@sjcrh/proteinpaint-server 2.140.1-0 → 2.140.1-2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.140.1-0",
+  "version": "2.140.1-2",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -63,8 +63,8 @@
     "@sjcrh/proteinpaint-python": "2.139.1",
     "@sjcrh/proteinpaint-r": "2.137.2-0",
     "@sjcrh/proteinpaint-rust": "2.138.3-7",
-    "@sjcrh/proteinpaint-shared": "2.138.3-7",
-    "@sjcrh/proteinpaint-types": "2.140.1-0",
+    "@sjcrh/proteinpaint-shared": "2.140.1-1",
+    "@sjcrh/proteinpaint-types": "2.140.1-2",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^9.4.1",

package/routes/aiProjectAdmin.js

@@ -4,18 +4,23 @@ const routePath = "aiProjectAdmin";
 const api = {
   endpoint: `${routePath}`,
   methods: {
+    get: {
+      //all requests
+      ...aiProjectAdminPayload,
+      init
+    },
     post: {
-      //edit
+      //'admin' -> edit
       ...aiProjectAdminPayload,
       init
     },
     delete: {
-      //delete
+      //'admin' -> delete
       ...aiProjectAdminPayload,
       init
     },
     put: {
-      //add
+      //'admin' -> add
       ...aiProjectAdminPayload,
       init
     }
@@ -25,22 +30,44 @@ function init({ genomes }) {
   return async (req, res) => {
     try {
       const query = req.query;
+      if (!query.genome || !query.dslabel) {
+        throw new Error("Genome and dataset label are required for aiProjectAdmin request.");
+      }
       const g = genomes[query.genome];
       const ds = g.datasets[query.dslabel];
       if (!ds.queries?.WSImages?.db)
-        return;
+        throw new Error("WSImages database not found.");
       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`
-      });
+      if (query.for === "list") {
+        const projects = getProjects(db.connection);
+        res.send(projects);
+      } else if (query.for === "admin") {
+        if (req.method === "PUT" || query.project.type === "new")
+          addProject(db.connection, query.project);
+        else if (req.method === "POST")
+          editProject(db.connection, query.project);
+        else if (req.method === "DELETE")
+          deleteProject(db.connection, query.project.id);
+        else
+          throw new Error('Invalid request method for="admin" in aiProjectAdmin route.');
+        res.status(200).send({
+          status: "ok",
+          message: `Project ${query.project.name} processed successfully`
+        });
+      } else if (query.for === "images") {
+        const q = ds.cohort.termdb.q;
+        const data = await q.getFilteredImages(query.project.filter);
+        res.status(200).send({
+          status: "ok",
+          data
+        });
+      } else {
+        res.send({
+          status: "error",
+          message: "Invalid request"
+        });
+      }
     } catch (e) {
       console.warn(e);
       res.status(500).send({
@@ -50,25 +77,104 @@ function init({ genomes }) {
     }
   };
 }
-function editProject() {
-  console.log(58, "called editProject");
+function getProjects(connection) {
+  const sql = "SELECT project.name as value, id FROM project";
+  return runSQL(connection, sql);
 }
-function deleteProject(connection, query) {
-  const sql = `DELETE FROM project WHERE id= ?`;
-  const params = [query.project.id];
-  runSQL(connection, sql, params, "delete");
+function editProject(connection, project) {
+  const stmts = [];
+  if (!project.id) {
+    const res = connection.prepare(`SELECT id FROM project WHERE name = ?`).get(project.name);
+    project.id = res.id;
+  }
+  if (project.images) {
+    stmts.push({
+      sql: `DELETE FROM project_images WHERE project_id = ? AND image NOT IN (${project.images.map(() => "?").join(",") || "''"})`,
+      params: [[project.id, ...project.images]]
+    });
+    const existingImg = connection.prepare(`SELECT 1 FROM project_images WHERE project_id = ? AND image = ?`);
+    const multiParams = [];
