@sjcrh/proteinpaint-server 2.144.0 → 2.145.1-0

package/dataset/termdb.test.js

@@ -213,6 +213,42 @@ function termdb_test_default() {
       // small list of terms for sunburst rings
       sunburst_twLst: [{ id: "sex", q: {} }]
     },
+    assayAvailability: {
+      // term used below must be annotated on samples rather than patients(root). otherwise matrix will pull wrong samples for geneVariant term
+      byDt: {
+        // snvindel, differentiating sample origin
+        1: {
+          byOrigin: {
+            germline: {
+              term_id: "assayavailability_germline",
+              label: "Germline",
+              // human readable label of this origin
+              yes: { value: ["1"] },
+              no: { value: ["2"] }
+            },
+            somatic: {
+              term_id: "wgs_curated",
+              label: "Somatic",
+              yes: { value: ["1"] },
+              no: { value: ["0"] }
+              // the category doesn't exist in termdb but is still supplied since somatic.no{} is required
+            }
+          }
+        },
+        // fusion
+        2: {
+          term_id: "assayavailability_fusion",
+          yes: { value: ["1"] },
+          no: { value: ["2"] }
+        },
+        // cnv
+        4: {
+          term_id: "assayavailability_cnv",
+          yes: { value: ["1"] },
+          no: { value: ["2"] }
+        }
+      }
+    },
     queries: {
       snvindel: {
         forTrack: true,
@@ -278,7 +314,8 @@ function termdb_test_default() {
       },
       rnaseqGeneCount: {
         storage_type: "HDF5",
-        file: "files/hg38/TermdbTest/rnaseq/TermdbTest.geneCounts.h5"
+        newformat: true,
+        file: "files/hg38/TermdbTest/rnaseq/TermdbTest.geneCounts.new.h5"
       },
       singleCell: {
         samples: {
@@ -312,42 +349,10 @@ function termdb_test_default() {
       WSImages: {
         type: "H&E",
         imageBySampleFolder: "files/hg38/TermdbTest/wsimages"
-      }
-    },
-    assayAvailability: {
-      // term used below must be annotated on samples rather than patients(root). otherwise matrix will pull wrong samples for geneVariant term
-      byDt: {
-        // snvindel, differentiating sample origin
-        1: {
-          byOrigin: {
-            germline: {
-              term_id: "assayavailability_germline",
-              label: "Germline",
-              // human readable label of this origin
-              yes: { value: ["1"] },
-              no: { value: ["2"] }
-            },
-            somatic: {
-              term_id: "wgs_curated",
-              label: "Somatic",
-              yes: { value: ["1"] },
-              no: { value: ["0"] }
-              // the category doesn't exist in termdb but is still supplied since somatic.no{} is required
-            }
-          }
-        },
-        // fusion
-        2: {
-          term_id: "assayavailability_fusion",
-          yes: { value: ["1"] },
-          no: { value: ["2"] }
-        },
-        // cnv
-        4: {
-          term_id: "assayavailability_cnv",
-          yes: { value: ["1"] },
-          no: { value: ["2"] }
-        }
+      },
+      trackLst: {
+        jsonFile: "files/hg38/TermdbTest/trackLst/facet.json",
+        activeTracks: ["bw 1", "bed 1"]
       }
     }
   };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.144.0",
+  "version": "2.145.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,10 +62,10 @@
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
     "@sjcrh/proteinpaint-python": "2.144.0",
-    "@sjcrh/proteinpaint-r": "2.137.2-0",
-    "@sjcrh/proteinpaint-rust": "2.143.0",
-    "@sjcrh/proteinpaint-shared": "2.143.0",
-    "@sjcrh/proteinpaint-types": "2.144.0",
+    "@sjcrh/proteinpaint-r": "2.145.1-0",
+    "@sjcrh/proteinpaint-rust": "2.145.1-0",
+    "@sjcrh/proteinpaint-shared": "2.145.1-0",
+    "@sjcrh/proteinpaint-types": "2.145.1-0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/gdc.grin2.run.js

