def test_context(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test")
niceCx_creatures.create_node(node_name="Fox")
try:
self.assertRaises(Exception, niceCx_creatures.set_context("hkjhnk"))
except Exception as e:
print('Bad context exception was caught')
def test_context(self):
niceCx_creatures = NiceCXNetwork()
niceCx_creatures.set_name("Test")
niceCx_creatures.create_node(node_name="Fox")
try:
self.assertRaises(Exception, niceCx_creatures.set_context("hkjhnk"))
except Exception as e:
print('Bad context exception was caught')
class NiceCXBuilder(object):
def __init__(self, cx=None, server=None, username='******', password='******', uuid=None, networkx_G=None, data=None, **attr):
from ndex2.nice_cx_network import NiceCXNetwork
self.nice_cx = NiceCXNetwork(user_agent='niceCx Builder')
self.node_id_lookup = {}
self.node_id_counter = 0
self.edge_id_counter = 0
self.node_inventory = {}
self.node_attribute_inventory = []
self.node_attribute_map = {}
self.edge_inventory = {}
self.edge_attribute_inventory = []
self.edge_attribute_map = {}
self.opaque_aspect_inventory = []
self.context_inventory = []
self.network_attribute_inventory = {}
self.user_base64 = None
self.username = None
self.password = None
if username and password:
self.username = username
self.password = password
if sys.version_info.major == 3:
encode_string = '%s:%s' % (username, password)
byte_string = encode_string.encode()
self.user_base64 = base64.b64encode(byte_string)#.replace('\n', '')
else:
self.user_base64 = base64.encodestring('%s:%s' % (username, password)).replace('\n', '')
def set_context(self, context):
"""
Set the @context information of the network. This information maps namespace prefixes to their defining URIs
Example:
``set_context({'pmid': 'https://www.ncbi.nlm.nih.gov/pubmed/'})``
:param context: dict of name, URI pairs
:type context: dict
:return: None
:rtype: none
"""
if isinstance(context, dict):
self.context_inventory = context
elif isinstance(context, list):
if len(context) > 0:
self.context_inventory = context[0]
def set_name(self, network_name):
"""
Set the network name
:param network_name: Network name
:type network_name: string
:return: None
:rtype:none
"""
self.network_attribute_inventory['name'] = {'n': 'name', 'v': network_name, 'd': 'string'}
def add_network_attribute(self, name=None, values=None, type=None, cx_element=None):
"""
Add an attribute to the network
:param name: Name of the attribute
:type name: str
:param values: The value(s) of the attribute
:type values: One of the allowable CX types. See `Supported data types`_
:param type: They type of data supplied in values. Default is string. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
add_this_network_attribute = {'n': name, 'v': values}
if type:
add_this_network_attribute['d'] = type
self.network_attribute_inventory[name] = add_this_network_attribute
def add_node(self, name=None, represents=None, id=None, data_type=None, map_node_ids=False):
"""
Adds a new node with the corresponding name and represents (external id)
:param node_name: Name of the node
:type node_name: str
:param represents: Representation of the node (alternate identifier)
:type represents: str
:param id:
:type id:
:return: Node ID
:rtype: int
"""
if self.node_inventory.get(name) is not None:
return self.node_inventory.get(name).get('@id')
if id:
node_id = id
else:
node_id = self.node_id_counter
self.node_id_counter += 1
add_this_node = {'@id': node_id, 'n': name}
if represents:
add_this_node['r'] = represents
if data_type:
add_this_node['d'] = data_type
self.node_inventory[name] = add_this_node
if map_node_ids:
self.node_id_lookup[name] = node_id
return node_id
def add_edge(self, source=None, target=None, interaction=None, id=None):
"""
Adds a new edge in the network by specifying source-interaction-target
:param source: The source node of this edge, either its id or the node object itself.
:type source: int, dict (with @id property)
:param target: The target node of this edge, either its id or the node object itself.
:type target: int, dict (with @id property)
:param interaction: The interaction that describes the relationship between the source and target nodes
:type interaction: str
:param id: Edge id for this edge. If none is provided the builder will create one
:type id: int
:return: Edge ID
:rtype: int
"""
if id is not None:
edge_id = id
else:
edge_id = self.edge_id_counter
self.edge_id_counter += 1
add_this_edge = {'@id': edge_id, 's': source, 't': target}
if interaction:
add_this_edge['i'] = interaction
else:
add_this_edge['i'] = 'interacts-with'
self.edge_inventory[edge_id] = add_this_edge
return edge_id
def add_node_attribute(self, property_of, name, values, type=None):
"""
Set an attribute of a node, where the node may be specified by its id or passed in as a node dict.
