@sjcrh/proteinpaint-server 2.114.0 → 2.115.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.114.0",
+  "version": "2.115.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -19,8 +19,9 @@
     "start": "tsx watch . /start.js",
     "test:unit": "tsx emitImports.js unit > serverTests.js && c8 tsx serverTests.js && rm -rf ./cache",
     "precombined:coverage": "tsx emitImports.js unit > serverTests.js",
-    "combined:coverage": "closeCoverageKey=test c8 --all --src=proteinpaint/server --experimental-monocart -r=v8 -r=html -r=json -r=markdown-summary -r=markdown-details -o=./.coverage tsx ./coverage.js & ",
+    "combined:coverage": "coverageKey=test c8 --all --src=proteinpaint/server --experimental-monocart -r=v8 -r=html -r=json -r=markdown-summary -r=markdown-details -o=./.coverage tsx ./coverage.js & ",
     "postcombined:coverage": "rm -rf ./cache",
+    "spec:coverage": "tsx test/relevant.js",
     "getconf": "../build/getConfigProp.js",
     "doc": "../augen/build.sh routes shared/types/routes shared/checkers ../public/docs/server",
     "mjs": "esbuild \"$DIR/*.ts\" --platform=node --outdir=\"$DIR\" --format=esm",
@@ -64,10 +65,10 @@
     "typescript": "^5.6.3"
   },
   "dependencies": {
-    "@sjcrh/augen": "2.113.0",
+    "@sjcrh/augen": "2.115.0",
     "@sjcrh/proteinpaint-rust": "2.114.0",
-    "@sjcrh/proteinpaint-shared": "2.114.0",
-    "@sjcrh/proteinpaint-types": "2.114.0",
+    "@sjcrh/proteinpaint-shared": "2.115.0",
+    "@sjcrh/proteinpaint-types": "2.115.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/correlationVolcano.js

@@ -5,6 +5,7 @@ import serverconfig from "../src/serverconfig.js";
 import { mayLog } from "#src/helpers.ts";
 import path from "path";
 import { getStdDev } from "#shared/descriptive.stats.js";
+import { formatElapsedTime } from "#shared/time.js";
 const minArrayLength = 3;
 const minSD = 0.05;
 const api = {
@@ -92,7 +93,9 @@ async function compute(q, ds, genome) {
   const output = {
     terms: JSON.parse(await run_R(path.join(serverconfig.binpath, "utils", "corr.R"), JSON.stringify(input)))
   };
-  mayLog("Time taken to run correlation analysis:", Date.now() - time1);
+  const elapsedMs = Date.now() - time1;
+  const formattedTime = formatElapsedTime(elapsedMs);
+  mayLog("Time taken to run correlation analysis:", formattedTime);
   for (const t of output.terms) {
     const t2 = {
       tw$id: t.id,

package/routes/samplewsimages.js

@@ -23,18 +23,7 @@ function init({ genomes }) {
       if (!ds)
         throw "invalid dataset name";
       const sampleId = query.sample_id;
-      if (ds.queries.WSImages.sources) {
-        const images2 = [];
-        if (ds.queries.WSImages.sources) {
-          images2.push({
-            filename: sampleId + "_fsspec.json",
-            metadata: ""
-          });
-        }
-        res.send({ sampleWSImages: images2 });
-        return;
-      }
-      const images = await ds.queries.WSImages.getWSImages({ sampleId });
+      const images = await ds.queries.WSImages.getWSImages(sampleId);
       res.send({ sampleWSImages: images });
     } catch (e) {
       console.log(e);
@@ -42,32 +31,31 @@ function init({ genomes }) {
     }
   };
 }
-function validate_query_getSampleWSImages(ds) {
-  const q = ds.queries?.WSImages;
-  if (!q)
+async function validate_query_getSampleWSImages(ds) {
+  if (!ds.queries?.WSImages)
     return;
-  nativeValidateQuery(ds);
+  validateQuery(ds);
 }
-function nativeValidateQuery(ds) {
-  ds.queries.WSImages.getWSImages = async (q) => {
-    return await getWSImages(ds, q.sampleId);
-  };
-}
-async function getWSImages(ds, sampleName) {
-  const sql = `SELECT wsimages.filename as filename, wsimages.metadata as metadata
-                 FROM wsimages
-                          INNER JOIN sampleidmap
-                                     ON wsimages.sample = sampleidmap.id
-                 WHERE sampleidmap.name = ?`;
-  const rows = ds.cohort.db.connection.prepare(sql).all(sampleName);
-  const images = [];
-  for (const row of rows) {
-    images.push({
-      filename: row.filename,
-      metadata: row.metadata
-    });
+function validateQuery(ds) {
+  if (typeof ds.queries.WSImages.getWSImages == "function") {
+    return;
   }
-  return images;
+  ds.queries.WSImages.getWSImages = async (sampleName) => {
+    const sql = `SELECT wsimages.filename as filename, wsimages.metadata as metadata
+					 FROM wsimages
+							  INNER JOIN sampleidmap
+										 ON wsimages.sample = sampleidmap.id
+					 WHERE sampleidmap.name = ?`;
+    const rows = ds.cohort.db.connection.prepare(sql).all(sampleName);
+    const images = [];
+    for (const row of rows) {
+      images.push({
+        filename: row.filename,
+        metadata: row.metadata
+      });
+    }
+    return images;
+  };
 }
 export {
   api,

