ function init({ genomes }) {
     res.send(data);
   };
 }
-async function trigger_getViolinPlotData(q, ds, genome) {
+async function trigger_getViolinPlotData(q, ds) {
   if (typeof q.tw?.term != "object" || typeof q.tw?.q != "object")
     throw "q.tw not of {term,q}";
   const term = q.tw.term;
@@ -53,9 +53,14 @@ async function trigger_getViolinPlotData(q, ds, genome) {
   if (q.divideTw)
     terms.push(q.divideTw);
   const data = await getData(
-    { terms, filter: q.filter, filter0: q.filter0, currentGeneNames: q.currentGeneNames },
-    ds,
-    genome
+    {
+      terms,
+      filter: q.filter,
+      filter0: q.filter0,
+      currentGeneNames: q.currentGeneNames,
+      __protected__: q.__protected__
+    },
+    ds
   );
   const sampleType = `All ${data.sampleType?.plural_name || "samples"}`;
   if (data.error)