@sjcrh/proteinpaint-server 2.70.4 → 2.72.0

package/dataset/termdb.test.js

@@ -194,39 +194,38 @@ var termdb_test_default = {
     topVariablyExpressedGenes: { src: "native" }
   },
   assayAvailability: {
-    // use "genetic_race" as fake sources of assay availability
+    // term used below must be annotated on samples rather than patients(root). otherwise matrix will pull wrong samples for geneVariant term
     byDt: {
       // snvindel, differentiating sample origin
       1: {
         byOrigin: {
           germline: {
-            term_id: "genetic_race",
+            term_id: "assayavailability_germline",
             label: "Germline",
             // human readable label of this origin
-            yes: { value: ["European Ancestry", "Asian Ancestry"] },
-            no: { value: ["Multi-Ancestry-Admixed", "African Ancestry"] }
+            yes: { value: ["1"] },
+            no: { value: ["2"] }
           },
           somatic: {
-            term_id: "genetic_race",
+            term_id: "wgs_curated",
             label: "Somatic",
-            yes: { value: ["European Ancestry", "African Ancestry"] },
-            no: { value: ["Multi-Ancestry-Admixed", "Asian Ancestry"] }
+            yes: { value: ["1"] },
+            no: { value: ["0"] }
+            // the category doesn't exist in termdb but is still supplied since somatic.no{} is required
           }
         }
       },
       // fusion
       2: {
-        //mutations are detected from RNAseq
-        term_id: "genetic_race",
-        yes: { value: ["European Ancestry", "African Ancestry"] },
-        no: { value: ["Asian Ancestry", "Multi-Ancestry-Admixed"] }
+        term_id: "assayavailability_fusion",
+        yes: { value: ["1"] },
+        no: { value: ["2"] }
       },
       // cnv
       4: {
-        // mutations are detected from Methylation
-        term_id: "genetic_race",
-        yes: { value: ["European Ancestry", "African Ancestry"] },
-        no: { value: ["Asian Ancestry", "Multi-Ancestry-Admixed"] }
+        term_id: "assayavailability_cnv",
+        yes: { value: ["1"] },
+        no: { value: ["2"] }
       }
     }
   }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.70.4",
+  "version": "2.72.0",
   "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/tough-cookie": "^4.0.5",
     "@typescript-eslint/eslint-plugin": "^5.60.0",
     "babel-loader": "^8.2.2",
     "esbuild": "^0.19.12",
@@ -82,6 +83,7 @@
     "node-fetch": "^2.6.1",
     "partjson": "^0.58.2",
     "tiny-async-pool": "^1.2.0",
+    "tough-cookie": "^4.1.4",
     "typedoc-plugin-missing-exports": "^2.0.1"
   },
   "repository": {

package/routes/gdc.topMutatedGenes.js

@@ -218,6 +218,7 @@ const queryV2 = {
       }
     };
     if (q.filter0) {
+      variables.ssmCase.content.push(JSON.parse(JSON.stringify(q.filter0)));
       variables.caseFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));
       variables.geneCaseFilter.content.push(JSON.parse(JSON.stringify(q.filter0)));
       variables.cnvLossFilters.content.push(JSON.parse(JSON.stringify(q.filter0)));

package/routes/samplewsimages.js

@@ -0,0 +1,50 @@
+import fs from "fs";
+import path from "path";
+import serverconfig from "#src/serverconfig.js";
+const api = {
+  endpoint: "samplewsimages",
+  methods: {
+    get: {
+      init,
+      request: {
+        typeId: "GetSampleWSImagesRequest"
+      },
+      response: {
+        typeId: "GetSampleWSImagesResponse"
+      }
+    },
+    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 sampleWSImagesPath = path.join(
+        `${serverconfig.tpmasterdir}/${ds.queries.WSImages.imageBySampleFolder}`,
+        sampleId
+      );
+      const sampleWSImages = await getWSImages(sampleWSImagesPath);
+      res.send({ sampleWSImages });
+    } catch (e) {
+      console.log(e);
+      res.status(404).send("Sample images not found");
+    }
+  };
+}
+async function getWSImages(sampleImagesPath) {
+  const files = await fs.promises.readdir(sampleImagesPath);
+  return files.filter((file) => [".svs", ".mrxs", ".scn", ".ndpi", ".tiff"].includes(path.extname(file)));
+}
+export {
+  api
+};

package/routes/termdb.config.js

@@ -177,11 +177,16 @@ function addNonDictionaryQueries(c, ds, genome) {
       q2.NIdata[k] = JSON.parse(JSON.stringify(q.NIdata[k]));
     }
   }
-  if (q.DZImages) {
+  if (q.DZImages && serverconfig.features.showDZImages) {
     q2.DZImages = {
       type: q.DZImages.type
     };
   }
+  if (q.WSImages && serverconfig.features.showWSImages) {
+    q2.WSImages = {
+      type: q.WSImages.type
+    };
+  }
   if (q.singleSampleGbtk) {
     q2.singleSampleGbtk = {};
     for (const k in q.singleSampleGbtk) {

