def app(tmpdir, request):
port = 8000
dictionary_setup(_app)
# this is to make sure sqlite is initialized
# for every unit test
reload(default_settings)
# fresh files before running
for filename in ['auth.sq3', 'index.sq3', 'alias.sq3']:
if os.path.exists(filename):
os.remove(filename)
indexd_app = get_indexd_app()
indexd_init(*INDEX_CLIENT['auth'])
indexd = Process(target=indexd_app.run, args=['localhost', port])
indexd.start()
wait_for_indexd_alive(port)
gencode_json = tmpdir.mkdir("slicing").join("test_gencode.json")
gencode_json.write(
json.dumps({
'a_gene': ['chr1', None, 200],
'b_gene': ['chr1', 150, 300],
'c_gene': ['chr1', 200, None],
'd_gene': ['chr1', None, None],
}))
def teardown():
for filename in ['auth.sq3', 'index.sq3', 'alias.sq3']:
if os.path.exists(filename):
os.remove(filename)
indexd.terminate()
wait_for_indexd_not_alive(port)
_app.config.from_object("sheepdog.test_settings")
_app.config["PATH_TO_SCHEMA_DIR"] = PATH_TO_SCHEMA_DIR
request.addfinalizer(teardown)
app_init(_app)
_app.logger.setLevel(os.environ.get("GDC_LOG_LEVEL", "WARNING"))
_app.jwt_public_keys = {
_app.config['USER_API']: {
'key-test':
utils.read_file('./integration/resources/keys/test_public_key.pem')
}
}
_app.auth = ArboristClient()
return _app
def app(tmpdir, request):
port = 8000
dictionary_setup(_app)
# this is to make sure sqlite is initialized
# for every unit test
reload(default_settings)
# fresh files before running
for filename in ["auth.sq3", "index.sq3", "alias.sq3"]:
if os.path.exists(filename):
os.remove(filename)
indexd_app = get_indexd_app()
indexd_init(*SIGNPOST["auth"])
indexd = Process(target=indexd_app.run, args=["localhost", port])
indexd.start()
wait_for_indexd_alive(port)
gencode_json = tmpdir.mkdir("slicing").join("test_gencode.json")
gencode_json.write(
json.dumps({
"a_gene": ["chr1", None, 200],
"b_gene": ["chr1", 150, 300],
"c_gene": ["chr1", 200, None],
"d_gene": ["chr1", None, None],
}))
def teardown():
for filename in ["auth.sq3", "index.sq3", "alias.sq3"]:
if os.path.exists(filename):
os.remove(filename)
indexd.terminate()
wait_for_indexd_not_alive(port)
_app.config.from_object("sheepdog.test_settings")
_app.config["PATH_TO_SCHEMA_DIR"] = PATH_TO_SCHEMA_DIR
request.addfinalizer(teardown)
app_init(_app)
_app.logger.setLevel(os.environ.get("GDC_LOG_LEVEL", "WARNING"))
_app.jwt_public_keys = {
_app.config["USER_API"]: {
"key-test":
utils.read_file("./integration/resources/keys/test_public_key.pem")
}
}
return _app
