@sjcrh/proteinpaint-server 2.191.3 → 2.191.4

package/routes/saveWSIAnnotation.js

@@ -1,151 +0,0 @@
-import { FlagStatus, SelectionPrefixes, checkSelectionType } from "#types";
-import { getDbConnection } from "#src/aiHistoDBConnection.ts";
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const query = req.query;
-      if (!query.genome) throw new Error(".genome is required for deleteWSIAnnotation request.");
-      if (!query.dslabel) throw new Error(".dslabel is required for deleteWSIAnnotation request.");
-      const g = genomes[query.genome];
-      if (!g) throw new Error("invalid genome name");
-      const ds = g.datasets[query.dslabel];
-      if (!ds) throw new Error("invalid dataset name");
-      if (typeof ds.queries?.WSImages?.saveWSIAnnotation === "function") {
-        const result = await ds.queries.WSImages.saveWSIAnnotation(query, req);
-        if (result?.status === "error") {
-          return res.status(500).send(result);
-        }
-      }
-      res.status(200).send({ status: "ok" });
-    } catch (e) {
-      console.warn(e);
-      res.status(500).send({
-        status: "error",
-        error: e?.message || String(e)
-      });
-    }
-  };
-}
-async function validate_query_saveWSIAnnotation(ds) {
-  if (!ds.queries?.WSImages?.db) return;
-  const connection = getDbConnection(ds);
-  if (!connection) {
-    return;
-  }
-  validateQuery(ds, connection);
-}
-function validateQuery(ds, connection) {
-  ds.queries.WSImages.saveWSIAnnotation = async (annotation, req) => {
-    try {
-      const { email = "" } = req.query.__protected__.clientAuthResult ?? {};
-      const tileSelection = annotation.tileSelection;
-      const timestamp = (/* @__PURE__ */ new Date()).toISOString();
-      const projectId = annotation.projectId;
-      const wsimageFilename = annotation.wsimage;
-      const coords = JSON.stringify(tileSelection.zoomCoordinates ?? []);
-      const flag = tileSelection.flag;
-      const classId = annotation.classId;
-      const isAnnotation = checkSelectionType(tileSelection, SelectionPrefixes.Annotation);
-      const isPrediction = checkSelectionType(tileSelection, SelectionPrefixes.Prediction);
-      const currentUser = connection.prepare("SELECT current_user FROM project WHERE id = ?").get(projectId);
-      if (!await ds.queries?.AIHalAuth?.checkAuthorization(req, "annotate", currentUser?.current_user ?? null)) {
-        return {
-          status: "error",
-          error: "logout"
-        };
-      }
-      if (!isAnnotation && !isPrediction) {
-        return {
-          status: "error",
-          error: `Invalid tileSelection id "${tileSelection.id}". Must start with "${SelectionPrefixes.Annotation}" or "${SelectionPrefixes.Prediction}".`
-        };
-      }
-      if (projectId == null || wsimageFilename == null) {
-        return {
-          status: "error",
-          error: "Missing required fields: projectId and wsimage."
-        };
-      }
-      const getImageIdSql = `
-				SELECT id
-				FROM project_images
-				WHERE project_id = ?
-				  AND image_path = ?
-				LIMIT 1
-			`;
-      const imageRow = connection.prepare(getImageIdSql).get(projectId, wsimageFilename);
-      if (!imageRow?.id) {
-        return {
-          status: "error",
-          error: `Image not found for project_id=${projectId} and image_path="${wsimageFilename}".`
-        };
-      }
-      const imageId = imageRow.id;
-      connection.prepare(
-        `DELETE FROM project_flagged_annotations
-					 WHERE project_id = ?
-					   AND image_id = ?
-					   AND coordinates = ?`
-      ).run(projectId, imageId, coords);
-      connection.prepare(
-        `DELETE FROM project_flagged_predictions
-					 WHERE project_id = ?
-					   AND image_id = ?
-					   AND coordinates = ?`
-      ).run(projectId, imageId, coords);
-      connection.prepare(
-        `DELETE FROM project_annotations
-					 WHERE project_id = ?
-					   AND image_id = ?
-					   AND coordinates = ?`
-      ).run(projectId, imageId, coords);
-      if (isAnnotation) {
-        if (tileSelection.flag === FlagStatus.Normal) {
-          connection.prepare(
-            `
-						INSERT INTO project_annotations (
-							project_id, user_id, coordinates, timestamp,class_id, image_id
-						) VALUES (?, ?, ?, ?, ?, ?)
