@sjcrh/proteinpaint-server 2.133.2 → 2.133.3-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.133.2",
+  "version": "2.133.3-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -65,7 +65,7 @@
     "@sjcrh/proteinpaint-r": "2.130.0",
     "@sjcrh/proteinpaint-rust": "2.133.0",
     "@sjcrh/proteinpaint-shared": "2.132.1-2",
-    "@sjcrh/proteinpaint-types": "2.133.0",
+    "@sjcrh/proteinpaint-types": "2.133.3-0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/sampleWsiAiApi.js

@@ -0,0 +1,33 @@
+import { sampleWsiAiApiPayload } from "#types/checkers";
+const routePath = "sampleWsiAiApi";
+const api = {
+  endpoint: `${routePath}`,
+  methods: {
+    get: {
+      ...sampleWsiAiApiPayload,
+      init
+    },
+    post: {
+      ...sampleWsiAiApiPayload,
+      init
+    }
+  }
+};
+function init() {
+  return async (req, res) => {
+    try {
+      const request = req.query;
+      console.log("sample wsi api request:", request);
+      res.status(200).send({ testKey: "completed" });
+    } catch (e) {
+      console.warn(e);
+      res.status(500).send({
+        status: "error",
+        error: e.message || e
+      });
+    }
+  };
+}
+export {
+  api
+};

package/routes/samplewsimages.js

@@ -1,4 +1,7 @@
 import { sampleWSImagesPayload } from "#types/checkers";
+import path from "path";
+import fs from "fs";
+import serverconfig from "#src/serverconfig.js";
 const api = {
   endpoint: "samplewsimages",
   methods: {
@@ -26,14 +29,40 @@ function init({ genomes }) {
       const wsimages = await ds.queries.WSImages.getWSImages(sampleId);
       if (ds.queries.WSImages.getWSIAnnotations) {
         for (const wsimage of wsimages) {
+          if (ds.queries.WSImages.makeGeoJson) {
+            await ds.queries.WSImages.makeGeoJson(sampleId, wsimage);
+          }
           const annotations = await ds.queries.WSImages.getWSIAnnotations(sampleId, wsimage.filename);
-          if (annotations) {
+          if (annotations && annotations.length > 0) {
             wsimage.overlays = annotations;
+            const annotationFilePath = path.join(
+              serverconfig.tpmasterdir,
+              ds.queries.WSImages.imageBySampleFolder,
+              sampleId,
+              annotations[0]
+            );
+            const annotationData = JSON.parse(fs.readFileSync(annotationFilePath, "utf8"));
+            if (!annotationData.features && !ds.queries.WSImages?.classes?.length) {
+              throw new Error(`No classes found for WSImage annotations in dataset ${ds.label}`);
+            }
+            wsimage.annotationsData = annotationData.features.map((d) => {
+              const featClass = ds.queries.WSImages?.classes?.find((f) => f.id == d.properties.class)?.label || d.properties.class;
+              return {
+                zoomCoordinates: d.properties.zoomCoordinates,
+                type: d.properties.type,
+                uncertainty: d.properties.uncertainty,
+                class: featClass
+              };
+            });
+            wsimage.classes = ds.queries?.WSImages?.classes;
+            wsimage.uncertainty = ds.queries?.WSImages?.uncertainty;
+            wsimage.activePatchColor = ds.queries?.WSImages?.activePatchColor || "#00e62a";
           }
           if (ds.queries.WSImages.getZoomInPoints) {
             const zoomInPoints = await ds.queries.WSImages.getZoomInPoints(
               sampleId,
-              wsimage.filename
+              wsimage.filename,
+              query.index
             );
             if (zoomInPoints) {
               wsimage.zoomInPoints = zoomInPoints;
@@ -41,6 +70,14 @@ function init({ genomes }) {
           }
         }
       }
+      if (ds.queries.WSImages.getWSIPredictionOverlay) {
+        for (const wsimage of wsimages) {
+          const predictionOverlay = await ds.queries.WSImages.getWSIPredictionOverlay(sampleId, wsimage.filename);
+          if (predictionOverlay) {
+            wsimage.predictionLayers = [predictionOverlay];
+          }
+        }
+      }
       res.send({ sampleWSImages: wsimages });
     } catch (e) {
       console.log(e);

