egauzens/forked-sparc-api

SPARC Portal API

Overview

This is the API service which is build as a Flask Application. It runs independent of the Nuxt.js web-application.

Requirements

Python 3

Make sure you have python 3 installed python3 --version

Running the app

python3 -m venv ./venv
. ./venv/bin/activate
pip install -r requirements.txt
gunicorn main:app

Testing

If you do not have the NIH SPARC portal user environment variables setup already:

1. Create a .env file with the configuration variables of the NIH SPARC portal user or add them to your bash profile.
2. If you created a separate file, run source {fileName}.env.

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

export PYTHONPATH=`pwd`
pip install -r requirements-dev.txt
pytest

External requirements of sparc-api

Pennsieve python client

Source: https://github.com/Pennsieve/pennsieve-python
Summary: Python client for the pennsieve data management platform
Used on sparc-api for: Getting emails for pennsieve users
Critical: no

Pennsieve Discover API

Source: https://developer.pennsieve.io/api/index.html
Summary: API endpoint for the Pennsieve Discovaer data management platform
Used on sparc-api for:

• Retrieving dataset awards
• Retrieving dataset metadata and sending it for the simcore endpoint Critical: no

Amazon Simple Email Service

Source: https://docs.aws.amazon.com/ses/index.html
Summary: Sends emails
Used on sparc-api for: Sending emails
Critical: no

SPARC Portal amazon s3

Source: https://aws.amazon.com/s3/
Summary: Cloud file storage
Used on sparc-api for: accessing pennsieve files for the portal (ie. displaying a scaffold)
Critical: yes

Biolucida

Source: https://www.mbfbioscience.com/biolucida
Summary: Image viewer and image repository
Used on sparc-api for: Retrieving images and image metadata. (These are displayed on sparc-app)
Critical: Critical for image display \

Scicrunch

Source: https://scicrunch.org/
Summary: Processes SPARC datasets, pulling out metadata from them to make them searchable
Used on sparc-api for:

• Searching across datasets
• Filtering on datasets
• Providing the contents of a dataset (ie. does it have a scaffold? Where is the scaffold file located?) Critical: Critical for much of the /maps page and some functionality of the /data page

Wrike

Source: https://www.wrike.com/
Summary: Project management software
Used on sparc-api for: Creates tickets from user feedback to be managed
Critical: no

Mail Chimp

Source: https://mailchimp.com/
Summary: Email service
Used on sparc-api for: Email subscriptions from sparc-app
Critical: no

oSparc

Source: https://osparc.io/
Summary: Biomedeical Modelling and simulation software
Used on sparc-api for: Running simulations from sparc-app
Critical: critical for running simulations from sparc-app

Nuerolucidia

Source: https://www.mbfbioscience.com/neurolucida
Summary: 3d Imaging software
Used on sparc-api for: Providing 3d images and metadata?
Critical: critical for the 3d images?

SCI_CRUNCH_INTERLEX

Source: unknown
Summary: Provides translation of medical terms
Used on sparc-api for: Converting terms between forms and finding similar terms
Critical: not sure

SendGrid

Source: https://sendgrid.com/
Summary: Sends emails
Used on sparc-api for: Sending an email to a user after they give feedback
Critical: no