@sjcrh/proteinpaint-server 2.69.0 → 2.69.1-1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.69.0",
+  "version": "2.69.1-1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -44,6 +44,7 @@
     "@babel/preset-typescript": "^7.21.4",
     "@babel/register": "^7.14.5",
     "@types/node": "^20.11.24",
+    "@types/qs": "^6.9.15",
     "@typescript-eslint/eslint-plugin": "^5.60.0",
     "babel-loader": "^8.2.2",
     "esbuild": "^0.19.12",
@@ -62,6 +63,7 @@
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
     "@sjcrh/proteinpaint-rust": "2.61.1",
+    "axios": "^1.7.2",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",
@@ -81,6 +83,7 @@
     "minimatch": "^3.1.2",
     "node-fetch": "^2.6.1",
     "partjson": "^0.58.2",
+    "qs": "^6.12.3",
     "tiny-async-pool": "^1.2.0",
     "typedoc-plugin-missing-exports": "^2.0.1"
   },

package/routes/genesetEnrichment.js

@@ -1,4 +1,5 @@
 import fs from "fs";
+import path from "path";
 import { spawn } from "child_process";
 import { Readable } from "stream";
 import serverconfig from "../src/serverconfig.js";
@@ -22,7 +23,20 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const results = await run_genesetEnrichment_analysis(req.query, genomes);
-      res.send(results);
+      if (!req.query.geneset_name) {
+        res.send(results);
+      } else {
+        res.sendFile(results, (err) => {
+          fs.unlink(results, (del_err) => {
+            if (del_err) {
+              console.error("Error deleting file " + results + ":", del_err);
+            }
+          });
+          if (err) {
+            res.status(404).send("Image not found");
+          }
+        });
+      }
     } catch (e) {
       res.send({ status: "error", error: e.message || e });
     }
@@ -36,7 +50,10 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     fold_change: q.fold_change,
     db: genomes[q.genome].termdbs.msigdb.cohort.db.connection.name,
     // For now msigdb has been added, but later databases other than msigdb may be used
-    gene_set_group: q.geneSetGroup
+    geneset_group: q.geneSetGroup,
+    cachedir: serverconfig.cachedir,
+    geneset_name: q.geneset_name,
+    pickle_file: q.pickle_file
   };
   const gsea_output = await run_gsea(
     `${serverconfig.binpath}/utils/gsea.py`,
@@ -44,14 +61,25 @@ async function run_genesetEnrichment_analysis(q, genomes) {
     // "/" is needed for python to accept the bracket "{" as a bracket
   );
   let result;
+  let data_found = false;
+  let image_found = false;
   for (const line of gsea_output.split("\n")) {
     if (line.startsWith("result: ")) {
       result = JSON.parse(line.replace("result: ", ""));
+      data_found = true;
+    } else if (line.startsWith("image: ")) {
+      result = JSON.parse(line.replace("image: ", ""));
+      image_found = true;
     } else {
       console.log(line);
     }
   }
-  return result;
+  if (data_found) {
+    return result;
+  } else if (image_found) {
+    const imagePath = path.join(serverconfig.cachedir, result.image_file);
+    return imagePath;
+  }
 }
 async function run_gsea(path2, data) {
   try {

package/routes/sampletiaimages.js

@@ -0,0 +1,51 @@
+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/termdb.config.js

@@ -182,6 +182,11 @@ function addNonDictionaryQueries(c, ds, genome) {
       type: q.DZImages.type
     };
   }
+  if (q.TiaImages) {
+    q2.TiaImages = {
+      type: q.TiaImages.type
+    };
+  }
   if (q.singleSampleGbtk) {
     q2.singleSampleGbtk = {};
     for (const k in q.singleSampleGbtk) {

package/routes/tiaimages.js

@@ -0,0 +1,83 @@
+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: `${routePath}`,
+  methods: {
+    get: {
+      init,
+      request: {
+        typeId: "any"
+      },
+      response: {
+        typeId: "any"
+      }
+    },
+    post: {
+      alternativeFor: "get",
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const g = genomes[req.query.genome];
+      if (!g)
+        throw "invalid genome name";
+      const ds = g.datasets[req.query.dslabel];
+      if (!ds)
+        throw "invalid dataset name";
+      const sampleId = req.query.sampleId;
+      if (!sampleId)
+        throw "invalid sampleId";
+      const sessionResponse = await axios.get("http://127.0.0.1:5000/tileserver/session_id", { withCredentials: true });
+      const setCookieHeader = sessionResponse.headers["set-cookie"];
+      const sessionId = setCookieHeader && setCookieHeader[0].split(";")[0].split("=")[1];
+      console.log("sessionId", sessionId);
+      const sampleTiaImagesPath = path.join(
+        `${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}/${images[0]}`;
+      const data = qs.stringify({ slide_path: fname });
+      const putResponse = await axios.put("http://127.0.0.1:5000/tileserver/slide", data, {
+        withCredentials: true,
+        headers: {
+          "Content-Type": "application/x-www-form-urlencoded",
+          Cookie: `session_id=${sessionId}`
+          // Include the session_id in the headers
+        }
+      });
+      const getResponse = await axios.get("http://127.0.0.1:5000/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

@@ -0,0 +1,40 @@
+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
+};