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 query_network(self, uuid, search_string, max_edges):
myConst = CX_CONSTANTS
niceCx = NiceCXNetwork()
#uuid = '7246d8cf-c644-11e6-b48c-0660b7976219'
search_terms_dict = {k:1 for k in search_string.split(',')}
solr = pysolr.Solr(solr_url + uuid + '/', timeout=10)
try:
results = solr.search(search_string, rows=10000)
#search_terms_array = [int(n['id']) for n in results.docs]
search_terms_array = {int(n['id']):1 for n in results.docs}
if(not search_terms_array):
return {'message': 'No nodes found'}
print('starting nodes 1')
#===================
# METADATA
#===================
available_aspects = []
for ae in (o for o in self.stream_aspect(uuid, 'metaData')):
available_aspects.append(ae.get(CX_CONSTANTS.METADATA_NAME))
mde = MetaDataElement(json_obj=ae)
niceCx.add_metadata(mde)
#available_aspects = ['edges', 'nodes'] # TODO - remove this
opaque_aspects = set(available_aspects).difference(known_aspects_min)
print(opaque_aspects)
#===================
# NODES
#===================
if 'nodes' in available_aspects:
for ae in (o for o in self.stream_aspect(uuid, 'nodes')):
if search_terms_array.get(ae.get(CX_CONSTANTS.ID)):
add_this_node = NodeElement(cx_fragment=ae)
niceCx.create_node(add_this_node)
else:
raise Exception('Network does not contain any nodes. Cannot query')
print('starting edges 1')
#===================
# EDGES
#===================
edge_count = 0
added_edges = 0
start_time = time.time()
if 'edges' in available_aspects:
for ae in (o for o in self.stream_aspect(uuid, 'edges')):
if niceCx.nodes.get(ae.get(CX_CONSTANTS.EDGE_SOURCE_NODE_ID_OR_SUBNETWORK)) is not None or niceCx.nodes.get(ae.get(CX_CONSTANTS.EDGE_TARGET_NODE_ID)) is not None:
add_this_edge = EdgeElement(cx_fragment=ae)
niceCx.create_edge(add_this_edge)
added_edges += 1
if edge_count % 5000 == 0:
print(edge_count)
#if edge_count > 30000:
# break
if added_edges > max_edges:
raise StopIteration('Max edges reached')
edge_count += 1
else:
raise Exception('Network does not contain any nodes. Cannot query')
print('Response time (Edge search): ' + str(time.time() - start_time))
print('starting nodes 2')
#===================
# NODES
#===================
for ae in (o for o in self.stream_aspect(uuid, 'nodes')):
if niceCx.get_missing_nodes().get(ae.get(CX_CONSTANTS.ID)):
add_this_node = NodeElement(cx_fragment=ae)
niceCx.create_node(add_this_node)
#====================
# NETWORK ATTRIBUTES
#====================
if 'networkAttributes' in available_aspects:
for ae in (o for o in self.stream_aspect(uuid, 'networkAttributes')):
add_this_network_attribute = NetworkAttributesElement(cx_fragment=ae)
niceCx.add_network_attribute(add_this_network_attribute)
#===================
# NODE ATTRIBUTES
#===================
if 'nodeAttributes' in available_aspects:
for ae in (o for o in self.stream_aspect(uuid, 'nodeAttributes')):
if niceCx.nodes.get(ae.get(CX_CONSTANTS.PROPERTY_OF)):
add_this_node_att = NodeAttributesElement(json_obj=ae)
niceCx.add_node_attribute(add_this_node_att)
#===================
# EDGE ATTRIBUTES
#===================
if 'edgeAttributes' in available_aspects:
for ae in (o for o in self.stream_aspect(uuid, 'edgeAttributes')):
if niceCx.edges.get(ae.get(CX_CONSTANTS.PROPERTY_OF)):
add_this_edge_att = EdgeAttributesElement(json_obj=ae)
niceCx.set_edge_attribute()
#===================
# NODE CITATIONS
#===================
if 'nodeCitations' in available_aspects:
