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 = loadndexncipidloader.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 = loadndexncipidloader.GENERATED_BY_ATTRIB
self.assertTrue(' ' + str(ndexncipidloader.__version__) in
net.get_network_attribute(norm_attr)['v'])
def test_set_wasderivedfrom(self):
net = NiceCXNetwork()
net.set_name('foo')
loader = NDExNciPidLoader(None)
loader._set_wasderivedfrom(net)
derived_attr = loadndexncipidloader.DERIVED_FROM_ATTRIB
self.assertEqual(
'<a href="ftp://' + loadndexncipidloader.DEFAULT_FTP_HOST + '/' +
loadndexncipidloader.DEFAULT_FTP_DIR + '/' +
'foo.owl.gz">foo.owl.gz</a>',
net.get_network_attribute(derived_attr)['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_set_network_attributes_from_style_network_complete_net(self):
net = NiceCXNetwork()
net.set_name(loadndexncipidloader.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_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_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 = loadndexncipidloader.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 = loadndexncipidloader.get_load_plan()
loader = NDExNciPidLoader(p)
loader._parse_load_plan()
self.assertTrue(isinstance(loader._loadplan, dict))