basic_rest_queries.py

"""
This sample file shows a simplistic example use of EDD's client-side REST API access. For a more
robust and realistic example, see sample_rest_queries.py.

To provide the most basic example, this script makes several simplifying assumptions that
aren't likely to hold true in real-world examples:

1) EDD always returns all results in a single REST query rather than needing to page result data
over multiple requests.

2) All the data included in the study are valid / current, and none have been marked "inactive",
e.g. by user experimentation with the study.

3) The study is fully populated with data.

4) There's no need to cross-reference REST API queries while drilling down into the hierarchy of
study data (e.g. filtering for line attributes, then only processing the related assays,
measurements, measurement types, etc.

5) There's no need to look up ICE entries referenced by EDD, e.g. to access detailed strain
information.

For a more full-featured / realistic example, see sample_rest_queries.py, which implements a
more realistic scenario in which all of these simplifying assumptions are accounted for.
"""
import argparse
import logging
import requests

from jbei.rest.clients.edd.api import EddApi
from jbei.rest.auth import EddSessionAuth
from logging.config import dictConfig
from requests.packages.urllib3.exceptions import InsecureRequestWarning

from . import settings

logger = logging.getLogger(__name__)

dictConfig(settings.LOGGING)

# silence library warnings if we're skipping SSL certificate verification for local
# testing. otherwise the warnings will swamp useful output from this script
if not settings.VERIFY_EDD_CERT:
    logger.warning('Skipping SSL certificate checking due to VERIFY_EDD_CERT setting. This '
                   'option should only be used for local testing!')
    requests.packages.urllib3.disable_warnings(InsecureRequestWarning)


def parse_arguments():
    ############################################################################################
    # Configure command line parameters. In this sample, username/password can be provided in a
    # local.py file, overridden at the command line, or the command line user is prompted
    # if they aren't provided by any other source.
    ############################################################################################
    parser = argparse.ArgumentParser(description='A sample script that demonstrates anticipated '
                                                 'use of EDD REST API to simplify integration '
                                                 'work for client applications.')
    parser.add_argument('study', help='the identifier for the study ')
    parser.add_argument('-username', '-u',
                        help='The username used to authenticate the EDD REST API'
                             'APIs. If provided, overrides username in the '
                             'settings file. If not provided, a user prompt will appear.')
    parser.add_argument('-password', '-p',
                        help='The password used to authenticate with both EDD & ICE APIs. If '
                             'provided, overrides the password provided in the settings file.  '
                             'If not provided, a user prompt will appear.')
    parser.add_argument('-edd_url', '-e', help='the URL to use in contacting EDD.')
    return parser.parse_args()


def main():

    args = parse_arguments()

    study_id = args.study
    base_url = args.edd_url if args.edd_url else getattr(settings, 'EDD_URL')
    username = args.username if args.username else getattr(settings, 'EDD_USERNAME', None)
    password = args.password if args.password else getattr(settings, 'EDD_PASSWORD', None)
    verify_ssl = getattr(settings, 'VERIFY_EDD_CERT', True)

    logger.info('Logging into EDD at %s...' % base_url)
    session_auth = EddSessionAuth.login(base_url=base_url, username=username, password=password,
                                        verify_ssl_cert=verify_ssl)

    if not session_auth:
        return

    edd = EddApi(session_auth, base_url)
    study = edd.get_study(study_id)
    lines = edd.search_lines(study_id=study_id)
    assays = edd.search_assays(study_id=study_id)
    measurements = edd.search_measurements(study_id=study_id)
    measurement_values = edd.search_values(study_id=study_id)

    # look up measurement types and units observed in this study
    for meas in measurements.results:
        measurement_type = edd.get_measurement_type(meas.measurement_type)

        # look up units used in the data
        units = edd.get_measurement_unit(meas.y_units)

    logger.info('Done reading data from study %s' % study_id)

    return 0


if __name__ == '__main__' or __name__ == 'edd.rest.scripts.basic_rest_queries':
    result = main()
    exit(result)