@sjcrh/proteinpaint-server 2.74.2 → 2.75.0

package/dataset/termdb.test.js

@@ -83,6 +83,15 @@ var termdb_test_default = {
         }
       },
       termid2totalsize2: {}
+      // about: {
+      // 	tab: {
+      // 		order: 4,
+      // 		topLabel: 'test',
+      // 		midLabel: 'test about',
+      // 		btmLabel: 'test'
+      // 	},
+      // 	html: 'Test'
+      // }
     },
     scatterplots: {
       plots: [

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.74.2",
+  "version": "2.75.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,7 +62,7 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.46.0",
-    "@sjcrh/proteinpaint-rust": "2.74.0",
+    "@sjcrh/proteinpaint-rust": "2.75.0",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/brainImaging.js

@@ -0,0 +1,99 @@
+import fs from "fs";
+import path from "path";
+import serverconfig from "#src/serverconfig.js";
+import { spawn } from "child_process";
+const api = {
+  endpoint: "brainImaging",
+  methods: {
+    get: {
+      init,
+      request: {
+        typeId: "GetBrainImagingRequest"
+      },
+      response: {
+        typeId: "GetBrainImagingResponse"
+      }
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const query = req.query;
+      const g = genomes[query.genome];
+      if (!g)
+        throw "invalid genome name";
+      const ds = g.datasets[query.dslabel];
+      if (!ds)
+        throw "invalid dataset name";
+      const brainImage = await getBrainImage(query, genomes);
+      res.send({ brainImage });
+    } catch (e) {
+      console.log(e);
+      res.status(404).send("Sample brain image not found");
+    }
+  };
+}
+async function getBrainImage(query, genomes) {
+  const ds = genomes[query.genome].datasets[query.dslabel];
+  const q = ds.queries.NIdata;
+  const key = query.refKey;
+  if (q[key].referenceFile && q[key].samples) {
+    const refFile = path.join(serverconfig.tpmasterdir, q[key].referenceFile);
+    const dirPath = path.join(serverconfig.tpmasterdir, q[key].samples);
+    const files = fs.readdirSync(dirPath).filter((file) => file.endsWith(".nii") && fs.statSync(path.join(dirPath, file)).isFile());
+    if (query.samplesOnly) {
+      const sampleNames = files.map((name) => name.split(".nii")[0]);
+      if (q[key].sampleColumns) {
+        const samples = {};
+        for (const s of sampleNames) {
+          const annoForOneS = { sample: s };
+          const sid = ds.cohort.termdb.q.sampleName2id(s);
+          for (const term of q[key].sampleColumns) {
+            const v = ds.cohort.termdb.q.getSample2value(term.termid, sid);
+            if (v[0]) {
+              annoForOneS[term.termid] = v[0].value;
+            }
+          }
+          samples[s] = annoForOneS;
+        }
+        return Object.values(samples);
+      }
+      return sampleNames;
+    }
+    return new Promise((resolve, reject) => {
+      const filePaths = query.selectedSampleFileNames.map((file) => path.join(dirPath, file));
+      const ps = spawn("python3", [
+        `${serverconfig.binpath}/../python/src/plotBrainImaging.py`,
+        refFile,
+        query.l,
+        query.f,
+        query.t,
+        ...filePaths
+      ]);
+      const imgData = [];
+      ps.stdout.on("data", (data) => {
+        imgData.push(data);
+      });
+      ps.stderr.on("data", (data) => {
+        console.error(`stderr: ${data}`);
+        reject(new Error(`Python script filed: ${data}`));
+      });
+      ps.on("close", (code) => {
+        if (code === 0) {
+          const imageBuffer = Buffer.concat(imgData);
+          const base64Data = imageBuffer.toString("base64");
+          const imgUrl = `data:image/png;base64,${base64Data}`;
+          resolve(imgUrl);
+        } else {
+          reject(new Error(`Python script exited with code ${code}`));
+        }
+      });
+    });
+  } else {
+    throw "no reference or sample files";
+  }
+}
+export {
+  api
+};

package/routes/samplewsimages.js

@@ -1,6 +1,3 @@
-import fs from "fs";
-import path from "path";
-import serverconfig from "#src/serverconfig.js";
 const api = {
   endpoint: "samplewsimages",
   methods: {
@@ -30,22 +27,42 @@ function init({ genomes }) {
       if (!ds)
         throw "invalid dataset name";
       const sampleId = query.sample_id;
-      const sampleWSImagesPath = path.join(
-        `${serverconfig.tpmasterdir}/${ds.queries.WSImages.imageBySampleFolder}`,
-        sampleId
-      );
-      const sampleWSImages = await getWSImages(sampleWSImagesPath);
-      res.send({ sampleWSImages });
+      const images = await ds.queries.WSImages.getWSImages({ sampleId });
+      res.send({ sampleWSImages: images });
     } 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)));
+function validate_query_getSampleWSImages(ds, genome) {
+  const q = ds.queries.WSImages;
+  if (!q)
+    return;
+  nativeValidateQuery(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
+    });
+  }
+  return images;
 }
 export {
-  api
+  api,
+  validate_query_getSampleWSImages
 };

package/routes/termdb.cohort.summary.js

@@ -23,7 +23,7 @@ function init({ genomes }) {
       if (!genome)
         throw "invalid genome";
       const [ds] = get_ds_tdb(genome, q);
-      res.send({ count: ds.cohort.termdb.q.getcohortsamplecount(q.cohort) });
+      res.send({ count: ds.cohort.termdb.q.getCohortSampleCount(q.cohort) });
     } catch (e) {
       res.send({ error: e.message || e });
       if (e.stack)

package/routes/termdb.config.js

@@ -62,6 +62,8 @@ function make(q, res, ds, genome) {
     c.chartConfigByType = tdb.chartConfigByType;
   if (tdb.multipleTestingCorrection)
     c.multipleTestingCorrection = tdb.multipleTestingCorrection;
+  if (tdb.neuroOncRegression)
+    c.neuroOncRegression = tdb.neuroOncRegression;
   if (tdb.helpPages)
     c.helpPages = tdb.helpPages;
   if (tdb.minTimeSinceDx)
@@ -80,6 +82,8 @@ function make(q, res, ds, genome) {
     c.useCasesExcluded = tdb.useCasesExcluded;
   if (tdb.excludedTermtypeByTarget)
     c.excludedTermtypeByTarget = tdb.excludedTermtypeByTarget;
+  if (tdb.about)
+    c.about = tdb.about;
   if (ds.assayAvailability)
     c.assayAvailability = ds.assayAvailability;
   if (ds.customTwQByType)