Merge pull request #22 from recogito/lwj/doc-updates

Doc updates

Author: lwjameson

.nvmrc

@@ -1 +1 @@
-18.18.2
+22.20.0

package.json

@@ -1,5 +1,5 @@
 {
-  "name": "starlight",
+  "name": "recogito.github.io",
   "type": "module",
   "version": "0.0.1",
   "scripts": {
@@ -16,4 +16,4 @@
     "sharp": "^0.34.3",
     "typescript": "^5.4.2"
   }
-}
+}

src/content/docs/guides/local-development.mdx

@@ -97,24 +97,6 @@ docker --version
    cd recogito-server
    ```
 
-   :::note[Supabase CLI Compatibility - pgsodium Extension]
-   If using Supabase CLI version 2.20.4 or later, you need to make a one-time fix to the migration file:
-
-   Edit `supabase/migrations/20230524173605_remote_commit.sql` and comment out line 13:
-   ```sql
-   -- CREATE EXTENSION IF NOT EXISTS "pgsodium" WITH SCHEMA "pgsodium";
-   ```
-
-   **Why this is needed:**
-   - Newer Supabase CLI versions don't pre-create the `pgsodium` schema in local development
-   - Supabase is [deprecating the pgsodium extension](https://supabase.com/docs/guides/database/extensions/pgsodium) and does not recommend its use for new projects
-   - Recogito doesn't use pgsodium's encryption features
-   - Your data remains secure: **Supabase projects are encrypted at rest by default** (SOC2 & HIPAA compliant)
-
-   **Production deployments:**
-   If your production instance was created before this change and already has pgsodium installed, it will continue to work. However, the extension is not actively used by Recogito, so this change is safe for all environments.
-   :::
-
 2. **Start Supabase locally**
 
    ```bash
@@ -200,36 +182,26 @@ docker --version
    The `supabase db reset` command only runs migrations - it doesn't populate roles and groups from config.json.
    :::
 
-7. **Create test users**
+7. **Create test users and run tests**
+
+   Recogito Server has a number of `Jest` tests that are in the `jest/tests/projects.test.ts` file. These tests verify some base functionality.  
+
+   To simplify the process going forward, modify the `run_tests.sh` file to be executable:
 
    ```bash
-   export SUPABASE_HOST=http://localhost:54321
-   export SUPABASE_SERVICE_KEY=<service_role_key from step 2>
-   export PROFESSOR_PW=password123
-   export STUDENT_PW=password123
-   export TUTOR_PW=password123
-   export READER_PW=password123
-   export INVITE_PW=password123
-   export PROFESSOR_GROUP_ID='f918b2f8-f587-4ee1-9f2d-35b3aed0b1e6'
-   node create-test-users.js -f config.json
+   chmod +x run_tests.sh
    ```
 
-   This creates test accounts for development:
-   - `[email protected]` / `password123`
-   - `[email protected]` / `password123`
-   - `[email protected]` / `password123`
-   - `[email protected]` / `password123`
-   - `[email protected]` / `password123`
-
-8. **Assign test users to organization groups**
+   Then execute the tests from the root directory of the repository:
 
    ```bash
-   export SUPABASE_HOST=http://localhost:54321
-   export SUPABASE_SERVICE_KEY=<service_role_key from step 2>
-   node assign-test-user-groups.js -f config.json
+   ./run_tests.sh
    ```
 
-   This assigns test users to appropriate groups:
+   The test script will create a number of test users that you can use locally to access the client and test fuctionality.
+
+   This creates test accounts for development:
+
    - `[email protected]` → Org Professor (can create projects)
    - `[email protected]` → Org Readers (read-only)
    - `[email protected]` → Org Readers (read-only)

src/content/docs/guides/self-hosting.mdx

@@ -109,6 +109,7 @@ ssh root@your_server_ip
 Update the system:
 ```bash
 apt update
+apt upgrade
 ```
 
