def test_create_from_tsv_manipulate_and_save(self):
print('Testing: mgdb_mutations.txt')
path_to_network = os.path.join(path_this, 'mgdb_mutations.txt')
with open(path_to_network, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='CDS Mutation', target_field='Gene Symbol', source_node_attr=['Primary Tissue', 'Histology', 'Genomic Locus'], target_node_attr=['Gene ID'], edge_interaction='variant-gene-relationship') #NiceCXNetwork()
nice_networkx = niceCx.to_networkx()
nice_pandas = niceCx.to_pandas_dataframe()
my_csv = nice_pandas.to_csv(sep='\t')
with open("pandas_to_cx_to_tsv_results.txt", "w") as text_file:
text_file.write(my_csv)
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('ndexbio.org', '2e8f9bdc-1e5f-11e8-b939-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_node_data_types_from_tsv(self):
self.assertFalse(upload_username == 'username')
path_to_network = os.path.join(path_this, 'mgdb_mutations.txt')
with open(path_to_network, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
print(df.head())
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='CDS Mutation', target_field='Gene Symbol',
source_node_attr=['Primary Tissue', 'Histology', 'Genomic Locus',
'Gene ID'], target_node_attr=['Gene ID'],
edge_interaction='variant-gene-relationship') #NiceCXNetwork()
found_string_type = False
for id, node in niceCx.get_nodes():
abc_node_attrs = niceCx.get_node_attributes(node)
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'string':
found_string_type = True
self.assertTrue(found_string_type)
def test_create_from_small_cx(self):
print('Testing: Pandas DataFrame.from_items')
my_cx = [
{"numberVerification":[{"longNumber":281474976710655}]},
{"metaData":[{"consistencyGroup":1,"elementCount":2,"idCounter":2,"name":"nodes","version":"1.0"},
{"consistencyGroup":1,"elementCount":1,"idCounter":1,"name":"edges","version":"1.0"}]},
{"nodes":[{"@id": 1, "n": "node1", "r": "ABC"}, {"@id": 2, "n": "node2", "r": "DEF"}]},
{"edges":[{"@id": 1, "s": 1, "t": 2, "i": "neighbor"}]},
{"status":[{"error":"","success":True}]}
]
#niceCx = NiceCXNetwork(cx=my_cx)
#data = [('Source', 'Target', 'interaction', 'EdgeProp'), ('ABC', 'DEF', 'interacts-with', 'Edge property 1'), ('DEF', 'XYZ', 'neighbor-of', 'Edge property 2')]
#df = pd.DataFrame.from_records(data)
#niceCx = NiceCXNetwork(pandas_df=df)
df = pd.DataFrame.from_items([('Source', ['ABC', 'DEF']),
('Target', ['DEF', 'XYZ']),
('Interaction', ['interacts-with', 'neighbor-of']),
('EdgeProp', [np.float(0.843), 1.2345])])
#niceCx = ndex2.create_empty_nice_cx() #NiceCXNetwork()
#niceCx.create_from_pandas(df, source_field='Source', target_field='Target', edge_attr=['EdgeProp'], edge_interaction='Interaction')
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='Source', target_field='Target', edge_attr=['EdgeProp'], edge_interaction='Interaction')
#niceCx = '' #NiceCXNetwork(server='public.ndexbio.org', uuid='f1dd6cc3-0007-11e6-b550-06603eb7f303')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
def test_create_from_tsv_manipulate_and_save(self):
path_to_network = os.path.join(path_this, 'mgdb_mutations.txt')
with open(path_to_network, 'rU') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='CDS Mutation', target_field='Gene Symbol', source_node_attr=['Primary Tissue', 'Histology', 'Genomic Locus'], target_node_attr=['Gene ID'], edge_interaction='variant-gene-relationship') #NiceCXNetwork()
nice_networkx = niceCx.to_networkx()
nice_pandas = niceCx.to_pandas_dataframe()
my_csv = nice_pandas.to_csv(sep='\t')
with open("pandas_to_cx_to_tsv_results.txt", "w") as text_file:
