@sjcrh/proteinpaint-server 2.138.3-2 → 2.138.3-5

package/dataset/protected.test.js

@@ -1,10 +1,14 @@
 import termdbTestInit from "./termdb.test.js";
+const minSampleSize = 10;
 function protected_test_default() {
   const ds = termdbTestInit();
   if (!ds.cohort)
     ds.cohort = { termdb: {} };
-  ds.cohort.termdb.hasMinSampleSize = (sampleCount) => {
-    return sampleCount >= 10;
+  ds.cohort.termdb.checkAccessToSampleData = (_, data) => {
+    return {
+      minSampleSize,
+      canAccess: data.sampleCount >= minSampleSize
+    };
   };
   return ds;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.138.3-2",
+  "version": "2.138.3-5",
   "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": "2.138.3-2",
+    "@sjcrh/proteinpaint-types": "2.138.3-5",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/aiProjectAdmin.js

@@ -39,7 +39,7 @@ function init({ genomes }) {
         addProject(db.connection, query);
       res.status(200).send({
         status: "ok",
-        message: `Project ${query.projectName} processed successfully`
+        message: `Project ${query.project.name} processed successfully`
       });
     } catch (e) {
       console.warn(e);
@@ -54,12 +54,12 @@ function editProject() {
   console.log(58, "called editProject");
 }
 function deleteProject(connection, query) {
-  const sql = `DELETE FROM Project WHERE id= ?`;
+  const sql = `DELETE FROM project WHERE id= ?`;
   const params = [query.project.id];
   runSQL(connection, sql, params, "delete");
 }
 function addProject(connection, query) {
-  const sql = `INSERT INTO Project (name) VALUES (?)`;
+  const sql = `INSERT INTO project (name) VALUES (?)`;
   const params = [query.project.name];
   runSQL(connection, sql, params, "add");
 }

package/routes/aiProjectList.js

@@ -35,7 +35,7 @@ function getProjects(ds) {
   if (!ds.queries?.WSImages?.db)
     return;
   const db = ds.queries.WSImages.db;
-  const sql = "SELECT project.name as value, id FROM Project";
+  const sql = "SELECT project.name as value, id FROM project";
   try {
     db.connection = connect_db(db.file, { readonly: false, fileMustExist: true });
     const rows = db.connection.prepare(sql).all();

package/routes/{filterTermValues.js → termdb.filterTermValues.js}

@@ -2,7 +2,7 @@ import { FilterTermValuesPayload } from "#types/checkers";
 import { getData, getSamplesPerFilter } from "../src/termdb.matrix.js";
 import { authApi } from "../src/auth.js";
 const api = {
-  endpoint: "filterTermValues",
+  endpoint: "termdb/filterTermValues",
   methods: {
     get: {
       ...FilterTermValuesPayload,

package/routes/{profileFormScores.js → termdb.profileFormScores.js}

@@ -1,7 +1,7 @@
 import { ProfileFormScoresPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 const api = {
-  endpoint: "profileFormScores",
+  endpoint: "termdb/profileFormScores",
   methods: {
     get: {
       ...ProfileFormScoresPayload,

package/routes/{profileScores.js → termdb.profileScores.js}

@@ -1,7 +1,7 @@
 import { ProfileScoresPayload } from "#types/checkers";
 import { getData } from "../src/termdb.matrix.js";
 const api = {
-  endpoint: "profileScores",
+  endpoint: "termdb/profileScores",
   methods: {
     get: {
       ...ProfileScoresPayload,