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_nice_cx_from_networkx(G):
"""
Create a NiceCXNetwork based on a networkx graph. The resulting NiceCXNetwork
contains the nodes edges and their attributes from the networkx graph and also
preserves the graph 'pos' attribute as a CX cartesian coordinates aspect.
:param G: networkx graph
:type G: networkx graph
:return: NiceCXNetwork
:rtype: NiceCXNetwork
"""
if G is None:
raise Exception('Networkx input is empty')
my_nicecx = NiceCXNetwork()
if G.graph.get('name'):
my_nicecx.set_name(G.graph.get('name'))
else:
my_nicecx.set_name('created from networkx')
my_nicecx.add_metadata_stub('networkAttributes')
for n, d in G.nodes_iter(data=True):
# =============
# ADD NODES
# =============
if d and d.get('name'):
my_nicecx.create_node(id=n,
node_name=d.get('name'),
node_represents=d.get('name'))
else:
my_nicecx.create_node(id=n, node_name=n, node_represents=n)
# ======================
# ADD NODE ATTRIBUTES
# ======================
for k, v in d.items():
attr_type = None
if isinstance(v, float):
attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
elif isinstance(v, int):
attr_type = ATTRIBUTE_DATA_TYPE.INTEGER
my_nicecx.set_node_attribute(n, k, v, type=attr_type)
index = 0
for u, v, d in G.edges_iter(data=True):
# =============
# ADD EDGES
# =============
my_nicecx.create_edge(id=index,
edge_source=u,
edge_target=v,
edge_interaction=d.get('interaction'))
# ==============================
# ADD EDGE ATTRIBUTES
# ==============================
for k, val in d.items():
if k != 'interaction':
attr_type = None
if isinstance(val, float):
attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
elif isinstance(val, int):
attr_type = ATTRIBUTE_DATA_TYPE.INTEGER
my_nicecx.set_edge_attribute(index, k, val, type=attr_type)
index += 1
my_nicecx.add_metadata_stub('nodes')
my_nicecx.add_metadata_stub('edges')
if my_nicecx.nodeAttributes:
my_nicecx.add_metadata_stub('nodeAttributes')
if my_nicecx.edgeAttributes:
my_nicecx.add_metadata_stub('edgeAttributes')
if hasattr(G, 'pos'):
aspect = _create_cartesian_coordinates_aspect_from_networkx(G)
my_nicecx.add_opaque_aspect('cartesianLayout', aspect)
my_nicecx.add_metadata_stub('cartesianLayout')
return my_nicecx
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
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(aspect_element)
return niceCx
else:
raise Exception('Server and uuid not specified')
def create_nice_cx_from_cx(cx):
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(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(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(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(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(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(aspect_element)
my_nicecx.add_metadata_stub(oa)
return my_nicecx
else:
raise Exception('CX is empty')