text_file.write(my_csv)
niceCx_from_netx = ndex2.create_nice_cx_from_networkx(nice_networkx)
# Restore template
niceCx_from_netx.apply_template('public.ndexbio.org', '72ef5c3a-caff-11e7-ad58-0ac135e8bacf')
niceCx_from_netx.set_name('Round trip from server to networkx to NDEx')
upload_message = niceCx_from_netx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def upload_file():
try:
data = request.files.get('file')
except Exception as e:
raise HTTPError(500, e)
if data and data.file:
if (request.query.alpha):
alpha = request.query.alpha
if (request.query.beta):
beta = request.query.beta
wb = xlrd.open_workbook(file_contents=data.file.read())
df = pd.read_excel(wb, engine='xlrd')
source_column = request.forms.get('source')
target_column = request.forms.get('target')
edge_column = request.forms.get('edge')
nice_cx = ndex2.create_nice_cx_from_pandas(
df,
source_field='CDS Mutation',
target_field='Gene Symbol',
source_node_attr=['Primary Tissue'],
target_node_attr=['Gene ID'],
edge_attr=[])
#upload_message = nice_cx.upload_to(upload_server, upload_username, upload_password)
nice_cx.print_summary()
def test_pandas_loading(self):
print('Testing: edge_list_network_adrian_small.txt')
path_to_network = os.path.join(path_this,
'edge_list_network_adrian_small.txt')
niceCxBuilder = NiceCXBuilder()
context = {
'signor': 'http://signor.uniroma2.it/relation_result.php?id=',
'BTO': 'http://identifiers.org/bto/BTO:',
'uniprot': 'http://identifiers.org/uniprot/',
'pubmed': 'http://identifiers.org/pubmed/',
'CID': 'http://identifiers.org/pubchem.compound/',
'SID': 'http://identifiers.org/pubchem.substance/',
'chebi': 'http://identifiers.org/chebi/CHEBI:'
}
with open(path_to_network, 'r') as tsvfile:
header = ['Source', 'Target']
df = pd.read_csv(tsvfile,
delimiter='\t',
engine='python',
names=header)
nice_cx = ndex2.create_nice_cx_from_pandas(
df) #NiceCXNetwork(pandas_df=df)
nice_cx.set_context(context)
upload_message = nice_cx.upload_to(upload_server, upload_username,
upload_password)
self.assertTrue('error' not in upload_message)
def test_create_from_pandas_with_headers2(self):
path_to_network = os.path.join(path_this, 'CTD_genes_pathways.txt')
with open(path_to_network, 'rU') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,
delimiter='\t',
engine='python',
names=header)
niceCx = NiceCXNetwork()
niceCx = ndex2.create_nice_cx_from_pandas(
df,
source_field='GeneSymbol',
target_field='PathwayName',
source_node_attr=['GeneID'],
target_node_attr=['Pathway Source'],
edge_attr=[])
#for k, v in niceCx.get_edges():
# print(k)
# print(v)
#niceCx.create_from_pandas(df, source_field='GeneSymbol', target_field='PathwayName', source_node_attr=['GeneID'], target_node_attr=['Pathway Source'], edge_attr=[])
#my_cx_json = niceCx.to_cx()
#print(json.dumps(my_cx_json))
upload_message = True #niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_pandas_loading(self):
print('Testing: edge_list_network_adrian_small.txt')
path_to_network = os.path.join(path_this, 'edge_list_network_adrian_small.txt')
niceCxBuilder = NiceCXBuilder()
context = {
'signor': 'http://signor.uniroma2.it/relation_result.php?id=',
'BTO': 'http://identifiers.org/bto/BTO:',
'uniprot': 'http://identifiers.org/uniprot/',
'pubmed': 'http://identifiers.org/pubmed/',
'CID': 'http://identifiers.org/pubchem.compound/',
'SID': 'http://identifiers.org/pubchem.substance/',
'chebi': 'http://identifiers.org/chebi/CHEBI:'
}
with open(path_to_network, 'r') as tsvfile:
header = ['Source', 'Target']
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