for ae in (o for o in self.stream_aspect(uuid, 'nodeCitations')):
for e_po in ae.get(CX_CONSTANTS.PROPERTY_OF):
if niceCx.get_nodes().get(e_po) is not None:
niceCx.add_node_citations_from_cx(ae)
#===================
# EDGE CITATIONS
#===================
ec_count = 0
if 'edgeCitations' in available_aspects:
for ae in (o for o in self.stream_aspect(uuid, 'edgeCitations')):
for e_po in ae.get(CX_CONSTANTS.PROPERTY_OF):
if niceCx.get_edges().get(e_po) is not None:
niceCx.add_edge_citations_from_cx(ae)
ec_count += 1
if ec_count % 500 == 0:
print(ec_count)
#===================
# CITATIONS
#===================
if 'citations' in available_aspects:
#======================================================
# FILTER CITATIONS IF THERE ARE EDGE OR NODE CITATIONS
# OTHERWISE ADD THEM ALL (NO-FILTER) -- TODO
#======================================================
for ae in (o for o in self.stream_aspect(uuid, 'citations')):
add_this_citation = CitationElement(cx_fragment=ae)
niceCx.add_citation(add_this_citation)
#===================
# OPAQUE ASPECTS
#===================
for oa in opaque_aspects:
objects = self.stream_aspect(uuid, oa)
obj_items = (o for o in objects)
for oa_item in obj_items:
aspect_element = AspectElement(oa_item, oa)
niceCx.add_opaque_aspect(aspect_element)
except SolrError as se:
if('404' in se.message):
ndex2.get_logger('SOLR').warning('Network not found ' + self.uuid + ' on ' + solr_url + ' server.')
raise Exception("Network not found (SOLR)")
else:
ndex2.get_logger('SOLR').warning('Network error ' + self.uuid + ' on ' + solr_url + ' server. ' + se.message)
raise Exception(se.message)
except StopIteration as si:
ndex2.get_logger('QUERY').warning("Found more than max edges. Raising exception")
raise StopIteration(si.message)
#nice_cx_json = niceCx.to_cx()
return niceCx
def create_from_server(self, server, username, password, uuid):
if server and uuid:
niceCx = NiceCXNetwork()
#===================
# METADATA
#===================
available_aspects = []
for ae in (o for o in self.stream_aspect(uuid, 'metaData')):
available_aspects.append(ae.get(CX_CONSTANTS.METADATA_NAME))
mde = MetaDataElement(json_obj=ae)
niceCx.add_metadata(mde)
#available_aspects = ['edges', 'nodes'] # TODO - remove this
opaque_aspects = set(available_aspects).difference(known_aspects_min)
print(opaque_aspects)
#====================
# NETWORK ATTRIBUTES
#====================
objects = self.stream_aspect(uuid, 'networkAttributes')
obj_items = (o for o in objects)
for network_item in obj_items:
add_this_network_attribute = NetworkAttributesElement(cx_fragment=network_item)
niceCx.add_network_attribute(add_this_network_attribute)
#===================
# NODES
#===================
objects = self.stream_aspect(uuid, 'nodes')
obj_items = (o for o in objects)
for node_item in obj_items:
add_this_node = NodeElement(cx_fragment=node_item)
niceCx.create_node(add_this_node)
#===================
# EDGES
#===================
objects = self.stream_aspect(uuid, 'edges')
obj_items = (o for o in objects)
for edge_item in obj_items:
add_this_edge = EdgeElement(cx_fragment=edge_item)
niceCx.create_edge(add_this_edge)
#===================
# NODE ATTRIBUTES
#===================
objects = self.stream_aspect(uuid, 'nodeAttributes')
obj_items = (o for o in objects)
for att in obj_items:
add_this_node_att = NodeAttributesElement(json_obj=att)
niceCx.add_node_attribute(add_this_node_att)
#===================
# EDGE ATTRIBUTES
#===================
