@sjcrh/proteinpaint-server 2.163.1 → 2.164.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.163.1",
+  "version": "2.164.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -62,11 +62,11 @@
   },
   "dependencies": {
     "@sjcrh/augen": "2.143.0",
-    "@sjcrh/proteinpaint-python": "2.162.0",
+    "@sjcrh/proteinpaint-python": "2.164.1",
     "@sjcrh/proteinpaint-r": "2.152.1-0",
     "@sjcrh/proteinpaint-rust": "2.157.0",
     "@sjcrh/proteinpaint-shared": "2.163.1",
-    "@sjcrh/proteinpaint-types": "2.163.1",
+    "@sjcrh/proteinpaint-types": "2.164.1",
     "@types/express": "^5.0.0",
     "@types/express-session": "^1.18.1",
     "better-sqlite3": "^12.4.1",

package/routes/aiProjectAdmin.js

@@ -154,17 +154,16 @@ function deleteProject(connection, projectId) {
   runMultiStmtSQL(connection, stmts, "delete");
 }
 function addProject(connection, project) {
-  if (!project.users || !Array.isArray(project.users) || project.users.length === 0) {
-    throw new Error("project.users must be a non-empty array of emails");
-  }
   const projectSql = `INSERT INTO project (name, filter)
                         VALUES (?, ?)`;
   const projectParams = [project.name, JSON.stringify(project.filter)];
   const row = runSQL(connection, projectSql, projectParams, "add");
-  const userSql = `INSERT INTO project_users (project_id, email)
-                     VALUES (?, ?)`;
-  const userParams = project.users.map((email) => [row.lastInsertRowid, email]);
-  runMultiStmtSQL(connection, [{ sql: userSql, params: userParams }], "add");
+  if (project.users) {
+    const userSql = `INSERT INTO project_users (project_id, email)
+                         VALUES (?, ?)`;
+    const userParams = project.users.map((email) => [row.lastInsertRowid, email]);
+    runMultiStmtSQL(connection, [{ sql: userSql, params: userParams }], "add");
+  }
   const classSql = `INSERT INTO project_classes (project_id, label, color, key_shortcut)
                       VALUES (?, ?, ?, ?)`;
   const classParams = project.classes.map((c) => [row.lastInsertRowid, c.label, c.color, c.key_shortcut || ""]);

package/routes/aiProjectSelectedWSImages.js

@@ -22,8 +22,20 @@ function init({ genomes }) {
       const ds = g.datasets[query.dslabel];
       if (!ds) throw "invalid dataset name";
       const projectId = query.projectId;
-      const wsimagesFilenames = query.wsimagesFilenames;
+      const wsimagesFilenamesArg = query.wsimagesFilenames;
+      let wsimagesFilenames = [];
       const wsimages = [];
+      if (Array.isArray(wsimagesFilenamesArg) && wsimagesFilenamesArg.length === 1 && wsimagesFilenamesArg[0] === "all") {
+        if (ds.queries?.WSImages?.getAllWSImages) {
+          try {
+            wsimagesFilenames = await ds.queries.WSImages.getAllWSImages(projectId);
+          } catch (e) {
+            console.error("Failed to get WSI image list via helper, falling back to provided param", e);
+          }
+        }
+      } else {
+        wsimagesFilenames = wsimagesFilenamesArg;
+      }
       if (ds.queries.WSImages.getWSIAnnotations) {
         for (const wsimageFilename of wsimagesFilenames) {
           const wsimage = {
@@ -84,6 +96,12 @@ function validateWSIAnnotationsQuery(ds, connection) {
           AND pa.status = 1
         ORDER BY pa.timestamp DESC, pa.id DESC
     `;
+  const GET_PROJECT_IMAGES_SQL = `
+        SELECT DISTINCT pi.image_path AS image_path
+        FROM project_images pi
+        WHERE pi.project_id = ?
+        ORDER BY pi.id
+    `;
   if (!ds.queries) ds.queries = {};
   if (!ds.queries.WSImages) ds.queries.WSImages = {};
   ds.queries.WSImages.getWSIAnnotations = async (projectId, filename) => {
@@ -103,7 +121,8 @@ function validateWSIAnnotationsQuery(ds, connection) {
         }
         return {
           zoomCoordinates: coords,
-          class: r.label ?? ""
+          class: r.label ?? "",
+          timestamp: r.timestamp
         };
       });
     } catch (error) {
@@ -111,6 +130,16 @@ function validateWSIAnnotationsQuery(ds, connection) {
       return [];
     }
   };
+  ds.queries.WSImages.getAllWSImages = async (projectId) => {
+    try {
+      const stmt = connection.prepare(GET_PROJECT_IMAGES_SQL);
+      const rows = stmt.all(projectId);
+      return (rows || []).map((r) => r.image_path);
+    } catch (error) {
+      console.error("Error loading project images list:", error);
+      return [];
+    }
+  };
 }
 function validateWSIClassesQuery(ds, connection) {
   if (!ds.queries) ds.queries = {};

package/routes/termdb.chat.js

@@ -2,6 +2,7 @@ import { ChatPayload } from "#types/checkers";
 import { run_rust } from "@sjcrh/proteinpaint-rust";
 import serverconfig from "../src/serverconfig.js";
 import { mayLog } from "#src/helpers.ts";
+import { run_python } from "@sjcrh/proteinpaint-python";
 const api = {
   endpoint: "termdb/chat",
   methods: {
@@ -23,7 +24,22 @@ function init({ genomes }) {
       if (!g) throw "invalid genome";
       const ds = g.datasets?.[q.dslabel];
       if (!ds) throw "invalid dslabel";
-      console.log("serverconfig:", serverconfig);
+      if (serverconfig.features.pythonChatBot) {
+        const chatbot_input2 = {
+          prompt: q.prompt,
+          genome: q.genome,
+          dslabel: q.dslabel
+          //terms_tsv_path: df
+        };
+        try {
+          const ai_output_data2 = await run_python("chatBot.py", JSON.stringify(chatbot_input2));
+          res.send(ai_output_data2);
+        } catch (error) {
+          const errmsg = "Error running chatBot Python script:" + error;
+          throw new Error(errmsg);
+        }
+        return;
+      }
       const serverconfig_ds_entries = serverconfig.genomes.find((genome) => genome.name == q.genome).datasets.find((dslabel) => dslabel.name == ds.label);
       console.log("serverconfig_ds_entries:", serverconfig_ds_entries);
       if (!serverconfig_ds_entries.aifiles) {