-					`
-          ).run(projectId, email, coords, timestamp, classId, imageId);
-        } else {
-          connection.prepare(
-            `
-				INSERT INTO project_flagged_annotations (
-					project_id, user_id, coordinates, timestamp, flagged,class_id, image_id
-				) VALUES (?, ?, ?, ?, ?, ?, ?)
-				`
-          ).run(projectId, email, coords, timestamp, flag, classId, imageId);
-        }
-      } else if (isPrediction) {
-        if (tileSelection.flag !== FlagStatus.Normal) {
-          const insertSql = `
-                    INSERT INTO project_flagged_predictions (project_id, user_email, prediction_class_id, coordinates, flag_type,image_id,timestamp)
-                    VALUES (?, ?, ?, ?, ?, ?, ?)
-                `;
-          const insertStmt = connection.prepare(insertSql);
-          insertStmt.run(
-            annotation.projectId,
-            email,
-            annotation.classId,
-            JSON.stringify(tileSelection.zoomCoordinates),
-            tileSelection.flag,
-            imageId,
-            timestamp
-          );
-        }
-      }
-      return { status: "ok" };
-    } catch (error) {
-      console.error("Error saving annotation:", error);
-      return {
-        status: "error",
-        error: error?.message || "Failed to save annotation"
-      };
-    }
-  };
-}
-export {
-  init,
-  validate_query_saveWSIAnnotation
-};

package/routes/wsimages.js

@@ -1,176 +0,0 @@
-import ky from "ky";
-import qs from "qs";
-import path from "path";
-import { CookieJar } from "tough-cookie";
-import { promisify } from "util";
-import SessionManager from "../src/wsisessions/SessionManager.ts";
-import { ShardManager } from "#src/sharding/ShardManager.ts";
-import { TileServerShardingAlgorithm } from "#src/sharding/TileServerShardingAlgorithm.ts";
-import serverconfig from "#src/serverconfig.js";
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const wSImagesRequest = req.query;
-      const g = genomes[wSImagesRequest.genome];
-      if (!g) throw new Error("Invalid genome name");
-      const ds = g.datasets[wSImagesRequest.dslabel];
-      if (!ds) throw new Error("Invalid dataset name");
-      const sampleId = wSImagesRequest.sampleId;
-      const wsimage = wSImagesRequest.wsimage;
-      const aiProjectId = wSImagesRequest.aiProjectId;
-      if (!sampleId && (!wsimage || !aiProjectId)) {
-        throw new Error("Invalid parameters: sampleId or both wsimage and aiProjectId must be provided");
-      }
-      const cookieJar = new CookieJar();
-      const setCookie = promisify(cookieJar.setCookie.bind(cookieJar));
-      const getCookieString = promisify(cookieJar.getCookieString.bind(cookieJar));
-      const wsiImagePath = await getWSImagePath(ds, wSImagesRequest);
-      const session = await getSessionId(ds, cookieJar, getCookieString, setCookie, wsiImagePath, aiProjectId);
-      const getWsiImageResponse = await getWsiImageDimensions(
-        session.imageSessionId,
-        getCookieString,
-        wsiImagePath
-      );
-      const payload = {
-        status: "ok",
-        wsiSessionId: session.imageSessionId,
-        overlays: session.overlays,
-        slide_dimensions: getWsiImageResponse.slide_dimensions,
-        mpp: getWsiImageResponse.mpp
-      };
-      res.status(200).json(payload);
-    } catch (e) {
-      console.warn(e);
-      res.status(500).send({
-        status: "error",
-        error: e.message || e
-      });
-    }
-  };
-}
-async function getWSImagePath(ds, wSImagesRequest) {
-  const mount = serverconfig.features?.tileserver?.mount;
-  if (!mount) throw new Error("No mount available for TileServer");
-  if (wSImagesRequest.sampleId) {
-    return path.join(
-      `${mount}/${ds.queries.WSImages.imageBySampleFolder}/${wSImagesRequest.sampleId}`,
-      wSImagesRequest.wsimage
-    );
-  } else {
-    return path.join(`${mount}/${ds.queries.WSImages.aiToolImageFolder}/`, wSImagesRequest.wsimage);
-  }
-}
-async function getSessionId(ds, cookieJar, getCookieString, setCookie, wsimage, projectId) {
-  const sessionManager = SessionManager.getInstance();
