def __init__(self, config="config/askomics.test.ini"):
"""Summary
Parameters
----------
config : str, optional
Description
"""
# Config
self.config = config
self.dir_path = tempfile.mkdtemp(prefix="askotest_")
self.db_path = "{}/database.db".format(self.dir_path)
# create app
self.app = create_app(config=self.config)
create_celery(self.app)
self.app.iniconfig.set('askomics', 'data_directory', self.dir_path)
self.app.iniconfig.set('askomics', 'database_path', self.db_path)
# context
self.ctx = self.app.app_context()
self.ctx.push()
# Client
self.client = self.app.test_client()
self.session = {}
# Galaxy
self.gurl = "http://localhost:8081"
self.gkey = "fakekey"
self.galaxy_history = None
self.init_database()
def __init__(self):
"""Get Args"""
parser = argparse.ArgumentParser(
description="Update base_url for all graphs")
parser.add_argument("-c",
"--config-file",
type=str,
help="AskOmics config file",
required=True)
parser.add_argument("-o",
"--old_url",
type=str,
help="Old base url",
required=True)
parser.add_argument("-n",
"--new_url",
type=str,
help="New base url",
required=True)
self.args = parser.parse_args()
if not (self.args.old_url and self.args.new_url):
print("Error: old_url and new_url must not be empty")
sys.exit(1)
self.check_urls(self.args.old_url, self.args.new_url)
self.application = create_app(config=self.args.config_file)
self.celery = create_celery(self.application)
self.session = {}
starter = Start(self.application, self.session)
starter.start()
def __init__(self):
"""Get Args"""
parser = argparse.ArgumentParser(
description="Upload files from a directory to AskOmics")
parser.add_argument("-c",
"--config-file",
type=str,
help="AskOmics config file",
required=True)
parser.add_argument("-d",
"--files-directory",
type=str,
help="Directory of files to upload",
required=True)
parser.add_argument("-k",
"--api-key",
type=str,
help="AskOmics user apikey",
required=True)
self.args = parser.parse_args()
self.application = create_app(config=self.args.config_file)
self.celery = create_celery(self.application)
self.session = {}
self.user = None
self.chunk_size = 1024 * 1024 * 10 # 10MB
starter = Start(self.application, self.session)
starter.start()
self.authenticate_user()
def __init__(self):
"""Get Args"""
parser = argparse.ArgumentParser(
description="Add a new user into AskOmics database")
parser.add_argument("-c",
"--config-file",
type=str,
help="AskOmics config file",
required=True)
parser.add_argument("-f",
"--first-name",
type=str,
help="User first name",
default="Ad")
parser.add_argument("-l",
"--last-name",
type=str,
help="User last name",
default="Min")
parser.add_argument("-u",
"--username",
type=str,
help="User username",
default="admin")
parser.add_argument("-p",
"--password",
type=str,
help="User password",
default="admin")
parser.add_argument("-e",
"--email",
type=str,
help="User email",
default="*****@*****.**")
parser.add_argument("-k",
"--api-key",
type=str,
help="User API key",
default="admin")
parser.add_argument("-g", "--galaxy-url", type=str, help="Galaxy URL")
parser.add_argument("-gk",
"--galaxy-apikey",
type=str,
help="Galaxy API key")
self.args = parser.parse_args()
self.application = create_app(config=self.args.config_file)
self.celery = create_celery(self.application)
self.session = {}
self.user = None
starter = Start(self.application, self.session)
starter.start()
def __init__(self):
"""Get Args"""
parser = argparse.ArgumentParser(
description="Update base_url for all graphs")
parser.add_argument("-c",
"--config-file",
type=str,
help="AskOmics config file",
required=True)
self.args = parser.parse_args()
self.application = create_app(config=self.args.config_file)
self.celery = create_celery(self.application)
self.session = {}
starter = Start(self.application, self.session)
starter.start()
celery : Celery
Celery object
"""
import sys
import traceback
from askomics.app import create_app, create_celery
from askomics.libaskomics.Dataset import Dataset
from askomics.libaskomics.DatasetsHandler import DatasetsHandler
from askomics.libaskomics.FilesHandler import FilesHandler
from askomics.libaskomics.Result import Result
from askomics.libaskomics.SparqlQueryBuilder import SparqlQueryBuilder
from askomics.libaskomics.SparqlQueryLauncher import SparqlQueryLauncher
app = create_app(config='config/askomics.ini')
celery = create_celery(app)
@celery.task(bind=True, name="integrate")
def integrate(self, session, data, host_url):
"""Integrate a file into the triplestore
Parameters
----------
session : dict
AskOmics session
data : dict
fileId: file to integrate
public: integrate as public or private data
host_url : string
AskOmics host url
from askomics.app import create_app, create_celery
application = create_app(config='config/askomics.ini')
celery = create_celery(application)
if __name__ == '__main__':
application.run()