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 create_nice_cx_from_server(server=None,
username=None,
password=None,
uuid=None):
"""
Create a NiceCXNetwork based on a network retrieved from NDEx, specified by its UUID.
If the network is not public, then username and password arguments for an account on
the server with permission to access the network must be supplied.
:param server: the URL of the NDEx server hosting the network.
:param username: the user name of an account with permission to access the network.
:param password: the password of an account with permission to access the network.
:param uuid: the UUID of the network.
:return: NiceCXNetwork
"""
if server and uuid:
my_nicecx = NiceCXNetwork()
# ===================
# METADATA
# ===================
available_aspects = []
md_aspect_iter = my_nicecx.get_aspect(uuid, 'metaData', server,
username, password)
if md_aspect_iter:
for ae in (o for o in md_aspect_iter):
available_aspects.append(ae.get(CX_CONSTANTS.METADATA_NAME))
mde = MetaDataElement(cx_fragment=ae)
my_nicecx.add_metadata(mde)
else:
if not username or not password:
raise Exception(
'Network is not available. Username and/or password not supplied'
)
else:
raise Exception('Network not available')
opaque_aspects = set(available_aspects).difference(known_aspects_min)
# ====================
# NETWORK ATTRIBUTES
# ====================
if 'networkAttributes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'networkAttributes', server,
username, password)
for network_item in objects:
my_nicecx.add_network_attribute(json_obj=network_item)
my_nicecx.add_metadata_stub('networkAttributes')
# ===================
# @CONTEXT
# ===================
if '@context' in available_aspects:
objects = my_nicecx.get_aspect(uuid, '@context', server, username,
password)
my_nicecx.set_context(objects)
if (my_nicecx.metadata.get('@context') is None):
my_nicecx.add_metadata_stub('@context')
else:
my_nicecx.metadata.get('@context').set_element_count(1)
# ===================
# NODES
# ===================
if 'nodes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'nodes', server, username,
password)
for node_item in objects:
my_nicecx.create_node(cx_fragment=node_item)
my_nicecx.add_metadata_stub('nodes')
# ===================
# EDGES
# ===================
if 'edges' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edges', server, username,
password)
for edge_item in objects:
my_nicecx.create_edge(cx_fragment=edge_item)
my_nicecx.add_metadata_stub('edges')
# ===================
# NODE ATTRIBUTES
# ===================
if 'nodeAttributes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'nodeAttributes', server,
username, password)
for att in objects:
# my_nicecx.set_node_attribute(att.get('po'), att.get('n'), att.get('v'), type=att.get('d'))
node_attribute_element = NodeAttributesElement(cx_fragment=att)
my_nicecx.nodeAttributeHeader.add(
node_attribute_element.get_name())
nodeAttrs = my_nicecx.nodeAttributes.get(
node_attribute_element.get_property_of())
if nodeAttrs is None:
nodeAttrs = []
my_nicecx.nodeAttributes[
node_attribute_element.get_property_of()] = nodeAttrs
nodeAttrs.append(node_attribute_element)
my_nicecx.add_metadata_stub('nodeAttributes')
# ===================
# EDGE ATTRIBUTES
# ===================
if 'edgeAttributes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edgeAttributes', server,
username, password)
for att in objects:
edge_attribute_element = EdgeAttributesElement(cx_fragment=att)
my_nicecx.edgeAttributeHeader.add(
edge_attribute_element.get_name())
edge_attrs = my_nicecx.edgeAttributes.get(att.get('po'))
if edge_attrs is None:
edge_attrs = []
my_nicecx.edgeAttributes[
edge_attribute_element.get_property_of()] = edge_attrs
edge_attrs.append(edge_attribute_element)
my_nicecx.add_metadata_stub('edgeAttributes')
# ===================
# CITATIONS
# ===================
if 'citations' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'citations', server, username,
password)
for cit in objects:
aspect_element = AspectElement(cit, 'citations')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('citations')
# ===================
# SUPPORTS
# ===================
if 'supports' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'supports', server, username,
password)
for sup in objects:
aspect_element = AspectElement(sup, 'supports')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('supports')
# ===================
# EDGE SUPPORTS
# ===================
if 'edgeSupports' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edgeSupports', server,
username, password)
for add_this_edge_sup in objects:
aspect_element = AspectElement(add_this_edge_sup,
'edgeSupports')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('edgeSupports')
# ===================
# NODE CITATIONS
# ===================
if 'nodeCitations' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'nodeCitations', server,
username, password)
for node_cit in objects:
aspect_element = AspectElement(node_cit, 'nodeCitations')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('nodeCitations')
# ===================
# EDGE CITATIONS
# ===================
if 'edgeCitations' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edgeCitations', server,
username, password)
for edge_cit in objects:
aspect_element = AspectElement(edge_cit, 'edgeCitations')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('edgeCitations')
# ===================
# OPAQUE ASPECTS
# ===================
for oa in opaque_aspects:
objects = my_nicecx.get_aspect(uuid, oa, server, username,
password)
for oa_item in objects:
aspect_element = AspectElement(oa_item, oa)
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub(oa)
else:
raise Exception('Server and uuid not specified')
return my_nicecx
def create_nice_cx_from_cx(cx):
"""
Create a NiceCXNetwork from a CX list.