package/routes/termdb.topMutatedGenes.js

@@ -0,0 +1,51 @@
+import { topMutatedGenePayload } from "#types/checkers";
+const api = {
+  endpoint: "termdb/topMutatedGenes",
+  methods: {
+    get: {
+      init,
+      ...topMutatedGenePayload
+    },
+    post: {
+      init,
+      ...topMutatedGenePayload
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const q = req.query;
+      const g = genomes[q.genome];
+      if (!g)
+        throw "genome missing";
+      const ds = g.datasets?.[q.dslabel];
+      if (!ds)
+        throw "ds missing";
+      if (!ds.queries?.topMutatedGenes)
+        throw "not supported by ds";
+      const genes = await ds.queries.topMutatedGenes.get(q);
+      const payload = { genes };
+      res.send(payload);
+    } catch (e) {
+      res.send({ status: "error", error: e.message || e });
+      if (e.stack)
+        console.log(e.stack);
+      else
+        console.trace(e);
+    }
+  };
+}
+function validate_query_getTopMutatedGenes(ds, genome) {
+  const q = ds.queries?.topMutatedGenes;
+  if (!q)
+    return;
+  if (typeof q.get == "function")
+    return;
+  q.get = async (param) => {
+  };
+}
+export {
+  api,
+  validate_query_getTopMutatedGenes
+};

package/routes/wsisamples.js

@@ -0,0 +1,74 @@
+import { wsiSamplesPayload } from "#types/checkers";
+const routePath = "wsisamples";
+const api = {
+  endpoint: `${routePath}`,
+  methods: {
+    get: {
+      ...wsiSamplesPayload,
+      init
+    },
+    post: {
+      ...wsiSamplesPayload,
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const query = req.query;
+      const g = genomes[query.genome];
+      if (!g)
+        throw new Error("Invalid genome name");
+      const ds = g.datasets[query.dslabel];
+      if (!ds)
+        throw "Invalid dslabel";
+      const images = await ds.queries.WSImages.getSamples();
+      const payload = {
+        samples: images
+      };
+      res.status(200).json(payload);
+    } catch (e) {
+      console.warn(e);
+      res.status(500).send({
+        status: "error",
+        error: e.message || e
+      });
+    }
+  };
+}
+async function validate_query_getWSISamples(ds) {
+  const q = ds.queries?.WSImages;
+  if (!q)
+    return;
+  validateQuery(ds);
+}
+function validateQuery(ds) {
+  if (typeof ds.queries.WSImages.getSamples == "function") {
+    return;
+  }
+  ds.queries.WSImages.getSamples = async () => {
+    const sql = `SELECT wsimages.sample as sample, wsimages.filename as filename, wsimages.metadata as metadata, sampleidmap.name as sampleName
+					 FROM wsimages
+					 INNER JOIN sampleidmap
+					 ON wsimages.sample = sampleidmap.id`;
+    try {
+      const rows = ds.cohort.db.connection.prepare(sql).all();
+      const sampleMap = {};
+      for (const row of rows) {
+        if (!sampleMap[row.sample]) {
+          sampleMap[row.sample] = { sampleId: row.sampleName, wsimages: [] };
+        }
+        sampleMap[row.sample].wsimages.push(row.filename);
+      }
+      return Object.values(sampleMap);
+    } catch (error) {
+      console.error("Error fetching samples:", error);
+      throw error;
+    }
+  };
+}
+export {
+  api,
+  validate_query_getWSISamples
+};