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https://github.com/int-brain-lab/ephys-atlas-web
https://github.com/int-brain-lab/ephys-atlas-web
Last synced: about 1 month ago
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- Host: GitHub
- URL: https://github.com/int-brain-lab/ephys-atlas-web
- Owner: int-brain-lab
- License: mit
- Created: 2023-02-03T12:47:55.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-13T15:14:05.000Z (3 months ago)
- Last Synced: 2024-09-15T01:25:40.166Z (3 months ago)
- Language: CSS
- Size: 5.11 MB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# IBL ephys atlas web app
## Running locally
### 1. Install requirements
Only tested on Ubuntu 22.04.
Install:
* A scientific Python distribution
* [svgo](https://github.com/svg/svgo)
* [inkscape](https://inkscape.org/)
```bash
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_.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`:
```
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
```
## 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:
```
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
WSGIProcessGroup features
WSGIApplicationGroup %{GLOBAL}
Require all granted
# !!!!!!!!!!!!!! IMPORTANT !!!!!!!!!!!!!!!!!!!!!
# 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
ErrorLog ${APACHE_LOG_DIR}/error_features.log
CustomLog ${APACHE_LOG_DIR}/access_features.log combined
```