@sjcrh/proteinpaint-server 2.142.0 → 2.143.0

package/routes/genomes.js

@@ -48,8 +48,7 @@ function init({ genomes }) {
     }
     let hasblat = false;
     for (const n in genomes) {
-      if (genomes[n].blat)
-        hasblat = true;
+      if (genomes[n].blat) hasblat = true;
     }
     res.send({
       genomes: hash,

package/routes/grin2.js

@@ -25,13 +25,10 @@ function init({ genomes }) {
       const request = req.query;
       console.log("[GRIN2] request:", request);
       const g = genomes[request.genome];
-      if (!g)
-        throw new Error("genome missing");
+      if (!g) throw new Error("genome missing");
       const ds = g.datasets?.[request.dslabel];
-      if (!ds)
-        throw new Error("ds missing");
-      if (!ds.queries?.singleSampleMutation)
-        throw new Error("singleSampleMutation query missing from dataset");
+      if (!ds) throw new Error("ds missing");
+      if (!ds.queries?.singleSampleMutation) throw new Error("singleSampleMutation query missing from dataset");
       const result = await runGrin2(g, ds, request);
       res.json(result);
     } catch (e) {
@@ -76,12 +73,14 @@ async function runGrin2(g, ds, request) {
   const pyInput = {
     genedb: path.join(serverconfig.tpmasterdir, g.genedb.dbfile),
     chromosomelist: {},
-    lesion: JSON.stringify(lesions)
+    lesion: JSON.stringify(lesions),
+    devicePixelRatio: request.devicePixelRatio,
+    plot_width: request.plot_width,
+    plot_height: request.plot_height
   };
   for (const c in g.majorchr) {
     if (ds.queries.singleSampleMutation.discoPlot?.skipChrM) {
-      if (c.toLowerCase() == "chrm")
-        continue;
+      if (c.toLowerCase() == "chrm") continue;
     }
     pyInput.chromosomelist[c] = g.majorchr[c];
   }
@@ -105,6 +104,7 @@ async function runGrin2(g, ds, request) {
   const response = {
     status: "success",
     pngImg: resultData.png[0],
+    plotData: resultData.plotData,
     topGeneTable: resultData.topGeneTable,
     totalGenes: resultData.totalGenes,
     showingTop: resultData.showingTop,
@@ -155,8 +155,7 @@ async function processSampleMlst(sampleName, mlst, startId, request) {
   for (const m of mlst) {
     switch (m.dt) {
       case dtsnvindel: {
-        if (!request.snvindelOptions)
-          break;
+        if (!request.snvindelOptions) break;
         const snvIndelLesion = filterAndConvertSnvIndel(sampleName, m, request.snvindelOptions);
         if (snvIndelLesion) {
           lesions.push(snvIndelLesion);
@@ -164,8 +163,7 @@ async function processSampleMlst(sampleName, mlst, startId, request) {
         break;
       }
       case dtcnv: {
-        if (!request.cnvOptions)
-          break;
+        if (!request.cnvOptions) break;
         const cnvLesion = filterAndConvertCnv(sampleName, m, request.cnvOptions);
         if (cnvLesion) {
           lesions.push(cnvLesion);
@@ -173,8 +171,7 @@ async function processSampleMlst(sampleName, mlst, startId, request) {
         break;
       }
       case dtfusionrna: {
-        if (!request.fusionOptions)
-          break;
+        if (!request.fusionOptions) break;
         const fusionLesion = filterAndConvertFusion(sampleName, m, request.fusionOptions);
         if (fusionLesion) {
           lesions.push(fusionLesion);
@@ -217,8 +214,7 @@ function filterAndConvertCnv(sampleName, entry, options) {
   }
   const isGain = entry.value >= options.gainThreshold;
   const isLoss = entry.value <= options.lossThreshold;
-  if (!isGain && !isLoss)
-    return null;
+  if (!isGain && !isLoss) return null;
   const lesionType = isGain ? "gain" : "loss";
   return [sampleName, entry.chr, entry.start, entry.stop, lesionType];
 }

