@sjcrh/proteinpaint-server 2.108.0 → 2.109.0

package/genome/hg38.js

@@ -42,8 +42,8 @@ var hg38_default = {
     },
     {
       __isgene: true,
-      name: "GENCODE v43",
-      file: "anno/gencode.v43.hg38.gz",
+      name: "GENCODE v47",
+      file: "anno/gencode.v47.hg38.gz",
       translatecoding: true,
       categories: {
         coding: { color: "#004D99", label: "Coding gene" },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.108.0",
+  "version": "2.109.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -60,8 +60,8 @@
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.99.0",
-    "@sjcrh/proteinpaint-shared": "2.108.0",
-    "@sjcrh/proteinpaint-types": "2.108.0",
+    "@sjcrh/proteinpaint-shared": "2.109.0",
+    "@sjcrh/proteinpaint-types": "2.109.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.maf.js

@@ -101,8 +101,10 @@ async function listMafFiles(q, ds) {
       if (normalTypeName)
         file.sample_types.push(normalTypeName);
     }
+    file.sample_types = [...new Set(file.sample_types)];
     files.push(file);
   }
+  files.sort((a, b) => b.file_size - a.file_size);
   const result = {
     files,
     filesTotal: re.data.pagination.total,

package/routes/termdb.DE.js

@@ -42,7 +42,22 @@ function init({ genomes }) {
         if (term_results.error)
           throw term_results.error;
       }
-      const results = await run_DE(req.query, ds, term_results);
+      let term_results2 = [];
+      if (q.tw2) {
+        const terms2 = [q.tw2];
+        term_results2 = await getData(
+          {
+            filter: q.filter,
+            filter0: q.filter0,
+            terms: terms2
+          },
+          ds,
+          genome
+        );
+        if (term_results2.error)
+          throw term_results2.error;
+      }
+      const results = await run_DE(req.query, ds, term_results, term_results2);
       res.send(results);
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
@@ -51,7 +66,7 @@ function init({ genomes }) {
     }
   };
 }
-async function run_DE(param, ds, term_results) {
+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)
@@ -68,6 +83,7 @@ async function run_DE(param, ds, term_results) {
   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;
@@ -75,7 +91,7 @@ async function run_DE(param, ds, term_results) {
     if (!n)
       continue;
     if (q.allSampleSet.has(n)) {
-      if (param.tw) {
+      if (param.tw && !param.tw2) {
         if (term_results.samples[s.sampleId]) {
           if (param.tw.q.mode == "continuous") {
             conf1_group1.push(term_results.samples[s.sampleId][param.tw.$id]["value"]);
@@ -84,14 +100,37 @@ async function run_DE(param, ds, term_results) {
           }
           group1names.push(n);
         }
+      } else if (!param.tw && param.tw2) {
+        if (term_results2.samples[s.sampleId]) {
+          if (param.tw2.q.mode == "continuous") {
+            conf2_group1.push(term_results2.samples[s.sampleId][param.tw2.$id]["value"]);
+          } else {
+            conf2_group1.push(term_results2.samples[s.sampleId][param.tw2.$id]["key"]);
+          }
+          group1names.push(n);
+        }
+      } else if (param.tw && param.tw2) {
+        if (term_results.samples[s.sampleId] && term_results2.samples[s.sampleId]) {
+          if (param.tw.q.mode == "continuous") {
+            conf1_group1.push(term_results.samples[s.sampleId][param.tw.$id]["value"]);
+          } else {
+            conf1_group1.push(term_results.samples[s.sampleId][param.tw.$id]["key"]);
+          }
+          if (param.tw2.q.mode == "continuous") {
+            conf2_group1.push(term_results2.samples[s.sampleId][param.tw2.$id]["value"]);
+          } else {
+            conf2_group1.push(term_results2.samples[s.sampleId][param.tw2.$id]["key"]);
+          }
+          group1names.push(n);
+        }
       } else {
         group1names.push(n);
       }
-    } else {
     }
   }
   const group2names = [];
   const conf1_group2 = [];
+  const conf2_group2 = [];
   for (const s of param.samplelst.groups[1].values) {
     if (!Number.isInteger(s.sampleId))
       continue;
@@ -99,7 +138,7 @@ async function run_DE(param, ds, term_results) {
     if (!n)
       continue;
     if (q.allSampleSet.has(n)) {
-      if (param.tw) {
+      if (param.tw && !param.tw2) {
         if (term_results.samples[s.sampleId]) {
           if (param.tw.q.mode == "continuous") {
             conf1_group2.push(term_results.samples[s.sampleId][param.tw.$id]["value"]);
@@ -108,10 +147,32 @@ async function run_DE(param, ds, term_results) {
           }
           group2names.push(n);
         }
+      } else if (!param.tw && param.tw2) {
+        if (term_results2.samples[s.sampleId]) {
+          if (param.tw2.q.mode == "continuous") {
+            conf2_group2.push(term_results2.samples[s.sampleId][param.tw2.$id]["value"]);
+          } else {
+            conf2_group2.push(term_results2.samples[s.sampleId][param.tw2.$id]["key"]);
+          }
+          group2names.push(n);
+        }
+      } else if (param.tw && param.tw2) {
+        if (term_results.samples[s.sampleId] && term_results2.samples[s.sampleId]) {
+          if (param.tw.q.mode == "continuous") {
+            conf1_group2.push(term_results.samples[s.sampleId][param.tw.$id]["value"]);
+          } else {
+            conf1_group2.push(term_results.samples[s.sampleId][param.tw.$id]["key"]);
+          }
+          if (param.tw2.q.mode == "continuous") {
+            conf2_group2.push(term_results2.samples[s.sampleId][param.tw2.$id]["value"]);
+          } else {
+            conf2_group2.push(term_results2.samples[s.sampleId][param.tw2.$id]["key"]);
+          }
+          group2names.push(n);
+        }
       } else {
         group2names.push(n);
       }
-    } else {
     }
   }
   const sample_size1 = group1names.length;
@@ -135,7 +196,14 @@ async function run_DE(param, ds, term_results) {
     expression_input.conf1 = [...conf1_group2, ...conf1_group1];
     expression_input.conf1_mode = param.tw.q.mode;
     if (new Set(expression_input.conf1).size === 1) {
-      throw "Confounding variable has only one value";
+      throw "Confounding variable 1 has only one value";
+    }
+  }
+  if (param.tw2) {
+    expression_input.conf2 = [...conf2_group2, ...conf2_group1];
+    expression_input.conf2_mode = param.tw2.q.mode;
+    if (new Set(expression_input.conf2).size === 1) {
+      throw "Confounding variable 2 has only one value";
     }
   }
   const sample_size_limit = 8;