nice_cx = ndex2.create_nice_cx_from_pandas(df) #NiceCXNetwork(pandas_df=df)
nice_cx.set_context(context)
upload_message = nice_cx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue('error' not in upload_message)
def test_node_data_types_from_tsv(self):
self.assertFalse(upload_username == 'username')
path_to_network = os.path.join(path_this, 'mgdb_mutations.txt')
with open(path_to_network, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,
delimiter='\t',
engine='python',
names=header)
print(df.head())
niceCx = ndex2.create_nice_cx_from_pandas(
df,
source_field='CDS Mutation',
target_field='Gene Symbol',
source_node_attr=[
'Primary Tissue', 'Histology', 'Genomic Locus', 'Gene ID'
],
target_node_attr=['Gene ID'],
edge_interaction='variant-gene-relationship') #NiceCXNetwork()
found_string_type = False
for id, node in niceCx.get_nodes():
abc_node_attrs = niceCx.get_node_attributes(node)
if abc_node_attrs is not None:
for node_attr in abc_node_attrs:
if node_attr.get('d') == 'string':
found_string_type = True
self.assertTrue(found_string_type)
def test_edit_network_attributes(self):
with open('SIMPLE_WITH_ATTRIBUTES.txt', 'rU') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,
delimiter='\t',
engine='python',
names=header)
niceCx = ndex2.create_nice_cx_from_pandas(
df,
source_field='SOURCE',
target_field='TARGET',
source_node_attr=['NODEATTR'],
target_node_attr=[],
edge_attr=['EDGEATTR']) #NiceCXNetwork()
for k, v in niceCx.get_nodes():
node_attr = niceCx.get_node_attribute(k, 'NODEATTR')
if node_attr:
niceCx.set_node_attribute(k, 'NODEATTR',
node_attr.get('v') + 'xyz')
print(node_attr)
for k, v in niceCx.get_edges():
edge_attr = niceCx.get_edge_attribute(k, 'EDGEATTR')
if edge_attr:
niceCx.set_edge_attribute(k, 'EDGEATTR',
edge_attr.get('v') + 'abc')
print(edge_attr)
my_cx_json = niceCx.to_cx()
print(json.dumps(my_cx_json))
def test_create_from_pandas_no_headers(self):
path_to_network = os.path.join(path_this, 'SIMPLE.txt')
with open(path_to_network, 'rU') as tsvfile:
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',header=None)
niceCx = ndex2.create_nice_cx_from_pandas(df) #NiceCXNetwork(pandas_df=df)
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_pandas_no_headers(self):
print('Testing: SIMPLE.txt')
path_to_network = os.path.join(path_this, 'SIMPLE.txt')
with open(path_to_network, 'r') as tsvfile:
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',header=None)
niceCx = ndex2.create_nice_cx_from_pandas(df) #NiceCXNetwork(pandas_df=df)
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_load_from_pandas(self):
path_to_network = os.path.join(path_this, 'SIMPLE3.txt')
with open(path_to_network, 'r') as tsvfile:
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',header=None)
#====================================
# BUILD NICECX FROM PANDAS DATAFRAME
#====================================
niceCx = ndex2.create_nice_cx_from_pandas(df) #NiceCXNetwork(pandas_df=df)
niceCx.apply_template('public.ndexbio.org', '56cbe15a-5f7e-11e8-a4bf-0ac135e8bacf')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
def test_load_from_pandas(self):
path_to_network = os.path.join(path_this, 'SIMPLE3.txt')
with open(path_to_network, 'r') as tsvfile:
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',header=None)
#====================================
# BUILD NICECX FROM PANDAS DATAFRAME
#====================================
niceCx = ndex2.create_nice_cx_from_pandas(df) #NiceCXNetwork(pandas_df=df)
niceCx.apply_template('public.ndexbio.org', '56cbe15a-5f7e-11e8-a4bf-0ac135e8bacf')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
