ChemReg 2.0 REST API

Chemical Curation and Data Management

Developer Setup

Required software

You'll need the following software installed on your machine to begin development.

• Python 3.8 or Conda
• Git
• Docker
• docker-compose (see Deploying with Docker page)

Running chemreg

Open up a terminal or command prompt for the following.

1. Clone the chemreg_django repository and enter into the downloaded directory.

git clone https://github.com/Chemical-Curation/chemcurator_django.git
cd chemcurator_django

2. Create your Python virtual environment.

Python 3.8 - Linux and macOS:

python3.8 -m venv .venv
source .venv/bin/activate

Python 3.8 - Windows:

python3.8 -m venv .venv
.venv\Scripts\activate.bat

Conda - Linux and macOS:

conda create -n chemreg python=3.8
source activate chemreg

Conda - Windows:

conda create -n chemreg python=3.8
activate chemreg

3. Install requirements.

3.0 - Install pre-requirements.

If you are on Windows, you will likely need the Microsoft Visual C++ 14.0 build tools

• Selecting the C++ libraries from the installer will be sufficient to build the python environment.

3.1 - Install requirements.

Install the Python requirements from the file w/in the /chemcurator_django repository:

pip install -r requirements.txt

4. Edit your configuration.

Make a copy of the "template.env" file and name it ".env". Change the uncommented attribute in .env to hold the following:

• Set DATABASE_URL=postgres://postgres:postgres@127.0.0.1:5432/chemreg

Note: A line in your .env preceded by "#" will be ignored.

5. Launch Docker services.

Note: These may take a while the first time you run them.

On linux/macOS you can use these commands, using the chemcurator_default network...

docker run \
    --volume=postgresql:/var/lib/postgres/data \
    -e POSTGRES_USER=postgres \
    -e POSTGRES_PASSWORD=postgres \
    -e POSTGRES_DB=chemreg \
    --name=postgresql \
    --network=chemcurator_default \
    --publish "5432:5432" \
    --detach \
    postgres:12.1

docker run \
    --volume=pgadmin4:/var/lib/pgadmin \
    -e "PGADMIN_DEFAULT_EMAIL=dev@epa.gov" \
    -e "PGADMIN_DEFAULT_PASSWORD=postgres" \
    -e "PGADMIN_LISTEN_PORT=5047" \
    --name=pgadmin4 \
    --network=chemcurator_default \
    --publish="5432:5432" \
    --detach \
    dpage/pgadmin4

Note: When adding a server to pgadmin4, use the postgres container name postgresql instead of localhost

On windows you can use these commands, using the network created...

docker network create --driver=bridge pgnetwork

docker run --publish 5432:5432 --volume=postgresql:/var/lib/postgres/data -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=postgres -e POSTGRES_DB=chemreg --name=postgresql --network=pgnetwork --detach postgres:12.1

docker run --publish 5047:80 --volume=pgadmin4:/var/lib/pgadmin -e "PGADMIN_DEFAULT_EMAIL=dev@epa.gov" -e "PGADMIN_DEFAULT_PASSWORD=postgres" --name=pgadmin4 --network=pgnetwork --detach dpage/pgadmin4

6. Install the git hook scripts.

This will initialize your git repository to run the .pre-commit-config.yaml whenever you go to commit changes.

pre-commit install

7. Migrate the database and start the runserver.

python manage.py migrate

Note: The variable URL_CONF variable in the .env file can be set to show admin or api urls. Be sure to set it appropriately before starting up the runserver.

For example, to run the API on port 8000 and the admin application on 8001:

python manage.py runserver 8000

(macOS syntax)

URL_CONF=admin python manage.py runserver 8001

(Windows syntax)

set URL_CONF=admin 

or

$env:URL_CONF = 'admin'

Then

python manage.py runserver 8001

8. Inspect.

You can now go to your browser and visit http://127.0.0.1:8000/ to see what the runserver is serving. And for to inspect the DB with the PGAdmin4 container visit http://localhost:5047/ and when prompted to sign in use the variables entered above when starting the container which are:

• Email Address : dev@epa.gov
• Password : postgres You can then right-click on "Servers" on the left and then provide a name in the "General" tab and then use the credentials used in the docker container
• Host : if using host network localhost ; if using pgnetwork postgresql
• Username : postgres
• Password : postgres

Finishing up your code changes

1. Lint your code.

We follow a code-style defined by the default settings of black. It automatically formats your code. The isort package handles the structure of imports in .py files. flake8 is used for PEP8 compliance. Tests will fail if this is not done. To format your code changes, run:

python manage.py lint

Note: The pre-commit hooks installed above will prevent a commit before this is done if any formatting is needed.

2. Build documentation

We use the Google style-guide for docstrings. Try to write good docstrings as you write functions.

The sphinx-autoapi package automatically crawls the source code and outputs the docs.

To build the documentation:

cd docs/
sphinx-build -b html . _build