:param property_of: Node ID to add the attribute to
:type property_of: int
:param name: Attribute name
:type name: str
:param value: A value or list of values of the attribute
:type value: list, string, int or float
:param type: The datatype of the attribute values, defaults is string. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
if property_of is None:
raise TypeError('Node value is None')
if name is None:
raise TypeError('Property name is None')
if values is None:
raise TypeError('Attribute value is None')
add_this_node_attribute = {'po': property_of, 'n': name, 'v': values}
if self.node_attribute_map.get(property_of) is None:
self.node_attribute_map[property_of] = {}
elif self.node_attribute_map[property_of].get(name) is not None:
# TODO - Raise warning/exception for duplicate attribute
return
if type:
if type == 'float' or type == 'double':
type = 'double'
try:
if not isinstance(values, float):
add_this_node_attribute['v'] = float(values)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
if type == 'list_of_float' or type == 'list_of_double':
try:
if isinstance(values, list):
for value in values:
if not isinstance(value, float):
value = float(value)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
type = 'list_of_double'
add_this_node_attribute['d'] = type
else:
use_this_value, attr_type = self._infer_data_type(values)
add_this_node_attribute['v'] = use_this_value
add_this_node_attribute['d'] = attr_type
if add_this_node_attribute['v'] is not None:
self.node_attribute_inventory.append(add_this_node_attribute)
self.node_attribute_map[property_of][name] = True
def add_edge_attribute(self, property_of=None, name=None, values=None, type=None):
"""
Set the value(s) of attribute of an edge, where the edge may be specified by its id or passed in an object.
Example:
``set_edge_attribute(0, 'weight', 0.5, type='float')``
or
``set_edge_attribute(edge, 'Disease', 'Atherosclerosis')``
:param property_of: Edge to add the attribute to
:type property_of: int or edge dict with @id attribute
:param name: Attribute name
:type name: str
:param values: A value or list of values of the attribute
:type values: list, string, int or float
:param type: The datatype of the attribute values, defaults to the python datatype of the values. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
if property_of is None:
raise TypeError('Edge value is None')
if name is None:
raise TypeError('Property name is None')
if values is None:
raise TypeError('Attribute value is None')
add_this_edge_attribute = {'po': property_of, 'n': name, 'v': values}
if self.edge_attribute_map.get(property_of) is None:
self.edge_attribute_map[property_of] = {}
elif self.edge_attribute_map[property_of].get(name) is not None:
return
if type:
if type == 'float' or type == 'double':
type = 'double'
try:
if not isinstance(values, float):
add_this_edge_attribute['v'] = float(values)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
if type == 'list_of_float' or type == 'list_of_double':
try:
if isinstance(values, list):
for value in values:
if not isinstance(value, float):
value = float(value)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
type = 'list_of_double'
add_this_edge_attribute['d'] = type
else:
use_this_value, attr_type = self._infer_data_type(values)
add_this_edge_attribute['v'] = use_this_value
add_this_edge_attribute['d'] = attr_type
if add_this_edge_attribute['v'] is not None:
self.edge_attribute_inventory.append(add_this_edge_attribute)
self.edge_attribute_map[property_of][name] = True
def add_opaque_aspect(self, oa_name, oa_list):
self.opaque_aspect_inventory.append({oa_name: oa_list})
#===================================
# methods to add data by fragment
#===================================
def _add_network_attributes_from_fragment(self, fragment):
self.nice_cx.networkAttributes.append(fragment)
def _add_node_from_fragment(self, fragment):
self.nice_cx.nodes[fragment.get('@id')] = fragment
def _add_edge_from_fragment(self, fragment):
self.nice_cx.edges[fragment.get('@id')] = fragment
def _add_node_attribute_from_fragment(self, fragment):
if self.nice_cx.nodeAttributes.get(fragment.get('po')) is None:
self.nice_cx.nodeAttributes[fragment.get('po')] = []
self.nice_cx.nodeAttributes[fragment.get('po')].append(fragment)
def _add_edge_attribute_from_fragment(self, fragment):
if self.nice_cx.edgeAttributes.get(fragment.get('po')) is None:
self.nice_cx.edgeAttributes[fragment.get('po')] = []
self.nice_cx.edgeAttributes[fragment.get('po')].append(fragment)
def _add_citation_from_fragment(self, fragment):
self.nice_cx.citations[fragment.get('@id')] = fragment
def _add_supports_from_fragment(self, fragment):