 Create a new user with sudo privileges:
@@ -125,6 +126,13 @@ ufw enable
 ufw status
 ```
 
+Best practice is to not utilize the `root` login except in special circumstances.  Go ahead and exit the instance and SSH in with the new `recogito` user.
+
+```bash
+exit
+ssh recogito@your_server_ip
+```
+
 ### 2. Install Nginx
 
 Install and configure the web server:
@@ -214,31 +222,31 @@ Use [Supabase JWT Generator](https://supabase.com/docs/guides/self-hosting/docke
 - **MINIO_ROOT_USER/PASSWORD**: MinIO dashboard credentials
 - **PGADMIN_ADMIN_EMAIL/PASSWORD**: pgAdmin web access
 
-### 6. Run Installation
+### 6. Configure Nginx Routes
 
-Execute the installation script:
-```bash
-sudo bash ./install-self-hosted-docker.sh
-```
+Copy and customize Nginx configuration files:
 
-Respond "Yes" to database push when prompted.
+#### Client Configuration
 
-### 7. Configure Nginx Routes
+You will need 5 URLs for this setup
 
-Copy and customize Nginx configuration files:
+- A client URL for accessing the Recogito Studio client
+- A server URL for API calls
+- A MinIO URL for accessing the MinIO dashboard
+- A pgAdmin URL for accessing pgAdmin
+- A Portainer URL for accessing the Portainer UI
 
-#### Client Configuration
 ```bash
-sudo cp ./nginx.client.example.com /etc/nginx/sites-available/client.example.com
-sudo nano /etc/nginx/sites-available/client.example.com
+sudo cp ./nginx.client.example.com /etc/nginx/sites-available/<your client url>
+sudo nano /etc/nginx/sites-available/<your client url>
 ```
 
 Replace `client.example.com` with your actual client domain.
 
 #### Server Configuration
 ```bash
-sudo cp ./nginx.server.example.com /etc/nginx/sites-available/server.example.com
-sudo nano /etc/nginx/sites-available/server.example.com
+sudo cp ./nginx.server.example.com /etc/nginx/sites-available/<your server url>
+sudo nano /etc/nginx/sites-available/<your server url>
 ```
 
 Update:
@@ -270,11 +278,11 @@ map $http_upgrade $connection_upgrade {
 #### Enable Sites
 Create symbolic links:
 ```bash
-sudo ln -s /etc/nginx/sites-available/server.example.com /etc/nginx/sites-enabled/
-sudo ln -s /etc/nginx/sites-available/client.example.com /etc/nginx/sites-enabled/
-sudo ln -s /etc/nginx/sites-available/pgadmin.example.com /etc/nginx/sites-enabled/
-sudo ln -s /etc/nginx/sites-available/minio.example.com /etc/nginx/sites-enabled/
-sudo ln -s /etc/nginx/sites-available/portainer.example.com /etc/nginx/sites-enabled/
+sudo ln -s /etc/nginx/sites-available/<your server url> /etc/nginx/sites-enabled/
+sudo ln -s /etc/nginx/sites-available/<your client url> /etc/nginx/sites-enabled/
+sudo ln -s /etc/nginx/sites-available/<your pgAdmin url> /etc/nginx/sites-enabled/
+sudo ln -s /etc/nginx/sites-available/<your MinIO url> /etc/nginx/sites-enabled/
+sudo ln -s /etc/nginx/sites-available/<your Portainer url> /etc/nginx/sites-enabled/
 ```
 
 Test and restart:
@@ -283,7 +291,7 @@ sudo nginx -t
 sudo systemctl restart nginx
 ```
 
-### 8. SSL Certificates with Let's Encrypt
+### 7. SSL Certificates with Let's Encrypt
 
 Install Certbot:
 ```bash
@@ -294,11 +302,11 @@ sudo ln -s /snap/bin/certbot /usr/bin/certbot
 
 Generate certificates for each domain:
 ```bash
-sudo certbot --nginx -d client.example.com
-sudo certbot --nginx -d server.example.com
-sudo certbot --nginx -d pgadmin.example.com
-sudo certbot --nginx -d minio.example.com
-sudo certbot --nginx -d portainer.example.com
+sudo certbot --nginx -d <your client url>
+sudo certbot --nginx -d <your server url>
+sudo certbot --nginx -d <your pgAdmin url>
+sudo certbot --nginx -d <your MinIO url>
+sudo certbot --nginx -d <your portainer url>
 ```
 
 Verify auto-renewal:
@@ -307,6 +315,15 @@ sudo systemctl status snap.certbot.renew.service
 sudo certbot renew --dry-run
 ```
 
+### 8. Run Installation
+
+Execute the installation script:
+```bash
+sudo bash ./install-self-hosted-docker.sh
+```
+
+Respond "Yes" to database push when prompted.
+
 ## Testing Your Installation
 
 ### Test Client Access

src/content/docs/reference/client-architecture.md

@@ -74,7 +74,6 @@ Layered annotation system:
 - Multiple layers per document
 - Context-based organization
 - Private/shared annotations
-- Version tracking
 
 ### Backend Integration