@sjcrh/proteinpaint-server 2.70.4-2 → 2.71.0

package/routes/sampletiaimages.js

@@ -1,51 +0,0 @@
-import fs from "fs";
-import path from "path";
-import serverconfig from "#src/serverconfig.js";
-const api = {
-  endpoint: "sampletiaimages",
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "GetSampleTiaImagesRequest"
-      },
-      response: {
-        typeId: "GetSampleTiaImagesResponse"
-      }
-    },
-    post: {
-      alternativeFor: "get",
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
-      const sampleId = req.query.sample_id;
-      const sampleTiaImagesPath = path.join(
-        `${serverconfig.tpmasterdir}/${ds.queries.TiaImages.imageBySampleFolder}`,
-        sampleId
-      );
-      console.log("sampleId", sampleId);
-      const sampleTiaImages = getTiaImages(sampleTiaImagesPath);
-      res.send({ sampleTiaImages });
-    } catch (e) {
-      console.log(e);
-      res.status(404).send("Sample images not found");
-    }
-  };
-}
-function getTiaImages(sampleImagesPath) {
-  const files = fs.readdirSync(sampleImagesPath);
-  return files.filter((file) => [".svs", ".mrxs"].includes(path.extname(file)));
-}
-export {
-  api
-};

package/routes/tiaimages.js

@@ -1,83 +0,0 @@
-import axios from "axios";
-import qs from "qs";
-import path from "path";
-import serverconfig from "#src/serverconfig.js";
-import fs from "fs";
-const routePath = "tiaimages";
-const api = {
-  endpoint: `${routePath}`,
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
-    },
-    post: {
-      alternativeFor: "get",
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    try {
-      const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
-      const sampleId = req.query.sampleId;
-      if (!sampleId)
-        throw "invalid sampleId";
-      const sessionResponse = await axios.get(`${serverconfig.tileServerURL}/tileserver/session_id`, { withCredentials: true });
-      const setCookieHeader = sessionResponse.headers["set-cookie"];
-      const sessionId = setCookieHeader && setCookieHeader[0].split(";")[0].split("=")[1];
-      console.log("sessionId", sessionId);
-      const sampleTiaImagesPath = path.join(
-        `${serverconfig.tpmasterdir}/${ds.queries.TiaImages.imageBySampleFolder}`,
-        sampleId
-      );
-      const images = getTiaImages(sampleTiaImagesPath);
-      const sampleTiaTileServer = path.join(
-        `${serverconfig.tileServerMount}/${ds.queries.TiaImages.imageBySampleFolder}`,
-        sampleId
-      );
-      const fname = `${sampleTiaTileServer}/${images[0]}`;
-      const data = qs.stringify({ slide_path: fname });
-      const putResponse = await axios.put(`${serverconfig.tileServerURL}/tileserver/slide`, data, {
-        withCredentials: true,
-        headers: {
-          "Content-Type": "application/x-www-form-urlencoded",
-          Cookie: `session_id=${sessionId}`
-          // Include the session_id in the headers
-        }
-      });
-      const getResponse = await axios.get(`${serverconfig.tileServerURL}/tileserver/slide`, {
-        withCredentials: true,
-        headers: {
-          Cookie: `session_id=${sessionId}`
-          // Include the session_id in the headers
-        }
-      });
-      res.status(200).json({ sessionId, slide_dimensions: getResponse.data.slide_dimensions });
-    } catch (e) {
-      console.log(e);
-      res.send({
-        status: "error",
-        error: e.error || e
-      });
-    }
-  };
-}
-function getTiaImages(sampleImagesPath) {
-  const files = fs.readdirSync(sampleImagesPath);
-  return files.filter((file) => [".svs", ".mrxs"].includes(path.extname(file)));
-}
-export {
-  api
-};

package/routes/tileserver.js

@@ -1,40 +0,0 @@
-import axios from "axios";
-import serverconfig from "#src/serverconfig.js";
-const routePath = "tileserver";
-const api = {
-  endpoint: `${routePath}/layer/slide/:sampleId/zoomify/:TileGroup/:z-:x-:y@1x.jpg`,
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "any"
-      },
-      response: {
-        typeId: "any"
-      }
-    },
-    post: {
-      alternativeFor: "get",
-      init
-    }
-  }
-};
-function init() {
-  return async (req, res) => {
-    try {
-      const { sampleId, TileGroup, z, x, y } = req.params;
-      const url = `${serverconfig.tileServerURL}/tileserver/layer/slide/${sampleId}/zoomify/${TileGroup}/${z}-${x}-${y}@1x.jpg`;
-      const response = await axios.get(url, { responseType: "arraybuffer" });
-      res.status(response.status).send(response.data);
-    } catch (error) {
-      if (error.response) {
-        res.status(error.response.status).send(error.response.data);
-      } else {
-        res.status(500).send("Internal Server Error");
-      }
-    }
-  };
-}
-export {
-  api
-};