self.nice_cx.supports[fragment.get('@id')] = fragment
def _add_edge_supports_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.edgeSupports[po_id] = fragment.get('supports')
def _add_node_citations_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.nodeCitations[po_id] = fragment.get('citations')
def _add_edge_citations_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.edgeCitations[po_id] = fragment.get('citations')
def get_nice_cx(self):
#==========================
# ADD CONTEXT
#==========================
if isinstance(self.context_inventory, dict):
self.nice_cx.set_context(self.context_inventory)
else:
for c in self.context_inventory:
self.nice_cx.set_context(c)
#=============================
# ASSEMBLE NETWORK ATTRIBUTES
#=============================
#{'n': 'name', 'v': network_name, 'd': 'string'}
for k, v in self.network_attribute_inventory.items():
self.nice_cx.add_network_attribute(name=v.get('n'), values=v.get('v'), type=v.get('d'))
#==========================
# ASSEMBLE NODES
#==========================
for k, v in self.node_inventory.items():
self.nice_cx.nodes[v.get('@id')] = v
#==========================
# ASSEMBLE NODE ATTRIBUTES
#==========================
for a in self.node_attribute_inventory:
property_of = a.get('po')
if self.nice_cx.nodeAttributes.get(property_of) is None:
self.nice_cx.nodeAttributes[property_of] = []
self.nice_cx.nodeAttributes[property_of].append(a)
#==========================
# ASSEMBLE EDGES
#==========================
for k, v in self.edge_inventory.items():
self.nice_cx.edges[k] = v
#==========================
# ASSEMBLE EDGE ATTRIBUTES
#==========================
for a in self.edge_attribute_inventory:
property_of = a.get('po')
if self.nice_cx.edgeAttributes.get(property_of) is None:
self.nice_cx.edgeAttributes[property_of] = []
self.nice_cx.edgeAttributes[property_of].append(a)
#==========================
# ASSEMBLE OPAQUE ASPECTS
#==========================
for oa in self.opaque_aspect_inventory:
for k, v in oa.items():
self.nice_cx.add_opaque_aspect(k, v)
return self.nice_cx
def get_frag_from_list_by_key(self, cx, key):
return_list = []
for aspect in cx:
if key in aspect:
if isinstance(aspect[key], list):
for a_item in aspect[key]:
return_list.append(a_item)
else:
return_list.append(aspect[key])
return return_list
def load_aspect(self, aspect_name):
#with open('Signal1.cx', mode='r') as cx_f:
with open('network1.cx', mode='r') as cx_f:
aspect_json = json.loads(cx_f.read())
for aspect in aspect_json:
if aspect.get(aspect_name) is not None:
return aspect.get(aspect_name)
def stream_all_aspects(self, uuid):
return ijson.items(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid), 'item')
def stream_aspect(self, uuid, aspect_name):
if aspect_name == 'metaData':
print('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect')
md_response = requests.get('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect')
json_respone = md_response.json()
return json_respone.get('metaData')
else:
#password_mgr = HTTPPasswordMgrWithDefaultRealm()
#top_level_url = 'http://dev2.ndexbio.org'
#password_mgr.add_password(None, top_level_url, self.username, self.password)
#handler = HTTPBasicAuthHandler(password_mgr)
#opener = build_opener(handler)
#install_opener(opener)
# Create an OpenerDirector with support for Basic HTTP Authentication...
#auth_handler = HTTPBasicAuthHandler()
#auth_handler.add_password(None, 'http://dev2.ndexbio.org', 'scratch', 'scratch')
#opener = build_opener(auth_handler)
# ...and install it globally so it can be used with urlopen.
#install_opener(opener)
request = Request('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/' + aspect_name)
base64string = base64.b64encode('%s:%s' % ('scratch', 'scratch'))
request.add_header("Authorization", "Basic %s" % base64string)
#result = urllib2.urlopen(request)
urlopen_result = None
try:
urlopen_result = urlopen(request) #'http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/' + aspect_name)
except HTTPError as e:
print(e.code)
return []
except URLError as e:
print('Other error')
print('URL Error %s' % e.message())
return []
return ijson.items(urlopen_result, 'item')
def stream_aspect_raw(self, uuid, aspect_name):
return ijson.parse(urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/' + aspect_name))
def _infer_data_type(self, val, split_string=False):
if val is None:
return None, None
attr_type = 'string'
if split_string:
if isinstance(val, str):
val = val.replace('"', '')
if ',' in val:
val = val.split(',')
elif ';' in val:
val = val.split(';')
processed_value = val
if isinstance(val, float) or isinstance(val, np.float) or isinstance(val, np.double):
if math.isnan(val):