package/routes/wsimages.js

@@ -3,6 +3,7 @@ import qs from "qs";
 import path from "path";
 import { CookieJar } from "tough-cookie";
 import { promisify } from "util";
+import { PredictionOverlayType } from "#types";
 import { wsImagesPayload } from "#types/checkers";
 import SessionManager from "../src/wsisessions/SessionManager.ts";
 import { ShardManager } from "#src/sharding/ShardManager.ts";
@@ -45,11 +46,16 @@ function init({ genomes }) {
       if (!mount)
         throw new Error("No mount available for TileServer");
       const wsiImagePath = path.join(`${mount}/${ds.queries.WSImages.imageBySampleFolder}/${sampleId}`, wsimage);
-      const sessionId = await getSessionId(ds, sampleId, cookieJar, getCookieString, setCookie, wsiImagePath);
-      const getWsiImageResponse = await getWsiImageDimensions(sessionId, getCookieString, wsiImagePath);
+      const session = await getSessionId(ds, sampleId, cookieJar, getCookieString, setCookie, wsiImagePath);
+      const getWsiImageResponse = await getWsiImageDimensions(
+        session.imageSessionId,
+        getCookieString,
+        wsiImagePath
+      );
       const payload = {
         status: "ok",
-        wsiSessionId: sessionId,
+        wsiSessionId: session.imageSessionId,
+        overlays: session.overlays,
         slide_dimensions: getWsiImageResponse.slide_dimensions
       };
       res.status(200).json(payload);
@@ -67,9 +73,9 @@ async function getSessionId(ds, sampleId, cookieJar, getCookieString, setCookie,
   const invalidateResult = await sessionManager.syncAndInvalidateSessions(wsimage);
   if (!invalidateResult)
     throw new Error("Session invalidation failed");
-  const sessionData = await sessionManager.getSession(wsimage);
-  if (sessionData) {
-    return sessionData.imageSessionId;
+  const session = await sessionManager.getSession(wsimage);
+  if (session) {
+    return session;
   }
   const tileServer = await sessionManager.getTileServerShard(wsimage);
   if (!tileServer)
@@ -82,6 +88,7 @@ async function getSessionId(ds, sampleId, cookieJar, getCookieString, setCookie,
   const sessionId = cookieString.match(/session_id=([^;]*)/)?.[1];
   if (!sessionId)
     throw new Error("session_id not found");
+  const overlays = [];
   const data = qs.stringify({ slide_path: wsimage });
   await ky.put(`${tileServer.url}/tileserver/slide`, {
     body: data,
@@ -92,25 +99,79 @@ async function getSessionId(ds, sampleId, cookieJar, getCookieString, setCookie,
     },
     hooks: getHooks(cookieJar, getCookieString, setCookie)
   });
-  await sessionManager.setSession(wsimage, sessionId, tileServer);
-  if (ds.queries.WSImages.getWSIAnnotations) {
-    const annotationFiles = await ds.queries.WSImages.getWSIAnnotations(sampleId, wsimage);
-    if (!annotationFiles)
-      throw new Error("No annotations files found");
+  if (ds.queries.WSImages.getWSIPredictionOverlay) {
+    const predictionOverlay = await ds.queries.WSImages.getWSIPredictionOverlay(sampleId, wsimage);
+    if (predictionOverlay) {
+      const mount = serverconfig.features?.tileserver?.mount;
+      const annotationsFilePath = path.join(
+        `${mount}/${ds.queries.WSImages.imageBySampleFolder}/${sampleId}`,
+        predictionOverlay
+      );
+      const annotationsData = qs.stringify({
+        overlay_path: annotationsFilePath
+      });
+      const layerNumber = await ky.put(`${tileServer.url}/tileserver/overlay`, {
+        body: annotationsData,
+        timeout: 5e4,
+        headers: {
