def __init__(self):
f = open('config.json', 'r', encoding="utf-8")
config = json.load(f)
self.logger = log.get_custom_logger(__name__)
self.product_code = config['productCode']
self.count = config['count']
self.period = config['period']
self.lot = config['lot']
code = 'XBTUSD' if self.product_code == 'BTC/USD' self.product_code
self.candle = Candle(code)
if config['isTest']:
apiKey = config['test']['key']
secret = config['test']['secret']
self.bitmex = ccxt.bitmex({
'apiKey': apiKey,
'secret': secret,
})
self.bitmex.urls['api'] = self.bitmex.urls['test']
else:
apiKey = config['real']['key']
secret = config['real']['secret']
self.bitmex = ccxt.bitmex({
'apiKey': apiKey,
'secret': secret,
})
self.order = Orders(self.bitmex)
def main():
import argparse
import os
parser = argparse.ArgumentParser()
parser.add_argument("--plateid", dest="plateid", action="store", help="The plate ID e.g. 'GEP00001_01'", required=True)
parser.add_argument("--file", dest="file", action="store", help="The Incucyte file e.g. 'GEP00001_01 data/20170127_GEP00001/GEP00001_01_incu.txt'.", required=True)
parser.add_argument("--clean", dest="clean", action="store_true", default=False, help="Clean database before loading?")
options = parser.parse_args()
log = logger.get_custom_logger(os.path.join(os.path.dirname(__file__), 'load_cell_growth.log'))
engine = sqlalchemy.create_engine(cfg['DATABASE_URI'])
Base.metadata.bind = engine
DBSession = sqlalchemy.orm.sessionmaker(bind=engine)
session = DBSession()
loader = CellGrowthLoader(session, options.file, options.plateid)
try:
if options.clean:
loader.clean()
loader.load()
session.commit()
except Exception as e:
log.exception(e)
session.rollback()
finally:
session.close()
def setUp(self):
import log as logger
self.log = logger.get_custom_logger()
self.current_path = os.path.abspath(os.path.dirname(__file__))
self.basedir = os.path.join(self.current_path,
'../testdata/processing/')
self.destdir = os.path.join(self.current_path, '../testdata/staging/')
self.runs = RunFolderList(self.basedir, self.destdir, None,
'130417_HWI-ST230_1122_C1YH9ACXX')
def setUp(self):
import log as logger
self.log = logger.get_custom_logger()
self.current_path = os.path.abspath(os.path.dirname(__file__))
self.basedir = os.path.join(self.current_path,
'../testdata/processing/')
self.destdir = os.path.join(self.current_path, '../testdata/staging/')
self.clusterdir = os.path.join(self.current_path,
'../testdata/lustre/')
self.runs = RunFolderList(processing_dir=self.basedir,
staging_dir=self.destdir,
cluster_dir=self.clusterdir)
def setUp(self):
import log as logger
self.log = logger.get_custom_logger()
self.current_path = os.path.abspath(os.path.dirname(__file__))
self.basedir = os.path.join(self.current_path,
'../testdata/processing/')
self.destdir = os.path.join(self.current_path, '../testdata/staging/')
self.clusterdir = os.path.join(self.current_path,
'../testdata/lustre/')
self.run_folder_name = '130417_HWI-ST230_1122_C1YH9ACXX'
self.run_folder = os.path.join(self.basedir, self.run_folder_name)
self.run = RunFolder(self.run_folder, self.destdir, self.clusterdir)
def setUp(self):
import data
import log as logger
from autoanalysis.config import cfg
self.log = logger.get_custom_logger()
self.current_path = os.path.abspath(os.path.dirname(__file__))
self.basedir = os.path.join(self.current_path, '../testdata/processing4publishing/')
self.stagingdir = os.path.join(self.current_path, '../testdata/staging4publishing/')
self.clusterdir = os.path.join(self.current_path, '../testdata/lustre/')
self.runs = data.RunFolderList(self.basedir, self.stagingdir, self.clusterdir)
self.PUBLISHING_ASSIGNED = cfg['PUBLISHING_ASSIGNED']
self.are_fastq_files_attached = True
self.glslims = GlsLims(use_dev_lims=True)
def main():
log = logger.get_custom_logger(os.path.join(os.path.dirname(__file__), 'load_ref_data.log'))
engine = sqlalchemy.create_engine(cfg['DATABASE_URI'])
Base.metadata.bind = engine
DBSession = sqlalchemy.orm.sessionmaker(bind=engine)
session = DBSession()
loader = RefLoader(session)
try:
loader.load_genomes()
loader.load_celllines()
session.commit()
except Exception as e:
log.exception(e)
session.rollback()
finally:
session.close()
def main():
log = logger.get_custom_logger(
os.path.join(os.path.dirname(__file__), 'delete_project.log'))
engine = sqlalchemy.create_engine(cfg['DATABASE_URI'])
Base.metadata.bind = engine
DBSession = sqlalchemy.orm.sessionmaker(bind=engine)
session = DBSession()
try:
project = session.query(Project).filter(
Project.geid == sys.argv[1]).first()
session.delete(project)
session.flush()
session.commit()
except Exception as e:
log.exception(e)
session.rollback()
finally:
session.close()
def main():
import argparse
import os
parser = argparse.ArgumentParser()
parser.add_argument("--plateid",
dest="plateid",
action="store",
help="The plate ID e.g. 'GEP00001_01'",
required=True)
parser.add_argument(
"--file",
dest="file",
action="store",
help=
"The InCell Western file e.g. 'data/20170127_GEP00001/GEP00001_01_ICW.csv'.",
required=True)
options = parser.parse_args()
log = logger.get_custom_logger(
os.path.join(os.path.dirname(__file__), 'load_protein_abundance.log'))
engine = sqlalchemy.create_engine(cfg['DATABASE_URI'])
Base.metadata.bind = engine
DBSession = sqlalchemy.orm.sessionmaker(bind=engine)
session = DBSession()
loader = ProteinAbundanceLoader(session, options.file, options.plateid)
try:
loader.load()
session.commit()
except Exception as e:
log.exception(e)
session.rollback()
finally:
session.close()
from log import get_custom_logger
log = get_custom_logger()
def before_all(context):
context.url = "https://api.spotify.com/v1/artists/"
context.token = "Bearer BQC25JXxyTjjsx8ZHtcX4v0pXzqYOifElXwOCnhjj4C5MFLRvwdlC339EDBqNl3z_NmmP9VYbXBPkB5CWA9KdnDEZc8zEJgBOMVf7zf9F4vqWHcC4ZBIUCHz7khpNCayug0alpe1YW90HRf2_2w"
log.info("Spotify OAuth token set to: " + context.token)
def before_scenario(context, scenario):
log.info("***************** SCENARIO STARTS: " + scenario.name +
" *****************")
def after_scenario(context, scenario):
log.info("****************** SCENARIO ENDS: " + scenario.name +
" ******************")
def __init__(self, exhange):
f = open('config.json', 'r', encoding="utf-8")
config = json.load(f)
self.exhange = exhange
self.product_code = config['productCode']
self.logger = log.get_custom_logger(__name__)