12-labours-api

Query API services for 12 Labours App

Overview

This is the API service providing query and data requests for the 12 Labours projects. This is currently implemented using fastapi.

Requirements

Python 3.6 or above

Make sure you have python 3 installed python3 --version.

Python version 3.9.0 used for this project.

Pip version 20.3.1 used for this project.

Environment variables

Here is the list of environment variables used by the app.

For production:

Please fill in the environment variables in the env.txt file and rename the file name to .env.

For deployment:

The environment variables template has been shown below:

QUERY_SECURE_KEY =
QUERY_ACCESS_TOKEN =

GEN3_ENDPOINT_URL =
GEN3_API_KEY =
GEN3_KEY_ID =
GEN3_PUBLIC_ACCESS =

IRODS_HOST =
IRODS_PASSWORD =
IRODS_PORT =
IRODS_USER =
IRODS_ZONE =
IRODS_ROOT_PATH =

ORTHANC_ENDPOINT_URL =
ORTHANC_USERNAME =
ORTHANC_PASSWORD =

Running the app

# Optional
$ pip install --upgrade pip
# Create the virtual environment
$ python3 -m venv ./venv
# Active the virtual environment
$ . ./venv/bin/activate
# Install all required dependencies
$ pip install -r requirements.txt
# Run the backend application, optional to use --port to run at specific port
$ uvicorn main:app (--port <port number>)

Database

Gen3 Data Commons

The connection between the backend and Gen3 Data Commons is directly through sending requests to Gen3 API. The backend will frequently request the access token to keep continuous interactions.

Gen3Submission(
    Gen3Auth(
        endpoint=Gen3Config.GEN3_ENDPOINT_URL,
        refresh_token={
            "api_key": Gen3Config.GEN3_API_KEY,
            "key_id": Gen3Config.GEN3_KEY_ID,
        },
    )
)

More information about the usage of this database in the documentation.

iRODS

iRODS provides Python SDK. Using the iRODSession to create the session to provide further features.

iRODSSession(
    host=iRODSConfig.IRODS_HOST,
    port=iRODSConfig.IRODS_PORT,
    user=iRODSConfig.IRODS_USER,
    password=iRODSConfig.IRODS_PASSWORD,
    zone=iRODSConfig.IRODS_ZONE,
)

Orthanc

Orthanc(
    OrthancConfig.ORTHANC_ENDPOINT_URL,
    username=OrthancConfig.ORTHANC_USERNAME,
    password=OrthancConfig.ORTHANC_PASSWORD,
)

More information about the usage of this database in the documentation.

Third-party packages

sgqlc

This package offers an easy to use GraphQL client.

More information about the usage of this package in the documentation.

Testing

If you do not have the 12 Labours portal user environment variables setup already:

1. Fill in the env.txt file with the configuration variables of the 12 Labours portal user.
2. Rename the file name to .env.

After the previous steps or if you already have those environment variables setup, run:

(Optional) If the app has not been run before, you should run the following commands first:

# Create the virtual environment
$ python3 -m venv ./venv
# Active the virtual environment
$ . ./venv/bin/activate
# Install all required dependencies
$ pip install -r requirements.txt

Otherwise, you only need to run the following commands:

# Install required dependencies for testing
$ pip install -r requirements-dev.txt
# Set the python path to the current diectory
$ export PYTHONPATH=.
# Run the pytest, optional to use --timeout= to limit the time for each test case
$ pytest (--timeout=<time in second>)

Developer Code Standards

Recommend to use following package to assist API development:

Black - The Uncompromising Code Formatter

Black makes code review faster by producing the smallest diffs possible. Blackened code looks the same regardless of the project you’re reading. Formatting becomes transparent after a while and you can focus on the content instead.

For official documentation, click here.

Pylint - Static code analyser

Pylint analyses your code without actually running it. It checks for errors, enforces a coding standard, looks for code smells, and can make suggestions about how the code could be refactored.

For official documentation, click here.

Mypy - Optional static typing for Python

Mypy is essentially a Python linter on steroids, and it can catch many programming errors by analyzing your program, without actually having to run it. Mypy has a powerful type system with features such as type inference, gradual typing, generics and union types.

isort

isort is a Python utility / library to sort imports alphabetically, and automatically separated into sections and by type.

For official documentation, click here.