def test_create_from_pandas_no_headers_3_columns(self):
path_to_network = os.path.join(path_this, 'SIMPLE3.txt')
with open(path_to_network, 'rU') as tsvfile:
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',header=None)
#====================================
# BUILD NICECX FROM PANDAS DATAFRAME
#====================================
niceCx = ndex2.create_nice_cx_from_pandas(df) #NiceCXNetwork(pandas_df=df)
niceCx.apply_template('public.ndexbio.org', '72ef5c3a-caff-11e7-ad58-0ac135e8bacf')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_pandas_with_headers2(self):
print('Testing: CTD_genes_pathways_small.txt')
path_to_network = os.path.join(path_this, 'CTD_genes_pathways_small.txt')
with open(path_to_network, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='GeneSymbol', target_field='PathwayName', source_node_attr=['GeneID'], target_node_attr=['Pathway Source'], edge_attr=[])
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_pandas_with_headers(self):
path_to_network = os.path.join(path_this, 'MDA1.txt')
with open(path_to_network, 'rU') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='Bait', target_field='Prey', source_node_attr=['AvePSM'], target_node_attr=['WD'], edge_attr=['Z', 'Entropy']) #NiceCXNetwork()
#niceCx.create_from_pandas(df, source_field='Bait', target_field='Prey', source_node_attr=['AvePSM'], target_node_attr=['WD'], edge_attr=['Z', 'Entropy'])
my_cx_json = niceCx.to_cx()
#print(json.dumps(my_cx_json, cls=DecimalEncoder))
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_big_tsv(self):
print('Testing: identifier_mappings_small.txt')
path_to_network = os.path.join(path_this, 'identifier_mappings_small.txt')
with open(path_to_network, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='Preferred_Name', target_field='Name',
source_node_attr=['Source'],
edge_interaction='neighbor-of')
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_create_from_pandas_with_headers(self):
print('Testing: MDA1.txt')
path_to_network = os.path.join(path_this, 'MDA1.txt')
with open(path_to_network, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='Bait', target_field='Prey', source_node_attr=['AvePSM'], target_node_attr=['WD'], edge_attr=['Z', 'Entropy']) #NiceCXNetwork()
#niceCx.create_from_pandas(df, source_field='Bait', target_field='Prey', source_node_attr=['AvePSM'], target_node_attr=['WD'], edge_attr=['Z', 'Entropy'])
my_cx_json = niceCx.to_cx()
#print(json.dumps(my_cx_json, cls=DecimalEncoder))
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_pandas(self):
df = pd.DataFrame.from_dict({'Source': ['a', 'b', 'c','e'],
'Target': ['b', 'c', 'd', 'f'],
'Interaction': ['touches', 'smells', 'tastes', 'hears'],
'color': ['red', 'blue', 'yellow', 'green'],
'size':['1', '2', '3', '4'],
'width': ['az', 'by', 'cx', 'mn']})
niceCx_df_with_headers = ndex2.create_nice_cx_from_pandas(df, source_field='Source', target_field='Target',
edge_attr=['color'],
edge_interaction='Interaction', source_node_attr=["size"],
target_node_attr=["width"])
upload_message = niceCx_df_with_headers.upload_to(upload_server, upload_username, upload_password)
niceCx_df_with_headers.print_summary()
self.assertTrue(upload_message)
def test_pandas(self):
df = pd.DataFrame.from_dict({'Source': ['a', 'b', 'c','e'],
'Target': ['b', 'c', 'd', 'f'],
'Interaction': ['touches', 'smells', 'tastes', 'hears'],
'color': ['red', 'blue', 'yellow', 'green'],
'size':['1', '2', '3', '4'],
'width': ['az', 'by', 'cx', 'mn']})
niceCx_df_with_headers = ndex2.create_nice_cx_from_pandas(df, source_field='Source', target_field='Target',
