def test_set_iconurl(self):
p = Param()
p.iconurl = 'hi'
loader = NDExNciPidLoader(p)
net = NiceCXNetwork()
loader._set_iconurl(net)
self.assertEqual('hi', net.get_network_attribute('__iconurl')['v'])
def test_add_node_types_in_network_to_report_empty_network(self):
loader = NDExNciPidLoader(None)
report = NetworkIssueReport('foo')
net = NiceCXNetwork()
net.set_name('foo')
loader._add_node_types_in_network_to_report(net, report)
self.assertEqual(set(), report.get_nodetypes())
def test_set_normalizationversion(self):
net = NiceCXNetwork()
net.set_name('foo')
loader = NDExNciPidLoader(None)
loader._set_normalization_version(net)
norm_attr = ndexloadncipid.NORMALIZATIONVERSION_ATTRIB
self.assertEqual('0.1', net.get_network_attribute(norm_attr)['v'])
def test_set_generatedby_in_network_attributes(self):
net = NiceCXNetwork()
net.set_name('foo')
loader = NDExNciPidLoader(None)
loader._set_generatedby_in_network_attributes(net)
norm_attr = ndexloadncipid.GENERATED_BY_ATTRIB
self.assertTrue(' ' + str(ndexncipidloader.__version__) in
net.get_network_attribute(norm_attr)['v'])
def test_update_network_system_properties_success(self):
net = NiceCXNetwork()
net.set_name('foo')
loader = NDExNciPidLoader(None)
loader._ndex = MagicMock()
loader._ndex.set_network_system_properties = MagicMock(return_value='')
perm_dict = {'index_level': 'ALL', 'showcase': True}
loader._update_network_system_properties('http://public.ndexbio.org'
'/v2/network/someid')
loader._ndex.set_network_system_properties.assert_called_with(
'someid', perm_dict)
def test_set_wasderivedfrom(self):
net = NiceCXNetwork()
net.set_name('foo')
loader = NDExNciPidLoader(None)
loader._set_wasderivedfrom(net)
derived_attr = ndexloadncipid.DERIVED_FROM_ATTRIB
self.assertEqual('<a href="ftp://' +
ndexloadncipid.DEFAULT_FTP_HOST +
'/' + ndexloadncipid.DEFAULT_FTP_DIR + '/' +
'foo.owl.gz">foo.owl.gz</a>',
net.get_network_attribute(derived_attr)['v'])
def test_apply_cytoscape_layout_ping_failed(self):
p = MagicMock()
p.layout = 'grid'
mockpy4 = MagicMock()
mockpy4.cytoscape_ping = MagicMock(side_effect=Exception('error'))
loader = NDExNciPidLoader(p, py4cyto=mockpy4)
net = NiceCXNetwork()
try:
loader._apply_cytoscape_layout(net)
self.fail('Expected NDExNciPidLoaderError')
except NDExNciPidLoaderError as e:
self.assertEqual('Cytoscape needs to be running '
'to run layout: grid', str(e))
def test_set_network_attributes_from_style_network_complete_net(self):
net = NiceCXNetwork()
net.set_name(ndexloadncipid.COMPLETE_INTERACTION_NAME)
templatenet = NiceCXNetwork()
templatenet.set_name('well')
templatenet.set_network_attribute('description', values='hi', type='string')
templatenet.set_network_attribute('organism', values='some', type='string')
loader = NDExNciPidLoader(None)
loader._template = templatenet
res = loader._set_network_attributes_from_style_network(net)
self.assertEqual(0, len(res))
self.assertTrue('This network' in net.get_network_attribute('description')['v'])
self.assertEqual('some', net.get_network_attribute('organism')['v'])
def test_set_network_attributes_from_style_network_description_set_org_not(self):
net = NiceCXNetwork()
net.set_name('foo')
templatenet = NiceCXNetwork()
templatenet.set_name('well')
templatenet.set_network_attribute('description', values='hi', type='string')
loader = NDExNciPidLoader(None)
loader._template = templatenet
res = loader._set_network_attributes_from_style_network(net)
self.assertEqual(1, len(res))
self.assertTrue('organism network' in res[0])
self.assertEqual('hi', net.get_network_attribute('description')['v'])
self.assertEqual(None, net.get_network_attribute('organism'))
def test_update_network_system_properties_exception_then_okay(self):
net = NiceCXNetwork()
net.set_name('foo')
loader = NDExNciPidLoader(None)
loader._ndex = MagicMock()
loader._networksystemproperty_wait = 0
loader._ndex.set_network_system_properties = MagicMock(side_effect=[Exception('foo'), ''])
perm_dict = {'index_level': 'ALL',
'showcase': True}
res = loader._update_network_system_properties('http://public.'