# do something (skip?)
processed_value = None
elif math.isinf(val):
processed_value = 'INFINITY'
attr_type = 'double' # CX spec dropped support for float and instead uses double precision
elif isinstance(val, int) or isinstance(val, np.int):
attr_type = 'integer'
elif isinstance(val, list):
if len(val) > 0:
if isinstance(val[0], float) or isinstance(val[0], np.float) or isinstance(val[0], np.double):
attr_type = 'list_of_double'
elif isinstance(val[0], int) or isinstance(val[0], np.int):
attr_type = 'list_of_integer'
else:
attr_type = 'list_of_string'
return processed_value, attr_type
class NiceCXBuilder(object):
def __init__(self,
cx=None,
server=None,
username='******',
password='******',
uuid=None,
networkx_G=None,
data=None,
**attr):
from ndex2.nice_cx_network import NiceCXNetwork
self.logger = logging.getLogger(__name__)
self.nice_cx = NiceCXNetwork(user_agent='niceCx Builder')
self.node_id_lookup = {}
self.node_id_counter = 0
self.edge_id_counter = 0
self.max_node_id = 0
self.max_edge_id = 0
self.node_inventory = {}
self.node_attribute_inventory = []
self.node_attribute_map = {}
self.edge_inventory = {}
self.edge_attribute_inventory = []
self.edge_attribute_map = {}
self.opaque_aspect_inventory = []
self.context_inventory = []
self.network_attribute_inventory = {}
self.user_base64 = None
self.username = None
self.password = None
if username and password:
self.username = username
self.password = password
if sys.version_info.major == 3:
encode_string = '%s:%s' % (username, password)
byte_string = encode_string.encode()
self.user_base64 = base64.b64encode(
byte_string) #.replace('\n', '')
else:
self.user_base64 = base64.encodestring(
'%s:%s' % (username, password)).replace('\n', '')
def set_context(self, context):
"""
Set the @context information of the network. This information
maps namespace prefixes to their defining URIs
Example:
``set_context({'pmid': 'https://www.ncbi.nlm.nih.gov/pubmed/'})``
:param context: dict of name, URI pairs
:type context: dict
:return: None
:rtype: none
"""
if isinstance(context, dict):
self.context_inventory = context
elif isinstance(context, list):
if len(context) > 0:
self.context_inventory = context[0]
def set_name(self, network_name):
"""
Set the network name
:param network_name: Network name
:type network_name: string
:return: None
:rtype:none
"""
self.network_attribute_inventory['name'] = {
'n': 'name',
'v': network_name,
'd': 'string'
}
def add_network_attribute(self,
name=None,
values=None,
type=None,
cx_element=None):
"""
Add an attribute to the network
:param name: Name of the attribute
:type name: str
:param values: The value(s) of the attribute
:type values: One of the allowable CX types. See `Supported data types`_
:param type: They type of data supplied in values. Default is string. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
add_this_network_attribute = {'n': name, 'v': values}
if type:
add_this_network_attribute['d'] = type
self.network_attribute_inventory[name] = add_this_network_attribute
def add_node(self,
name=None,
represents=None,
id=None,
data_type=None,
map_node_ids=False):
"""
Adds a new node with the corresponding name and represents (external id)
:param node_name: Name of the node
:type node_name: str
:param represents: Representation of the node (alternate identifier)
:type represents: str
:param id:
:type id:
:return: Node ID
:rtype: int
"""
if self.node_inventory.get(name) is not None:
return self.node_inventory.get(name).get('@id')
if id:
node_id = id
else:
node_id = self.node_id_counter
self.node_id_counter += 1
if node_id > self.max_node_id:
self.max_node_id = node_id
add_this_node = {'@id': node_id, 'n': name}
if represents:
add_this_node['r'] = represents
if data_type:
add_this_node['d'] = data_type
self.node_inventory[name] = add_this_node
if map_node_ids:
self.node_id_lookup[name] = node_id
return node_id
def add_edge(self, source=None, target=None, interaction=None, id=None):
"""
Adds a new edge in the network by specifying source-interaction-target
:param source: The source node of this edge, either its id or the node object itself.
:type source: int, dict (with @id property)
:param target: The target node of this edge, either its id or the node object itself.
:type target: int, dict (with @id property)
:param interaction: The interaction that describes the relationship between the source and target nodes
:type interaction: str
:param id: Edge id for this edge. If none is provided the builder will create one
:type id: int
:return: Edge ID
:rtype: int
"""
if id is not None:
edge_id = id
else:
edge_id = self.edge_id_counter
self.edge_id_counter += 1
if edge_id > self.max_edge_id:
self.max_edge_id = edge_id
add_this_edge = {'@id': edge_id, 's': source, 't': target}
if interaction:
add_this_edge['i'] = interaction
else:
add_this_edge['i'] = 'interacts-with'
self.edge_inventory[edge_id] = add_this_edge
return edge_id
def add_node_attribute(self, property_of, name, values, type=None):
"""
Set an attribute of a node, where the node may be specified by its id or passed in as a node dict.
