An API for use by NASA-Genelab to fetch Gene SPOKEsigs

Application Setup

Requirements

• Python 3.6 (API has been tested on Python 3.6.9)
• MySQL

Clone this repo and install dependencies to a virtualenv

Clone this repo

Create a virtualenv and activate it

Then install dependencies to that virtualenv as follows:

pip install -r requirements.txt

Setup the configuration file

Create a config file or use the template given in the repo named "nasa_spokesig_api.conf.example". Remove the ".example" suffix from the filename.

Give MySQL credentials such as username and password. Provide database name as gene_spokesig in the mysql section of the config file.

Provide data paths to the data section of the config file.

Note: column_mapping_file in the data section of the config file should be named as a .tsv file. Its okay even if you don't have this file. This will be generated later. Now, just give a name (along with the path) that you want this file to be called.

Then:

• Save it as ".nasa_spokesig_api.conf" to the home folder (~)

OR

• Save it as "nasa_spokesig_api.conf" to "/etc" folder

Create column map file

To create this file (which is given in the data section of the config file as column_mapping_file), run the following:

python -m nasa_api.bin.create_column_mappings

Create database and tables

Next, to create database and tables in MySQL, run the following:

python -m nasa_api.bin.create_db_and_tables

Populate the database

To populate database in MySQL, run the following:

python -m nasa_api.bin.populate_db

Note: This could take some time to complete (in the order of minutes)

Run unit tests

python -m unittest discover tests.unit

Start the app

python -m nasa_api.app

This runs the Flask development server, which is really only meant for testing.

If you want to run it in production, it's recommended to use WSGI, pointed at nasa_api.app:app.

Test the API using Swagger UI

Open the browser.

Type http://localhost:5555/nasa_api/v1/swagger

This will show a Swagger UI for the API as per OpenAPI Specification.

You can see details regarging this API and also documentation of endpoints in this Swagger UI.

You can also try making API calls from the Swagger UI.