package/routes/termdb.topVariablyExpressedGenes.js

@@ -1,9 +1,9 @@
 import path from "path";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
-import got from "got";
 import serverconfig from "#src/serverconfig.js";
 import { get_samples } from "#src/termdb.sql.js";
 import { makeFilter } from "#src/mds3.gdc.js";
+import { cachedFetch } from "#src/utils.js";
 const api = {
   endpoint: "termdb/topVariablyExpressedGenes",
   methods: {
@@ -120,11 +120,12 @@ function gdcValidateQuery(ds, genome) {
     const { host, headers } = ds.getHostHeaders(q);
     const url = path.join(host.geneExp, "/gene_expression/gene_selection");
     try {
-      const response = await got.post(url, {
+      const response = await cachedFetch(url, {
+        method: "POST",
         headers,
-        body: JSON.stringify(getGeneSelectionArg(q))
+        body: getGeneSelectionArg(q)
       });
-      const re = JSON.parse(response.body);
+      const re = response.body;
       const genes = [];
       if (!Array.isArray(re.gene_selection))
         throw "re.gene_selection[] is not array";

package/routes/tileserver.js

@@ -0,0 +1,42 @@
+import ky from "ky";
+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 ky.get(url);
+      const buffer = await response.arrayBuffer();
+      res.status(response.status).send(Buffer.from(buffer));
+    } catch (error) {
+      if (error.response) {
+        const errorBody = await error.response.arrayBuffer();
+        res.status(error.response.status).send(Buffer.from(errorBody));
+      } else {
+        res.status(500).send("Internal Server Error");
+      }
+    }
+  };
+}
+export {
+  api
+};

package/routes/wsimages.js

@@ -0,0 +1,115 @@
+import ky from "ky";
+import qs from "qs";
+import path from "path";
+import serverconfig from "#src/serverconfig.js";
+import { CookieJar } from "tough-cookie";
+import { promisify } from "util";
+const routePath = "wsimages";
+const api = {
+  endpoint: `${routePath}`,
+  methods: {
+    get: {
+      init,
+      request: {
+        typeId: "any"
+      },
+      response: {
+        typeId: "any"
+      }
+    },
+    post: {
+      alternativeFor: "get",
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const g = genomes[req.query.genome];
+      if (!g)
+        throw "invalid genome name";
+      const ds = g.datasets[req.query.dslabel];
+      if (!ds)
+        throw "invalid dataset name";
+      const sampleId = req.query.sampleId;
+      if (!sampleId)
+        throw "invalid sampleId";
+      const wsimage = req.query.wsimage;
+      if (!wsimage)
+        throw "invalid wsimage";
+      const cookieJar = new CookieJar();
+      const setCookie = promisify(cookieJar.setCookie.bind(cookieJar));
+      const getCookieString = promisify(cookieJar.getCookieString.bind(cookieJar));
+      await ky.get(`${serverconfig.tileServerURL}/tileserver/session_id`, {
+        hooks: {
+          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);
+              }
+            }
+          ]
+        }
+      });
+      const cookieString = await getCookieString(`${serverconfig.tileServerURL}/tileserver/session_id`);
+      const sessionId = cookieString.match(/session_id=([^;]*)/)?.[1];
+      const sampleWsiTileServer = path.join(
+        `${serverconfig.tileServerMount}/${ds.queries.WSImages.imageBySampleFolder}/${sampleId}`,
+        wsimage
+      );
+      const data = qs.stringify({ slide_path: sampleWsiTileServer });
+      await ky.put(`${serverconfig.tileServerURL}/tileserver/slide`, {
+        body: data,
+        headers: {
+          "Content-Type": "application/x-www-form-urlencoded",
+          Cookie: `session_id=${sessionId}`
+          // Include the session_id in the headers
+        },
+        hooks: {
+          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);
+              }
+            }
+          ]
+        }
+      });
+      const getWsiImageResponse = await ky.get(`${serverconfig.tileServerURL}/tileserver/slide`, {
+        hooks: {
+          beforeRequest: [
+            async (request) => {
+              const cookie = await getCookieString(request.url);
+              request.headers.set("Cookie", cookie);
+            }
+          ]
+        }
+      }).json();
+      res.status(200).json({ sessionId, slide_dimensions: getWsiImageResponse.slide_dimensions });
+    } catch (e) {
+      console.log(e);
+      res.send({
+        status: "error",
+        error: e.error || e
+      });
+    }
+  };
+}
+export {
+  api
+};