+    for (const img of project.images) {
+      const exists = existingImg.get(project.id, img);
+      if (!exists)
+        multiParams.push([project.id, img]);
+    }
+    if (multiParams.length > 0) {
+      const insertImg = `INSERT INTO project_images (project_id, image) VALUES (?, ?)`;
+      stmts.push({ sql: insertImg, params: multiParams });
+    }
+  }
+  if (project.filter) {
+    stmts.push({
+      sql: `UPDATE project SET filter = ? WHERE id = ?`,
+      params: [[JSON.stringify(project.filter), project.id]]
+    });
+  }
+  if (project.classes) {
+    stmts.push({
+      sql: `DELETE FROM project_classes WHERE project_id = ? AND name NOT IN (${project.classes.map(() => "?").join(",") || "''"})`,
+      params: [project.id, ...project.classes.map((c) => c.name)]
+    });
+    const existingClasses = connection.prepare(`SELECT 1 FROM project_classes WHERE project_id = ? AND name = ?`);
+    const multiParams = [];
+    for (const cls of project.classes) {
+      const exists = existingClasses.get(project.id, cls.name);
+      if (!exists)
+        multiParams.push([project.id, cls.name, cls.color, cls.key_shortcut || ""]);
+    }
+    if (multiParams.length > 0) {
+      const insertClass = `INSERT INTO project_classes (project_id, name, color, key_shortcut) VALUES (?, ?, ?, ?)`;
+      stmts.push({ sql: insertClass, params: multiParams });
+    }
+  }
+  runMultiStmtSQL(connection, stmts, "add");
+}
+function deleteProject(connection, projectId) {
+  if (!projectId)
+    throw new Error("Invalid project ID [aiProjectAdmin route deleteProject()]");
+  const stmts = [
+    { sql: "DELETE FROM project_annotations WHERE project_id = ?", params: [[projectId]] },
+    { sql: "DELETE FROM project_classes WHERE project_id = ?", params: [[projectId]] },
+    { sql: "DELETE FROM project_images WHERE project_id = ?", params: [[projectId]] },
+    { sql: "DELETE FROM project_users WHERE project_id = ?", params: [[projectId]] },
+    { sql: "DELETE FROM project WHERE id = ?", params: [[projectId]] }
+  ];
+  runMultiStmtSQL(connection, stmts, "delete");
 }
-function addProject(connection, query) {
-  const sql = `INSERT INTO project (name) VALUES (?)`;
-  const params = [query.project.name];
-  runSQL(connection, sql, params, "add");
+function addProject(connection, project) {
+  const projectSql = `INSERT INTO project (name, filter) VALUES (?, ?)`;
+  const projectParams = [project.name, JSON.stringify(project.filter)];
+  const rows = runSQL(connection, projectSql, projectParams, "add");
+  const classSql = `INSERT INTO project_classes (project_id, name, color, key_shortcut) VALUES (?, ?, ?, ?)`;
+  const classParams = project.classes.map((c) => [rows.lastInsertRowid, c.label, c.color, c.key_shortcut || ""]);
+  for (const params of classParams) {
+    runSQL(connection, classSql, params, "add");
+  }
 }
 function runSQL(connection, sql, params = [], errorText = "fetch") {
   try {
-    const rows = connection.prepare(sql).run(params);
-    return rows;
+    if (!params.length) {
+      return connection.prepare(sql).all();
+    }
+    return connection.prepare(sql).run(params);
+  } catch (e) {
+    console.error(`Error executing SQL for ${errorText}: ${e.message || e}`);
+    throw new Error(`Failed to ${errorText} projects`);
+  }
+}
+function runMultiStmtSQL(connection, stmts, errorText = "execute") {
+  const transaction = connection.transaction((batch) => {
+    for (const { sql, params = [] } of batch) {
+      const sqlStmt = connection.prepare(sql);
+      for (const item of params) {
+        sqlStmt.run(item);
+      }
+    }
+  });
+  try {
+    transaction(stmts);
   } catch (e) {
-    console.error(`Error executing SQL for ${errorText}:`, e);
+    console.error(`Error executing transaction for ${errorText}: ${e.message || e}`);
     throw new Error(`Failed to ${errorText} projects`);
   }
 }