@sjcrh/proteinpaint-server 2.138.3-1 → 2.138.3-4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.138.3-1",
+  "version": "2.138.3-4",
   "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": "2.138.3-0",
+    "@sjcrh/proteinpaint-types": "2.138.3-4",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/aiProjectAdmin.js

@@ -0,0 +1,77 @@
+import { aiProjectAdminPayload } from "#types/checkers";
+import { connect_db } from "../src/utils.js";
+const routePath = "aiProjectAdmin";
+const api = {
+  endpoint: `${routePath}`,
+  methods: {
+    post: {
+      //edit
+      ...aiProjectAdminPayload,
+      init
+    },
+    delete: {
+      //delete
+      ...aiProjectAdminPayload,
+      init
+    },
+    put: {
+      //add
+      ...aiProjectAdminPayload,
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const query = req.query;
+      const g = genomes[query.genome];
+      const ds = g.datasets[query.dslabel];
+      if (!ds.queries?.WSImages?.db)
+        return;
+      const db = ds.queries.WSImages.db;
+      db.connection = connect_db(db.file, { readonly: false, fileMustExist: true });
+      if (req.method === "POST")
+        editProject();
+      if (req.method === "DELETE")
+        deleteProject(db.connection, query);
+      if (req.method === "PUT")
+        addProject(db.connection, query);
+      res.status(200).send({
+        status: "ok",
+        message: `Project ${query.project.name} processed successfully`
+      });
+    } catch (e) {
+      console.warn(e);
+      res.status(500).send({
+        status: "error",
+        error: e.message || e
+      });
+    }
+  };
+}
+function editProject() {
+  console.log(58, "called editProject");
+}
+function deleteProject(connection, query) {
+  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 params = [query.project.name];
+  runSQL(connection, sql, params, "add");
+}
+function runSQL(connection, sql, params = [], errorText = "fetch") {
+  try {
+    const rows = connection.prepare(sql).run(params);
+    return rows;
+  } catch (e) {
+    console.error(`Error executing SQL for ${errorText}:`, e);
+    throw new Error(`Failed to ${errorText} projects`);
+  }
+}
+export {
+  api
+};

package/routes/aiProjectList.js

@@ -0,0 +1,50 @@
+import { aiProjectListPayload } from "#types/checkers";
+import { connect_db } from "../src/utils.js";
+const routePath = "aiProjectList";
+const api = {
+  endpoint: `${routePath}`,
+  methods: {
+    get: {
+      ...aiProjectListPayload,
+      init
+    },
+    post: {
+      ...aiProjectListPayload,
+      init
+    }
+  }
+};
+function init({ genomes }) {
+  return async (req, res) => {
+    try {
+      const query = req.query;
+      const g = genomes[query.genome];
+      const ds = g.datasets[query.dslabel];
+      const projects = getProjects(ds);
+      res.send(projects);
+    } catch (e) {
+      console.warn(e);
+      res.status(500).send({
+        status: "error",
+        error: e.message || e
+      });
+    }
+  };
+}
+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";
+  try {
+    db.connection = connect_db(db.file, { readonly: false, fileMustExist: true });
+    const rows = db.connection.prepare(sql).all();
+    return rows;
+  } catch (e) {
+    console.error("Error fetching projects:", e);
+    throw new Error("Failed to fetch projects");
+  }
+}
+export {
+  api
+};

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,