package/routes/termdb.cluster.js

@@ -74,6 +74,12 @@ async function getResult(q, ds, genome) {
     ;
     ({ term2sample2value, byTermId, bySampleId } = await ds.queries[q.dataType].get(_q));
   }
+  for (const [term, obj] of term2sample2value) {
+    if (Object.keys(obj).length === 0) {
+      term2sample2value.delete(term);
+      delete byTermId[term];
+    }
+  }
   if (term2sample2value.size == 0)
     throw "no data";
   if (term2sample2value.size == 1) {
@@ -227,7 +233,7 @@ async function validateNative(q, ds, genome) {
   q.get = async (param) => {
     const limitSamples = await mayLimitSamples(param, q.samples, ds);
     if (limitSamples?.size == 0) {
-      return { term2sample2value: /* @__PURE__ */ new Set(), byTermId: {}, bySampleId: {} };
+      return { term2sample2value: /* @__PURE__ */ new Map(), byTermId: {}, bySampleId: {} };
     }
     const bySampleId = {};
     const samples = q.samples || [];

package/routes/termdb.config.js

@@ -123,7 +123,8 @@ function addScatterplots(c, ds) {
       colorColumn: p.colorColumn,
       sampleType: p.sampleType,
       coordsColumns: p.coordsColumns,
-      settings: p.settings,
+      settings: { sampleScatter: p.settings },
+      //the client settings are under sampleScatter so we add it here to avoid adding it in the dataset
       sampleCategory: p.sampleCategory
     };
   });