def test_bad_node_attr(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
fox_node = niceCx_creatures.create_node(node_name=453)
niceCx_creatures.add_node_attribute(property_of=fox_node, name='Color', values=['Red',"tree"])
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_bad_node_attr(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test Network")
fox_node = niceCx_creatures.create_node(node_name=453)
niceCx_creatures.add_node_attribute(property_of=fox_node, name='Color', values=['Red',"tree"])
upload_message = niceCx_creatures.upload_to(upload_server, upload_username, upload_password)
self.assertTrue(upload_message)
def test_add_int_attr(self):
niceCx = NiceCXNetwork()
int_node = niceCx.create_node(node_name="testint")
niceCx.add_node_attribute(property_of=int_node, name='Size', values=1, type="integer")
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', uuid=UUID, username=upload_username, password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "integer")
def test_add_lst_flt(self):
niceCx = NiceCXNetwork()
list_float_node = niceCx.create_node(node_name="testlstflt")
niceCx.add_node_attribute(property_of=list_float_node, name='Too many scores', values=[15.3,43.6,-34.0,43.3], type="list_of_float")
upload_message = niceCx.upload_to(upload_server, upload_username, upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(server='dev.ndexbio.org', uuid=UUID, username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "list_of_double")
def test_add_lst_int(self):
niceCx = NiceCXNetwork()
list_int_node = niceCx.create_node(node_name="testlstint")
niceCx.add_node_attribute(property_of=list_int_node,
name='Too many sizes',
values=[1, 2, 3, 4, 5],
type="list_of_integer")
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(
server='dev.ndexbio.org',
uuid=UUID,
username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "list_of_integer")
def test_add_flt(self):
niceCx = NiceCXNetwork()
float_node = niceCx.create_node(node_name="testflt")
niceCx.add_node_attribute(property_of=float_node,
name='Score',
values=1.0,
type="float")
upload_message = niceCx.upload_to(upload_server, upload_username,
upload_password)
UUID = upload_message.split('/')[-1]
time.sleep(1)
imported_cx = ndex2.create_nice_cx_from_server(
server='dev.ndexbio.org',
uuid=UUID,
username=upload_username,
password=upload_password)
for i in imported_cx.get_node_attributes(0):
self.assertEqual(i.get('d'), "double")
def test_simple_create(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Food Web")
fox_node = niceCx_creatures.create_node(node_name='Fox')
mouse_node = niceCx_creatures.create_node(node_name='Mouse')
bird_node = niceCx_creatures.create_node(node_name='Bird')
fox_bird_edge = niceCx_creatures.create_edge(
edge_source=fox_node,
edge_target=bird_node,
edge_interaction='interacts-with')
fox_mouse_edge = niceCx_creatures.create_edge(
edge_source=fox_node,
edge_target=mouse_node,
edge_interaction='interacts-with')
niceCx_creatures.add_node_attribute(property_of=fox_node,
name='Color',
values='Red')
niceCx_creatures.add_node_attribute(property_of=mouse_node,
name='Color',
values='Gray')
niceCx_creatures.add_node_attribute(property_of=bird_node,
name='Color',
values='Blue')
niceCx_creatures.add_edge_attribute(property_of=fox_mouse_edge,
name='Hunted',
values='On the ground')
print(niceCx_creatures.get_node_attribute(fox_node, 'Color'))
def test_simple_create(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Food Web")
fox_node = niceCx_creatures.create_node(node_name='Fox')
mouse_node = niceCx_creatures.create_node(node_name='Mouse')
bird_node = niceCx_creatures.create_node(node_name='Bird')
fox_bird_edge = niceCx_creatures.create_edge(edge_source=fox_node, edge_target=bird_node, edge_interaction='interacts-with')
fox_mouse_edge = niceCx_creatures.create_edge(edge_source=fox_node, edge_target=mouse_node, edge_interaction='interacts-with')
niceCx_creatures.add_node_attribute(property_of=fox_node, name='Color', values='Red')
niceCx_creatures.add_node_attribute(property_of=mouse_node, name='Color', values='Gray')
niceCx_creatures.add_node_attribute(property_of=bird_node, name='Color', values='Blue')
niceCx_creatures.add_edge_attribute(property_of=fox_mouse_edge, name='Hunted', values='On the ground')
print(niceCx_creatures.get_node_attribute(fox_node, 'Color'))
class NiceCxAssembler(object):
"""Assembles a Nice CX network from a set of INDRA Statements.
