reorganize and cleanup

api/common.py

@@ -22,8 +22,8 @@ def load_yaml(file):
         data = yaml.safe_load(file)
     return data 
 
-common_config  = load_yaml('common_config.yaml')
-preview_config  = load_yaml('preview_config.yaml')
+common_config  = load_yaml('config/common.yaml')
+preview_config  = load_yaml('config/preview.yaml')
 
 # GLOBAL VARIABLES
 BOOK_PATHS = f"{common_config['DATA_ROOT_PATH']}/{common_config['JB_ROOT_FOLDER']}/*/*/*/*.tar.gz"

api/neurolibre_celery_tasks.py

@@ -24,9 +24,9 @@
 # from myst_libre.rees import REES
 # from myst_libre.builders import MystBuilder
 
-preview_config = load_yaml('preview_config.yaml')
-preprint_config = load_yaml('preprint_config.yaml')
-common_config  = load_yaml('common_config.yaml')
+preview_config = load_yaml('config/preview.yaml')
+preprint_config = load_yaml('config/preprint.yaml')
+common_config  = load_yaml('config/common.yaml')
 
 config_keys = [
     'DOI_PREFIX', 'DOI_SUFFIX', 'JOURNAL_NAME', 'PAPERS_PATH', 'BINDER_REGISTRY',

api/neurolibre_common_api.py

@@ -15,7 +15,7 @@
 # Document registration of the following endpoints must be performed by the app that 
 # imports this blueprint.
 
-common_config  = load_yaml('common_config.yaml')
+common_config  = load_yaml('config/common.yaml')
 DATA_ROOT_PATH = common_config['DATA_ROOT_PATH']
 JOURNAL_NAME = common_config['JOURNAL_NAME']
 

api/neurolibre_preprint_api.py

@@ -37,8 +37,8 @@
 app = flask.Flask(__name__)
 
 # Load configurations from YAML files and update Flask app config
-preprint_config = load_yaml('preprint_config.yaml')
-common_config = load_yaml('common_config.yaml')
+preprint_config = load_yaml('config/preprint.yaml')
+common_config = load_yaml('config/common.yaml')
 app.config.update(preprint_config)
 app.config.update(common_config)
 

api/neurolibre_preview_api.py

@@ -31,8 +31,8 @@
 app = flask.Flask(__name__)
 
 # Load and update app configuration from YAML files
-preview_config = load_yaml('preview_config.yaml')
-common_config = load_yaml('common_config.yaml')
+preview_config = load_yaml('config/preview.yaml')
+common_config = load_yaml('config/common.yaml')
 app.config.update(preview_config)
 app.config.update(common_config)
 

api/preprint.py

@@ -23,8 +23,8 @@
 
 load_dotenv()
 
-common_config  = load_yaml('common_config.yaml')
-preprint_config  = load_yaml('preprint_config.yaml')
+common_config  = load_yaml('config/common.yaml')
+preprint_config  = load_yaml('config/preprint.yaml')
 
 BINDER_REGISTRY = common_config['BINDER_REGISTRY']
 DATA_ROOT_PATH = common_config['DATA_ROOT_PATH']

systemd/doc.md

@@ -2,7 +2,7 @@
 
 ### Prerequisites
 
-Check that the `redis-server` service is (installed and) running:
+* Check that the `redis-server` service is (installed and) running:
 
 ```bash
 sudo systemctl status redis-server
@@ -16,6 +16,8 @@ sudo systemctl start redis-server
 
 The redis server is expected to run on port 6379 (by celery).
 
+* Check that a python virtual environment has been created and the dependencies (`<full-stack-server>/api/requirements.txt`) have been installed to that environment.
+
 ### Starting the Celery service
 
 #### Copy over systemd and environment files
@@ -25,7 +27,7 @@ sudo cp <full-stack-server>/api/systemd/neurolibre-celery.service /etc/systemd/s
 sudo cp <full-stack-server>/api/systemd/default/celery /etc/default/
 ```
 
-Make sure that the `neurolibre-server` file has correct permissions after copying:
+Make sure that the `celery` file has correct permissions after copying:
 
 ```bash
 sudo chown ubuntu:ubuntu /etc/default/celery
@@ -89,4 +91,77 @@ To clear the cache, simply delete the `__pycache__` folder in the root directory
 
 ```bash
 rm -rf <full-stack-server>/api/__pycache__
-```
+```
+
+## Starting NeuroLibre Full Stack Server
+
+### Prerequisites
+
+* Check that a python virtual environment has been created and the dependencies (`<full-stack-server>/api/requirements.txt`) have been installed to that environment.
+
+* Ensure that the ubuntu dependencies are installed from the apt.txt file:
+
+```bash
+sudo apt-get install -y $(cat <full-stack-server>/api/apt.txt)
+```
+
+* Ensure that you placed `.env` file in the `<full-stack-server>/api` directory with the correct parameters. See `<full-stack-server>/api/env_template/env.<server-type>.template` files as examples.
+
+* Ensure that the YAML configuration files are properly set for the server type:
+
+- `<full-stack-server>/api/config/common.yaml` (common parameters for both server types)
+- `<full-stack-server>/api/config/<server-type>.yaml` (server type specific parameters)
+
+#### Copy over systemd and environment files
+
+```bash
+sudo cp <full-stack-server>/api/systemd/neurolibre-<server-type>.service /etc/systemd/system/
+sudo cp <full-stack-server>/api/systemd/default/neurolibre-server /etc/default/
+```
+
+Make sure that the `neurolibre-server` file has correct permissions after copying:
+
+```bash
+sudo chown ubuntu:ubuntu /etc/default/neurolibre-server
+sudo chmod 644 /etc/default/neurolibre-server
+```
+
+> Note: The `/etc/default/neurolibre-server` file is a shared environment file containing parameters for both server types (preview and preprint).
+
+* Now you can start the service:
+
+```bash
+sudo systemctl start neurolibre-<server-type>
+```
+
+* Check the status of the service:
+
+```bash
+sudo systemctl status neurolibre-<server-type>
+```
+
+* Enable the service to start at boot:
+
+```bash
+sudo systemctl enable neurolibre-<server-type>
+```
+
+##### If the server is not starting
+
+To see the logs:
+
+```bash
+sudo journalctl -xn 100 -u neurolibre-<server-type>
+```
+
+* Make sure that you copied over the environment file properly with the correct parameters.
+
+* Make sure that the **YAML configuration files** for the respective server corresponds to the resources available in your system.
+
+* If you have made any changes to these, make sure to restart the service for your changes to take effect:
+
+```bash
+sudo systemctl restart neurolibre-<server-type>
+```
+
+* Make sure that you have a `.env` file.