Merge pull request #406 from FAIMS/projects-api

Projects API

package.json

@@ -27,7 +27,7 @@
     "express-handlebars": "7.1.2",
     "express-rate-limit": "^7.1.5",
     "express-validator": "7.0.1",
-    "faims3-datamodel": "github:FAIMS/faims3-data-model#v1.1.0",
+    "faims3-datamodel": "github:FAIMS/faims3-data-model#v1.1.1",
     "fast-check": "2.25.0",
     "gts": "3.1.1",
     "handlebars": "4.7.7.",

src/api/routes.ts

@@ -31,6 +31,7 @@ import {
   updateNotebook,
   streamNotebookRecordsAsCSV,
   streamNotebookFilesAsZip,
+  getProjects,
 } from '../couchdb/notebooks';
 import {requireAuthenticationAPI} from '../middleware';
 import {initialiseDatabases} from '../couchdb';
@@ -74,6 +75,16 @@ api.post('/initialise/', async (req, res) => {
   res.json({success: true});
 });
 
+api.get('/directory/', requireAuthenticationAPI, async (req, res) => {
+  // get the directory of notebooks on this server
+  if (req.user) {
+    const projects = await getProjects(req.user);
+    res.json(projects);
+  } else {
+    res.json([]);
+  }
+});
+
 api.get('/notebooks/', requireAuthenticationAPI, async (req, res) => {
   // get a list of notebooks from the db
   if (req.user) {
@@ -318,7 +329,7 @@ api.post('/users/:id/admin', requireAuthenticationAPI, async (req, res) => {
       .status(401)
       .json({
         error:
-         'you do not have permission to modify user permissions for this server',
+          'you do not have permission to modify user permissions for this server',
       })
       .end();
   }

src/buildconfig.ts

@@ -210,7 +210,6 @@ function google_client_secret(): string {
   }
 }
 
-
 function get_providers_to_use(): string[] {
   const providers = process.env.CONDUCTOR_AUTH_PROVIDERS;
   if (providers === '' || providers === undefined) {

src/couchdb/index.ts

@@ -25,8 +25,7 @@ import {
   COUCHDB_INTERNAL_URL,
   LOCAL_COUCHDB_AUTH,
 } from '../buildconfig';
-import {ProjectID} from 'faims3-datamodel';
-import {ProjectObject} from '../datamodel/database';
+import {ProjectID, ProjectObject} from 'faims3-datamodel';
 import {
   initialiseDirectoryDB,
   initialiseProjectsDB,

src/couchdb/notebooks.ts

@@ -20,17 +20,17 @@
 
 import PouchDB from 'pouchdb';
 import {getProjectsDB} from '.';
-import {CLUSTER_ADMIN_GROUP_NAME} from '../buildconfig';
+import {CLUSTER_ADMIN_GROUP_NAME, COUCHDB_PUBLIC_URL} from '../buildconfig';
 import {
   ProjectID,
   getProjectDB,
+  ProjectObject,
   resolve_project_id,
   notebookRecordIterator,
   addDesignDocsForNotebook,
 } from 'faims3-datamodel';
 import {
   ProjectMetadata,
-  ProjectObject,
   ProjectUIFields,
   ProjectUIModel,
   PROJECT_METADATA_PREFIX,
@@ -53,6 +53,39 @@ import {userHasPermission} from './users';
 PouchDB.plugin(securityPlugin);
 import {Stringifier, stringify} from 'csv-stringify';
 
+/**
+ * getProjects - get the internal project documents that reference
+ * the project databases that the front end will connnect to
+ * @param user - only return projects visible to this user
+ */
+export const getProjects = async (
+  user: Express.User
+): Promise<ProjectObject[]> => {
+  const projects: ProjectObject[] = [];
+
+  const projects_db = getProjectsDB();
+  if (projects_db) {
+    const res = await projects_db.allDocs({
+      include_docs: true,
+    });
+    res.rows.forEach(e => {
+      if (e.doc !== undefined && !e.id.startsWith('_')) {
+        const doc = e.doc as any;
+        if (userHasPermission(user, e.id, 'read')) {
+          delete doc._rev;
+          const project = doc as unknown as ProjectObject;
+          // add database connection details
+          if (project.metadata_db)
+            project.metadata_db.base_url = COUCHDB_PUBLIC_URL;
+          if (project.data_db) project.data_db.base_url = COUCHDB_PUBLIC_URL;
+          projects.push(project);
+        }
+      }
+    });
+  }
+  return projects;
+};
+
 /**
  * getNotebooks -- return an array of notebooks from the database
  * @oaram user - only return notebooks that this user can see