package/routes/healthcheck.js

@@ -17,12 +17,9 @@ function init({ genomes }) {
       if (q.dslabel) {
         for (const gn in genomes) {
           const ds = genomes[gn]?.datasets?.[q.dslabel];
-          if (!ds?.getHealth)
-            continue;
-          if (!health.byDataset)
-            health.byDataset = {};
-          if (!health.byDataset[q.dslabel])
-            health.byDataset[q.dslabel] = {};
+          if (!ds?.getHealth) continue;
+          if (!health.byDataset) health.byDataset = {};
+          if (!health.byDataset[q.dslabel]) health.byDataset[q.dslabel] = {};
           health.byDataset[q.dslabel][gn] = ds.getHealth(ds);
         }
       }

package/routes/hicdata.js

@@ -24,16 +24,14 @@ function init() {
       res.send(payload);
     } catch (e) {
       res.send({ error: e?.message || e });
-      if (e instanceof Error && e.stack)
-        console.log(e);
+      if (e instanceof Error && e.stack) console.log(e);
     }
   };
 }
 function handle_hicdata(q) {
   return new Promise((resolve, reject) => {
     const [e, file] = fileurl({ query: q });
-    if (e)
-      reject({ error: "illegal file name" });
+    if (e) reject({ error: "illegal file name" });
     const matrixType = q.matrixType == "log(oe)" ? "oe" : q.matrixType ? q.matrixType : "observed";
     const par = [matrixType, q.nmeth || "NONE", file, q.pos1, q.pos2, q.isfrag ? "FRAG" : "BP", q.resolution];
     const ps = spawn(serverconfig.hicstraw, par);
@@ -63,10 +61,8 @@ function handle_hicdata(q) {
     ps.stderr.on("data", (i) => erroutput.push(i));
     ps.on("close", () => {
       const err = erroutput.join("");
-      if (err)
-        reject({ error: err });
-      if (linenot3fields)
-        reject({ error: linenot3fields + " lines have other than 3 fields" });
+      if (err) reject({ error: err });
+      if (linenot3fields) reject({ error: linenot3fields + " lines have other than 3 fields" });
       if (fieldnotnumerical)
         reject({ error: fieldnotnumerical + " lines have non-numerical values in any of the 3 fields" });
       resolve({ items });

package/routes/hicgenome.js

@@ -22,8 +22,7 @@ function init() {
     const data = [];
     const erroutput = [];
     const [e, file] = fileurl({ query });
-    if (e)
-      res.send({ error: "illegal file name" });
+    if (e) res.send({ error: "illegal file name" });
     const matrixType = req.query.matrixType == "log(oe)" ? "oe" : req.query.matrixType ? req.query.matrixType : "observed";
     const promises = req.query.chrlst.map((lead, i) => {
       return req.query.chrlst.slice(0, i + 1).map((follow, j) => {
@@ -55,10 +54,8 @@ function init() {
             data.push({ items, lead, follow });
             ps.stderr.on("data", (i2) => erroutput.push(`${lead} - ${follow}: `, i2));
             ps.on("close", () => {
-              if (erroutput.length)
-                reject({ error: erroutput.join("") });
-              if (linenot3fields)
-                reject({ error: `${linenot3fields} lines have other than 3 fields` });
+              if (erroutput.length) reject({ error: erroutput.join("") });
+              if (linenot3fields) reject({ error: `${linenot3fields} lines have other than 3 fields` });
               if (fieldnotnumerical)
                 reject(`${fieldnotnumerical} lines have non-numerical values in any of the 3 fields`);
               resolve();
@@ -69,8 +66,7 @@ function init() {
     }).flat();
     Promise.allSettled(promises).then(() => res.send({ data, error: erroutput.join("") })).catch((e2) => {
       res.send({ error: e2?.message || e2 });
-      if (e2 instanceof Error && e2.stack)
-        console.log(e2);
+      if (e2 instanceof Error && e2.stack) console.log(e2);
     });
   };
 }

package/routes/hicstat.js

@@ -18,8 +18,7 @@ function init() {
   return async (req, res) => {
     try {
       const [e, file, isurl] = fileurl(req);
-      if (e)
-        throw "illegal file name";
+      if (e) throw "illegal file name";
       if (!isurl) {
         await file_is_readable(file);
       }
@@ -27,8 +26,7 @@ function init() {
       res.send({ out });
     } catch (e) {
       res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack)
-        console.log(e);
+      if (e instanceof Error && e.stack) console.log(e);
     }
   };
 }

package/routes/img.js

@@ -28,8 +28,7 @@ function init() {
 async function sendImage(req, res) {
   const [e, file] = utils.fileurl(req, true);
   try {
-    if (e)
-      throw "invalid image file";
+    if (e) throw "invalid image file";
     const data = await fs.promises.readFile(file);
     const ext = path.extname(file).substring(1);
     const image = {