edge_attr=['color'],
edge_interaction='Interaction', source_node_attr=["size"],
target_node_attr=["width"])
upload_message = niceCx_df_with_headers.upload_to(upload_server, upload_username, upload_password)
niceCx_df_with_headers.print_summary()
self.assertTrue(upload_message)
def test_create_nice_cx_from_pandas_with_sif(self):
data = {
'source': ['Node 1', 'Node 2'],
'target': ['Node 2', 'Node 3'],
'interaction': ['helps', 'hurts']
}
df = pd.DataFrame.from_dict(data)
# on older versions of pandas this order is not consistent
# so setting it explicitly
df = df[['source', 'target', 'interaction']]
net = ndex2.create_nice_cx_from_pandas(df)
self.assertEqual(2, len(net.get_edges()))
self.assertEqual(3, len(net.get_nodes()))
for node_id, node in net.get_nodes():
self.assertEqual(
{
'@id': node_id,
'n': 'Node ' + str(node_id + 1),
'r': 'Node ' + str(node_id + 1)
}, node)
for edge_id, edge in net.get_edges():
if edge_id == 0:
self.assertEqual({
'@id': 0,
's': 0,
't': 1,
'i': 'helps'
}, edge)
elif edge_id == 1:
self.assertEqual({
'@id': 1,
's': 1,
't': 2,
'i': 'hurts'
}, edge)
else:
self.fail('Unexpected edge: ' + str(edge))
def test_edit_network_attributes(self):
with open('SIMPLE_WITH_ATTRIBUTES.txt', 'rU') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split('\t')]
df = pd.read_csv(tsvfile,delimiter='\t',engine='python',names=header)
niceCx = ndex2.create_nice_cx_from_pandas(df, source_field='SOURCE', target_field='TARGET', source_node_attr=['NODEATTR'], target_node_attr=[], edge_attr=['EDGEATTR']) #NiceCXNetwork()
for k, v in niceCx.get_nodes():
node_attr = niceCx.get_node_attribute(k, 'NODEATTR')
if node_attr:
niceCx.set_node_attribute(k, 'NODEATTR', node_attr.get('v') + 'xyz')
print(node_attr)
for k, v in niceCx.get_edges():
edge_attr = niceCx.get_edge_attribute(k, 'EDGEATTR')
if edge_attr:
niceCx.set_edge_attribute(k, 'EDGEATTR', edge_attr.get('v') + 'abc')
print(edge_attr)
my_cx_json = niceCx.to_cx()
print(json.dumps(my_cx_json))
def test_create_nice_cx_from_networkx_roundtrip_no_attrs(self):
net = ndex2.nice_cx_network.NiceCXNetwork()
node_one = net.create_node('Node 1')
node_two = net.create_node('Node 2')
net.create_edge(edge_source=node_one, edge_target=node_two)
net_df = net.to_pandas_dataframe(include_attributes=True)
net_roundtrip = ndex2.create_nice_cx_from_pandas(net_df,
source_field='source',
target_field='target')
self.assertEqual(
'created from pandas by '
'ndex2.create_nice_cx_from_pandas()', net_roundtrip.get_name())
self.assertEqual(1, len(net_roundtrip.get_edges()))
self.assertEqual(2, len(net_roundtrip.get_nodes()))
self.assertEqual((0, {
'@id': 0,
's': 0,
't': 1,
'i': 'interacts-with'
}),
list(net_roundtrip.get_edges())[0])
for node_id, node_obj in net_roundtrip.get_nodes():
if node_id == 0:
self.assertEqual({
'@id': 0,
'n': 'Node 1',
'r': 'Node 1'
}, node_obj)
elif node_id == 1:
self.assertEqual({
'@id': 1,
'n': 'Node 2',
'r': 'Node 2'
}, node_obj)
else:
self.fail('Invalid node: ' + str(node_obj))
def upload_file():
try:
data = request.files.get('file')
node_data = request.files.get('nodeFile')
except Exception as e:
raise HTTPError(500, e)
if data and data.file:
if (request.query.alpha):
alpha = request.query.alpha
if (request.query.beta):
beta = request.query.beta
source_column = request.forms.get('source')
target_column = request.forms.get('target')
edge_column = request.forms.get('edge')
node_file_id_col = request.forms.get('nodeFileIDColumn')
with tempfile.NamedTemporaryFile('wb', delete=False) as f:
f.write(data.file.read())
f_name = f.name
f.close()
with open(f_name, 'r') as tsvfile:
