GEM-NET Members Portal

A user portal to gather useful info, data, and analytics for team members.

The homepage of this app features:

• a list of upcoming events from the team Google Calendar
• counts of shipment requests by status, from the Strains app
• a list of the most recently modified documents from the Team Drive.
• links to external resources, including the team website, the Strains app, Slack, Benchling, and Asana.

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 Portal by using conda to install the virtual environment specified by the supplied environment files.

• environment.lock.yaml specifies all precise version numbers.
• environment.abstract.yaml specifies packages without version numbers.

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

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

Activate the environment using conda activate portal.

Dependencies via pip

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

pip install -r requirements.txt

Other requirements

• This app assumes that the Strains app (https://github.com/gem-net/strains) is already set up and running.

env files

The env files specifies configuration detail that is not suitable for hard-coding. A demo env files, .env_demo has been provided, which you should update and rename to .env.

The env file is used to specify:

• The path to the app-specific python environment (includes bin and lib subdirectories).
• The Flask environment (development, testing, or production) and port
• G Suite credentials data
• the Team Drive alphanumeric ID
• the directory ID for the Compounds protocols folder within the Team Drive
• a path to save a local copy of the protocols listing ('compounds.pickle')
• development and production database details for the Strains app
• Asana workspace info and credentials

.env_demo:

PY_HOME=/path/to/python/environment/dir
FLASK_ENV=production
FLASK_RUN_PORT=5100
GOOGLE_CLIENT_ID=xxxx-yyyy.apps.googleusercontent.com
GOOGLE_SECRET=zzzz
SERVICE_ACCOUNT_FILE=/path/to/service-account-key.json
CREDENTIALS_AS_USER=admin@example.com
GROUP_KEY=fakegroupkey
TEAM_DRIVE_ID=xxxxxxxxxxxxxxxxx
CALENDAR_ID=example.com_12345abc1234@group.calendar.google.com
COMPOUNDS_DIR_ID=yyyyyyyyyyy
COMPOUNDS_PICKLE=compounds.pickle
DATABASE_URL_DEV=mysql+pymysql://fakeuser:fakepassword@127.0.0.1:3306/strains_dev
DATABASE_URL=mysql+pymysql://fakeuser:fakepassword@127.0.0.1:3306/strains
DB_NAME_DEV=strains_dev
DB_NAME=strains
DB_HOST=localhost
SQLALCHEMY_ECHO=False
ASANA_TOKEN=0/123456789abcdef
ASANA_WORKSPACE_ID=1234567890
ASANA_TEAM_ID=0987654321

Note that there are four rows corresponding to Google credentials data. GOOGLE_CLIENT_ID and GOOGLE_SECRET are for an OAuth client ID, used during the login process. SERVICE_ACCOUNT_FILE is used to specify a JSON credentials file corresponding to a service account with domain-wide delegation, and CREDENTIALS_AS_USER specifies a corresponding user with privileges to mimic.

Running the app

The app can be served by running either the start_portal.sh script or, when the python environment is activated, by executing the command flask run. In both cases the flask executable serves the app on the port specified in your .env file. With the port set as e.g. 5100, the app will then be accessible from your browser at http://localhost:5100.