FLASK PROTEOMICS API

This is an API based on Proteomics API. Json data was fetched using:

https://www.proteomicsdb.org/proteomicsdb/logic/api/proteinpeptideresult.xsodata/InputParams(PROTEINFILTER='Q92769')/Results?$select=ENTRY_NAME,PROTEIN_NAME,CHROMOSOME_NAME,GENE_NAME,STRAND,PEPTIDE_SEQUENCE,PEPTIDE_MASS,PUBMEDID&$format=json
I left out some fields because I wanted to make a simple schema.

ENVIRONMENT VARIABLES

Be sure to setup FLASK_APP environment variable.

ex.

export FLASK_APP=protein-api.py

RUNNING APP

After setting the environment variables, you can:

1. Test the app

flask test

2. Initialize DB

flask db init flask migrate -m "Initial migration" will make a migration script. flask db upgrade is equivalent to calling db.create_all()

3. Populate DB with test data.

flask populate will add protein sequences from cleaned-protein.json file.

4. Run the api locally (default will be localhost:5000) with

flask run

Authentication

The application uses flask-httpauth for JWT token authentication.

TESTING HTTP REQUESTS

Using httpie http --json GET http://127.0.0.1:5000/api/v1/proteins/ Either way using Postman you can receive/send json data.

HOW TO USE THE API

5 routes:

1. GET http://localhost:5000/api/v1/proteins/
   GET ALL ENTRIES
2. GET http://localhost:5000/api/v1/protein/{id}
   GET single entry with specified id. e.g. [...]/protein/5
3. POST http://localhost:5000/api/v1/proteins/ {json}
   CREATE a new protein entry
4. PUT http://localhost:5000/api/v1/protein/{id}
   UPDATE protein's pubmed id
5. DELETE http://localhost:5000/api/v1/protein/{id}
   DELETE protein entry with id e.g. [...]/protein/5