@sjcrh/proteinpaint-server 2.83.0 → 2.85.0

package/src/serverconfig.js

@@ -67,6 +67,15 @@ if (!('allow_env_overrides' in serverconfig) && serverconfig.debugmode) {
 	serverconfig.allow_env_overrides = true
 }
 
+//if jwt is enabled, check for JWT_SECRET environment variable
+if (serverconfig.jwt) {
+	const jwtSecret = process.env.JWT_SECRET
+	if (!jwtSecret) {
+		throw `JWT_SECRET is not set as an environment variable.`
+	}
+	serverconfig.jwt.secret = jwtSecret
+}
+
 if (!serverconfig.binpath) {
 	const pkfile = process.argv.find(n => n.includes('/build'))
 	if (pkfile) {

package/routes/termdb.getnumericcategories.js

@@ -1,91 +0,0 @@
-import * as termdbsql from "#src/termdb.sql.js";
-const api = {
-  endpoint: "termdb/numericcategories",
-  methods: {
-    get: {
-      init,
-      request: {
-        typeId: "getnumericcategoriesRequest"
-      },
-      response: {
-        typeId: "getnumericcategoriesResponse"
-      },
-      examples: [
-        {
-          request: {
-            body: {
-              genome: "hg38-test",
-              dslabel: "TermdbTest",
-              embedder: "localhost",
-              tid: "aaclassic_5",
-              filter: {
-                type: "tvslst",
-                in: true,
-                join: "",
-                lst: [
-                  {
-                    tag: "cohortFilter",
-                    type: "tvs",
-                    tvs: {
-                      term: {
-                        name: "Cohort",
-                        type: "categorical",
-                        values: { ABC: { label: "ABC" }, XYZ: { label: "XYZ" } },
-                        id: "subcohort",
-                        isleaf: false,
-                        groupsetting: { disabled: true }
-                      },
-                      values: [{ key: "ABC", label: "ABC" }]
-                    }
-                  }
-                ]
-              }
-            }
-          },
-          response: {
-            header: { status: 200 }
-          }
-        }
-      ]
-    },
-    post: {
-      alternativeFor: "get",
-      init
-    }
-  }
-};
-function init({ genomes }) {
-  return async (req, res) => {
-    const q = req.query;
-    try {
-      const g = genomes[req.query.genome];
-      if (!g)
-        throw "invalid genome name";
-      const ds = g.datasets[req.query.dslabel];
-      if (!ds)
-        throw "invalid dataset name";
-      const tdb = ds.cohort.termdb;
-      if (!tdb)
-        throw "invalid termdb object";
-      await trigger_getnumericcategories(q, res, tdb, ds);
-    } catch (e) {
-      res.send({ error: e instanceof Error ? e.message : e });
-      if (e instanceof Error && e.stack)
-        console.log(e);
-    }
-  };
-}
-async function trigger_getnumericcategories(q, res, tdb, ds) {
-  if (!q.tid)
-    throw ".tid missing";
-  const arg = {
-    ds,
-    term_id: q.tid,
-    filter: q.filter
-  };
-  const lst = await termdbsql.get_summary_numericcategories(arg);
-  res.send({ lst });
-}
-export {
-  api
-};