package/routes/isoformlst.js

@@ -21,20 +21,16 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const g = genomes[q.genome];
-      if (!g)
-        throw "invalid genome";
-      if (!Array.isArray(q.lst))
-        throw ".lst missing";
+      if (!g) throw "invalid genome";
+      if (!Array.isArray(q.lst)) throw ".lst missing";
       const lst = [];
       for (const isoform of q.lst) {
-        if (g.genomicNameRegexp.test(isoform))
-          continue;
+        if (g.genomicNameRegexp.test(isoform)) continue;
         const tmp = g.genedb.getjsonbyisoform.all(isoform);
         lst.push(
           tmp.map((i) => {
             const j = JSON.parse(i.genemodel);
-            if (i.isdefault)
-              j.isdefault = true;
+            if (i.isdefault) j.isdefault = true;
             return j;
           })
         );
@@ -42,10 +38,8 @@ function init({ genomes }) {
       res.send({ lst });
     } catch (e) {
       res.send({ error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
-      else
-        console.trace(e);
+      if (e.stack) console.log(e.stack);
+      else console.trace(e);
     }
   };
 }

package/routes/ntseq.js

@@ -17,21 +17,17 @@ function init({ genomes }) {
   return async function handle_ntseq(req, res) {
     try {
       const q = req.query;
-      if (!q.coord)
-        throw "coord missing";
+      if (!q.coord) throw "coord missing";
       const g = genomes[q.genome];
-      if (!g)
-        throw "invalid genome";
-      if (!g.genomefile)
-        throw "no sequence file available";
+      if (!g) throw "invalid genome";
+      if (!g.genomefile) throw "no sequence file available";
       const seq = await get_fasta(g, q.coord);
       res.send({
         seq: seq.split("\n").slice(1).join("")
       });
     } catch (e) {
       res.send({ error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
     }
   };
 }

package/routes/pdomain.js

@@ -21,20 +21,16 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const gn = q.genome;
-      if (!gn)
-        throw "no genome";
+      if (!gn) throw "no genome";
       const g = genomes[gn];
-      if (!g)
-        throw "invalid genome " + gn;
+      if (!g) throw "invalid genome " + gn;
       if (!g.proteindomain) {
         return res.send({ lst: [] });
       }
-      if (!Array.isArray(q.isoforms))
-        throw "isoforms[] missing";
+      if (!Array.isArray(q.isoforms)) throw "isoforms[] missing";
       const lst = [];
       for (const isoform of q.isoforms) {
-        if (g.genomicNameRegexp.test(isoform))
-          continue;
+        if (g.genomicNameRegexp.test(isoform)) continue;
         const tmp = g.proteindomain.getbyisoform.all(isoform);
         lst.push({
           name: isoform,
@@ -48,8 +44,7 @@ function init({ genomes }) {
       res.send({ lst });
     } catch (e) {
       res.send({ error: e.message || e });
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
     }
   };
 }

package/routes/sampledzimages.js

@@ -20,11 +20,9 @@ function init({ genomes }) {
     const q = req.query;
     try {
       const g = genomes[q.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets[q.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
+      if (!ds) throw "invalid dataset name";
       const sampleId = q.sample_id || "";
       const sampleDZImagesPath = path.join(
         `${serverconfig.tpmasterdir}/${ds.queries.DZImages.imageBySampleFolder}`,