:param property_of: Node ID to add the attribute to
:type property_of: int
:param name: Attribute name
:type name: str
:param value: A value or list of values of the attribute
:type value: list, string, int or float
:param type: The datatype of the attribute values, defaults is string. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
if property_of is None:
raise TypeError('Node value is None')
if name is None:
raise TypeError('Property name is None')
if values is None:
raise TypeError('Attribute value is None')
add_this_node_attribute = {'po': property_of, 'n': name, 'v': values}
if self.node_attribute_map.get(property_of) is None:
self.node_attribute_map[property_of] = {}
elif self.node_attribute_map[property_of].get(name) is not None:
# TODO - Raise warning/exception for duplicate attribute
return
if type:
if type == 'float' or type == 'double':
type = 'double'
try:
if not isinstance(values, float):
add_this_node_attribute['v'] = float(values)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
if type == 'list_of_float' or type == 'list_of_double':
try:
if isinstance(values, list):
for value in values:
if not isinstance(value, float):
value = float(value)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
type = 'list_of_double'
add_this_node_attribute['d'] = type
else:
use_this_value, attr_type = self._infer_data_type(values)
add_this_node_attribute['v'] = use_this_value
add_this_node_attribute['d'] = attr_type
if add_this_node_attribute['v'] is not None:
self.node_attribute_inventory.append(add_this_node_attribute)
self.node_attribute_map[property_of][name] = True
def add_edge_attribute(self,
property_of=None,
name=None,
values=None,
type=None):
"""
Set the value(s) of attribute of an edge, where the edge may be specified by its id or passed in an object.
Example:
``set_edge_attribute(0, 'weight', 0.5, type='float')``
or
``set_edge_attribute(edge, 'Disease', 'Atherosclerosis')``
:param property_of: Edge to add the attribute to
:type property_of: int or edge dict with @id attribute
:param name: Attribute name
:type name: str
:param values: A value or list of values of the attribute
:type values: list, string, int or float
:param type: The datatype of the attribute values, defaults to the python datatype of the values. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
if property_of is None:
raise TypeError('Edge value is None')
if name is None:
raise TypeError('Property name is None')
if values is None:
raise TypeError('Attribute value is None')
add_this_edge_attribute = {'po': property_of, 'n': name, 'v': values}
if self.edge_attribute_map.get(property_of) is None:
self.edge_attribute_map[property_of] = {}
elif self.edge_attribute_map[property_of].get(name) is not None:
return
if type:
if type == 'float' or type == 'double':
type = 'double'
try:
if not isinstance(values, float):
add_this_edge_attribute['v'] = float(values)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
if type == 'list_of_float' or type == 'list_of_double':
try:
if isinstance(values, list):
for value in values:
if not isinstance(value, float):
value = float(value)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
type = 'list_of_double'
add_this_edge_attribute['d'] = type
else:
use_this_value, attr_type = self._infer_data_type(values)
add_this_edge_attribute['v'] = use_this_value
add_this_edge_attribute['d'] = attr_type
if add_this_edge_attribute['v'] is not None:
self.edge_attribute_inventory.append(add_this_edge_attribute)
self.edge_attribute_map[property_of][name] = True
def add_opaque_aspect(self, oa_name, oa_list):
self.opaque_aspect_inventory.append({oa_name: oa_list})
#===================================
# methods to add data by fragment
#===================================
def _add_network_attributes_from_fragment(self, fragment):
self.nice_cx.networkAttributes.append(fragment)
def _add_node_from_fragment(self, fragment):
node_id = fragment.get('@id')
if node_id > self.max_node_id:
self.max_node_id = node_id
self.nice_cx.nodes[node_id] = fragment
def _add_edge_from_fragment(self, fragment):
edge_id = fragment.get('@id')
if edge_id > self.max_edge_id:
self.max_edge_id = edge_id
self.nice_cx.edges[edge_id] = fragment
def _add_node_attribute_from_fragment(self, fragment):
if self.nice_cx.nodeAttributes.get(fragment.get('po')) is None:
self.nice_cx.nodeAttributes[fragment.get('po')] = []
self.nice_cx.nodeAttributes[fragment.get('po')].append(fragment)
def _add_edge_attribute_from_fragment(self, fragment):
if self.nice_cx.edgeAttributes.get(fragment.get('po')) is None:
self.nice_cx.edgeAttributes[fragment.get('po')] = []
self.nice_cx.edgeAttributes[fragment.get('po')].append(fragment)
def _add_citation_from_fragment(self, fragment):
self.nice_cx.citations[fragment.get('@id')] = fragment
def _add_supports_from_fragment(self, fragment):
self.nice_cx.supports[fragment.get('@id')] = fragment
def _add_edge_supports_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.edgeSupports[po_id] = fragment.get('supports')
def _add_node_citations_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.nodeCitations[po_id] = fragment.get('citations')