@@ -48,7 +48,11 @@ async function runGrin2(genomes, req, res) {
   const pyInput = {
     genedb: path.join(serverconfig.tpmasterdir, g.genedb.dbfile),
     chromosomelist: {},
-    lesion: ""
+    lesion: "",
+    devicePixelRatio: parsedRequest.devicePixelRatio || 2,
+    plot_width: parsedRequest.plot_width || 1e3,
+    plot_height: parsedRequest.plot_height || 400,
+    pngDotRadius: parsedRequest.pngDotRadius || 2
   };
   for (const c in g.majorchr) {
     if (ds.queries.singleSampleMutation?.discoPlot?.skipChrM) {
@@ -89,6 +93,7 @@ async function runGrin2(genomes, req, res) {
   const topGeneTable = resultData.topGeneTable || null;
   const totalProcessTime = downloadTimeToPrint + grin2AnalysisTimeToPrint;
   return res.json({
+    resultData,
     pngImg,
     topGeneTable,
     rustResult: parsedRustResult,

package/routes/termdb.DE.js

@@ -204,7 +204,12 @@ async function run_DE(param, ds, term_results, term_results2) {
   const sample_size_limit = 8;
   if (group1names.length <= sample_size_limit && group2names.length <= sample_size_limit || param.method == "edgeR" || param.method == "limma") {
     const time12 = (/* @__PURE__ */ new Date()).valueOf();
-    const result2 = JSON.parse(await run_R("edge.R", JSON.stringify(expression_input)));
+    let result2;
+    if (q.newformat) {
+      result2 = JSON.parse(await run_R("edge_newh5.R", JSON.stringify(expression_input)));
+    } else {
+      result2 = JSON.parse(await run_R("edge.R", JSON.stringify(expression_input)));
+    }
     mayLog("Time taken to run edgeR:", formatElapsedTime(Date.now() - time12));
     param.method = "edgeR";
     const ql_imagePath = path.join(serverconfig.cachedir, result2.edgeR_ql_image_name[0]);
@@ -254,15 +259,30 @@ async function validate_query_rnaseqGeneCount(ds) {
     if (ds.queries.rnaseqGeneCount.storage_type == "text") {
       samples = (await get_header_txt(q.file, null)).split("	").slice(4);
     } else if (ds.queries.rnaseqGeneCount.storage_type == "HDF5") {
-      const get_samples_from_hdf5 = {
-        input_file: q.file,
-        data_type: "get_samples"
-      };
-      const time1 = (/* @__PURE__ */ new Date()).valueOf();
-      const result = await run_rust("DEanalysis", JSON.stringify(get_samples_from_hdf5));
-      const time2 = (/* @__PURE__ */ new Date()).valueOf();
-      mayLog("Time taken to query gene expression:", time2 - time1, "ms");
-      samples = result.split(",");
+      if (q.newformat) {
+        const get_samples_from_hdf5 = {
+          hdf5_file: q.file,
+          validate: true
+        };
+        const time1 = (/* @__PURE__ */ new Date()).valueOf();
+        const result = await run_rust("readH5", JSON.stringify(get_samples_from_hdf5));
+        const time2 = (/* @__PURE__ */ new Date()).valueOf();
+        mayLog("Time taken to query gene expression:", time2 - time1, "ms");
+        const vr = JSON.parse(result);
+        if (vr.status !== "success") throw vr.message;
+        if (!Array.isArray(vr.samples)) throw "HDF5 file has no samples, please check file.";
+        samples = vr.samples;
+      } else {
+        const get_samples_from_hdf5 = {
+          input_file: q.file,
+          data_type: "get_samples"
+        };
+        const time1 = (/* @__PURE__ */ new Date()).valueOf();
+        const result = await run_rust("DEanalysis", JSON.stringify(get_samples_from_hdf5));
+        const time2 = (/* @__PURE__ */ new Date()).valueOf();
+        mayLog("Time taken to query gene expression:", time2 - time1, "ms");
+        samples = result.split(",");
+      }
     } else throw "unknown storage type:" + ds.queries.rnaseqGeneCount.storage_type;
     q.allSampleSet = new Set(samples);
     const unknownSamples = [];

package/routes/termdb.boxplot.js

@@ -140,7 +140,7 @@ function setUncomputableValues(values) {
 function parseValues(q, data, sampleType, isLog, overlayTerm, divideTerm) {
   const chart2plot2values = /* @__PURE__ */ new Map();
   const uncomputableValues = {};
-  let absMin = null, absMax = null;
+  let absMin = Infinity, absMax = -Infinity;
   for (const val of Object.values(data.samples)) {
     const value = val[q.tw.$id];
     if (!Number.isFinite(value?.value)) continue;
@@ -175,8 +175,8 @@ function parseValues(q, data, sampleType, isLog, overlayTerm, divideTerm) {
     if (!plot2values.has(plot)) plot2values.set(plot, []);
     const values = plot2values.get(plot);
     values.push(value.value);
-    if (absMin === null || value.value < absMin) absMin = value.value;
-    if (absMax === null || value.value > absMax) absMax = value.value;
+    if (value.value < absMin) absMin = value.value;
+    if (value.value > absMax) absMax = value.value;
   }
   return { absMax, absMin, chart2plot2values, uncomputableValues };
 }