The C-GEM Strains app

This app consists of two sub-apps which must run simultaneously:

• a Bokeh server app, with code in bk_server;
• a Flask app, with code in oauth.

The Bokeh server app is used to generate the interactive bar chart and table on the homepage. It interacts with the user-facing Flask app, which provides the rest of the application interface and responds to HTTP requests.

Setup instructions

Python package dependencies

The code in this repository assumes a Python 3 environment. You can use either conda or pip as described below.

Dependencies via conda

You can replicate the environment used to run the C-GEM Strains app by using conda to install the virtual environment specified by the supplied environment file, environment.lock.yaml. This file specifies all dependendices, including precise version numbers.

With a Conda distribution installed, you can create a virtual environment as follows:

conda env create -n strains -f environment.lock.yaml

Activate the environment using conda activate strains.

Dependencies via pip

As an alternative to conda, you can use pip to install dependencies, using:

pip install -r requirements.txt

Environment file

A single environment file (.env) is used to specify all variables specific to your server. A demo file (.env.demo) has been provided, which you should update and rename to .env. If you wish to keep multiple env files to define different setups (e.g. a development environment), this is also possible by setting the ENV_NAME environment variable -- e.g. export ENV_NAME=.env.dev will cause the bokeh server and flask app to use the configuration in a file called .env.dev in the root source directory.

The environment file is used to specify:

• your flask environment (i.e. 'development', 'testing', or 'production')
• the location of your python virtual environment (full path to directory that includes the bin/ and lib/ subdirectories).
• the URL where the app will be made available (could be 'localhost')
• the server address (e.g. 'localhost' or IP address)
• port numbers for running the Bokeh server and Flask app
• a location for saving a local copy of downloaded strains data
• the path to a GSuite credentials file, in JSON format. The corresponding user must have read permission on the corresponding Strains sheet in Team Drive.
• a username for service account authorization
• the local URL for the bokeh server
• development and production database details
• the id ('group key') for the Team Drive, used by the Directory API
• mail server configuration for user alerts

Database setup

Database tables (used for tracking shipment requests and discussion) are defined in oauth/models.py and will be created automatically by SQLAlchemy, triggered by the line db.create_all() at the end of the module. Before running the apps for the first time, first make sure that you have created the database using the credentials you provided in the env file.

Running the apps

If you are using a custom environment file (as described above), remember to set the ENV_NAME environment variable prior to starting the apps.

The Bokeh server app should be started first, and can be initiated by running the start_strains_bokeh.sh script. This sets up the environment and runs the appropriate bokeh serve command to start the Bokeh server.

The Flask app can be initiated by running the start_strains.sh script, which contains the appropriate flask run command.

Once both components are running, the combined app will be accessible in your browser at the URL you specified in the env file.