@sjcrh/proteinpaint-server 2.62.0 → 2.63.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.62.0",
+  "version": "2.63.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",

package/routes/termdb.config.js

@@ -85,6 +85,7 @@ function make(q, res, ds, genome) {
   addScatterplots(c, ds);
   addMatrixplots(c, ds);
   addGenomicQueries(c, ds, genome);
+  addImageQueries(c, ds);
   res.send({ termdbConfig: c });
 }
 function addRestrictAncestries(c, tdb) {
@@ -94,6 +95,13 @@ function addRestrictAncestries(c, tdb) {
     return { name: i.name, tvs: i.tvs, PCcount: i.PCcount };
   });
 }
+function addImageQueries(c, ds) {
+  const q = ds.queries;
+  const q2 = c.queries;
+  if (q.images) {
+    q2.images = {};
+  }
+}
 function addScatterplots(c, ds) {
   if (!ds.cohort.scatterplots)
     return;

package/routes/termdb.getSampleImages.js

@@ -0,0 +1,67 @@
+import path from "path";
+import fs from "fs";
+import serverconfig from "#src/serverconfig.js";
+const api = {
+  endpoint: "termdb/getSampleImages",
+  methods: {
+    all: {
+      init,
+      request: {
+        typeId: "TermdbGetSampleImagesRequest"
+      },
+      response: {
+        typeId: "TermdbGetSampleImagesResponse"
+      }
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const q = req.query;
+      const sampleId = q.sampleId;
+      const genome = genomes[q.genome];
+      if (!genome)
+        throw "invalid genome";
+      const ds = genome.datasets?.[q.dslabel];
+      if (!ds)
+        throw "invalid dslabel";
+      const images = await ds.queries.images.getSampleImages({ sampleId });
+      res.send({ images });
+    } catch (e) {
+      res.send({ status: "error", error: e.message || e });
+    }
+  };
+}
+function validate_query_getSampleImages(ds, genome) {
+  const q = ds.queries.images;
+  if (!q)
+    return;
+  nativeValidateQuery(ds);
+}
+function nativeValidateQuery(ds) {
+  ds.queries.images.getSampleImages = async (q) => {
+    const folder = ds.queries.images.folder;
+    const images = await getSampleImages(ds, folder, q.sampleId);
+    return images;
+  };
+}
+async function getSampleImages(ds, folder, sampleId) {
+  const sql = `SELECT * FROM images WHERE sample = ${sampleId}`;
+  const rows = ds.cohort.db.connection.prepare(sql).all();
+  const images = [];
+  for (const row of rows) {
+    const file = path.join(serverconfig.tpmasterdir, folder, row.fileName);
+    if (!fs.existsSync(file))
+      throw new Error(`File ${row.fileName} does not exist`);
+    const data = await fs.promises.readFile(file);
+    images.push({
+      src: "data:image/jpeg;base64," + Buffer.from(data).toString("base64")
+    });
+  }
+  return images;
+}
+export {
+  api,
+  validate_query_getSampleImages
+};