'ndexbio.org'
'/v2/network/someid')
self.assertEqual(None, res)
loader._ndex.set_network_system_properties.assert_called_with('someid',
perm_dict)
cnt = loader._ndex.set_network_system_properties.call_count
self.assertEqual(2, cnt)
def test_apply_cytoscape_layout_networks_not_in_dict(self):
temp_dir = tempfile.mkdtemp()
try:
p = MagicMock()
p.layout = 'grid'
p.sifdir = temp_dir
mockpy4 = MagicMock()
mockpy4.import_network_from_file = MagicMock(return_value={})
loader = NDExNciPidLoader(p, py4cyto=mockpy4)
net = NiceCXNetwork()
for x in range(10):
net.create_node('node' + str(x))
try:
loader._apply_cytoscape_layout(net)
self.fail('Expected NDExNciPidLoaderError')
except NDExNciPidLoaderError as e:
self.assertTrue(str(e).startswith('Error network view'))
finally:
shutil.rmtree(temp_dir)
def test_apply_cytoscape_layout_networks_success(self):
temp_dir = tempfile.mkdtemp()
try:
p = MagicMock()
p.layout = 'grid'
p.sifdir = temp_dir
mockpy4 = MagicMock()
imp_res = {'networks': ['netid']}
mockpy4.import_network_from_file = MagicMock(return_value=imp_res)
mockpy4.export_network = MagicMock(return_value='')
loader = NDExNciPidLoader(p, py4cyto=mockpy4)
loader._ndexextra.extract_layout_aspect_from_cx = MagicMock(return_value={'cartesianLayout': []})
net = NiceCXNetwork()
for x in range(10):
net.create_node('node' + str(x))
loader._apply_cytoscape_layout(net)
self.assertEqual([{'cartesianLayout': []}],
net.get_opaque_aspect('cartesianLayout'))
finally:
shutil.rmtree(temp_dir)
def test_parse_config(self):
temp_dir = tempfile.mkdtemp()
try:
p = Param()
p.profile = 'foo'
conf = os.path.join(temp_dir, 'blah.conf')
p.conf = conf
with open(conf, 'w') as f:
f.write('[' + p.profile + ']' + '\n')
f.write(NDExUtilConfig.USER + ' = bob\n')
f.write(NDExUtilConfig.PASSWORD + ' = pass\n')
f.write(NDExUtilConfig.SERVER + ' = server\n')
f.flush()
loader = NDExNciPidLoader(p)
loader._parse_config()
self.assertEqual('bob', loader._user)
self.assertEqual('pass', loader._pass)
self.assertEqual('server', loader._server)
finally:
shutil.rmtree(temp_dir)
def test_apply_simple_spring_layout(self):
net = NiceCXNetwork()
for x in range(2):
net.create_node('node' + str(x))
loader = NDExNciPidLoader(None)
loader._apply_simple_spring_layout(net)
res = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(2, len(res))
self.assertTrue('node' in res[0])
self.assertTrue(res[0]['node'] >= 0)
self.assertTrue('x' in res[0])
self.assertTrue('y' in res[0])
self.assertTrue('node' in res[1])
self.assertTrue(res[1]['node'] >= 1)
self.assertTrue('x' in res[1])
self.assertTrue('y' in res[1])
net = NiceCXNetwork()
for x in range(10):
net.create_node('node' + str(x))
loader._apply_simple_spring_layout(net)
self.assertEqual(10,
len(net.get_opaque_aspect('cartesianLayout')))
net = NiceCXNetwork()
for x in range(20):
net.create_node('node' + str(x))
loader._apply_simple_spring_layout(net)
self.assertEqual(20,
len(net.get_opaque_aspect('cartesianLayout')))
net = NiceCXNetwork()
for x in range(100):
net.create_node('node' + str(x))
loader._apply_simple_spring_layout(net)
self.assertEqual(100,
len(net.get_opaque_aspect('cartesianLayout')))
def test_set_type(self):
loader = NDExNciPidLoader(None)
net = NiceCXNetwork()
net.set_name('foo')
loader._set_type(net)
self.assertEqual(['pathway'],
net.get_network_attribute('networkType')['v'])
net.set_name(ndexloadncipid.COMPLETE_INTERACTION_NAME)
loader._set_type(net)
self.assertEqual(['pathway', 'interactome'],
net.get_network_attribute('networkType')['v'])
def test_update_network_system_properties_failure(self):
net = NiceCXNetwork()
net.set_name('foo')
loader = NDExNciPidLoader(None)
loader._ndex = MagicMock()
loader._networksystemproperty_retry = 1
loader._networksystemproperty_wait = 0
loader._ndex.set_network_system_properties = MagicMock(return_value='error')
perm_dict = {'index_level': 'ALL',
'showcase': True}
res = loader._update_network_system_properties('http://public.'
'ndexbio.org'
'/v2/network/someid')
self.assertTrue('After 1 retries' in res)
loader._ndex.set_network_system_properties.assert_called_with('someid',
perm_dict)
def test_normalize_context_prefixes(self):
loader = NDExNciPidLoader(None)
self.assertEqual(None,
loader._normalize_context_prefixes(None))
# try with value that shouldn't change
self.assertEqual('foo',
loader._normalize_context_prefixes('foo'))
# try uniprot knowledgebase:
self.assertEqual('uniprot:hi',
loader._normalize_context_prefixes('uniprot '
'knowledgebase:'
'hi'))
# try kegg compound:
self.assertEqual('kegg.compound:hi',
loader._normalize_context_prefixes('kegg compound:'
'hi'))
# try UniProt:
self.assertEqual('uniprot:yo',
loader._normalize_context_prefixes('UniProt:'
'yo'))
def test_get_style_template(self):
p = Param()
p.style = ndexloadncipid.get_style()
loader = NDExNciPidLoader(p)
loader._load_style_template()
self.assertTrue(loader._template is not None)
def test_parse_load_plan(self):
p = Param()
p.loadplan = ndexloadncipid.get_load_plan()
loader = NDExNciPidLoader(p)
loader._parse_load_plan()
self.assertTrue(isinstance(loader._loadplan, dict))
