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Tracking the C3G projects

Test suite on main branch
Test suite on dev branch

This is an API to access and modify the C3G data processing tracking database.

Install

We recommend using postgress in producton, but the project is fully compatible with sqlite. We also publish container on quay.io and test or system using podman.

From GitHub with sqlite (best for developer):

Sqlite needs to be installed on your machine. Here, you will deploy a development instance of the app and be able to modify the code in the repo with auto-reload

git clone  [email protected]:c3g/project_tracking.git
cd project_tracking
git checkout dev # If you are developing from the dev branch!
python -m venv venv
source ./venv/bin/activate
pip install --upgrade pip
pip install -e  .
# Setting the db url is optional, the default will be in the app installation folder
export C3G_SQLALCHEMY_DATABASE_URI="sqlite:////tmp/my_test_db.sql"
# initialyse the db
flask --app project_tracking init-db
# run the app
flask --app project_tracking --debug run

By default, falsk will run the server on http://127.0.0.1:5000. You can test that everything is fine with curl in a terminal:

$ curl http://127.0.0.1:5000/
Welcome to the TechDev tracking API!
# The help api is also available. It lists all the server urls.
$ curl http://127.0.0.1:5000/help
----------
URL:
        /
DOC:
        Welcome page

[...]

Once the server is running, you can still initialise the database, you can even flush it clear of any entry with:

# WARNING this will erase all entry to you Database!
flask  --app project_tracking init-db --flush --db-uri "sqlite:////tmp/my_test_db.sql"

Using podman and sqlite:

We have a quay.io repo for the project There are a dev release and version releases. The latest tag relates to the latest release.

SQLITE_DB_FOLDER=<folder on host with WR access>
podman run -v $SQLITE_DB_FOLDER:/sqlite:Z -it --rm -p 8000:8000 -e C3G_INIT_DB=1 quay.io/c3genomics/project_tracking:dev

The app runs on port 8000 inside the container, the -e C3G_INIT_DB=1 option will the db in $SQLITE_DB_FOLDER/tracking_db.sql.

From GitHub using postgress:

postgress needs to be installed with a database names <DB_NAME>, assessible by user <POSTGRESS_USER>, with a pasword <POSTGRESS_PW>

git clone  [email protected]:c3g/project_tracking.git
cd project_tracking
python -m venv venv
source ./venv/bin/activate
pip install .[postgres]
C3G_SQLALCHEMY_DATABASE_URI="postgresql+psycopg2://<POSTGRESS_USER>:<POSTGRESS_PW>@<POSTGRESS_HOST>/<DB_NAME>?client_encoding=utf8"
gunicorn -w 4 'project_tracking:create_app()'

Using podman and postgress:

Here we expect postgres to be listening to the localhost (127.0.0.1) interface. The podman option --network slirp4netns:allow_host_loopback=true options makes it so that the host 127.0.0.1 interface is reachable with the 10.0.2.2 adress inside the container. That is why the C3G_SQLALCHEMY_DATABASE_URI is set to that value.

podman pull quay.io/c3genomics/project_tracking:dev
export C3G_SQLALCHEMY_DATABASE_URI="postgresql+psycopg2://<POSTGRESS_USER>:<POSTGRESS_PW>@10.0.2.2/<POSTGRESS_DB_NAME>?client_encoding=utf8"
podman secret create --env C3G_SQLALCHEMY_DATABASE_URI C3G_SQLALCHEMY_DATABASE_URI
podman run --secret C3G_SQLALCHEMY_DATABASE_URI,type=env -p 8000:8000 -e C3G_INIT_DB=1 --network slirp4netns:allow_host_loopback=true quay.io/c3genomics/project_tracking:dev

Install from pypi:

No release yet

Run tests

Once you have modified the code, you can run the test to make sure you have not broken anything. In the git repo:

pip install -e  .[tests]
pytest -v