+          "Content-Type": "application/x-www-form-urlencoded",
+          Cookie: `session_id=${sessionId}`
+        },
+        hooks: getHooks(cookieJar, getCookieString, setCookie)
+      }).json();
+      const overlay = {
+        layerNumber,
+        predictionOverlayType: PredictionOverlayType.PREDICTION
+      };
+      overlays.push(overlay);
+    }
+  }
+  if (ds.queries.WSImages.getWSIUncertaintyOverlay) {
+    const uncertaintyOverlay = await ds.queries.WSImages.getWSIUncertaintyOverlay(sampleId, wsimage);
+    if (uncertaintyOverlay) {
+      const mount = serverconfig.features?.tileserver?.mount;
+      const annotationsFilePath = path.join(
+        `${mount}/${ds.queries.WSImages.imageBySampleFolder}/${sampleId}`,
+        uncertaintyOverlay
+      );
+      const annotationsData = qs.stringify({
+        overlay_path: annotationsFilePath
+      });
+      const layerNumber = await ky.put(`${tileServer.url}/tileserver/overlay`, {
+        body: annotationsData,
+        timeout: 5e4,
+        headers: {
+          "Content-Type": "application/x-www-form-urlencoded",
+          Cookie: `session_id=${sessionId}`
+        },
+        hooks: getHooks(cookieJar, getCookieString, setCookie)
+      }).json();
+      const overlay = {
+        layerNumber,
+        predictionOverlayType: PredictionOverlayType.UNCERTAINTY
+      };
+      overlays.push(overlay);
+    }
+  }
+  const sessionData = await sessionManager.setSession(wsimage, sessionId, tileServer, overlays);
+  if (ds.queries.WSImages.getWSIPredictionPatches) {
+    const predictionPatches = await ds.queries.WSImages.getWSIPredictionPatches(sampleId, wsimage);
+    if (!predictionPatches)
+      throw new Error("No prediction files found");
     const mount = serverconfig.features?.tileserver?.mount;
     if (!mount)
       throw new Error("No mount available for TileServer");
-    if (annotationFiles.length > 0) {
-      for (const annotationFile of annotationFiles) {
-        const annotationsFilePath = path.join(
+    if (predictionPatches.length > 0) {
+      for (const predictionPatch of predictionPatches) {
+        const predictionFilePath = path.join(
           `${mount}/${ds.queries.WSImages.imageBySampleFolder}/${sampleId}`,
-          annotationFile
+          predictionPatch
         );
-        const annotationsData = qs.stringify({
-          overlay_path: annotationsFilePath
+        const predictionsData = qs.stringify({
+          overlay_path: predictionFilePath
         });
         await ky.put(`${tileServer.url}/tileserver/overlay`, {
-          body: annotationsData,
+          body: predictionsData,
           timeout: 5e4,
           headers: {
             "Content-Type": "application/x-www-form-urlencoded",
@@ -121,8 +182,8 @@ async function getSessionId(ds, sampleId, cookieJar, getCookieString, setCookie,
       }
       const cmapData = qs.stringify({
         cmap: JSON.stringify({
-          keys: ["annotation"],
-          values: [ds.queries.WSImages.annotationsColor]
+          keys: ["prediction", "annotation"],
+          values: [ds.queries.WSImages.predictionColor, ds.queries.WSImages.annotationsColor]
         })
       });
       await ky.put(`${tileServer.url}/tileserver/cmap`, {
@@ -136,7 +197,7 @@ async function getSessionId(ds, sampleId, cookieJar, getCookieString, setCookie,
       });
     }
   }
-  return sessionId;
+  return sessionData;
 }
 async function getWsiImageDimensions(sessionId, getCookieString, wsimage) {
   const shardManager = ShardManager.getInstance();