def _add_edge_citations_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.edgeCitations[po_id] = fragment.get('citations')
def get_nice_cx(self):
#==========================
# ADD CONTEXT
#==========================
if isinstance(self.context_inventory, dict):
self.nice_cx.set_context(self.context_inventory)
else:
for c in self.context_inventory:
self.nice_cx.set_context(c)
#=============================
# ASSEMBLE NETWORK ATTRIBUTES
#=============================
#{'n': 'name', 'v': network_name, 'd': 'string'}
for k, v in self.network_attribute_inventory.items():
self.nice_cx.add_network_attribute(name=v.get('n'),
values=v.get('v'),
type=v.get('d'))
#==========================
# ASSEMBLE NODES
#==========================
for k, v in self.node_inventory.items():
self.nice_cx.nodes[v.get('@id')] = v
#==========================
# ASSEMBLE NODE ATTRIBUTES
#==========================
for a in self.node_attribute_inventory:
property_of = a.get('po')
if self.nice_cx.nodeAttributes.get(property_of) is None:
self.nice_cx.nodeAttributes[property_of] = []
self.nice_cx.nodeAttributes[property_of].append(a)
#==========================
# ASSEMBLE EDGES
#==========================
for k, v in self.edge_inventory.items():
self.nice_cx.edges[k] = v
#==========================
# ASSEMBLE EDGE ATTRIBUTES
#==========================
for a in self.edge_attribute_inventory:
property_of = a.get('po')
if self.nice_cx.edgeAttributes.get(property_of) is None:
self.nice_cx.edgeAttributes[property_of] = []
self.nice_cx.edgeAttributes[property_of].append(a)
#==========================
# ASSEMBLE OPAQUE ASPECTS
#==========================
for oa in self.opaque_aspect_inventory:
for k, v in oa.items():
self.nice_cx.add_opaque_aspect(k, v)
# Fixes issue #60 where there are problems adding
# new nodes/edges to networks generated
#
self.nice_cx.node_int_id_generator = self.max_node_id + 1
self.nice_cx.edge_int_id_generator = self.max_edge_id + 1
return self.nice_cx
def get_frag_from_list_by_key(self, cx, key):
return_list = []
for aspect in cx:
if key in aspect:
if isinstance(aspect[key], list):
for a_item in aspect[key]:
return_list.append(a_item)
else:
return_list.append(aspect[key])
return return_list
def _infer_data_type(self, val, split_string=False):
"""
Gets data type of **val** and returns an updated **val** value
that conforms to the data type inferred
Okay this is kinda complicated, but this code leverages :python:`isinstance`
to determine data types
:param val: Value to infer data type from
:param split_string: If ``True`` split **val** if it is type :py:func:`str`
and it contains ``,`` or ``;``. Order matters if both
``,`` and ``;`` are found **val** is split by ``,``
:type split_string: bool
:return: (processed value, CX data type), if **val** is ``None`` then ``(None, None)`` is
returned
:rtype tuple
"""
if val is None:
return None, None
attr_type = 'string'
if split_string:
if isinstance(val, str):
val = val.replace('"', '')
if ',' in val:
val = val.split(',')
elif ';' in val:
val = val.split(';')
if isinstance(val, float) or isinstance(val, np.float) or isinstance(
val, np.double):
if math.isnan(val):
# do something (skip?)
val = None
elif math.isinf(val):
val = 'INFINITY'
return val, 'double'
if isinstance(val, bool):
# fix for https://github.com/ndexbio/ndex2-client/issues/83
# a boolean is a sub type of int so bool must be tested first
return val, 'boolean'
if isinstance(val, int) or isinstance(val, np.int):
return val, 'integer'
if isinstance(val, list):
# if the list is empty just set data type to list_of_string
# fix for https://github.com/ndexbio/ndex2-client/issues/90
attr_type = 'list_of_string'
if len(val) > 0:
if isinstance(val[0], float) or isinstance(
val[0], np.float) or isinstance(val[0], np.double):
attr_type = 'list_of_double'
elif isinstance(val[0], bool):
# fix for https://github.com/ndexbio/ndex2-client/issues/83
# a boolean is a sub type of int so bool must be tested first
attr_type = 'list_of_boolean'
elif isinstance(val[0], int) or isinstance(val[0], np.int):
attr_type = 'list_of_integer'
return val, attr_type
class NiceCXBuilder(object):
def __init__(self,
cx=None,
server=None,
username='******',
password='******',
uuid=None,
networkx_G=None,
data=None,
**attr):
from ndex2.nice_cx_network import NiceCXNetwork
self.nice_cx = NiceCXNetwork(user_agent='niceCx Builder')
self.node_id_lookup = {}
self.node_id_counter = 0
self.edge_id_counter = 0
self.node_inventory = {}
self.node_attribute_inventory = []
self.node_attribute_map = {}
self.edge_inventory = {}
self.edge_attribute_inventory = []
self.edge_attribute_map = {}
self.opaque_aspect_inventory = []
self.context_inventory = []
self.network_attribute_inventory = {}
self.user_base64 = None
self.username = None
self.password = None
if username and password:
self.username = username
self.password = password
if sys.version_info.major == 3:
encode_string = '%s:%s' % (username, password)
byte_string = encode_string.encode()
self.user_base64 = base64.b64encode(
byte_string) #.replace('\n', '')
else:
self.user_base64 = base64.encodestring(
'%s:%s' % (username, password)).replace('\n', '')
def set_context(self, context):
"""
Set the @context information of the network. This information maps namespace prefixes to their defining URIs
Example:
``set_context({'pmid': 'https://www.ncbi.nlm.nih.gov/pubmed/'})``
:param context: dict of name, URI pairs
:type context: dict
:return: None
:rtype: none
"""
if isinstance(context, dict):
self.context_inventory = context
elif isinstance(context, list):
if len(context) > 0:
self.context_inventory = context[0]
def set_name(self, network_name):
"""
Set the network name
:param network_name: Network name
:type network_name: string
:return: None
:rtype:none
"""
self.network_attribute_inventory['name'] = {
'n': 'name',
'v': network_name,
'd': 'string'
}
def add_network_attribute(self,
name=None,
values=None,
type=None,
cx_element=None):
"""
Add an attribute to the network
:param name: Name of the attribute
:type name: str
:param values: The value(s) of the attribute
:type values: One of the allowable CX types. See `Supported data types`_
:param type: They type of data supplied in values. Default is string. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
add_this_network_attribute = {'n': name, 'v': values}
if type:
add_this_network_attribute['d'] = type
self.network_attribute_inventory[name] = add_this_network_attribute
def add_node(self,
name=None,
represents=None,
id=None,
data_type=None,
map_node_ids=False):
"""
Adds a new node with the corresponding name and represents (external id)
:param node_name: Name of the node
:type node_name: str
:param represents: Representation of the node (alternate identifier)
:type represents: str
:param id:
:type id:
:return: Node ID
:rtype: int
"""
if self.node_inventory.get(name) is not None:
return self.node_inventory.get(name).get('@id')
if id:
node_id = id
else:
node_id = self.node_id_counter
self.node_id_counter += 1
add_this_node = {'@id': node_id, 'n': name}
if represents:
add_this_node['r'] = represents
if data_type:
add_this_node['d'] = data_type
self.node_inventory[name] = add_this_node
if map_node_ids:
self.node_id_lookup[name] = node_id
return node_id
def add_edge(self, source=None, target=None, interaction=None, id=None):
"""
Adds a new edge in the network by specifying source-interaction-target
:param source: The source node of this edge, either its id or the node object itself.
:type source: int, dict (with @id property)
:param target: The target node of this edge, either its id or the node object itself.
:type target: int, dict (with @id property)
:param interaction: The interaction that describes the relationship between the source and target nodes
:type interaction: str
:param id: Edge id for this edge. If none is provided the builder will create one
:type id: int
:return: Edge ID
:rtype: int
"""
if id is not None:
edge_id = id
else:
edge_id = self.edge_id_counter
self.edge_id_counter += 1
add_this_edge = {'@id': edge_id, 's': source, 't': target}
if interaction:
add_this_edge['i'] = interaction
else:
add_this_edge['i'] = 'interacts-with'
self.edge_inventory[edge_id] = add_this_edge
return edge_id
def add_node_attribute(self, property_of, name, values, type=None):
"""
Set an attribute of a node, where the node may be specified by its id or passed in as a node dict.
:param property_of: Node ID to add the attribute to
:type property_of: int
:param name: Attribute name
:type name: str
:param value: A value or list of values of the attribute
:type value: list, string, int or float
:param type: The datatype of the attribute values, defaults is string. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
if property_of is None:
raise TypeError('Node value is None')
if name is None:
raise TypeError('Property name is None')
if values is None:
raise TypeError('Attribute value is None')
add_this_node_attribute = {'po': property_of, 'n': name, 'v': values}
if self.node_attribute_map.get(property_of) is None:
self.node_attribute_map[property_of] = {}
elif self.node_attribute_map[property_of].get(name) is not None:
# TODO - Raise warning/exception for duplicate attribute
return
if type:
if type == 'float' or type == 'double':
type = 'double'
try:
if not isinstance(values, float):
add_this_node_attribute['v'] = float(values)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
if type == 'list_of_float' or type == 'list_of_double':
try:
if isinstance(values, list):
for value in values:
if not isinstance(value, float):
value = float(value)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
type = 'list_of_double'
add_this_node_attribute['d'] = type
else:
use_this_value, attr_type = self._infer_data_type(values)
add_this_node_attribute['v'] = use_this_value
add_this_node_attribute['d'] = attr_type
if add_this_node_attribute['v'] is not None:
self.node_attribute_inventory.append(add_this_node_attribute)
self.node_attribute_map[property_of][name] = True
def add_edge_attribute(self,
property_of=None,
name=None,
values=None,
type=None):
"""
Set the value(s) of attribute of an edge, where the edge may be specified by its id or passed in an object.
