@sjcrh/proteinpaint-server 2.206.1 → 2.207.0

package/dataset/termdb.test.js

@@ -447,11 +447,12 @@ function termdb_test_default() {
         // .ome.tif extension is required for the JPEG-2000 OME-TIFF reader
         // in wsi_tile.py open_slide() to engage
         tiffFileSuffix: "morphology.ome.tif",
-        nucleusBoundariesFileSuffix: "nucleus_boundaries.csv",
-        cellBoundariesFileSuffix: "cell_boundaries.csv",
-        geneExpressionFileSuffix: "gene_expression.h5",
+        // consolidated h5ad: the single source for boundaries, annotations
+        // and expression (the per-file *FileSuffix fallbacks exist for
+        // datasets without one; this fixture's companion CSVs/h5 were removed)
+        spatialDataFileSuffix: "spatial.h5ad",
         // default viewer settings, overridable in the burger menu
-        geneExpression: "PTPRC",
+        cellTypes: true,
         annotationLevel: 1
       },
       trackLst: {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.206.1",
+  "version": "2.207.0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -57,11 +57,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.204.0",
-    "@sjcrh/proteinpaint-python": "2.204.0",
+    "@sjcrh/proteinpaint-python": "2.207.0",
     "@sjcrh/proteinpaint-r": "2.204.0",
-    "@sjcrh/proteinpaint-rust": "2.206.0",
-    "@sjcrh/proteinpaint-shared": "2.206.0",
-    "@sjcrh/proteinpaint-types": "2.206.0",
+    "@sjcrh/proteinpaint-rust": "2.207.0",
+    "@sjcrh/proteinpaint-shared": "2.207.0",
+    "@sjcrh/proteinpaint-types": "2.207.0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/brainImaging.js

@@ -36,10 +36,14 @@ function init({ genomes }) {
 async function getBrainImage(query, genomes, plane, index) {
   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);
+  if (q.checkDataAccess) {
+    if (!q.checkDataAccess(query)) throw "no access";
+  }
+  const ref = q.references[query.refKey];
+  if (!ref) throw "invalid refKey";
+  if (ref.referenceFile && ref.samples) {
+    const refFile = path.join(serverconfig.tpmasterdir, ref.referenceFile);
+    const dirPath = path.join(serverconfig.tpmasterdir, ref.samples);
     const terms = [];
     const divideByTW = query.divideByTW;
     const overlayTW = query.overlayTW;
@@ -55,37 +59,43 @@ async function getBrainImage(query, genomes, plane, index) {
     if (data.error) throw data.error;
     const divideByCat = {};
     const uniqueOverlayTwCats = /* @__PURE__ */ new Set();
+    const getCategories = (tw, value) => {
+      const keys = value.values ? value.values.map((v) => v.key) : [value.key];
+      return keys.map((k) => tw.term.values?.[k]?.label || k);
+    };
     for (const sampleName of selectedSampleNames) {
       const sampleId = ds.sampleName2Id.get(sampleName);
       const sampleData = data.samples[sampleId];
       const samplePath = path.join(dirPath, sampleName) + ".nii";
-      let divideCategory = "default";
+      let divideCategories = ["default"];
       let overlayCategory = "default";
       if (divideByTW && sampleData) {
         const value = sampleData[divideByTW.$id];
-        if (value) divideCategory = divideByTW.term.values?.[value.key]?.label || value.key;
+        if (value) divideCategories = getCategories(divideByTW, value);
       }
       if (overlayTW && sampleData) {
         const value = sampleData[overlayTW.$id];
         if (value) {
-          overlayCategory = overlayTW.term.values?.[value.key]?.label || value.key;
+          overlayCategory = getCategories(overlayTW, value).join(", ");
           uniqueOverlayTwCats.add(overlayCategory);
         }
       }
-      if (!divideByCat[divideCategory]) divideByCat[divideCategory] = {};
-      if (!query.legendFilter?.includes(overlayCategory)) {
-        if (!divideByCat[divideCategory][overlayCategory]) {
-          let color = overlayTW?.term?.values?.[overlayCategory]?.color;
-          if (overlayTW && isNumericTerm(overlayTW.term)) {
-            const bins = data.refs.byTermId[overlayTW.$id].bins;
-            color = bins.find((b) => b.label == overlayCategory).color;
+      for (const divideCategory of divideCategories) {
+        if (!divideByCat[divideCategory]) divideByCat[divideCategory] = {};
+        if (!query.legendFilter?.includes(overlayCategory)) {
+          if (!divideByCat[divideCategory][overlayCategory]) {
+            let color = overlayTW?.term?.values?.[overlayCategory]?.color;
+            if (overlayTW && isNumericTerm(overlayTW.term)) {
+              const bins = data.refs.byTermId[overlayTW.$id].bins;
+              color = bins.find((b) => b.label == overlayCategory).color;
+            }
+            divideByCat[divideCategory][overlayCategory] = {
+              samples: [],
+              color
+            };
           }
-          divideByCat[divideCategory][overlayCategory] = {
-            samples: [],
-            color
-          };
+          divideByCat[divideCategory][overlayCategory].samples.push(samplePath);
         }
-        divideByCat[divideCategory][overlayCategory].samples.push(samplePath);
       }
     }
     const k2c = getColors(uniqueOverlayTwCats.size);

package/routes/brainImagingSamples.js

@@ -22,15 +22,19 @@ function init({ genomes }) {
 async function getBrainImageSamples(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 dirPath = path.join(serverconfig.tpmasterdir, q[key].samples);
+  if (q.checkDataAccess) {
+    if (!q.checkDataAccess(query)) throw "no access";
+  }
+  const ref = q.references[query.refKey];
+  if (!ref) throw "invalid refKey";
+  if (ref.referenceFile && ref.samples) {
+    const dirPath = path.join(serverconfig.tpmasterdir, ref.samples);
     const files = (await fs.promises.readdir(dirPath, { withFileTypes: true })).filter((f) => f.isFile() && f.name.endsWith(".nii")).map((f) => f.name);
     let sampleNames = files.map((name) => name.split(".nii")[0]);
     sampleNames = await filterSampleNamesByAccess(query, ds, sampleNames);
     if (query.samplesOnly) return sampleNames.map((name) => ({ sample: name }));
-    if (q[key].sampleColumns) {
-      const terms = q[key].sampleColumns.map((term) => {
+    if (ref.sampleColumns) {
+      const terms = ref.sampleColumns.map((term) => {
         const termjson = ds.cohort.termdb.q.termjsonByOneid(term.termid);
         return {
           $id: term.termid,
@@ -46,11 +50,11 @@ async function getBrainImageSamples(query, genomes) {
         const sid = ds.cohort.termdb.q.sampleName2id(s);
         const sampleData = data.samples?.[sid];
         if (sampleData) {
-          for (const term of q[key].sampleColumns) {
+          for (const term of ref.sampleColumns) {
             const v = sampleData[term.termid];
-            if (v?.value !== void 0) {
-              annoForOneS[term.termid] = v.value;
-            }
+            if (!v) continue;
+            if (v.values) annoForOneS[term.termid] = v.values.map((x) => x.key).join(", ");
+            else if (v.value !== void 0) annoForOneS[term.termid] = v.value;
           }
         }
         samples[s] = annoForOneS;