@sjcrh/proteinpaint-server 2.152.0 → 2.153.1-2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.152.0",
+  "version": "2.153.1-2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -61,16 +61,16 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
-    "@sjcrh/proteinpaint-python": "2.151.0",
-    "@sjcrh/proteinpaint-r": "2.149.0",
-    "@sjcrh/proteinpaint-rust": "2.150.0",
-    "@sjcrh/proteinpaint-shared": "2.152.0",
-    "@sjcrh/proteinpaint-types": "2.152.0",
+    "@sjcrh/proteinpaint-python": "2.153.0",
+    "@sjcrh/proteinpaint-r": "2.152.1-0",
+    "@sjcrh/proteinpaint-rust": "2.152.1-0",
+    "@sjcrh/proteinpaint-shared": "2.153.1-2",
+    "@sjcrh/proteinpaint-types": "2.153.1-2",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
-    "better-sqlite3": "^9.4.1",
+    "better-sqlite3": "^12.4.1",
     "body-parser": "^1.15.2",
-    "canvas": "~3.1.0",
+    "canvas": "~3.1.2",
     "compression": "^1.6.2",
     "connect-redis": "^6.1.3",
     "cookie-parser": "^1.4.5",

package/routes/aiProjectAdmin.js

@@ -1,5 +1,5 @@
 import { aiProjectAdminPayload } from "#types/checkers";
-import { getDbConnection } from "#src/aiHistoDBConnection.js";
+import { getDbConnection } from "#src/aiHistoDBConnection.ts";
 import { runMultiStmtSQL, runSQL } from "#src/runSQLHelpers.ts";
 const api = {
   endpoint: "aiProjectAdmin",
@@ -165,5 +165,6 @@ function addProject(connection, project) {
   runMultiStmtSQL(connection, [{ sql: classSql, params: classParams }], "add");
 }
 export {
-  api
+  api,
+  getImages
 };

package/routes/aiProjectTrainModel.js

@@ -1,6 +1,8 @@
 import { aiProjectTrainModelPayload } from "#types/checkers";
 import { TileServerSessionsHandler } from "#src/wsisessions/TileServerSessionsHandler.ts";
 import SessionManager from "#src/wsisessions/SessionManager.ts";
+import { getDbConnection } from "#src/aiHistoDBConnection.js";
+import { getImages } from "#routes/aiProjectAdmin.js";
 const api = {
   endpoint: "aiProjectTrainModel",
   methods: {
@@ -18,13 +20,17 @@ function init({ genomes }) {
   return async function(req, res) {
     try {
       const query = req.query;
-      console.log(query);
       const g = genomes[query.genome];
       if (!g) throw "invalid genome name";
       const ds = g.datasets[query.dslabel];
       if (!ds) throw "invalid dataset name";
       if (typeof ds.queries.WSImages.retrainModel == "function") {
-        await ds.queries.WSImages.retrainModel(query.projectId);
+        const connection = getDbConnection(ds);
+        const project = {
+          id: query.projectId
+        };
+        const wsimages = getImages(connection, project);
+        await ds.queries.WSImages.retrainModel(query.projectId, wsimages);
         try {
           const handler = new TileServerSessionsHandler();
           const sessionMgr = SessionManager.getInstance();

