@sjcrh/proteinpaint-server 2.151.1-0 → 2.152.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.151.1-0",
+  "version": "2.152.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,13 +62,13 @@
   "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": "2.150.0",
-    "@sjcrh/proteinpaint-types": "2.151.1-0",
+    "@sjcrh/proteinpaint-r": "2.152.1-0",
+    "@sjcrh/proteinpaint-rust": "2.152.1-0",
+    "@sjcrh/proteinpaint-shared": "2.152.0",
+    "@sjcrh/proteinpaint-types": "2.152.1-0",
     "@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",
     "compression": "^1.6.2",

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/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];