monarch-initiative/phenopacket-scraper-api

Name: phenopacket-scraper-api

Owner: Monarch Initiative

Description: REST API for phenopacket-scraper

Created: 2016-06-23 19:16:17.0

Updated: 2016-06-28 20:15:26.0

Pushed: 2016-08-23 18:36:41.0

Homepage: null

Size: 21

Language: Python

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README

Phenopacket-Scraper Api

REST API for phenopacket-scraper

Setup:

To get the project's source code, clone the github repository:

$ git clone https://github.com/monarch-initiative/phenopacket-scraper-api.git

Install VirtualEnv using the following:

$ [sudo] pip install virtualenv

Create and activate your virtual environment (with python 3):

$ virtualenv -p python3 venv
$ source venv/bin/activate

Clone the phenopacket-python respository:

$ git clone https://github.com/phenopackets/phenopacket-python.git

Install it in your virtual environment:

$ cd phenopacket-python
$ ../venv/bin/python setup.py install

Add this to the end of ~/.profile or ~/.bash_profile file to add phenopacket-python directory to your python environment variables:

$ export PYTHONPATH=$PYTHONPATH:[path of phenopacket-python directory]

For Example:

$ export PYTHONPATH=$PYTHONPATH:/Users/Gauss/Home/phenopacket-python

Install all the required packages:

$ venv/bin/pip3 install -r requirements.txt

Create your database and the superuser by running this from the phenopacketscraper/ directory of the repository:

$ python manage.py migrate
$ python manage.py createsuperuser

Usage

To run the server enter the following in the 'phenopacketscraper/' directory of the repository

$ python manage.py runserver

Now you can go to your browser and test the api using:

http://localhost:8000/api/test/

To scrape data from a url you can enter the following in your browser:

http://localhost:8000/api/scrape/?url=[url]

To annotate data from a url you can enter the following in your browser:

http://localhost:8000/api/annotate/?url=[url]

To generate phenopacket of a given webpage you can enter the following in your browser:

http://localhost:8000/api/phenopacket/?url=[url]

Or by using curl in your terminal. For annotation you can enter the following

$ curl -H 'Accept: application/json; indent=4' http://localhost:8000/api/annotate/?url=[url]

For instance you can use http://molecularcasestudies.cshlp.org/content/2/2/a000703.abstract in place of [url] for testing.

To generate phenopackets you can enter the following in your terminal:

$ curl -H 'Accept: application/json; indent=4' http://localhost:8000/api/phenopacket/?url=[url]

To run the test cases, enter the following in the 'phenopacketscraper/' directory of the repository

$ python manage.py test