def test_query_with_login(self):
"""A properly authenticated query sould return a dictionary.
"""
sbh_query = sbha.SynBioHubQuery(sbha.SD2Constants.SD2_SERVER)
sbh_query.login(self.user, self.password)
result = sbh_query.query_design_inducers()
self.assertEqual(type(result), dict)
def test_query_without_login(self):
"""An exception should be raised if a query is run without calling login first.
"""
sbh_query = sbha.SynBioHubQuery(sbha.SD2Constants.SD2_SERVER)
with self.assertRaises(SPARQLWrapper.SPARQLExceptions.Unauthorized) as exc:
# Silence the warning generated by SPARQLWrapper when
# text/html is received instead of JSON
with warnings.catch_warnings():
warnings.simplefilter("ignore")
result = sbh_query.query_design_inducers()
def test_wrong_user(self):
sbh_query = sbha.SynBioHubQuery(sbha.SD2Constants.SD2_SERVER)
with self.assertRaises(SPARQLWrapper.SPARQLExceptions.Unauthorized) as exc:
sbh_query.login('Not_the_U5eR', self.password)
def test_login(self):
sbh_query = sbha.SynBioHubQuery(sbha.SD2Constants.SD2_SERVER)
result = sbh_query.login(self.user, self.password)
self.assertEqual(result, None)
def __init__(self, url):
self._url = url
self._query = sbha.SynBioHubQuery(url)
def main(argv=None):
args = parse_args(argv)
# Init logging
init_logging(args.debug)
# Get SynBioHub password
sbh_password = os.getenv('SBH_PASSWORD')
if sbh_password is None:
raise Exception('Environment does not contain SBH_PASSWORD')
if args.staging:
sbh_query = sbha.SynBioHubQuery(sbha.SD2Constants.SD2_STAGING_SERVER,
spoofed_url=sbha.SD2Constants.SD2_SERVER)
else:
sbh_query = sbha.SynBioHubQuery(sbha.SD2Constants.SD2_SERVER)
logging.info('Authenticating to {}'.format(sbh_query._server))
sbh_query.login(args.user, sbh_password)
logging.info('Authentication complete')
# --------------------------------------------------
# for s, title in find_grna(sbh_query):
# if 'gRNA Gene' in title:
# logging.info('%s %s', s, title)
# return
# --------------------------------------------------
# coll = 'https://hub.sd2e.org/user/sd2e/design/yeast_gates_plasmids/1'
# coll_members = format_query_result(sbh_query, sbh_query.query_collection_members([coll]))
# for m in sorted(coll_members):
# logging.info('yeast_gates_plasmid: %s', m)
# --------------------------------------------------
# Tell me about this thing...
# subj = 'https://hub.sd2e.org/user/sd2e/design/anno_120009203/1'
# for p, o in subject_info(sbh_query, subj):
# logging.info('%s %s %s', subj, p, o)
# return
# --------------------------------------------------
# things = so_query(sbh_query, SBOL_FUNCTIONAL_COMPONENT)
# for thing in things:
# logging.info('%s ----> %s', thing['s'], thing['o'])
# sys.exit(0)
# definers = subjects_for(sbh_query, SBOL_DEFINITION, 'https://hub.sd2e.org/user/sd2e/design/anno_120009203/1')
gene = R10_GRNA_GENE
gene = R3_GRNA_GENE
data_frame = find_construct_experiments(sbh_query, gene)
logging.info('Found %d experiments', data_frame.size)
sys.exit(0)
for x in results:
logging.info('%s', x)
title = title_for(sbh_query, x)
logging.info('\ttitle: %s', title)
# for triple in results[x]:
# logging.info('\t%r', triple)
logging.info('--------------------------------------------------')
sys.exit(0)
cp_members = {}
for cp in CHALLENGE_PROBLEMS:
cp_members[cp] = format_query_result(sbh_query, sbh_query.query_collection_members([cp]))
for cp in cp_members:
actual_members = set(members).intersection(set(cp_members[cp]))
for m in actual_members:
logging.info('Component of %s (%s)', m, cp)
titles = title_for(sbh_query, m)
for title in titles:
logging.info('%s title: %s', m, title)
logging.info('Chain: %r', [(cp, SBOL_MEMBER, m)] + results[m])
import sys
import logging
import synbiohub_adapter as sbha
import sbh_prospector as sbhp
"""Find all the strains contained in all the members of the yeast
gates challenge problem.
"""
# Enter the sd2e SynBioHub password
SBH_USER = '******'
SBH_PASSWORD = '******'
# Authenticate to SynBioHub
sbh_query = sbha.SynBioHubQuery(sbha.SD2Constants.SD2_SERVER)
sbh_query.login(SBH_USER, SBH_PASSWORD)
# First get all the members of the yeast gates challenge problem
yg_members = sbhp.objects_for(sbh_query,
sbha.SD2Constants.YEAST_GATES_DESIGN_COLLECTION,
sbhp.SBOL_MEMBER)
print('Found {} yeast gate challenge problem members'.format(len(yg_members)))
# Iterate through the members, finding contained strains
all_strains = []
print('Looking for strains...', end='', flush=True)
yg_count = 0
for yg in yg_members:
# print(yg)
strains = sbhp.find_contained_strains(sbh_query, yg)
all_strains.extend(strains)
