Run pATLAS locally

Docker compose (recommended)

You can run pATLAS locally without much requirements by using patlas-compose. This will automatically handle the installation of the version 1.5.2 of pATLAS and launch the service in a local instance. For that you just require:

• docker
• docker-compose

Then, follow this simple steps:

• Clone the repository patlas-compose.

git clone https://github.com/bfrgoncalves/patlas-compose

• Enter the patlas-compose folder

cd patlas-compose

• Launch the compose:

docker-compose up

• Wait for the line * Running on http://0.0.0.0:5000/ (Press CTRL+C to quit) to show up, meaning that the service is now running.

• Access on 127.0.0.1:5000 or 0.0.0.0:5000.

From scratch (alternatively)

pATLAS can be run locally if you have PostgreSQL installed and configured. After, you just need to:

1) Clone this repository:

git clone https://github.com/tiagofilipe12/pATLAS

2) Create your custom database version or generate the default pATLAS database or download sql file from version 1.6.1 (the tar.gz archive). Note: if you download the sql file from version 1.6.1 you may skip steps 3 to 4 and continue with step 5.

3) Make sure all the necessary files are in place.

• by default pATLAS generates a import_to_vivagraph.json file in the folder <tag_provided_to_o_flag>/results. Place this file in the patlas/db_manager/db_app/static/json folder.
• change session to read the new import_to_vivagraph.json file by changing from false to true a variable named devel in patlas/db_manager/db_app/static/js/pATLASGlobals.js

4) Create the database that the front end will run:

createdb <your_database>

5) load the generated sql file

6) Install backend dependencies:

# within the root directory of this repository
pip install -r requirements.txt

7) Install frontend dependencies:

# change directory to static direcoty where `index.html` will look for
# its depdendenies
cd patlas/db_manager/db_app/static/
# then install them (package.json is located in this directory)
yarn install

8) Compile node modules so that the html can understand, using webpack:

# You can also user a local installation of webpack.
# entry-point.js is the config file where all the imported modules are
# called
node_modules/webpack/bin/webpack.js entry-point.js

9) Then execute the script run.py.

# within the root directory of this repository
cd patlas/db_manager
./run.py <your_database>

Note: the database name is utterly important to properly say to the frontend where to get the data.

10) Go to 127.0.0.1:5000.

Optimization of the resources usage by the web page

Using the devel = true isn't very efficient, so you can allow the force directed graph to render in a devel = true session, then when you are satisfied pause the force layout using the buttons available in pATLAS and click at the same time Shift+Ctrl+Space. This will take a while but eventually it will generate a file named filtered.json. Once you have this file you can add it to the patlas/db_manager/db_app/static/json folder and change the devel variable to false. This will use the previously saved positions to render a pre rendered network.