Parameters
----------
stmts : Optional[list[indra.statements.Statement]]
A list of INDRA Statements to be assembled.
network_name : Optional[str]
The name of the network to be assembled. Default: indra_assembled
Attributes
----------
network : ndex2.nice_cx_network.NiceCXNetwork
A Nice CX network object that is assembled from Statements.
"""
def __init__(self, stmts=None, network_name=None):
self.statements = stmts if stmts else []
self.network = NiceCXNetwork()
self.network.set_network_attribute(
'name', (network_name if network_name else 'indra_assembled'))
self.node_keys = {}
self.context_prefixes = {
'pubmed': 'https://identifiers.org/pubmed:',
'hgnc.symbol': 'https://identifiers.org/hgnc.symbol:'
}
def make_model(self, self_loops=False, network_attributes=None):
"""Return a Nice CX network object after running assembly.
Parameters
----------
self_loops : Optional[bool]
If False, self-loops are excluded from the network. Default: False
network_attributes : Optional[dict]
A dictionary containing attributes to be added to the
assembled network.
Returns
-------
ndex2.nice_cx_network.NiceCXNetwork
The assembled Nice CX network.
"""
for stmt in self.statements:
agents = stmt.agent_list()
not_none_agents = [a for a in agents if a is not None]
if len(not_none_agents) < 2:
continue
for a1, a2 in itertools.combinations(not_none_agents, 2):
a1_id = self.add_node(a1)
a2_id = self.add_node(a2)
if not self_loops and a1_id == a2_id:
continue
edge_id = self.add_edge(a1_id, a2_id, stmt)
self.network.set_network_attribute('@context',
json.dumps(self.context_prefixes))
if network_attributes:
for k, v in network_attributes.items():
self.network.set_network_attribute(k, v, 'string')
return self.network
def add_node(self, agent):
"""Add an Agent to the network as a node."""
agent_key = self.get_agent_key(agent)
# If the node already exists
if agent_key in self.node_keys:
return self.node_keys[agent_key]
# If the node doesn't exist yet
db_ns, db_id = agent.get_grounding()
# TODO: handle more represents name spaces
if db_ns == 'HGNC':
represents = 'hgnc.symbol:%s' % agent.name
else:
represents = None
node_id = self.network.create_node(agent.name,
node_represents=represents)
self.node_keys[agent_key] = node_id
# Add db_refs as aliases
db_refs_list = [
'%s:%s' % (db_name, db_id)
for db_name, db_id in agent.db_refs.items()
if db_name in url_prefixes
]
if db_refs_list:
self.network.add_node_attribute(property_of=node_id,
name='aliases',
values=db_refs_list,
type='list_of_string')
# Add the type of the node, inferred from grounding
if db_ns:
mapped_type = db_ns_type_mappings.get(db_ns)
if mapped_type:
self.network.add_node_attribute(property_of=node_id,
name='type',
values=mapped_type,
type='string')
return node_id
def add_edge(self, a1_id, a2_id, stmt):
"""Add a Statement to the network as an edge."""
stmt_type = stmt.__class__.__name__
edge_id = self.network.create_edge(a1_id, a2_id, stmt_type)
evs = []
for ev in stmt.evidence:
# We skip evidences with no PMID
if not ev.pmid:
continue
# We take a maximum 200 character snippet of the evidence text
if not ev.text:
ev_txt = 'Evidence text not available.'
elif len(ev.text) > 200:
ev_txt = ev.text[:200] + '...'
else:
ev_txt = ev.text
# Construct a clickable PMID link with the source and evidence text
ev_str = ('<a target="_blank" '
'href="https://identifiers.org/pubmed:%s">'
'pubmed:%s</a> (%s) %s') % (ev.pmid, ev.pmid,
ev.source_api, ev_txt)
evs.append((ev_str, 0 if ev.text is None else 1))
# Reorder to have ones with text first
evs = sorted(evs, key=lambda x: x[1], reverse=True)
# Cap at 10 pieces of evidence
evs = [e[0] for e in evs[:10]]
self.network.set_edge_attribute(edge_id,
'citation',
evs,
type='list_of_string')
return edge_id
def print_model(self):
"""Return the CX string of the assembled model."""
