def setUp(self):
logging.info("Creating test sqlite database")
copy2(dirpath + "/test_pipeline.db.template",
dirpath + "/test_pipeline.db")
logging.info("Connecting to hive test sqlite database " + dirpath +
"/test_pipeline.db")
self.hive = HiveInstance("sqlite:///" + dirpath + "/test_pipeline.db")
def get_hive(process):
if process not in hives.keys():
if process not in process_lookup.keys():
raise ProcessNotFoundError("Process " + str(process) +
" not known")
hives[process] = HiveInstance(process_lookup[process]['hive_uri'])
return hives[process]
def get_hive(process):
if process not in hives:
if process not in process_lookup:
raise ProcessNotFoundError('Process %s not known' % process)
hives[process] = HiveInstance(process_lookup[process]['hive_uri'])
return hives[process]
from ensembl_prodinf.exceptions import HTTPRequestError
from ensembl_prodinf.config import load_config_json
app = Flask(__name__, instance_relative_config=True)
app.config.from_object('db_config')
app.analysis = app.config["HIVE_ANALYSIS"]
app.blacklisted_status_hosts = set(app.config['BLACKLISTED_STATUS_HOSTS'])
app.config['SWAGGER'] = {
'title': 'Database copy REST endpoints',
'uiversion': 2
}
swagger = Swagger(app)
app.hive = HiveInstance(app.config["HIVE_URI"])
app.logger.addHandler(app_logging.file_handler(__name__))
app.logger.addHandler(app_logging.default_handler())
app.logger.info(app.config)
app.servers = load_config_json(app.config['SERVER_URIS_FILE'])
def is_running(pid):
try:
os.kill(pid, 0)
except OSError as err:
return False
return True
def get_hive():
global hive
if hive is None:
hive = HiveInstance(app.config["HIVE_URI"])
return hive