package/routes/samplewsimages.js

@@ -1,7 +1,4 @@
 import { sampleWSImagesPayload } from "#types/checkers";
-import path from "path";
-import fs from "fs";
-import serverconfig from "#src/serverconfig.js";
 const api = {
   endpoint: "samplewsimages",
   methods: {
@@ -20,71 +17,11 @@ function init({ genomes }) {
     try {
       const query = req.query;
       const g = genomes[query.genome];
-      if (!g)
-        throw "invalid genome name";
+      if (!g) throw "invalid genome name";
       const ds = g.datasets[query.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
+      if (!ds) throw "invalid dataset name";
       const sampleId = query.sample_id;
       const wsimages = await ds.queries.WSImages.getWSImages(sampleId);
-      if (ds.queries.WSImages.getWSIAnnotations) {
-        for (const wsimage of wsimages) {
-          if (ds.queries.WSImages.makeGeoJson) {
-            await ds.queries.WSImages.makeGeoJson(sampleId, wsimage);
-          }
-          const annotations = await ds.queries.WSImages.getWSIAnnotations(sampleId, wsimage.filename);
-          if (annotations && annotations.length > 0) {
-            wsimage.overlays = annotations;
-            const annotationFilePath = path.join(
-              serverconfig.tpmasterdir,
-              ds.queries.WSImages.imageBySampleFolder,
-              sampleId,
-              annotations[0]
-            );
-            const annotationData = JSON.parse(fs.readFileSync(annotationFilePath, "utf8"));
-            if (!annotationData.features && !ds.queries.WSImages?.classes?.length) {
-              throw new Error(`No classes found for WSImage annotations in dataset ${ds.label}`);
-            }
-            wsimage.annotationsData = annotationData.features.map((d) => {
-              const featClass = ds.queries.WSImages?.classes?.find((f) => f.id == d.properties.class)?.label || d.properties.class;
-              return {
-                zoomCoordinates: d.properties.zoomCoordinates,
-                uncertainty: d.properties.uncertainty,
-                class: featClass
-              };
-            }).slice(15, 20);
-            wsimage.classes = ds.queries?.WSImages?.classes;
-            wsimage.uncertainty = ds.queries?.WSImages?.uncertainty;
-            wsimage.activePatchColor = ds.queries?.WSImages?.activePatchColor;
-          }
-          if (ds.queries.WSImages.getWSIPredictionPatches) {
-            const predictionsFile = await ds.queries.WSImages.getWSIPredictionPatches(sampleId, wsimage.filename);
-            const predictionsFilePath = path.join(
-              serverconfig.tpmasterdir,
-              ds.queries.WSImages.imageBySampleFolder,
-              sampleId,
-              predictionsFile[0]
-            );
-            const predictionsData = JSON.parse(fs.readFileSync(predictionsFilePath, "utf8"));
-            wsimage.predictions = predictionsData.features.map((d) => {
-              const featClass = ds.queries.WSImages?.classes?.find((f) => f.id == d.properties.class)?.label || d.properties.class;
-              return {
-                zoomCoordinates: d.properties.zoomCoordinates,
-                uncertainty: d.properties.uncertainty,
-                class: featClass
-              };
-            }).slice(0, 15);
-          }
-        }
-      }
-      if (ds.queries.WSImages.getWSIPredictionOverlay) {
-        for (const wsimage of wsimages) {
-          const predictionOverlay = await ds.queries.WSImages.getWSIPredictionOverlay(sampleId, wsimage.filename);
-          if (predictionOverlay) {
-            wsimage.predictionLayers = [predictionOverlay];
-          }
-        }
-      }
       res.send({ sampleWSImages: wsimages });
     } catch (e) {
       console.log(e);
@@ -93,8 +30,7 @@ function init({ genomes }) {
   };
 }
 async function validate_query_getSampleWSImages(ds) {
-  if (!ds.queries?.WSImages)
-    return;
+  if (!ds.queries?.WSImages) return;
   validateQuery(ds);
 }
 function validateQuery(ds) {

