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