return self.network.to_cx()
@staticmethod
def get_agent_key(agent):
return agent.name
def get_nice_cx_network_from_clusterfile(inputfile):
"""
:param inputfile:
:return:
"""
network = NiceCXNetwork()
network.set_name('clustertocx from ' + str(os.path.basename(os.path.dirname(inputfile))))
with open(inputfile, 'r') as f:
data = f.read()
node_map = {}
protein_map = {}
for line in data.split(';'):
slist = line.split(',')
if len(slist) != 3:
sys.stderr.write(line + ' does not have appropriate number of columns. skipping\n')
continue
if slist[2].startswith('c-c'):
target_is_protein = False
else:
target_is_protein = True
if slist[0] not in node_map:
source_node_id = network.create_node(slist[0])
node_map[slist[0]] = source_node_id
network.add_node_attribute(property_of=source_node_id, name='suid', values=int(slist[0]), type='long')
network.add_node_attribute(property_of=source_node_id, name='type', values='term', type='string')
else:
source_node_id = node_map[slist[0]]
if target_is_protein:
if slist[0] not in protein_map:
protein_map[slist[0]] = set()
protein_map[slist[0]].add(slist[1])
else:
if slist[1] not in protein_map[slist[0]]:
protein_map[slist[0]].add(slist[1])
else:
target_node_id = network.create_node(slist[1])
network.create_edge(source_node_id, target_node_id, 'Child-Parent')
network.add_node_attribute(property_of=target_node_id, name='suid', values=int(slist[1]), type='long')
network.add_node_attribute(property_of=target_node_id, name='type', values='term', type='string')
node_map[slist[1]] = target_node_id
for nodename in protein_map:
genelist = protein_map[nodename]
if len(genelist) > 0:
genesymbol_list = []
for entry in genelist:
genesymbol_list.append(entry)
network.add_node_attribute(property_of=node_map[nodename], name='member', values=genesymbol_list,
type='list_of_string')
network.add_node_attribute(property_of=node_map[nodename], name='type', values='complex', type='string',
overwrite=True)
del node_map
del protein_map
return network
# #### set_node_attribute(node, attribute_name, values, type=None, subnetwork=None)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
node_id = NiceCX_creatures.create_node("new node")
NiceCX_creatures.set_node_attribute(node_id, "new attribute",
"new attribute value is xxxx")
# #### *add_node_attribute(node, attribute_name, values)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
node_id = NiceCX_creatures.create_node("new node")
NiceCX_creatures.add_node_attribute(node_id, "new attribute",
"new attribute value is xxxx")
# #### get_node_attribute(node, attribute_name, subnetwork=None)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
node_id = NiceCX_creatures.create_node("new node")
NiceCX_creatures.set_node_attribute(node_id, "new attribute",
"new attribute value is nnnn")
NiceCX_creatures.get_node_attribute(node_id, "new attribute")
# ##### get_node_attribute_objects(node, attribute_name)
# In[ ]:
graph_id_manager = GraphIdManager()
for gpml_node in dom.findall("ns3:Group", NAMESPACES):
# add_cx_node_from_gpml(cx_network, gpml_node)
group_id = gpml_node.get("GroupId")
graph_id = gpml_node.get("GraphId")
if graph_id is None:
graph_id = graph_id_manager.generate_and_record()
cx_node = cx_network.create_node(node_name=graph_id)
entities_by_id[graph_id] = cx_node
group_id_to_entity_id[group_id] = cx_node
# TODO: some GPML elements have default ShapeType of Rectangle, but
# the default Shape for CX is Ellipse.
cx_network.add_node_attribute(property_of=cx_node,
name="Shape",
values="Rectangle")
# text_label = gpml_node.get("TextLabel")
# if text_label:
# cx_network.add_node_attribute(
# property_of=cx_node, name="shared name", values=text_label
# )
for name, value in sorted(gpml_node.items()):
kv = process_kv(name, value)
cx_network.add_node_attribute(property_of=cx_node,
name=kv["key"],
values=kv["value"])
for gpml_node in dom.findall("ns3:DataNode", NAMESPACES):
add_cx_node_from_gpml(cx_network, gpml_node)
