def test_write_nice_cx_to_file(self):
temp_dir = tempfile.mkdtemp()
try:
p = MagicMock()
p.datadir = temp_dir
p.profile = 'foo'
p.organismloadplan = ndexloadbiogrid.get_organism_load_plan()
p.chemicalloadplan = ndexloadbiogrid.get_chemical_load_plan()
p.organismstyle = ndexloadbiogrid.get_organism_style()
p.chemstyle = ndexloadbiogrid.get_chemical_style()
p.biogridversion = '1.0.0'
p.skipdownload = False
loader = NdexBioGRIDLoader(p)
loader._network = NiceCXNetwork()
loader._network.create_node('hi')
loader._network.set_name('name')
cxfile = os.path.join(temp_dir, 'some.cx')
loader._write_nice_cx_to_file(cxfile)
self.assertTrue(os.path.isfile(cxfile))
checknet = ndex2.create_nice_cx_from_file(cxfile)
self.assertEqual('name', checknet.get_name())
finally:
shutil.rmtree(temp_dir)
def test_parse_arguments_defaults(self):
fakeargs = ['datadir']
pargs = ndexloadbiogrid._parse_arguments('desc', fakeargs)
self.assertEqual('datadir', pargs.datadir)
self.assertEqual('ndexbiogridloader', pargs.profile)
self.assertEqual('4.2.191', pargs.biogridversion)
self.assertEqual(ndexloadbiogrid.get_organism_load_plan(),
pargs.organismloadplan)
self.assertEqual(ndexloadbiogrid.get_chemical_load_plan(),
pargs.chemicalloadplan)
self.assertEqual(ndexloadbiogrid.get_organism_style(),
pargs.organismstyle)
self.assertEqual(ndexloadbiogrid.get_chemical_style(),
pargs.chemicalstyle)
def test_update_or_upload_with_retry(self):
temp_dir = tempfile.mkdtemp()
try:
p = MagicMock()
p.datadir = os.path.join(temp_dir, 'datadir')
p.profile = 'foo'
p.organismloadplan = ndexloadbiogrid.get_organism_load_plan()
p.chemicalloadplan = ndexloadbiogrid.get_chemical_load_plan()
p.organismstyle = ndexloadbiogrid.get_organism_style()
p.chemstyle = ndexloadbiogrid.get_chemical_style()
p.biogridversion = '1.0.0'
p.skipdownload = False
loader = NdexBioGRIDLoader(p)
loader._ndex = MagicMock()
cxfile = os.path.join(temp_dir, 'file.cx')
with open(cxfile, 'wb') as f:
f.write(b'hello')
loader._ndex.save_cx_stream_as_new_network = MagicMock(
side_effect=Exception('error'))
res = loader._update_or_upload_with_retry(cxfile=cxfile,
network_name='foo',
network_uuid=None,
maxretries=1,
retry_sleep=0)
self.assertEqual(2, res)
loader._ndex.update_cx_network = MagicMock(
side_effect=Exception('error'))
res = loader._update_or_upload_with_retry(cxfile=cxfile,
network_name='foo',
network_uuid='1234',
maxretries=1,
retry_sleep=0)
self.assertEqual(2, res)
loader._ndex.save_cx_stream_as_new_network = MagicMock(
return_value={})
res = loader._update_or_upload_with_retry(cxfile=cxfile,
network_name='foo',
maxretries=1,
retry_sleep=0)
self.assertEqual(0, res)
finally:
shutil.rmtree(temp_dir)
def test_apply_simple_spring_layout(self):
net = NiceCXNetwork()
n_one = net.create_node('node1')
n_two = net.create_node('node2')
net.create_edge(n_one, n_two, 'links')
p = MagicMock()
p.datadir = 'datadir'
p.profile = 'foo'
p.organismloadplan = ndexloadbiogrid.get_organism_load_plan()
p.chemicalloadplan = ndexloadbiogrid.get_chemical_load_plan()
p.organismstyle = ndexloadbiogrid.get_organism_style()
p.chemstyle = ndexloadbiogrid.get_chemical_style()
p.biogridversion = '1.0.0'
p.skipdownload = False
loader = NdexBioGRIDLoader(p)
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(2, len(aspect))
# try with 19 nodes
net = NiceCXNetwork()
for x in range(0, 19):
net.create_node(str(x))
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(19, len(aspect))
# try with 99 nodes
net = NiceCXNetwork()
for x in range(0, 99):
net.create_node(str(x))
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(99, len(aspect))
# try with 101 nodes
net = NiceCXNetwork()
for x in range(0, 101):
net.create_node(str(x))
loader._apply_simple_spring_layout(net)
aspect = net.get_opaque_aspect('cartesianLayout')
self.assertEqual(101, len(aspect))
def test_check_if_data_dir_exists(self):
