def get_queries():
"""Get galaxy queries (json datasets)
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
history_id = None
if request.method == 'POST':
if request.get_json():
history_id = request.get_json().get("history_id")
try:
galaxy = Galaxy(current_app, session)
ginfo = galaxy.get_datasets_and_histories(history_id, query=True)
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'datasets': [],
'histories': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'datasets': ginfo['datasets'],
'histories': ginfo['histories'],
'error': False,
'errorMessage': ''
})
def add_galaxy_account(self, user, url, apikey):
"""Add a Galaxy account
Parameters
----------
user : dict
Previous user info
url : string
Galaxy URL
apikey : string
Galaxy API key
Returns
-------
dict
Updated user
"""
database = Database(self.app, self.session)
galaxy = Galaxy(self.app, self.session, url, apikey)
valid = galaxy.check_galaxy_instance()
error_message = "Not a valid Galaxy"
if valid:
error_message = ""
query = '''
INSERT INTO galaxy_accounts VALUES(
NULL,
?,
?,
?
)
'''
database.execute_sql_query(
query, (self.session["user"]["id"], url, apikey))
user["galaxy"] = {"url": url, "apikey": apikey}
return {
"error": not valid,
"error_message": error_message,
"user": user
}
def update_galaxy_account(self, user, url, apikey):
"""Update a Galaxy account
Parameters
----------
user : dict
Previous user info
url : string
Galaxy URL
apikey : string
Galaxy API key
Returns
-------
dict
Updated user
"""
database = Database(self.app, self.session)
galaxy = Galaxy(self.app, self.session, url, apikey)
valid = galaxy.check_galaxy_instance()
error_message = "Not a valid Galaxy"
if valid:
error_message = ""
query = '''
UPDATE galaxy_accounts SET
url = ?,
apikey = ?
WHERE user_id = ?
'''
database.execute_sql_query(
query, (url, apikey, self.session["user"]["id"]))
user["galaxy"] = {"url": url, "apikey": apikey}
return {
"error": not valid,
"error_message": error_message,
"user": user
}
def upload_datasets():
"""Download a galaxy datasets into AskOmics
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
files_utils = FilesUtils(current_app, session)
disk_space = files_utils.get_size_occupied_by_user() if "user" in session else None
if session["user"]["quota"] > 0 and disk_space >= session["user"]["quota"]:
return jsonify({
'errorMessage': "Exceeded quota",
"error": True
}), 400
data = request.get_json()
if not (data and data.get("datasets_id")):
return jsonify({
'error': True,
'errorMessage': "Missing datasets_id parameter"
}), 400
datasets_id = data["datasets_id"]
try:
galaxy = Galaxy(current_app, session)
galaxy.download_datasets(datasets_id)
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'error': False,
'errorMessage': ''
})
def get_dataset_content():
"""Download a galaxy datasets into AskOmics
Returns
-------
json
dataset_content: content of the requested Galaxy dataset
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
if not (data and data.get("dataset_id")):
return jsonify({
'error': True,
'errorMessage': "Missing dataset_id parameter"
}), 400
dataset_id = data["dataset_id"]
try:
galaxy = Galaxy(current_app, session)
dataset_content = galaxy.get_dataset_content(dataset_id)
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'dataset_content': {},
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'dataset_content': json.loads(dataset_content),
'error': False,
'errorMessage': ''
})