objects = self.stream_aspect(uuid, 'edgeAttributes')
obj_items = (o for o in objects)
for att in obj_items:
add_this_edge_att = EdgeAttributesElement(json_obj=att)
niceCx.add_edge_attribute(add_this_edge_att)
#===================
# CITATIONS
#===================
objects = self.stream_aspect(uuid, 'citations')
obj_items = (o for o in objects)
for cit in obj_items:
add_this_citation = CitationElement(cx_fragment=cit)
niceCx.add_citation(add_this_citation)
#===================
# SUPPORTS
#===================
objects = self.stream_aspect(uuid, 'supports')
obj_items = (o for o in objects)
for sup in obj_items:
add_this_supports = SupportElement(cx_fragment=sup)
niceCx.add_support(add_this_supports)
#===================
# NODE CITATIONS
#===================
objects = self.stream_aspect(uuid, 'nodeCitations')
obj_items = (o for o in objects)
for node_cit in obj_items:
niceCx.add_node_citations_from_cx(node_cit)
#===================
# EDGE CITATIONS
#===================
objects = self.stream_aspect(uuid, 'edgeCitations')
obj_items = (o for o in objects)
for edge_cit in obj_items:
niceCx.add_edge_citations_from_cx(edge_cit)
#===================
# OPAQUE ASPECTS
#===================
for oa in opaque_aspects:
objects = self.stream_aspect(uuid, oa)
obj_items = (o for o in objects)
for oa_item in obj_items:
aspect_element = AspectElement(oa_item, oa)
niceCx.add_opaque_aspect_element(aspect_element)
return niceCx
else:
raise Exception('Server and uuid not specified')
def test_nice_cx_model(self):
niceCx = NiceCXNetwork()
#main_map = NdexGraph(server='http://dev2.ndexbio.org', username='******', password='******', uuid='7246d8cf-c644-11e6-b48c-0660b7976219')
uuid = '6b968fd2-02a4-11e6-b550-06603eb7f303'
#====================
# NETWORK QUERY
#====================
networkQuery = NetworkQuery()
networkQuery.query_network('40f1def0-3aa4-11e7-b12f-0660b7976219',
'HSPA5,HSPA4')
my_na = NodeAttributesElement(
subnetwork=1,
property_of=11,
name=22,
values=33,
type=ATTRIBUTE_DATA_TYPE.convert_to_data_type('string'))
#====================
# NETWORK ATTRIBUTES
#====================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/nodes'), 'item')
objects = loadAspect('networkAttributes')
obj_items = (o for o in objects)
for network_item in obj_items:
add_this_network_attribute = NetworkAttributesElement(
cx_fragment=network_item)
niceCx.add_network_attribute(add_this_network_attribute)
#===================
# NODES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/nodes'), 'item')
objects = loadAspect('nodes')
obj_items = (o for o in objects)
for node_item in obj_items:
add_this_node = NodeElement(json_obj=node_item)
niceCx.create_node(add_this_node)
#===================
# EDGES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/edges'), 'item')
objects = loadAspect('edges')
obj_items = (o for o in objects)
for edge_item in obj_items:
add_this_edge = EdgeElement(json_obj=edge_item)
niceCx.create_edge(add_this_edge)
#===================
# NODE ATTRIBUTES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/nodeAttributes'), 'item')
objects = loadAspect('nodeAttributes')
obj_items = (o for o in objects)
for att in obj_items:
add_this_node_att = NodeAttributesElement(json_obj=att)
niceCx.add_node_attribute(add_this_node_att)
#===================
# EDGE ATTRIBUTES
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/edgeAttributes'), 'item')
objects = loadAspect('edgeAttributes')
obj_items = (o for o in objects)
for att in obj_items:
