def setUp(self):
"""Set up the configuration to access the triplestore
Use the config file test.virtuoso.ini to not interfere with
production data
"""
self.settings = get_appsettings('configs/tests.ini', name='main')
self.settings['askomics.upload_user_data_method'] = 'insert'
self.request = testing.DummyRequest()
self.config = testing.setUp(request=self.request)
self.config.add_route('load_data_into_graph', '/load_data_into_graph')
self.config.scan()
self.request.session['username'] = '******'
self.request.session['blocked'] = False
self.request.session['group'] = 'base'
self.request.session['graph'] = 'urn:sparql:test_askomics:jdoe'
self.request.host_url = 'http://localhost:6543'
self.request.json_body = {}
SetupTests(self.settings, self.request.session)
self.tps = InterfaceTpsDb(self.settings, self.request)
self.askview = AskView(self.request)
self.askview.settings = self.settings
def test_delete_graph(self):
"""Test delete_graph method
Insert 2 datasets, and test delete_graph on one. Also test if
start point return only one datasets
"""
# empty tps
self.tps.clean_up()
# load a test
timestamp_people = self.tps.load_people(
) # need the timestamp of people to delete it
timestamp_instruments = self.tps.load_instruments()
# Delete only the people graph
self.request.json_body = {
'named_graph':
['urn:sparql:test_askomics:jdoe:people_tsv_' + timestamp_people]
}
data = self.askview.delete_graph()
assert data is None
# test if start point return only one entity
askview2 = AskView(self.request)
askview2.settings = self.settings
data = askview2.start_points()
assert len(data["nodes"]) == 1
# test if startpoint return only instruments
expected_result = {
'nodes': {
self.settings['askomics.prefix'] + 'Instruments': {
'public': False,
'label': 'Instruments',
'uri': self.settings['askomics.prefix'] + 'Instruments',
'private': True,
'g': 'urn:sparql:test_askomics:jdoe:instruments_tsv_' +
timestamp_instruments,
'endpoint': 'http://localhost:8890/sparql'
}
},
'galaxy': False
}
assert data == expected_result
def test_delete_graph(self):
"""Test delete_graph method
Insert 2 datasets, and test delete_graph on one. Also test if
start point return only one datasets
"""
# empty tps
self.tps.clean_up()
# load a test
timestamp_people = self.tps.load_people() # need the timestamp of people to delete it
timestamp_instruments = self.tps.load_instruments()
# Delete only the people graph
self.request.json_body = {
'named_graph': ['urn:sparql:test_askomics:jdoe:people_tsv_' + timestamp_people]
}
data = self.askview.delete_graph()
assert data is None
# test if start point return only one entity
askview2 = AskView(self.request)
askview2.settings = self.settings
data = askview2.start_points()
assert len(data["nodes"]) == 1
# test if startpoint return only instruments
expected_result = {
'nodes': {
'http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#Instruments':
{
'public': False,
'label': 'Instruments',
'uri':
'http://www.semanticweb.org/irisa/ontologies/2016/1/igepp-ontology#Instruments',
'private': True,
'g':
'urn:sparql:test_askomics:jdoe:instruments_tsv_' + timestamp_instruments
}
}
}
assert data == expected_result
def setUp(self):
"""Set up the configuration to access the triplestore
Use the config file test.virtuoso.ini to not interfere with
production data
"""
self.settings = get_appsettings('configs/test.virtuoso.ini', name='main')
self.settings['askomics.upload_user_data_method'] = 'insert'
self.request = testing.DummyRequest()
self.config = testing.setUp(request=self.request)
self.config.add_route('load_data_into_graph', '/load_data_into_graph')
self.config.scan()
self.request.session['username'] = '******'
self.request.session['blocked'] = False
self.request.session['group'] = 'base'
self.request.session['graph'] = 'urn:sparql:test_askomics:jdoe'
self.request.host_url = 'http://localhost:6543'
self.request.json_body = {}
# Create the user dir if not exist
self.temp_directory = self.settings['askomics.files_dir'] + '/upload/' + self.request.session['username']
if not os.path.isdir(self.temp_directory):
os.makedirs(self.temp_directory)
# Set the upload dir
self.request.session['upload_directory'] = self.temp_directory
# Copy files if directory is empty
if not os.listdir(self.temp_directory):
files = ['people.tsv', 'instruments.tsv', 'play_instrument.tsv', 'transcript.tsv', 'qtl.tsv', 'small_data.gff3', 'turtle_data.ttl', 'bed_example.bed']
for file in files:
src = os.path.join(os.path.dirname(__file__), "..", "test-data") + '/' + file
dst = self.request.session['upload_directory'] + '/' + file
copyfile(src, dst)
self.tps = InterfaceTPS(self.settings, self.request)
self.askview = AskView(self.request)
self.askview.settings = self.settings
em = EndpointManager(self.settings, self.request.session)
em.drop()
def setUp(self):
self.settings = get_appsettings('configs/development.virtuoso.ini',
name='main')
self.request = testing.DummyRequest()
self.config = testing.setUp(request=self.request)
self.config.add_route('load_data_into_graph', '/load_data_into_graph')
self.config.scan()
self.request.session['upload_directory'] = os.path.join(
os.path.dirname(__file__), "..", "test-data")
self.temp_directory = tempfile.mkdtemp()
self.it = InterfaceTPS(self.settings, self.request)
self.askview = AskView(self.request)
self.askview.settings = self.settings
self.timestamp = str(time.time())
def test_empty_database(self):
"""Test the empty_database method
Insert data and test empty_database. Also test if
start point return no results after deletion
"""
# empty tps
self.tps.clean_up()
# load a test
self.tps.load_people()
self.tps.load_instruments()
data = self.askview.empty_database()
assert data == {} # if success, return an empty dict
# test if start point return no data
askview2 = AskView(self.request)
askview2.settings = self.settings
data = askview2.start_points()
assert data == {'nodes': {}}