@sjcrh/proteinpaint-server 2.170.1 → 2.171.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.170.1",
+  "version": "2.171.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,11 +62,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
-    "@sjcrh/proteinpaint-python": "2.169.0",
+    "@sjcrh/proteinpaint-python": "2.171.0-0",
     "@sjcrh/proteinpaint-r": "2.152.1-0",
-    "@sjcrh/proteinpaint-rust": "2.170.0",
-    "@sjcrh/proteinpaint-shared": "2.170.1",
-    "@sjcrh/proteinpaint-types": "2.170.1",
+    "@sjcrh/proteinpaint-rust": "2.171.0",
+    "@sjcrh/proteinpaint-shared": "2.171.0-0",
+    "@sjcrh/proteinpaint-types": "2.171.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/aiProjectAdmin.js

@@ -61,6 +61,7 @@ function init({ genomes }) {
       } else if (query.for === "filterImages") {
         const q = ds.cohort.termdb.q;
         const data = await q.getFilteredImages(query.project.filter);
+        data.selectedImages = await ds.queries?.WSImages?.selectWSIImages();
         res.status(200).send({
           status: "ok",
           data

package/routes/grin2.js

@@ -6,16 +6,7 @@ import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { mayLog } from "#src/helpers.ts";
 import { get_samples } from "#src/termdb.sql.js";
 import { read_file, file_is_readable } from "#src/utils.js";
-import {
-  dtsnvindel,
-  dtcnv,
-  dtfusionrna,
-  dtsv,
-  dt2lesion,
-  optionToDt,
-  formatElapsedTime,
-  MANHATTAN_LOG_QVALUE_CUTOFF
-} from "#shared";
+import { dtsnvindel, dtcnv, dtfusionrna, dtsv, dt2lesion, optionToDt, formatElapsedTime } from "#shared";
 import crypto from "crypto";
 const MAX_LESIONS_PER_TYPE = serverconfig.features.grin2maxLesionPerType || 11e4;
 const api = {
@@ -115,9 +106,6 @@ async function runGrin2(g, ds, request) {
     lesionTypeMap: buildLesionTypeMap(availableDataTypes)
   };
   for (const c in g.majorchr) {
-    if (ds.queries.singleSampleMutation.discoPlot?.skipChrM) {
-      if (c.toLowerCase() == "chrm") continue;
-    }
     pyInput.chromosomelist[c] = g.majorchr[c];
   }
   const grin2AnalysisStart = Date.now();
@@ -141,7 +129,9 @@ async function runGrin2(g, ds, request) {
     png_dot_radius: request.pngDotRadius,
     lesion_type_colors: request.lesionTypeColors,
     q_value_threshold: request.qValueThreshold,
-    log_cutoff: MANHATTAN_LOG_QVALUE_CUTOFF
+    max_capped_points: request.maxCappedPoints,
+    hard_cap: request.hardCap,
+    bin_size: request.binSize
   };
   const manhattanPlotStart = Date.now();
   const rsResult = await run_rust("manhattan_plot", JSON.stringify(rustInput));
@@ -214,12 +204,14 @@ async function processSampleData(samples, ds, request, tracker) {
       await file_is_readable(filepath);
       const mlst = JSON.parse(await read_file(filepath));
       const { sampleLesions, contributedTypes } = await processSampleMlst(sample.name, mlst, request, tracker);
-      lesions.push(...sampleLesions);
+      const skipChrM = ds.queries.singleSampleMutation.discoPlot?.skipChrM;
+      const filteredLesions = skipChrM ? sampleLesions.filter((lesion) => lesion[1].toLowerCase() !== "chrm") : sampleLesions;
+      lesions.push(...filteredLesions);
       for (const type of contributedTypes) {
         samplesPerType.get(type)?.add(sample.name);
       }
       processingSummary.processedSamples += 1;
-      processingSummary.totalLesions += sampleLesions.length;
+      processingSummary.totalLesions += filteredLesions.length;
       if (allTypesCapped(tracker)) {
         const remaining = samples.length - 1 - i;
         if (remaining > 0) processingSummary.unprocessedSamples += remaining;

package/routes/termdb.config.js

@@ -143,7 +143,8 @@ function addNonDictionaryQueries(c, ds, genome) {
       // some of the stuff here are to provide user-selectable choices
       // e.g. computing methods, info fields, populations.
       details: q.snvindel.details,
-      populations: q.snvindel.populations
+      populations: q.snvindel.populations,
+      mafFilter: q.snvindel.mafFilter
     };
     if (q.snvindel.byisoform?.processTwsInOneQuery) q2.snvindel.byisoform = { processTwsInOneQuery: true };
   }