def add_galaxy(self, url, key):
"""Connect a galaxy account to Askomics
add triples for the url of galaxy, and the user api key
:param self; url: the galaxy url
:type self; url: string
:param key: the galaxy user api key
:type key: string
"""
# try to connect to the galaxy server
galaxy = GalaxyConnector(self.settings, self.session, url, key)
try:
galaxy.check_galaxy_instance()
except Exception as e:
raise e
database = DatabaseConnector(self.settings, self.session)
query = '''
INSERT INTO galaxy_accounts VALUES(
NULL,
?,
?,
?
)
'''
database.execute_sql_query(query, (self.get_user_id_by_username(), url, key))
def test_check_galaxy_instance(self):
"""Test the check_galaxy_instance method"""
galaxy_connector = GalaxyConnector(self.settings, self.request.session,
self.galaxy['url'],
self.galaxy['key'])
assert galaxy_connector.check_galaxy_instance() is True
def test_send_json_to_history(self):
"""Test the send_json_to_history method"""
galaxy_connector = GalaxyConnector(self.settings, self.request.session,
self.galaxy['url'],
self.galaxy['key'])
galaxy_connector.send_json_to_history('hello world')
assert self.interface_galaxy.check_dataset_presence(
'askomics_query_', start_with=True) is True
def test_upload_files(self):
"""Test upload_files method"""
galaxy_connector = GalaxyConnector(self.settings, self.request.session,
self.galaxy['url'],
self.galaxy['key'])
galaxy_connector.upload_files([self.datasets['hello']['dataset_id']])
assert self.interface_galaxy.check_uploaded_files(
self.temp_directory) is True
def test_upload_files(self):
"""Test upload_files method"""
galaxy_connector = GalaxyConnector(self.settings, self.request.session,
self.galaxy['url'],
self.galaxy['key'])
galaxy_connector.upload_files([self.datasets['hello']['dataset_id']])
assert self.interface_galaxy.check_uploaded_files(
self.settings['askomics.files_dir'] + '/' +
self.request.session['username'] + '/upload/') is True
def test_get_file_content(self):
"""Test get_file_content method"""
galaxy_connector = GalaxyConnector(self.settings, self.request.session,
self.galaxy['url'],
self.galaxy['key'])
content = galaxy_connector.get_file_content(
self.datasets['hello']['dataset_id'])
expected_content = 'hello world\n'
assert content == expected_content
def test_send_to_history(self):
"""Test the send_to_history method"""
galaxy_connector = GalaxyConnector(self.settings, self.request.session,
self.galaxy['url'],
self.galaxy['key'])
param_manager = ParamManager(self.settings, self.request.session)
src_file = param_manager.get_upload_directory()
filepath = src_file + 'play_instrument.tsv'
galaxy_connector.send_to_history(filepath, 'play_instrument.tsv',
'tabular')
assert self.interface_galaxy.check_dataset_presence(
'play_instrument.tsv') is True
def add_galaxy(self, url, key):
"""Connect a galaxy account to Askomics
add triples for the url of galaxy, and the user api key
:param self; url: the galaxy url
:type self; url: string
:param key: the galaxy user api key
:type key: string
"""
# try to connect to the galaxy server
galaxy = GalaxyConnector(self.settings, self.session, url, key)
try:
galaxy.check_galaxy_instance()
except Exception as e:
raise e
query_laucher = QueryLauncher(self.settings, self.session)
sqa = SparqlQueryAuth(self.settings, self.session)
query_laucher.execute_query(
sqa.add_galaxy(self.username, url, key).query)
def test_get_datasets_and_histories(self):
"""Test the get_datasets_and_histories method"""
galaxy_connector = GalaxyConnector(self.settings, self.request.session,
self.galaxy['url'],
self.galaxy['key'])
# Test with history id
result = galaxy_connector.get_datasets_and_histories(
['tabular'], history_id=self.history_id)
created_history = {
'name': 'askomics_test',
'id': self.history_id,
'selected': True
}
assert isinstance(result, dict)
assert len(result) == 2
assert 'datasets' in result
assert 'histories' in result
assert created_history in result['histories']
# Test without history id
result = galaxy_connector.get_datasets_and_histories(['tabular'])
created_history = {
'name': 'askomics_test',
'id': self.history_id,
'selected': True
}
assert isinstance(result, dict)
assert len(result) == 2
assert 'datasets' in result
assert 'histories' in result
assert created_history in result['histories']