:param cx: a list in CX format
:return: NiceCXNetwork
"""
my_nicecx = NiceCXNetwork()
if cx:
# ===================
# METADATA
# ===================
available_aspects = []
for ae in (
o
for o in my_nicecx.get_frag_from_list_by_key(cx, 'metaData')):
available_aspects.append(ae.get(CX_CONSTANTS.METADATA_NAME))
mde = MetaDataElement(cx_fragment=ae)
my_nicecx.add_metadata(mde)
opaque_aspects = set(available_aspects).difference(known_aspects_min)
# ====================
# NETWORK ATTRIBUTES
# ====================
if 'networkAttributes' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(
cx, 'networkAttributes')
for network_item in objects:
add_this_network_attribute = NetworkAttributesElement(
cx_fragment=network_item)
my_nicecx.add_network_attribute(
network_attribute_element=add_this_network_attribute)
my_nicecx.add_metadata_stub('networkAttributes')
# ===================
# NODES
# ===================
if 'nodes' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'nodes')
for node_item in objects:
my_nicecx.create_node(cx_fragment=node_item)
my_nicecx.add_metadata_stub('nodes')
# ===================
# EDGES
# ===================
if 'edges' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'edges')
for edge_item in objects:
my_nicecx.create_edge(cx_fragment=edge_item)
my_nicecx.add_metadata_stub('edges')
# ===================
# NODE ATTRIBUTES
# ===================
if 'nodeAttributes' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'nodeAttributes')
for att in objects:
# my_nicecx.set_node_attribute(None, None, None, cx_fragment=att)
node_attribute_element = NodeAttributesElement(cx_fragment=att)
my_nicecx.nodeAttributeHeader.add(
node_attribute_element.get_name())
nodeAttrs = my_nicecx.nodeAttributes.get(
node_attribute_element.get_property_of())
if nodeAttrs is None:
nodeAttrs = []
my_nicecx.nodeAttributes[
node_attribute_element.get_property_of()] = nodeAttrs
nodeAttrs.append(node_attribute_element)
my_nicecx.add_metadata_stub('nodeAttributes')
# ===================
# EDGE ATTRIBUTES
# ===================
if 'edgeAttributes' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'edgeAttributes')
for att in objects:
#my_nicecx.set_edge_attribute(None, None, None, cx_fragment=att)
edge_attribute_element = EdgeAttributesElement(cx_fragment=att)
my_nicecx.edgeAttributeHeader.add(
edge_attribute_element.get_name())
edge_attrs = my_nicecx.edgeAttributes.get(att.get('po'))
if edge_attrs is None:
edge_attrs = []
my_nicecx.edgeAttributes[
edge_attribute_element.get_property_of()] = edge_attrs
edge_attrs.append(edge_attribute_element)
my_nicecx.add_metadata_stub('edgeAttributes')
# ===================
# CITATIONS
# ===================
if 'citations' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'citations')
for cit in objects:
aspect_element = AspectElement(cit, 'citations')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('citations')
# ===================
# SUPPORTS
# ===================
if 'supports' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'supports')
for sup in objects:
aspect_element = AspectElement(sup, 'supports')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('supports')
# ===================
# EDGE SUPPORTS
# ===================
if 'edgeSupports' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'edgeSupports')
for add_this_edge_sup in objects:
aspect_element = AspectElement(add_this_edge_sup,
'edgeSupports')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('edgeSupports')
# ===================
# NODE CITATIONS
# ===================
if 'nodeCitations' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'nodeCitations')
for node_cit in objects:
aspect_element = AspectElement(node_cit, 'nodeCitations')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('nodeCitations')
# ===================
# EDGE CITATIONS
# ===================
if 'edgeCitations' in available_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, 'edgeCitations')
for edge_cit in objects:
aspect_element = AspectElement(edge_cit, 'edgeCitations')
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub('edgeCitations')
# ===================
# OPAQUE ASPECTS
# ===================
for oa in opaque_aspects:
objects = my_nicecx.get_frag_from_list_by_key(cx, oa)
for oa_item in objects:
aspect_element = AspectElement(oa_item, oa)
my_nicecx.add_opaque_aspect_element(aspect_element)
my_nicecx.add_metadata_stub(oa)
return my_nicecx
else:
raise Exception('CX is empty')
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)
def create_nice_cx_from_server(server=None,
username=None,
password=None,
uuid=None):
if server and uuid:
my_nicecx = NiceCXNetwork()
#===================
# METADATA
#===================
available_aspects = []