src/datamodel/database.ts

@@ -18,14 +18,7 @@
  *   TODO
  */
 
-import {
-  NonUniqueProjectID,
-  RecordID,
-  RevisionID,
-  AttributeValuePairID,
-  ProjectID,
-  ListingID,
-} from 'faims3-datamodel';
+import {RecordID, RevisionID, AttributeValuePairID} from 'faims3-datamodel';
 
 export const UI_SPECIFICATION_NAME = 'ui-specification';
 export const PROJECT_SPECIFICATION_PREFIX = 'project-specification';
@@ -40,18 +33,6 @@ export interface PouchAttachments {
   [key: string]: any; // any for now until we work out what we need
 }
 
-export interface ConnectionInfo {
-  proto: string;
-  host: string;
-  port: number;
-  lan?: boolean;
-  db_name: string;
-  auth?: {
-    username: string;
-    password: string;
-  };
-}
-
 /**
  * User-facing description of an Authentication mechanism.
  * The actual auth mechanisms are stored in authconfig.ts in the FAIMS3-conductor
@@ -63,89 +44,11 @@ export type AuthInfo = {
   name: string;
 };
 
-export type PossibleConnectionInfo =
-  | undefined
-  | {
-      proto?: string | undefined;
-      host?: string | undefined;
-      port?: number | undefined;
-      lan?: boolean | undefined;
-      db_name?: string | undefined;
-      auth?: {
-        username: string;
-        password: string;
-      };
-    };
-
-export type DirectoryEntry =
-  | undefined
-  | {
-      _id: string;
-      name: string;
-      description: string;
-      people_db?: PossibleConnectionInfo;
-      projects_db?: PossibleConnectionInfo;
-      auth_mechanisms: {[key: string]: AuthInfo};
-    };
-
-export interface ListingsObject {
-  _id: string;
-  name: string;
-  description: string;
-  projects_db?: PossibleConnectionInfo;
-  auth_mechanisms: {[key: string]: AuthInfo};
-}
-
-export interface NonNullListingsObject extends ListingsObject {
-  projects_db: ConnectionInfo;
-}
-
-export interface ActiveDoc {
-  _id: ProjectID;
-  listing_id: string;
-  project_id: NonUniqueProjectID;
-  username: string | null;
-  password: string | null;
-  friendly_name?: string;
-  is_sync: boolean;
-}
-
 export interface LocalAuthDoc {
   _id: string; //Corresponds to a listings ID
   dc_token: string;
 }
 
-/**
- * Describes a project, with connection, name, description, and schema
- * Part of the Projects DB
- * Do not use with UI code; sync code only
- */
-export interface ProjectObject {
-  _id: string;
-  name: string;
-  description?: string;
-  data_db?: PossibleConnectionInfo;
-  metadata_db?: PossibleConnectionInfo;
-  last_updated?: string;
-  created?: string;
-  status?: string;
-}
-
-export type ProjectsList = {
-  [key: string]: ProjectObject;
-};
-
-export interface ProjectInformation {
-  project_id: ProjectID;
-  name: string;
-  description?: string;
-  last_updated?: string;
-  created?: string;
-  status?: string;
-  listing_id: ListingID;
-  non_unique_project_id: NonUniqueProjectID;
-}
-
 export interface EncodedProjectMetadata {
   _id: string; // optional as we may want to include the raw json in places
   _rev?: string; // optional as we may want to include the raw json in places

views/notebook-landing.handlebars

@@ -157,7 +157,7 @@
         </div>
         <div class="modal-footer">
           <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
-          <button type="button" class="btn btn-warning">Update Notebook</button>
+          <button type="button" class="btn btn-warning" onclick="uploadNotebookHandler()">Update Notebook</button>
         </div>
       </div>
     </div>
@@ -245,10 +245,9 @@ const copyToClipboard = (text) => {
   }
 
 
-  const uploadNotebookHandler = (event) => {
-    event.preventDefault();
+  const uploadNotebookHandler = () => {
     const url = '/api/notebooks/{{notebook.project_id}}';
-    const form = event.target;
+    const form = document.querySelector('#upload-notebook-form');
     const fileInput = form.querySelector('[name="notebook"]');
     if (fileInput) {
       // parse the contents of the uploaded file as JSON