def test_add_pathway_info(self):
fargs = FakeArgs()
fargs.conf = 'hi'
fargs.iconurl = 'http://myicon'
fargs.edgecollapse = False
fargs.profile = 'profile'
fargs.datadir = '/foo'
fargs.visibility = 'PUBLIC'
loader = LoadSignorIntoNDEx(fargs, None)
net = NiceCXNetwork()
loader._add_pathway_info(net, 'Human', True, 'mypathway')
net_attr = net.get_network_attribute('description')
self.assertEqual(
'This network contains all the Human' +
' interactions currently available ' + 'in SIGNOR', net_attr['v'])
net_attr = net.get_network_attribute('organism')
self.assertEqual('H**o sapiens (human)', net_attr['v'])
net_attr = net.get_network_attribute('rightsHolder')
self.assertEqual('Prof. Gianni Cesareni', net_attr['v'])
net_attr = net.get_network_attribute('reference')
self.assertTrue('<a href="https://doi.org/10.1093/nar/gkv1048" '
'target="_blank">doi: 10.1093'
'/nar/gkv1048</a>' in net_attr['v'])
def test_wasderivedfrom(self):
fargs = FakeArgs()
fargs.conf = 'hi'
fargs.profile = 'profile'
fargs.datadir = '/foo'
fargs.visibility = 'PUBLIC'
loader = LoadSignorIntoNDEx(fargs, None)
net = NiceCXNetwork()
loader._set_wasderivedfrom(net, 'foo')
res = net.get_network_attribute(ndexloadsignor.DERIVED_FROM_ATTRIB)
self.assertEqual(
'https://signor.uniroma2.it/pathway_browser.php?'
'organism=&pathway_list=foo', res['v'])
# try with is_full_pathway false
net = NiceCXNetwork()
loader._set_wasderivedfrom(net, 'foo', is_full_pathway=False)
res = net.get_network_attribute(ndexloadsignor.DERIVED_FROM_ATTRIB)
self.assertEqual(
'https://signor.uniroma2.it/pathway_browser.php?'
'organism=&pathway_list=foo', res['v'])
# try with is_full_pathway true
net = NiceCXNetwork()
loader._set_wasderivedfrom(net, 'foo', is_full_pathway=True)
res = net.get_network_attribute(ndexloadsignor.DERIVED_FROM_ATTRIB)
self.assertEqual('https://signor.uniroma2.it', res['v'])
def test_set_type(self):
fargs = FakeArgs()
fargs.conf = 'hi'
fargs.profile = 'profile'
fargs.datadir = '/foo'
fargs.visibility = 'PUBLIC'
loader = LoadSignorIntoNDEx(fargs, None)
net = NiceCXNetwork()
# test default
net.set_name('foo')
loader._set_type(net)
res = net.get_network_attribute('networkType')
self.assertEqual(['pathway', 'Signalling Pathway'], res['v'])
# test disease pathway
net.set_name('fsgs')
loader._set_type(net)
res = net.get_network_attribute('networkType')
self.assertEqual(['pathway', 'Disease Pathway'], res['v'])
# test cancer pathway
net.set_name('prostate cancer')
loader._set_type(net)
res = net.get_network_attribute('networkType')
self.assertEqual(['pathway', 'Cancer Pathway'], res['v'])
#test interactome True
net.set_name('some name')
loader._set_type(net, is_human_fullpathway=True)
res = net.get_network_attribute('networkType')
self.assertEqual(['interactome', 'pathway', 'Signalling Pathway'],
res['v'])
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_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_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_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_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_add_network_attribute_duplicate_add(self):
net = NiceCXNetwork()
net.add_network_attribute(name='foo',
values=['a', 'b'],
type='list_of_string')
res = net.get_network_attribute('foo')
self.assertEqual('list_of_string', res['d'])
# add duplicate with no type
net.add_network_attribute(name='foo',
values=['a', 'b'])
res = net.get_network_attribute('foo')
self.assertTrue('d' not in res)
net.add_network_attribute(name='foo',
values=4,
type='integer')
res = net.get_network_attribute('foo')
self.assertEqual('integer', res['d'])
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_set_edgecollapse_notes_with_edgecollapse_false(self):
fargs = FakeArgs()
fargs.conf = '/ho'
fargs.profile = 'hi'
fargs.datadir = '/'
fargs.visibility = 'PUBLIC'
fargs.edgecollapse = False
loader = LoadSignorIntoNDEx(fargs, None)
net = NiceCXNetwork()
loader._set_edgecollapse_notes(net)
res = net.get_network_attribute(ndexloadsignor.NOTES_ATTRIB)
self.assertEqual(None, res)
def test_set_iconurl(self):
fargs = FakeArgs()
fargs.conf = 'hi'
fargs.profile = 'profile'
fargs.datadir = '/foo'
fargs.iconurl = 'hi'
fargs.visibility = 'PUBLIC'
loader = LoadSignorIntoNDEx(fargs, None)
net = NiceCXNetwork()
loader._set_iconurl(net)
res = net.get_network_attribute('__iconurl')
self.assertEqual('hi', res['v'])