md_aspect_iter = my_nicecx.get_aspect(uuid, 'metaData', server,
username, password)
if md_aspect_iter:
for ae in (o for o in md_aspect_iter):
available_aspects.append(ae.get(CX_CONSTANTS.METADATA_NAME))
mde = MetaDataElement(cx_fragment=ae)
my_nicecx.add_metadata(mde)
else:
if not username or not password:
raise Exception(
'Network is not available. Username and/or password not supplied'
)
else:
raise Exception('Network not available')
opaque_aspects = set(available_aspects).difference(known_aspects_min)
#====================
# NETWORK ATTRIBUTES
#====================
if 'networkAttributes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'networkAttributes', server,
username, password)
for network_item in objects:
my_nicecx.add_network_attribute(json_obj=network_item)
my_nicecx.add_metadata_stub('networkAttributes')
#===================
# NODES
#===================
if 'nodes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'nodes', server, username,
password)
for node_item in objects:
my_nicecx.create_node(cx_fragment=node_item)
my_nicecx.add_metadata_stub('nodes')
#===================
# EDGES
#===================
if 'edges' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edges', server, username,
password)
for edge_item in objects:
my_nicecx.create_edge(cx_fragment=edge_item)
my_nicecx.add_metadata_stub('edges')
#===================
# NODE ATTRIBUTES
#===================
if 'nodeAttributes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'nodeAttributes', server,
username, password)
for att in objects:
#my_nicecx.set_node_attribute(att.get('po'), att.get('n'), att.get('v'), type=att.get('d'))
node_attribute_element = NodeAttributesElement(cx_fragment=att)
my_nicecx.nodeAttributeHeader.add(
node_attribute_element.get_name())
nodeAttrs = my_nicecx.nodeAttributes.get(
node_attribute_element.get_property_of())
if nodeAttrs is None:
nodeAttrs = []
my_nicecx.nodeAttributes[
node_attribute_element.get_property_of()] = nodeAttrs
nodeAttrs.append(node_attribute_element)
my_nicecx.add_metadata_stub('nodeAttributes')
#===================
# EDGE ATTRIBUTES
#===================
if 'edgeAttributes' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edgeAttributes', server,
username, password)
for att in objects:
edge_attribute_element = EdgeAttributesElement(cx_fragment=att)
my_nicecx.edgeAttributeHeader.add(
edge_attribute_element.get_name())
edge_attrs = my_nicecx.edgeAttributes.get(att.get('po'))
if edge_attrs is None:
edge_attrs = []
my_nicecx.edgeAttributes[
edge_attribute_element.get_property_of()] = edge_attrs
edge_attrs.append(edge_attribute_element)
my_nicecx.add_metadata_stub('edgeAttributes')
#===================
# CITATIONS
#===================
if 'citations' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'citations', server, username,
password)
for cit in objects:
aspect_element = AspectElement(cit, 'citations')
my_nicecx.add_opaque_aspect(aspect_element)
my_nicecx.add_metadata_stub('citations')
#===================
# SUPPORTS
#===================
if 'supports' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'supports', server, username,
password)
for sup in objects:
aspect_element = AspectElement(sup, 'supports')
my_nicecx.add_opaque_aspect(aspect_element)
my_nicecx.add_metadata_stub('supports')
#===================
# EDGE SUPPORTS
#===================
if 'edgeSupports' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edgeSupports', server,
username, password)
for add_this_edge_sup in objects:
aspect_element = AspectElement(add_this_edge_sup,
'edgeSupports')
my_nicecx.add_opaque_aspect(aspect_element)
my_nicecx.add_metadata_stub('edgeSupports')
#===================
# NODE CITATIONS
#===================
if 'nodeCitations' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'nodeCitations', server,
username, password)
for node_cit in objects:
aspect_element = AspectElement(node_cit, 'nodeCitations')
my_nicecx.add_opaque_aspect(aspect_element)
my_nicecx.add_metadata_stub('nodeCitations')
#===================
# EDGE CITATIONS
#===================
if 'edgeCitations' in available_aspects:
objects = my_nicecx.get_aspect(uuid, 'edgeCitations', server,
username, password)
for edge_cit in objects:
aspect_element = AspectElement(edge_cit, 'edgeCitations')
my_nicecx.add_opaque_aspect(aspect_element)
my_nicecx.add_metadata_stub('edgeCitations')
#===================
# OPAQUE ASPECTS
#===================
for oa in opaque_aspects:
objects = my_nicecx.get_aspect(uuid, oa, server, username,
password)
for oa_item in objects:
aspect_element = AspectElement(oa_item, oa)
my_nicecx.add_opaque_aspect(aspect_element)
my_nicecx.add_metadata_stub(oa)
else:
raise Exception('Server and uuid not specified')
return my_nicecx