@sjcrh/proteinpaint-server 2.138.1 → 2.138.3-0

package/dataset/protected.test.js

@@ -0,0 +1,13 @@
+import termdbTestInit from "./termdb.test.ts";
+function protected_test_default() {
+  const ds = termdbTestInit();
+  if (!ds.cohort)
+    ds.cohort = { termdb: {} };
+  ds.cohort.termdb.hasMinSampleSize = (sampleCount) => {
+    return sampleCount >= 10;
+  };
+  return ds;
+}
+export {
+  protected_test_default as default
+};

package/dataset/termdb.test.js

@@ -36,7 +36,6 @@ function termdb_test_default() {
       },
       termdb: {
         allowedTermTypes: ["geneVariant"],
-        //minSampleSizeForFilterCharts: 100, // 20,
         displaySampleIds: () => true,
         // allow to display sample-level data
         timeUnit: "years",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.138.1",
+  "version": "2.138.3-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -64,7 +64,7 @@
     "@sjcrh/proteinpaint-r": "2.137.2-0",
     "@sjcrh/proteinpaint-rust": "2.137.2-0",
     "@sjcrh/proteinpaint-shared": "2.137.3",
-    "@sjcrh/proteinpaint-types": "2.138.1",
+    "@sjcrh/proteinpaint-types": "2.138.3-0",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/filterTermValues.js

@@ -28,7 +28,29 @@ function init({ genomes }) {
     }
   };
 }
-function getList(samplesPerFilter, filtersData, tw) {
+async function getFilters(query, ds, res) {
+  if (!query.filterByUserSites)
+    authApi.mayAdjustFilter(query, ds, query.terms);
+  try {
+    const samplesPerFilter = await getSamplesPerFilter(query, ds);
+    const filtersData = await getData(
+      {
+        terms: query.terms,
+        __protected__: query.__protected__
+      },
+      ds
+    );
+    const tw2List = {};
+    for (const tw of query.terms) {
+      tw2List[tw.term.id] = getList(samplesPerFilter, filtersData, tw, query.showAll);
+    }
+    res.send({ ...tw2List });
+  } catch (e) {
+    console.log(e);
+    res.send({ error: e.message || e });
+  }
+}
+function getList(samplesPerFilter, filtersData, tw, showAll) {
   const values = Object.values(tw.term.values);
   values.sort((v1, v2) => v1.label.localeCompare(v2.label));
   const twSamples = samplesPerFilter[tw.term.id];
@@ -42,28 +64,14 @@ function getList(samplesPerFilter, filtersData, tw) {
   for (const value of values) {
     const label = value.label.replace(/["']/g, "");
     const disabled = !sampleValues.includes(value.key || value.label);
+    if (!showAll && disabled)
+      continue;
     filteredValues.push({ value: value.key || value.label, label, disabled });
   }
   filteredValues.unshift({ label: "", value: "" });
   filteredValues.sort((a, b) => a.label.localeCompare(b.label));
   return filteredValues;
 }
-async function getFilters(query, ds, res) {
-  if (!query.filterByUserSites)
-    authApi.mayAdjustFilter(query, ds, query.terms);
-  try {
-    const samplesPerFilter = await getSamplesPerFilter(query, ds);
-    const filtersData = await getData({ terms: query.terms, __protected__: query.__protected__ }, ds);
-    const tw2List = {};
-    for (const tw of query.terms) {
-      tw2List[tw.term.id] = getList(samplesPerFilter, filtersData, tw);
-    }
-    res.send({ ...tw2List });
-  } catch (e) {
-    console.log(e);
-    res.send({ error: e.message || e });
-  }
-}
 export {
   api
 };

package/routes/samplewsimages.js

@@ -49,24 +49,31 @@ function init({ genomes }) {
               const featClass = ds.queries.WSImages?.classes?.find((f) => f.id == d.properties.class)?.label || d.properties.class;
               return {
                 zoomCoordinates: d.properties.zoomCoordinates,
-                type: d.properties.type,
                 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 || "#00e62a";
+            wsimage.activePatchColor = ds.queries?.WSImages?.activePatchColor;
           }
-          if (ds.queries.WSImages.getZoomInPoints) {
-            const zoomInPoints = await ds.queries.WSImages.getZoomInPoints(
+          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,
-              wsimage.filename,
-              query.index
+              predictionsFile[0]
             );
-            if (zoomInPoints) {
-              wsimage.zoomInPoints = zoomInPoints;
-            }
+            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);
           }
         }
       }