@sjcrh/proteinpaint-server 2.157.0 → 2.158.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.157.0",
+  "version": "2.158.0",
   "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": "2.157.0",
+    "@sjcrh/proteinpaint-python": "2.158.0",
     "@sjcrh/proteinpaint-r": "2.152.1-0",
     "@sjcrh/proteinpaint-rust": "2.157.0",
     "@sjcrh/proteinpaint-shared": "2.157.0",
-    "@sjcrh/proteinpaint-types": "2.157.0",
+    "@sjcrh/proteinpaint-types": "2.158.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",
     "body-parser": "^1.15.2",
-    "canvas": "~3.1.2",
+    "canvas": "~3.2.0",
     "compression": "^1.6.2",
     "connect-redis": "^6.1.3",
     "cookie-parser": "^1.4.5",
@@ -80,7 +80,7 @@
     "express-basic-auth": "^1.1.5",
     "express-session": "^1.18.1",
     "got": "^14.2.0",
-    "image-size": "^0.5.5",
+    "image-size": "^0.9.7",
     "jsonwebtoken": "^9.0.0",
     "ky": "^1.2.1",
     "micromatch": "^4.0.5",

package/routes/grin2.js

@@ -118,7 +118,9 @@ async function runGrin2(g, ds, request) {
     plot_width: request.width,
     plot_height: request.height,
     device_pixel_ratio: request.devicePixelRatio,
-    png_dot_radius: request.pngDotRadius
+    png_dot_radius: request.pngDotRadius,
+    lesion_type_colors: request.lesionTypeColors,
+    q_value_threshold: request.qValueThreshold
   };
   const manhattanPlotStart = Date.now();
   const rsResult = await run_rust("manhattan_plot", JSON.stringify(rustInput));

package/routes/img.js

@@ -2,7 +2,7 @@ import { imgPayload } from "#types/checkers";
 import path from "path";
 import fs from "fs";
 import * as utils from "../src/utils.js";
-import imagesize from "image-size";
+import { imageSize } from "image-size";
 const api = {
   endpoint: "img",
   methods: {
@@ -31,9 +31,10 @@ async function sendImage(req, res) {
     if (e) throw "invalid image file";
     const data = await fs.promises.readFile(file);
     const ext = path.extname(file).substring(1);
+    const { width, height } = imageSize(file);
     const image = {
       src: `data:image/${ext};base64,${Buffer.from(data).toString("base64")}`,
-      size: imagesize(file)
+      size: `${width}x${height}`
     };
     res.send({ ...image });
   } catch (e2) {

package/routes/termdb.DE.js

@@ -7,7 +7,7 @@ import { get_ds_tdb } from "../src/termdb.js";
 import { run_R } from "@sjcrh/proteinpaint-r";
 import { mayLog } from "#src/helpers.ts";
 import serverconfig from "../src/serverconfig.js";
-import imagesize from "image-size";
+import { imageSize } from "image-size";
 import { get_header_txt } from "#src/utils.js";
 import { formatElapsedTime } from "@sjcrh/proteinpaint-shared/time.js";
 const api = {
@@ -254,9 +254,10 @@ function validateGroups(sample_size1, sample_size2, group1names, group2names) {
 async function readFileAndDelete(file, key, response) {
   const plot = await fs.promises.readFile(file);
   const plotBuffer = Buffer.from(plot).toString("base64");
+  const { width, height } = imageSize(file);
   const obj = {
     src: `data:image/png;base64,${plotBuffer}`,
-    size: imagesize(file),
+    size: `${width}x${height}`,
     key
   };
   response[key] = obj;

package/routes/wsimages.js

@@ -77,7 +77,15 @@ async function getWSImagePath(ds, wSImagesRequest) {
 }
 async function getSessionId(ds, cookieJar, getCookieString, setCookie, wsimage, projectId) {
   const sessionManager = SessionManager.getInstance();
-  const invalidateResult = await sessionManager.syncAndInvalidateSessions(wsimage);
+  const maxSessions = serverconfig.features?.tileserver?.maxSessions;
+  const maxIdleTime = serverconfig.features?.tileserver?.maxIdleTime;
+  const invalidationThreshold = serverconfig.features?.tileserver?.invalidationThreshold;
+  const invalidateResult = await sessionManager.syncAndInvalidateSessions(
+    wsimage,
+    maxSessions,
+    maxIdleTime,
+    invalidationThreshold
+  );
   if (!invalidateResult) throw new Error("Session invalidation failed");
   const session = await sessionManager.getSession(wsimage);
   if (session) {