temp_dir = tempfile.mkdtemp()
try:
p = MagicMock()
p.datadir = temp_dir
p.profile = 'foo'
p.organismloadplan = ndexloadbiogrid.get_organism_load_plan()
p.chemicalloadplan = ndexloadbiogrid.get_chemical_load_plan()
p.organismstyle = ndexloadbiogrid.get_organism_style()
p.chemstyle = ndexloadbiogrid.get_chemical_style()
p.biogridversion = '1.0.0'
p.skipdownload = False
loader = NdexBioGRIDLoader(p)
self.assertTrue(loader._check_if_data_dir_exists())
p.datadir = os.path.join(temp_dir, 'foo')
loader = NdexBioGRIDLoader(p)
self.assertFalse(loader._check_if_data_dir_exists())
finally:
shutil.rmtree(temp_dir)
def setupClass(self):
unittest.TestCase.setUp(self)
self.__class__._data_dir = ndexloadbiogrid.get_datadir()
self.__class__._testing_dir = ndexloadbiogrid.get_testsdir()
self.__class__._biogrid_files_dir = os.path.join(
self.__class__._testing_dir, 'biogrid_files')
self._the_args = {
'profile': 'ndexbiogridloader',
'biogridversion': '3.5.175',
'datadir': self.__class__._biogrid_files_dir,
'organismloadplan': ndexloadbiogrid.get_organism_load_plan(),
'chemicalloadplan': ndexloadbiogrid.get_chemical_load_plan(),
'organismstyle': ndexloadbiogrid.get_organism_style(),
'chemicalstyle': ndexloadbiogrid.get_chemical_style()
}
self._the_args = dotdict(self._the_args)
self.__class__.NdexBioGRIDLoader = NdexBioGRIDLoader(self._the_args)
self.__class__.NdexBioGRIDLoader._parse_config()
self.__class__.organism_entries_expected = [
['BIOGRID-ORGANISM-Zea_mays', 'Maize, 4577, Zea mays', 'Z. mays'],
[
'BIOGRID-ORGANISM-Xenopus_laevis',
'African clawed frog, 8355, Xenopus laevis', 'X. laevis'
],
[
'BIOGRID-ORGANISM-Saccharomyces_cerevisiae_S288c',
'Baker\'s yeast, 559292', 'S. cerevisiae'
],
[
'BIOGRID-ORGANISM-Rattus_norvegicus',
'Norway rat, 10116, Rattus norvegicus', 'R. norvegicus'
],
[
'BIOGRID-ORGANISM-Mus_musculus',
'House mouse, 10090, Mus musculus', 'M. musculus'
],
[
'BIOGRID-ORGANISM-Human_papillomavirus_16',
'HPV, 10566, Human papillomavirus', 'HPV'
],
[
'BIOGRID-ORGANISM-Human_Immunodeficiency_Virus_2',
'HIV-2, 11709, Human immunodeficiency virus 2', 'HIV-2'
],
[
'BIOGRID-ORGANISM-Human_Immunodeficiency_Virus_1',
'HIV-1, 11676, Human immunodeficiency virus 1', 'HIV-1'
],
[
'BIOGRID-ORGANISM-Homo_sapiens', 'Human, 9606, H**o sapiens',
'H. sapiens'
],
[
'BIOGRID-ORGANISM-Drosophila_melanogaster',
'Fruit fly, 7227, Drosophila melanogaster', 'D. melanogaster'
],
[
'BIOGRID-ORGANISM-Danio_rerio', 'Zebrafish, 7955, Danio rerio',
'D. rerio'
],
[
'BIOGRID-ORGANISM-Caenorhabditis_elegans',
'Roundworm, 6239, Cenorhabditis elegans', 'C. elegans'
],
[
'BIOGRID-ORGANISM-Arabidopsis_thaliana_Columbia',
'Thale cress, 3702, Arabidopsis thaliana', 'A. thaliana'
]
]
self.__class__.chemicals_entries_expected = [[
'BIOGRID-CHEMICALS', 'Human, 9606, H**o sapiens', 'H. sapiens'
]]
self.__class__._ndex = self.NdexBioGRIDLoader._create_ndex_connection()
self.assertIsNotNone(self.__class__._ndex,
'Unable to to create NDEx client connection')
status_code = self.NdexBioGRIDLoader._download_biogrid_files()
self.assertEqual(status_code, 0,
'Unable to download required biogrid files ')
net_summaries, status_code = self.NdexBioGRIDLoader._load_network_summaries_for_user(
)
self.assertEqual(status_code, 0, 'Unable to get netwok summaries')
self.__class__.NdexBioGRIDLoader._load_chemical_style_template()
self.__class__.NdexBioGRIDLoader._load_organism_style_template()
self.__class__._organism_template = self.__class__.NdexBioGRIDLoader.__getattribute__(
'_organism_style_template')
self.__class__._chemical_template = self.__class__.NdexBioGRIDLoader.__getattribute__(
'_chem_style_template')
def test_get_organism_style(self):
res = ndexloadbiogrid.get_organism_style()
self.assertTrue(os.path.isfile(res))
net = ndex2.create_nice_cx_from_file(res)
props = net.get_opaque_aspect('cyVisualProperties')
self.assertTrue(isinstance(props, list))