@sjcrh/proteinpaint-server 2.66.0 → 2.67.1-0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.66.0",
+  "version": "2.67.1-0",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -30,7 +30,7 @@
     "pretest": "tsc && ./test/pretest.js",
     "prepare": "ts-patch install",
     "pretest:type": "npm run checkers",
-    "pretest:integration": "tsc --esModuleInterop genome/*.ts dataset/*.ts",
+    "pretest:integration": "tsc",
     "test:integration": "echo 'TODO: server integration tests'",
     "test:tsc": "tsc --esModuleInterop --noEmit --allowImportingTsExtensions ./shared/types/test/*.type.spec.ts"
   },

package/routes/termdb.categories.js

@@ -79,11 +79,10 @@ function init({ genomes }) {
   };
 }
 async function trigger_getcategories(q, res, tdb, ds, genome) {
-  const $id = Math.random().toString();
-  const tw = { $id, term: q.term, q: q.term1_q || getDefaultQ(q.term, q) };
+  const $id = q.tw.$id;
   const arg = {
     filter: q.filter,
-    terms: [tw],
+    terms: [q.tw],
     currentGeneNames: q.currentGeneNames,
     // optional, from mds3 mayAddGetCategoryArgs()
     rglst: q.rglst
@@ -93,7 +92,7 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
   if (data.error)
     throw data.error;
   const lst = [];
-  if (q.term.type == "geneVariant") {
+  if (q.tw.term.type == "geneVariant" && !q.tw.q.groupsetting.inuse) {
     const samples = data.samples;
     const dtClassMap = /* @__PURE__ */ new Map();
     if (ds.assayAvailability?.byDt) {
@@ -154,15 +153,15 @@ async function trigger_getcategories(q, res, tdb, ds, genome) {
       lst.push({
         samplecount: count,
         key,
-        label: data.refs?.byTermId?.[$id]?.events?.find((e) => e.event === key).label || q.term?.values?.[key]?.label || key
+        label: data.refs?.byTermId?.[$id]?.events?.find((e) => e.event === key).label || q.tw.term?.values?.[key]?.label || key
       });
     }
   }
   const orderedLabels = getOrderedLabels(
-    q.term,
+    q.tw.term,
     data.refs?.byTermId?.[$id]?.bins || [],
     data.refs?.byTermId?.[$id]?.events,
-    q.term1_q
+    q.tw.q
   );
   if (orderedLabels.length) {
     lst.sort((a, b) => orderedLabels.indexOf(a.label) - orderedLabels.indexOf(b.label));

package/routes/termdb.config.js

@@ -191,10 +191,6 @@ function addNonDictionaryQueries(c, ds, genome) {
     q2.rnaseqGeneCount = true;
   }
   if (q.singleCell) {
-    const plots = "plots" in q.singleCell.data ? q.singleCell.data.plots.map((p) => ({
-      name: p.name,
-      colorColumn: p.colorColumn.name
-    })) : [];
     q2.singleCell = {
       samples: {
         firstColumnName: q.singleCell.samples.firstColumnName,
@@ -204,12 +200,17 @@ function addNonDictionaryQueries(c, ds, genome) {
       data: {
         sameLegend: q.singleCell.data.sameLegend,
         refName: q.singleCell.data.refName,
-        plots
+        plots: q.singleCell.data.plots.map((p) => {
+          return { name: p.name, colorColumn: p.colorColumn.name };
+        })
       }
     };
     if (q.singleCell.geneExpression) {
       q2.singleCell.geneExpression = {};
     }
+    if (q.singleCell.DEgenes) {
+      q2.singleCell.DEgenes = { columnName: q.singleCell.DEgenes.columnName };
+    }
   }
   if (q.images) {
     q2.images = {};

package/routes/termdb.singlecellDEgenes.js

@@ -0,0 +1,51 @@
+import { gdc_validate_query_singleCell_DEgenes } from "#src/mds3.gdc.js";
+const api = {
+  endpoint: "termdb/singlecellDEgenes",
+  methods: {
+    all: {
+      init,
+      request: {
+        typeId: "TermdbSinglecellDEgenesRequest"
+      },
+      response: {
+        typeId: "TermdbSinglecellDEgenesResponse"
+      }
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    const q = req.query;
+    let result;
+    try {
+      const g = genomes[q.genome];
+      if (!g)
+        throw "invalid genome name";
+      const ds = g.datasets[q.dslabel];
+      if (!ds)
+        throw "invalid dataset name";
+      if (!ds.queries?.singleCell?.DEgenes)
+        throw "not supported on this dataset";
+      result = await ds.queries.singleCell.DEgenes.get(q);
+    } catch (e) {
+      if (e.stack)
+        console.log(e.stack);
+      result = {
+        status: e.status || 400,
+        error: e.message || e
+      };
+    }
+    res.send(result);
+  };
+}
+async function validate_query_singleCell_DEgenes(ds) {
+  if (ds.queries.singleCell.DEgenes.src == "gdcapi") {
+    gdc_validate_query_singleCell_DEgenes(ds);
+  } else {
+    throw "unknown singleCell.DEgenes.src";
+  }
+}
+export {
+  api,
+  validate_query_singleCell_DEgenes
+};

package/routes/termdb.singlecellSamples.js

@@ -3,11 +3,12 @@ import path from "path";
 import { read_file } from "#src/utils.js";
 import run_R from "#src/run_R.js";
 import serverconfig from "#src/serverconfig.js";
+import { validate_query_singleCell_DEgenes } from "./termdb.singlecellDEgenes.ts";
 import { gdc_validate_query_singleCell_samples, gdc_validate_query_singleCell_data } from "#src/mds3.gdc.js";
 const api = {
   endpoint: "termdb/singlecellSamples",
   methods: {
-    get: {
+    all: {
       init,
       request: {
         typeId: "TermdbSinglecellsamplesRequest"
@@ -15,10 +16,6 @@ const api = {
       response: {
         typeId: "TermdbSinglecellsamplesResponse"
       }
-    },
-    post: {
-      alternativeFor: "get",
-      init
     }
   }
 };
@@ -73,6 +70,9 @@ async function validate_query_singleCell(ds, genome) {
       throw "unknown singleCell.geneExpression.src";
     }
   }
+  if (q.DEgenes) {
+    validate_query_singleCell_DEgenes(ds);
+  }
 }
 async function validateSamplesNative(S, ds) {
   const samples = {};

package/routes/termdb.termsbyids.js

@@ -39,7 +39,9 @@ function init({ genomes }) {
   };
 }
 async function trigger_gettermsbyid(q, res, tdb) {
-  const terms = {};
+  const terms = {
+    terms: {}
+  };
   for (const id of q.ids) {
     const term = tdb.q.termjsonByOneid(id);
     if (term) {