header = [h.strip() for h in tsvfile.readline().split(',')]
edge_attrs = [
e for e in header
if e not in [source_column, target_column, edge_column]
]
df = pd.read_csv(tsvfile,
delimiter=',',
engine='python',
names=header)
nice_cx = ndex2.create_nice_cx_from_pandas(
df,
source_field=source_column,
target_field=target_column,
source_node_attr=[],
target_node_attr=[],
edge_attr=edge_attrs,
edge_interaction=edge_column) #NiceCXNetwork()
if node_data and node_data.file:
with tempfile.NamedTemporaryFile('wb', delete=False) as f2:
f2.write(node_data.file.read())
f_name2 = f2.name
f2.close()
with open(f_name2, 'r') as tsvfile2:
header2 = [h.strip() for h in tsvfile2.readline().split(',')]
dtype_set = {h_n: str for h_n in header2}
df2 = pd.read_csv(tsvfile2,
delimiter=',',
engine='python',
names=header2,
dtype=dtype_set)
for index, row in df2.iterrows():
node_name_lookup = {
node.get('n'): node.get('@id')
for node_id, node in nice_cx.get_nodes()
}
node_id = node_name_lookup.get(row[node_file_id_col])
for header_column in header2:
if header_column != node_file_id_col:
if header_column == 'name':
nice_cx.add_node_attribute(
property_of=node_id,
name='name_attr',
values=row[header_column])
else:
nice_cx.add_node_attribute(
property_of=node_id,
name=header_column,
values=row[header_column])
upload_message = nice_cx.upload_to(upload_server, upload_username,
upload_password)
nice_cx.print_summary()
return upload_message
# #### *ndex2.create_nice_cx_from_networkx(networkx)
# In[ ]:
#create an Empty NetworkX
G = nx.Graph()
nice_cx_from_networkx = ndex2.create_nice_cx_from_networkx(G)
# #### *ndex2.create_nice_cx_from_pandas(dataframe)
# In[ ]:
#create an Empty Pandas Dataframe
df = pd.DataFrame()
nice_cx_from_pandas = ndex2.create_nice_cx_from_pandas(df)
# #### *ndex2.create_nice_cx_from_server(server, username=None, password=None, uuid=None)
# In[ ]:
uuid = "1c69beff-1229-11e6-a039-06603eb7f303"
nice_cx_from_server = ndex2.create_nice_cx_from_server(
server='http://public.ndexbio.org', uuid=uuid)
nice_cx_from_server.print_summary()
# #### create_node(name, represents=None)
# In[ ]:
#Starting with an Empty Network
def push_to_ndex(biggim_id,
username='******',
password='******',
server="http://public.ndexbio.org",
network_name=None,
network_set_name=None,
network_set_description=None):
glogger.debug("Looking for biggim request [%s]" % (biggim_id))
request_status = get_request_status(biggim_id)
while request_status['status'] == 'running':
time.sleep(1)
request_status = get_request_status(biggim_id)
glogger.debug("Request search response[%s]" % (str(request_status)))
if request_status['status'] == 'complete':
csvs = request_status['request_uri']
else:
glogger.error("Error attempting to get [%s]" % (biggim_id))
return request_status
if network_set_name is None:
network_set_name = "Anonymous"
network_set_description = "Biggim network"
if network_name is None:
network_name = "Biggim - [%s]" % (biggim_id, )
try:
my_ndex = ndex2.Ndex2(server, username, password)
my_ndex.update_status()
except Exception as inst:
glogger.exception("Could not access account %s with password %s" %
(username, password))
return {'status': 'error', 'message': "Invalid authentication to NDEX"}
user = my_ndex.get_user_by_username(username)
if network_set_name is None:
network_set = "Anonymous"
network_set_description = "Autogenerated biggim ndex file. CSV source at %s" % csv_url
ctr = 0
ndex_urls = []
ndex_ids = []
public_url = []
for csv_url in csvs:
df = pandas.read_csv(csv_url)
df.loc[:, 'Interaction'] = 'coexpression'
non_att = ['GPID', 'Gene1', 'Gene2', 'Interaction']
