from brain.utils.general import get_yaml_loader
from pgpasslib import getpass
# Read in the db connection configuration
dbconfigfile = 'dbconfig.ini'
dbconfigfile = os.path.join(os.path.dirname(os.path.abspath(__file__)),
dbconfigfile)
try:
with open(dbconfigfile, 'r') as ff:
rawfile = ff.read()
except IOError as e:
raise RuntimeError('IOError: Could not open dbconfigfile {0}:{1}'.format(
dbconfigfile, e))
dbdict = yaml.load(rawfile, Loader=get_yaml_loader())
# select the appropriate configuration from config
if config.db:
db_info = dbdict[config.db]
try:
if 'password' not in db_info:
db_info['password'] = getpass(db_info['host'], db_info['port'],
db_info['database'], db_info['user'])
except KeyError:
raise RuntimeError('ERROR: invalid server configuration')
else:
raise RuntimeError(
'Error: could not determine db to connect to: {0}'.format(config.db))
# this format is only usable with PostgreSQL 9.2+
from brain.utils.general import get_yaml_loader
import pytest
import yaml
import os
# @pytest.fixture()
# def page(client, request, init_api):
# blue, endpoint = request.param
# page = ApiPage(client, 'api', endpoint)
# yield page
query_data = yaml.load(open(
os.path.abspath(
os.path.join(os.path.dirname(__file__),
'../data/query_test_data.dat'))),
Loader=get_yaml_loader())
@pytest.fixture()
def params(release):
return {'release': release}
@pytest.fixture()
def data(release):
return query_data[release]
def get_query_params(release, paramdisplay):
q = Query(mode='local', release=release)
if paramdisplay == 'best':
if template not in templates[release]:
templates[release].append(template)
return bintypes, templates
bintypes, templates = populate_bintypes_templates(releases)
# TODO reduce modes to only local and remote
modes = ['local', 'remote', 'auto'] # to loop over modes (see mode fixture)
dbs = ['db', 'nodb'] # to loop over dbs (see db fixture)
origins = ['file', 'db', 'api'] # to loop over data origins (see data_origin fixture)
# Galaxy and Query data is stored in a YAML file
with open(os.path.join(os.path.dirname(__file__), 'data/galaxy_test_data.dat')) as f:
galaxy_data = yaml.load(f, Loader=get_yaml_loader())
with open(os.path.join(os.path.dirname(__file__), 'data/query_test_data.dat')) as f:
query_data = yaml.load(f, Loader=get_yaml_loader())
@pytest.fixture(scope='session', params=releases)
def release(request):
"""Yield a release."""
if travis and request.param not in travis.new_releases:
pytest.skip('Skipping non-requested release')
return request.param
def _get_release_generator_chain():
"""Return all valid combinations of (release, bintype, template)."""
from __future__ import print_function, division, absolute_import
from tests.api.conftest import ApiPage
from marvin.tools.query import Query
from marvin.utils.datamodel.query.base import bestparams
from brain.utils.general import get_yaml_loader
import pytest
import yaml
import os
# @pytest.fixture()
# def page(client, request, init_api):
# blue, endpoint = request.param
# page = ApiPage(client, 'api', endpoint)
# yield page
query_data = yaml.load(open(os.path.abspath(os.path.join(os.path.dirname(__file__), '../data/query_test_data.dat'))), Loader=get_yaml_loader())
@pytest.fixture()
def params(release):
return {'release': release}
@pytest.fixture()
def data(release):
return query_data[release]
def get_query_params(release, paramdisplay):
q = Query(mode='local', release=release)
if paramdisplay == 'best':