IBL ephys atlas web app

Running locally

1. Install requirements

Only tested on Ubuntu 22.04.

Install:

• A scientific Python distribution
• svgo
• inkscape

sudo apt-get install npm
sudo npm install --global http-server

2. Clone the repository

git clone https://github.com/int-brain-lab/ephys-atlas-web.git

3. Get the data

You can either obtain the generated data directly, or generate it from the input data.

3.1. Generate the data from input files

Get the following files from Cyrille and put them here:

data/pqt/allen_regions.pqt
data/pqt/beryl_regions.pqt
data/pqt/cosmos_regions.pqt
data/pqt/features_for_viz_mappings.pqt

Then, run python tools/process.py.

3.2. Alternatively, obtain the data directly

These files are generated by the tools/process.py script. If you obtain these files and put them at their expected location, you don't have to run tools/process.py.

* data/json/colormaps.json          the colormaps
* data/json/features_<fset>.json    all features for all supported mappings (fset=ephys, ...)
* data/json/regions.json            names of the brain regions
* data/json/slices.json             all SVG data, 84M (~30MB compressed) loaded once at initial startup
* data/css/region_colors.css        default brain region colors

4. Run the static HTTP server

Run ./run.sh (which just calls python -m http.server as this is a severless static web application for now).

Deployment

• Clone the repository.
• You also need to upload the files listed in section 3.2 above.

Apache configuration file, for example /etc/apache2/sites-available/atlas.conf:

<VirtualHost *:80>
    ServerAdmin [email protected]
    ServerName atlas.internationalbrainlab.org
    DocumentRoot /path/to/ephys-atlas-web
    AddOutputFilterByType DEFLATE application/javascript application/json
    ErrorLog ${APACHE_LOG_DIR}/error.log
    CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>

Fix CORS issues

You can add this in /etc/apache2/apache2.conf:

# NOTE: setup CORS policy for all websites
Header set Access-Control-Allow-Origin *
Header set Access-Control-Allow-Methods: "GET, POST, OPTIONS, PUT, DELETE"
Header set Access-Control-Allow-Headers "Origin, X-Requested-With, Content-Type, Accept, Content-Encoding"

Serving the flask features server

• Create /.ibl/globalkey with f9134149-fcb5-4142-a0eb-4e76a0811cf9.
• Apache configuration:

<VirtualHost *:443>
    ServerName features.internationalbrainlab.org

    WSGIDaemonProcess features user=ubuntu group=www-data threads=5 python-home=/var/www/ibl_website/atlas2/venv python-path=/var/www/ibl_website/atlas2/
    WSGIScriptAlias / /var/www/ibl_website/atlas2/features.wsgi

    <Directory /var/www/ibl_website/atlas2>
        WSGIProcessGroup features
        WSGIApplicationGroup %{GLOBAL}
        Require all granted
    </Directory>

    # !!!!!!!!!!!!!! IMPORTANT !!!!!!!!!!!!!!!!!!!!!
    <LocationMatch ".*">
        # necessary if when using token-based authentication, to ensure the Authentication
        # HTTP header is not removed when being passed to django via WSGI
        CGIPassAuth On
    </LocationMatch>

    ErrorLog ${APACHE_LOG_DIR}/error_features.log
    CustomLog ${APACHE_LOG_DIR}/access_features.log combined
</VirtualHost>