edge_attr = [c for c in df.columns if c not in non_att]
df.loc[:, 'Gene1'] = df.apply(lambda x: "ncbigene:%i" % x['Gene1'],
axis=1)
df.loc[:, 'Gene2'] = df.apply(lambda x: "ncbigene:%i" % x['Gene2'],
axis=1)
niceCx_df_with_headers = ndex2.create_nice_cx_from_pandas(
df,
source_field='Gene1',
target_field='Gene2',
edge_attr=edge_attr,
edge_interaction='Interaction')
# add gene context for lookup
context = [{'ncbigene': 'http://identifiers.org/ncbigene/'}]
niceCx_df_with_headers.set_name("%s - [%i]" % (network_name, ctr))
ndex_network_url = niceCx_df_with_headers.upload_to(
server, username, password, visibility='PUBLIC')
ndex_urls.append(ndex_network_url)
ndex_network_uuid = ndex_network_url.split('/')[-1]
ndex_ids.append(ndex_network_uuid)
public_url.append("http://www.ndexbio.org/#/network/%s" %
(ndex_network_uuid, ))
ctr += 1
net_set_uuid = None
network_sets = my_ndex.get('/user/%s/networksets' % user['externalId'])
for ns in network_sets:
if ns['name'] == network_set_name:
net_set_uuid = ns['externalId']
if net_set_uuid is None:
net_set_url = my_ndex.create_networkset(network_set_name,
network_set_description)
net_set_uuid = net_set_url.split('/')[-1]
my_ndex.add_networks_to_networkset(net_set_uuid, [ndex_network_uuid])
return {
'status': 'complete',
'request_id': biggim_id,
'ndex_network_url': ndex_urls,
'ndex_network_uuid': ndex_ids,
'ndex_public_url': public_url
}
def test_create_nice_cx_from_networkx_roundtrip_with_attrs(self):
net = ndex2.nice_cx_network.NiceCXNetwork()
node_one = net.create_node('Node 1')
node_two = net.create_node('Node 2')
net.set_node_attribute(node_one, 'somestrfield', 'hi')
edge_one = net.create_edge(edge_source=node_one,
edge_target=node_two,
edge_interaction='breaks')
net.set_edge_attribute(edge_one, 'somestrfield', 'bye')
net.set_opaque_aspect(ndex2.constants.CARTESIAN_LAYOUT_ASPECT,
[{
'node': node_one,
'x': 1.0,
'y': 2.0
}, {
'node': node_two,
'x': 3.0,
'y': 4.0
}])
net.set_name('mynetwork')
net_df = net.to_pandas_dataframe(include_attributes=True)
net_roundtrip = ndex2.create_nice_cx_from_pandas(
net_df,
source_field='source',
target_field='target',
edge_interaction='interaction',
edge_attr=['somestrfield'],
source_node_attr=['source_somestrfield'])
self.assertEqual(
'created from pandas by '
'ndex2.create_nice_cx_from_pandas()', net_roundtrip.get_name())
self.assertEqual(1, len(net_roundtrip.get_edges()))
self.assertEqual(2, len(net_roundtrip.get_nodes()))
self.assertEqual((0, {
'@id': 0,
's': 0,
't': 1,
'i': 'breaks'
}),
list(net_roundtrip.get_edges())[0],
'\n\n' + str(net_df.head()))
for node_id, node_obj in net_roundtrip.get_nodes():
if node_id == 0:
self.assertEqual({
'@id': 0,
'n': 'Node 1',
'r': 'Node 1'
}, node_obj)
elif node_id == 1:
self.assertEqual({
'@id': 1,
'n': 'Node 2',
'r': 'Node 2'
}, node_obj)
else:
self.fail('Invalid node: ' + str(node_obj))
n_a = net_roundtrip.get_node_attribute(node_one, 'source_somestrfield')
self.assertEqual(
{
'po': 0,
'n': 'source_somestrfield',
'v': 'hi',
'd': 'string'
}, n_a)
n_a = net_roundtrip.get_edge_attribute(node_one, 'somestrfield')
self.assertEqual(
{
'po': 0,
'n': 'somestrfield',
'v': 'bye',
'd': 'string'
}, n_a)
def test_create_nice_cx_from_pandas_with_invalidstr(self):
try:
ndex2.create_nice_cx_from_pandas('invalid')
self.fail('Expected Exception')
except AttributeError as e:
self.assertTrue('object has no' in str(e))
def test_create_nice_cx_from_pandas_with_none(self):
try:
ndex2.create_nice_cx_from_pandas(None)
self.fail('AssertionError')
except AttributeError as e:
self.assertTrue('NoneType' in str(e))