add_this_edge_att = EdgeAttributesElement(json_obj=att)
niceCx.add_edge_attribute(add_this_edge_att)
#===================
# CITATIONS
#===================
#objects = ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/edgeAttributes'), 'item')
objects = loadAspect('citations')
obj_items = (o for o in objects)
for cit in obj_items:
add_this_citation = CitationElement(cx_fragment=cit)
niceCx.add_citation(add_this_citation)
#===================
# SUPPORTS
#===================
objects = loadAspect('supports')
obj_items = (o for o in objects)
for sup in obj_items:
add_this_supports = SupportElement(cx_fragment=sup)
niceCx.add_support(add_this_supports)
#===================
# NODE CITATIONS
#===================
objects = loadAspect('nodeCitations')
obj_items = (o for o in objects)
for node_cit in obj_items:
niceCx.add_node_citations_from_cx(node_cit)
#===================
# EDGE CITATIONS
#===================
objects = loadAspect('edgeCitations')
obj_items = (o for o in objects)
for edge_cit in obj_items:
niceCx.add_edge_citations_from_cx(edge_cit)
nice_cx_json = niceCx.to_cx()
# serialized = pickle.dumps(niceCx, protocol=0)
# print 'Serialized memory:', sys.getsizeof(serialized)
print('starting to_pandas_dataframe')
niceCx.to_pandas_dataframe()
parser = ijson.parse(
urlopen('http://dev2.ndexbio.org/v2/network/' + uuid +
'/aspect/nodes'))
node_id, node_n, node_r = '', '', ''
edge_id, edge_s, edge_t, edge_i = '', '', '', ''
node_matches = {}
edge_matches = {}
edge_connected = {}
node_found = False
edge_found = False
count = 0
done_searching = False
start_time = time.time()
for prefix, event, value in parser:
if (prefix) == ('item.@id'):
if count % 10000 == 0:
print(count)
count += 1
node_id = value
elif (prefix) == ('item.n'):
node_n = value
node_found = True
elif (prefix) == ('item.r'):
node_r = value
if node_found:
node_matches[node_id] = {'n': node_n, 'r': node_r}
add_this_node = NodeElement(id=node_id,
node_name=node_n,
node_represents=node_r)
niceCx.create_node(add_this_node)
node_found = False
else:
# No represents found
if node_found:
node_matches[node_id] = {'n': node_n}
add_this_node = NodeElement(id=node_id, node_name=node_n)
niceCx.create_node(add_this_node)
node_found = False
print('Response time (Node search): ' + str(time.time() - start_time))
start_time = time.time()
print(edge_matches)
print(node_matches)
parser = ijson.parse(
urlopen('http://dev2.ndexbio.org/v2/network/' + uuid +
'/aspect/edges'))
for prefix, event, value in parser:
if (prefix) == ('item.@id'):
edge_id = value
elif (prefix) == ('item.s'):
edge_s = value
edge_found = True
elif (prefix) == ('item.t'):
edge_t = value
edge_found = True
elif (prefix) == ('item.i'):
edge_i = value
if edge_found:
edge_matches[edge_id] = {
's': edge_s,
't': edge_t,
'i': edge_i
}
add_this_edge = EdgeElement(id=edge_id,
edge_source=edge_s,
edge_target=edge_t,
edge_interaction=edge_i)
niceCx.create_edge(add_this_edge)
edge_connected[edge_s] = 1
edge_connected[edge_t] = 1
edge_found = False
else:
# No interaction found
if edge_found:
edge_matches[edge_id] = {'s': edge_s, 't': edge_t}
add_this_edge = EdgeElement(id=edge_id,
edge_source=edge_s,
edge_target=edge_t)
niceCx.create_edge(add_this_edge)
edge_connected[edge_s] = 1
edge_connected[edge_t] = 1
edge_found = False
print('Response time (Edge search): ' + str(time.time() - start_time))
start_time = time.time()
print(edge_matches)
print(node_matches)
self.assertTrue(niceCx is not None)
