def main():
"""Main program for gresq dashboard.
"""
parser = argparse.ArgumentParser()
parser.add_argument("--nanohub",
action="store_true",
default=False,
help="Configure for nanohub.")
parser.add_argument("--test",
action="store_true",
default=False,
help="Test configuration.")
parser.add_argument(
"--release_db",
action="store_true",
default=False,
help="Configure database for release version.",
)
parser.add_argument(
"--box_config_path",
default="../box_config.json",
type=str,
help="Path to box config.",
)
parser.add_argument(
"--db_config_path",
default="",
type=str,
help="Path to database config secrets.",
)
parser.add_argument(
"--db_mode",
default="development",
type=str,
help="Database mode: development, testing, or production",
)
parser.add_argument("-v",
"--verbose",
help="increase output verbosity",
action="store_true")
kwargs = vars(parser.parse_args())
if kwargs["verbose"]:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
admin_group = 31804
submit_group = 31595
# Set configuration prefix to search for when setting db config
db_debug = True
db_config_prefix = None
if kwargs["db_mode"].lower() == "development":
db_config_prefix = "DEV_DATABASE"
elif kwargs["db_mode"].lower() == "production":
db_config_prefix = "PROD_DATABASE"
db_debug = False
elif kwargs["db_mode"] == "testing":
db_config_prefix = "TEST_DATABASE"
db_config_suffix = ""
dbconfig_file = kwargs["db_config_path"]
if kwargs["nanohub"] == True:
mode = "nanohub"
groups = os.getgroups()
if admin_group in groups:
privileges = {"read": True, "write": True, "validate": True}
db_config_suffix = "_ADMIN"
dbconfig_file = os.path.join(kwargs["db_config_path"], "admin",
"db_config.py")
elif submit_group in groups:
privileges = {"read": True, "write": True, "validate": False}
db_config_suffix = "_WRITE"
dbconfig_file = os.path.join(kwargs["db_config_path"], "submit",
"db_config.py")
else:
privileges = {"read": True, "write": False, "validate": False}
db_config_suffix = "_READ"
dbconfig_file = os.path.join(kwargs["db_config_path"], "readonly",
"db_config.py")
else:
mode = "local"
privileges = {"read": True, "write": True, "validate": True}
logging.info(dbconfig_file)
# logging.debug(db_config_prefix)
# logging.debug(kwargs['db_config_path'])
db_conf = Config(
prefix=db_config_prefix,
suffix=db_config_suffix,
debug=db_debug,
dbconfig_file=dbconfig_file,
)
# logging.debug(db_conf.DATABASEURI)
# logging.debug(db_conf.DATABASEARGS)
dal.init_db(db_conf, privileges=privileges)
box_config_path = os.path.abspath(kwargs["box_config_path"])
app = QtGui.QApplication([])
dashboard = GSADashboard(
mode=mode,
box_config_path=box_config_path,
privileges=privileges,
test=kwargs["test"],
)
dashboard.show()
sys.exit(app.exec_())
import os
from gresq.config import Config
from gresq.database import dal, Base
from gresq.database.models import Sample
import logging
logging.basicConfig(level=logging.DEBUG)
config_prefix = "DEV_DATABASE"
config_suffix = "_ADMIN"
conf = Config(prefix=config_prefix,
suffix=config_suffix,
debug=True,
try_secrets=False)
dal.init_db(conf, privileges={"read": True, "write": True, "validate": True})
with dal.session_scope(autocommit=True) as sess:
for s in sess.query(Sample).all():
sess.delete(s)
dal.Session().close()
#print(Base.metadata.tables)
ret = Base.metadata.drop_all(bind=dal.engine)
print(f"ret: {ret}")
def get_status(source_id):
mdf = MDFAdaptor()
return mdf.get_status(source_id)
def upload_file(file_path, folder_name=None):
box_adaptor = BoxAdaptor(box_config_path)
upload_folder = box_adaptor.create_upload_folder(folder_name=folder_name)
box_file = box_adaptor.upload_file(upload_folder, file_path,
str(uuid.uuid4()))
return box_file.get_shared_link_download_url(access='open')
dal.init_db(config['production'])
with dal.session_scope() as session:
samples = session.query(Sample)
print(samples)
for sample in samples:
if sample.raman_files and len(sample.raman_files) > 0:
print(sample.id)
sample_dict = sample.json_encodable()
recipe_box_file = stage_upload(sample_dict,
raman_files=sample.raman_files,
sem_files=sample.sem_files,
json_name='mdf')