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'])