-  const maxSessions = serverconfig.features?.tileserver?.maxSessions;
-  const maxIdleTime = serverconfig.features?.tileserver?.maxIdleTime;
-  const invalidationThreshold = serverconfig.features?.tileserver?.invalidationThreshold;
-  const invalidateResult = await sessionManager.syncAndInvalidateSessions(
-    wsimage,
-    maxSessions,
-    maxIdleTime,
-    invalidationThreshold
-  );
-  if (!invalidateResult) throw new Error("Session invalidation failed");
-  const session = await sessionManager.getSession(wsimage);
-  if (session) {
-    return session;
-  }
-  const tileServer = await sessionManager.getTileServerShard(wsimage);
-  if (!tileServer) throw new Error("No TileServer shard available");
-  await ky.get(`${tileServer.url}/tileserver/session_id`, {
-    timeout: 5e4,
-    hooks: getHooks(cookieJar, getCookieString, setCookie)
-  });
-  const cookieString = await getCookieString(`${tileServer.url}/tileserver/session_id`);
-  const sessionId = cookieString.match(/session_id=([^;]*)/)?.[1];
-  if (!sessionId) throw new Error("session_id not found");
-  const overlays = [];
-  const data = qs.stringify({ slide_path: wsimage });
-  await ky.put(`${tileServer.url}/tileserver/slide`, {
-    body: data,
-    timeout: 5e4,
-    headers: {
-      "Content-Type": "application/x-www-form-urlencoded",
-      Cookie: `session_id=${sessionId}`
-    },
-    hooks: getHooks(cookieJar, getCookieString, setCookie)
-  });
-  if (ds.queries.WSImages.getPredictionLayers) {
-    const predictionLayers = await ds.queries.WSImages.getPredictionLayers(projectId, wsimage);
-    if (predictionLayers) {
-      const resolveFilename = (key) => {
-        if (!predictionLayers) return void 0;
-        if (predictionLayers instanceof Map) return predictionLayers.get(key) ?? void 0;
-        return predictionLayers[key] ?? void 0;
-      };
-      const pushOverlayForKey = async (key, predictionOverlayType) => {
-        const overlayPath = resolveFilename(key);
-        if (!overlayPath) return;
-        const annotationsData = qs.stringify({
-          overlay_path: overlayPath
-        });
-        const layerNumber = await ky.put(`${tileServer.url}/tileserver/overlay`, {
-          body: annotationsData,
-          timeout: 5e4,
-          headers: {
-            "Content-Type": "application/x-www-form-urlencoded",
-            Cookie: `session_id=${sessionId}`
-          },
-          hooks: getHooks(cookieJar, getCookieString, setCookie)
-        }).json();
-        const overlay = {
-          layerNumber,
-          predictionOverlayType
-        };
-        overlays.push(overlay);
-      };
-      await pushOverlayForKey("Prediction", "Prediction");
-      await pushOverlayForKey("Uncertainty", "Uncertainty");
-    }
-  }
-  const sessionData = await sessionManager.setSession(wsimage, sessionId, tileServer, overlays);
-  return sessionData;
-}
-async function getWsiImageDimensions(sessionId, getCookieString, wsimage) {
-  const shardManager = ShardManager.getInstance();
-  const tileServer = await shardManager.shardingAlgorithmsMap?.get(TileServerShardingAlgorithm.TILE_SERVER_SHARDING_KEY)?.getShard(wsimage);
-  if (!tileServer) {
-    throw new Error("No tile server");
-  }
-  return await ky.get(`${tileServer.url}/tileserver/slide`, {
-    timeout: 12e4,
-    hooks: {
-      beforeRequest: [
-        async (request) => {
-          let cookie = await getCookieString(request.url);
-          if (!cookie) {
-            cookie = `session_id=${sessionId}`;
-          }
-          request.headers.set("Cookie", cookie);
-        }
-      ]
-    }
-  }).json();
-}
-function getHooks(cookieJar, getCookieString, setCookie) {
-  return {
-    beforeRequest: [
-      async (request) => {
-        const cookie = await getCookieString(request.url);
-        request.headers.set("Cookie", cookie);
-      }
-    ],
-    afterResponse: [
-      async (request, options, response) => {
-        const setCookieHeader = response.headers.get("set-cookie");
-        if (setCookieHeader) {
-          await setCookie(setCookieHeader, request.url);
-        }
-      }
-    ]
-  };
-}
-export {
-  init
-};