package/routes/saveWSIAnnotation.js

@@ -0,0 +1,100 @@
+import { saveWSIAnnotationPayload } from "#types/checkers";
+import { getDbConnection } from "#src/aiHistoDBConnection.ts";
+const routePath = "saveWSIAnnotation";
+const api = {
+  endpoint: `${routePath}`,
+  methods: {
+    post: {
+      ...saveWSIAnnotationPayload,
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const query = req.query;
+      if (!query.genome) throw new Error(".genome is required for deleteWSIAnnotation request.");
+      if (!query.dslabel) throw new Error(".dslabel is required for deleteWSIAnnotation request.");
+      const g = genomes[query.genome];
+      if (!g) throw new Error("invalid genome name");
+      const ds = g.datasets[query.dslabel];
+      if (!ds) throw new Error("invalid dataset name");
+      if (typeof ds.queries?.WSImages?.saveWSIAnnotation === "function") {
+        const result = await ds.queries.WSImages.saveWSIAnnotation(query);
+        if (result?.status === "error") {
+          return res.status(500).send(result);
+        }
+      }
+      res.status(200).send({ status: "ok" });
+    } catch (e) {
+      console.warn(e);
+      res.status(500).send({
+        status: "error",
+        error: e?.message || String(e)
+      });
+    }
+  };
+}
+async function validate_query_saveWSIAnnotation(ds) {
+  if (!ds.queries?.WSImages?.db) return;
+  const connection = getDbConnection(ds);
+  if (!connection) {
+    return;
+  }
+  validateQuery(ds, connection);
+}
+function validateQuery(ds, connection) {
+  ds.queries.WSImages.saveWSIAnnotation = async (annotation) => {
+    try {
+      const timestamp = (/* @__PURE__ */ new Date()).toISOString();
+      const projectId = annotation.projectId;
+      const wsimageFilename = annotation.wsimage;
+      const coords = JSON.stringify(annotation.coordinates ?? []);
+      const status = 1;
+      const classId = annotation.classId;
+      if (projectId == null || wsimageFilename == null) {
+        return {
+          status: "error",
+          error: "Missing required fields: projectId and wsimage."
+        };
+      }
+      const getImageIdSql = `
+				SELECT id
+				FROM project_images
+				WHERE project_id = ?
+				  AND image_path = ?
+				LIMIT 1
+			`;
+      const getImageStmt = connection.prepare(getImageIdSql);
+      const imageRow = getImageStmt.get(projectId, wsimageFilename);
+      if (!imageRow?.id) {
+        return {
+          status: "error",
+          error: `Image not found for project_id=${projectId} and image_path="${wsimageFilename}".`
+        };
+      }
+      const imageId = imageRow.id;
+      const insertSql = `
+				INSERT INTO project_annotations (
+					project_id, user_id, coordinates, timestamp, status, class_id, image_id
+				) VALUES (?, ?, ?, ?, ?, ?, ?)
+			`;
+      const insertStmt = connection.prepare(insertSql);
+      const userRow = connection.prepare(`SELECT id FROM project_users WHERE project_id = ? ORDER BY id ASC LIMIT 1`).get(projectId);
+      const userId = userRow?.id;
+      insertStmt.run(projectId, userId, coords, timestamp, status, classId, imageId);
+      return { status: "ok" };
+    } catch (error) {
+      console.error("Error saving annotation:", error);
+      return {
+        status: "error",
+        error: error?.message || "Failed to save annotation"
+      };
+    }
+  };
+}
+export {
+  api,
+  validate_query_saveWSIAnnotation
+};

package/routes/snp.js

@@ -22,28 +22,22 @@ function init({ genomes }) {
     try {
       const q = req.query;
       const n = q.genome;
-      if (!n)
-        throw "no genome";
+      if (!n) throw "no genome";
       const results = await searchSNP(q, genomes[n]);
       res.send({ results });
     } catch (e) {
-      if (e.stack)
-        console.log(e.stack);
+      if (e.stack) console.log(e.stack);
       return res.send({ error: e.message || e });
     }
   };
 }
 async function searchSNP(q, genome) {
-  if (!genome)
-    throw "invalid genome";
-  if (!genome.snp)
-    throw "snp is not configured for this genome";
+  if (!genome) throw "invalid genome";
+  if (!genome.snp) throw "snp is not configured for this genome";
   const hits = [];
   if (q.byCoord) {
-    if (genome.genomicNameRegexp.test(q.chr))
-      throw "invalid chr name";
-    if (!Array.isArray(q.ranges))
-      throw "ranges not an array";
+    if (genome.genomicNameRegexp.test(q.chr)) throw "invalid chr name";
+    if (!Array.isArray(q.ranges)) throw "ranges not an array";
     for (const r of q.ranges) {
       if (!Number.isInteger(r.start) || !Number.isInteger(r.stop) || r.start < 0 || r.stop < r.start)
         throw "invalid start/stop";
@@ -61,18 +55,15 @@ async function searchSNP(q, genome) {
               break;
             }
           }
-          if (missing)
-            continue;
+          if (missing) continue;
         }
         hits.push(hit);
       }
     }
   } else if (q.byName) {
-    if (!Array.isArray(q.lst))
-      throw ".lst[] missing";
+    if (!Array.isArray(q.lst)) throw ".lst[] missing";
     for (const n of q.lst) {
-      if (genome.genomicNameRegexp.test(n))
-        continue;
+      if (genome.genomicNameRegexp.test(n)) continue;
       const snps = await utils.query_bigbed_by_name(genome.snp.bigbedfile, n);
       for (const snp of snps) {
         const hit = snp2hit(snp);