package/routes/grin2.js

@@ -153,6 +153,10 @@ function allTypesCapped(tracker) {
 }
 async function processSampleData(samples, ds, request, tracker) {
   const lesions = [];
+  const samplesPerType = /* @__PURE__ */ new Map();
+  for (const [type] of tracker.entries()) {
+    samplesPerType.set(type, /* @__PURE__ */ new Set());
+  }
   const processingSummary = {
     totalSamples: samples.length,
     processedSamples: 0,
@@ -174,8 +178,11 @@ async function processSampleData(samples, ds, request, tracker) {
     try {
       await file_is_readable(filepath);
       const mlst = JSON.parse(await read_file(filepath));
-      const { sampleLesions } = await processSampleMlst(sample.name, mlst, request, tracker);
+      const { sampleLesions, contributedTypes } = await processSampleMlst(sample.name, mlst, request, tracker);
       lesions.push(...sampleLesions);
+      for (const type of contributedTypes) {
+        samplesPerType.get(type)?.add(sample.name);
+      }
       processingSummary.processedSamples += 1;
       processingSummary.totalLesions += sampleLesions.length;
       if (allTypesCapped(tracker)) {
@@ -195,35 +202,61 @@ async function processSampleData(samples, ds, request, tracker) {
     }
   }
   processingSummary.processedLesions = lesions.length;
+  const lesionCounts = {
+    total: lesions.length,
+    byType: {}
+  };
+  const lesionTypeCounts = {};
+  for (const lesion of lesions) {
+    const lesionType = lesion[4];
+    lesionTypeCounts[lesionType] = (lesionTypeCounts[lesionType] || 0) + 1;
+  }
   for (const [type, info] of tracker.entries()) {
-    if (info.count >= MAX_LESIONS_PER_TYPE) {
-      let label;
-      switch (type) {
-        case dtsnvindel:
-          label = "mutation";
-          break;
-        case dtcnv:
-          label = "CNV (gain/loss)";
-          break;
-        case dtfusionrna:
-          label = "fusion";
-          break;
-        case dtsv:
-          label = "structural variant";
-          break;
-        default:
-          label = `type ${type}`;
-          break;
+    const isCapped = info.count >= MAX_LESIONS_PER_TYPE;
+    switch (type) {
+      case dtsnvindel:
+        lesionCounts.byType["mutation"] = {
+          count: lesionTypeCounts["mutation"] || 0,
+          capped: isCapped,
+          samples: samplesPerType.get(type)?.size || 0
+        };
+        break;
+      case dtcnv: {
+        const sampleCount = samplesPerType.get(type)?.size || 0;
+        lesionCounts.byType["gain"] = {
+          count: lesionTypeCounts["gain"] || 0,
+          capped: isCapped,
+          samples: sampleCount
+        };
+        lesionCounts.byType["loss"] = {
+          count: lesionTypeCounts["loss"] || 0,
+          capped: isCapped,
+          samples: sampleCount
+        };
+        break;
       }
-      mayLog(
-        `[GRIN2] Warning: ${label} lesions reached the per-type cap of ${MAX_LESIONS_PER_TYPE.toLocaleString()}. No further ${label} lesions were processed.`
-      );
+      case dtfusionrna:
+        lesionCounts.byType["fusion"] = {
+          count: lesionTypeCounts["fusion"] || 0,
+          capped: isCapped,
+          samples: samplesPerType.get(type)?.size || 0
+        };
+        break;
+      case dtsv:
+        lesionCounts.byType["sv"] = {
+          count: lesionTypeCounts["sv"] || 0,
+          capped: isCapped,
+          samples: samplesPerType.get(type)?.size || 0
+        };
+        break;
     }
   }
+  processingSummary.lesionCounts = lesionCounts;
   return { lesions, processingSummary };
 }
 async function processSampleMlst(sampleName, mlst, request, tracker) {
   const sampleLesions = [];
+  const contributedTypes = /* @__PURE__ */ new Set();
   for (const m of mlst) {
     switch (m.dt) {
       case dtsnvindel: {
@@ -236,6 +269,7 @@ async function processSampleMlst(sampleName, mlst, request, tracker) {
         if (les && entry) {
           entry.count++;
           sampleLesions.push(les);
+          contributedTypes.add(dtsnvindel);
         }
         break;
       }
@@ -249,6 +283,7 @@ async function processSampleMlst(sampleName, mlst, request, tracker) {
         if (les && cnv) {
           cnv.count++;
           sampleLesions.push(les);
+          contributedTypes.add(dtcnv);
         }
         break;
       }
@@ -273,6 +308,7 @@ async function processSampleMlst(sampleName, mlst, request, tracker) {
             sampleLesions.push(les);
             fusion.count++;
           }
+          contributedTypes.add(dtfusionrna);
         }
         break;
       }
@@ -297,6 +333,7 @@ async function processSampleMlst(sampleName, mlst, request, tracker) {
             sampleLesions.push(les);
             sv.count++;
           }
+          contributedTypes.add(dtsv);
         }
         break;
       }
@@ -304,7 +341,7 @@ async function processSampleMlst(sampleName, mlst, request, tracker) {
         break;
     }
   }
-  return { sampleLesions };
+  return { sampleLesions, contributedTypes };
 }
 function filterAndConvertSnvIndel(sampleName, entry, options) {
   if (!options?.consequences) {

package/routes/termdb.profileFormScores.js

@@ -1,5 +1,5 @@
 import { ProfileFormScoresPayload } from "#types/checkers";
-import { getScoresData } from "./termdb.profileScores.js";
+import { getScoresData } from "./termdb.profileScores.ts";
 const api = {
   endpoint: "termdb/profileFormScores",
   methods: {

package/routes/termdb.violin.js

@@ -1,5 +1,5 @@
 import { violinPayload } from "#types/checkers";
-import { scaleLinear, scaleLog, extent } from "d3";
+import { scaleLinear, scaleLog } from "d3";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import { getData } from "../src/termdb.matrix.js";
 import { createCanvas } from "canvas";
@@ -181,7 +181,7 @@ async function createCanvasImg(q, result, ds) {
     const chart = result.charts[k];
     const plot2Values = {};
     for (const plot of chart.plots) plot2Values[plot.label] = plot.values;
-    const densities = await getDensities(plot2Values, result.min, result.max);
+    const densities = await getDensities(plot2Values);
     let axisScale;
     const useLog = q.unit == "log";
     if (useLog) {
@@ -229,12 +229,11 @@ async function createCanvasImg(q, result, ds) {
   }
 }
 async function getDensity(values) {
-  const [min, max] = extent(values);
-  const result = await getDensities({ plot: values }, min, max);
+  const result = await getDensities({ plot: values });
   return result.plot;
 }
-async function getDensities(plot2Values, min, max) {
-  const plot2Density = JSON.parse(await run_R("density.R", JSON.stringify({ plot2Values, min, max })));
+async function getDensities(plot2Values) {
+  const plot2Density = JSON.parse(await run_R("density.R", JSON.stringify({ plot2Values })));
   const densities = {};
   for (const plot in plot2Density) {
     const result = plot2Density[plot];