Example:
``set_edge_attribute(0, 'weight', 0.5, type='float')``
or
``set_edge_attribute(edge, 'Disease', 'Atherosclerosis')``
:param property_of: Edge to add the attribute to
:type property_of: int or edge dict with @id attribute
:param name: Attribute name
:type name: str
:param values: A value or list of values of the attribute
:type values: list, string, int or float
:param type: The datatype of the attribute values, defaults to the python datatype of the values. See `Supported data types`_
:type type: str
:return: None
:rtype: None
"""
if property_of is None:
raise TypeError('Edge value is None')
if name is None:
raise TypeError('Property name is None')
if values is None:
raise TypeError('Attribute value is None')
add_this_edge_attribute = {'po': property_of, 'n': name, 'v': values}
if self.edge_attribute_map.get(property_of) is None:
self.edge_attribute_map[property_of] = {}
elif self.edge_attribute_map[property_of].get(name) is not None:
return
if type:
if type == 'float' or type == 'double':
type = 'double'
try:
if not isinstance(values, float):
add_this_edge_attribute['v'] = float(values)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
if type == 'list_of_float' or type == 'list_of_double':
try:
if isinstance(values, list):
for value in values:
if not isinstance(value, float):
value = float(value)
except ValueError as e:
raise ValueError('Value was not of type %s' % type)
type = 'list_of_double'
add_this_edge_attribute['d'] = type
else:
use_this_value, attr_type = self._infer_data_type(values)
add_this_edge_attribute['v'] = use_this_value
add_this_edge_attribute['d'] = attr_type
if add_this_edge_attribute['v'] is not None:
self.edge_attribute_inventory.append(add_this_edge_attribute)
self.edge_attribute_map[property_of][name] = True
def add_opaque_aspect(self, oa_name, oa_list):
self.opaque_aspect_inventory.append({oa_name: oa_list})
#===================================
# methods to add data by fragment
#===================================
def _add_network_attributes_from_fragment(self, fragment):
self.nice_cx.networkAttributes.append(fragment)
def _add_node_from_fragment(self, fragment):
self.nice_cx.nodes[fragment.get('@id')] = fragment
def _add_edge_from_fragment(self, fragment):
self.nice_cx.edges[fragment.get('@id')] = fragment
def _add_node_attribute_from_fragment(self, fragment):
if self.nice_cx.nodeAttributes.get(fragment.get('po')) is None:
self.nice_cx.nodeAttributes[fragment.get('po')] = []
self.nice_cx.nodeAttributes[fragment.get('po')].append(fragment)
def _add_edge_attribute_from_fragment(self, fragment):
if self.nice_cx.edgeAttributes.get(fragment.get('po')) is None:
self.nice_cx.edgeAttributes[fragment.get('po')] = []
self.nice_cx.edgeAttributes[fragment.get('po')].append(fragment)
def _add_citation_from_fragment(self, fragment):
self.nice_cx.citations[fragment.get('@id')] = fragment
def _add_supports_from_fragment(self, fragment):
self.nice_cx.supports[fragment.get('@id')] = fragment
def _add_edge_supports_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.edgeSupports[po_id] = fragment.get('supports')
def _add_node_citations_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.nodeCitations[po_id] = fragment.get('citations')
def _add_edge_citations_from_fragment(self, fragment):
for po_id in fragment.get('po'):
self.nice_cx.edgeCitations[po_id] = fragment.get('citations')
def get_nice_cx(self):
#==========================
# ADD CONTEXT
#==========================
if isinstance(self.context_inventory, dict):
self.nice_cx.set_context(self.context_inventory)
else:
for c in self.context_inventory:
self.nice_cx.set_context(c)
#=============================
# ASSEMBLE NETWORK ATTRIBUTES
#=============================
#{'n': 'name', 'v': network_name, 'd': 'string'}
for k, v in self.network_attribute_inventory.items():
self.nice_cx.add_network_attribute(name=v.get('n'),
values=v.get('v'),
type=v.get('d'))
#==========================
# ASSEMBLE NODES
#==========================
for k, v in self.node_inventory.items():
self.nice_cx.nodes[v.get('@id')] = v
#==========================
# ASSEMBLE NODE ATTRIBUTES
#==========================
for a in self.node_attribute_inventory:
property_of = a.get('po')
if self.nice_cx.nodeAttributes.get(property_of) is None:
self.nice_cx.nodeAttributes[property_of] = []
self.nice_cx.nodeAttributes[property_of].append(a)
#==========================
# ASSEMBLE EDGES
#==========================
for k, v in self.edge_inventory.items():
self.nice_cx.edges[k] = v
#==========================
# ASSEMBLE EDGE ATTRIBUTES
#==========================
for a in self.edge_attribute_inventory:
property_of = a.get('po')
if self.nice_cx.edgeAttributes.get(property_of) is None:
self.nice_cx.edgeAttributes[property_of] = []
self.nice_cx.edgeAttributes[property_of].append(a)
#==========================
# ASSEMBLE OPAQUE ASPECTS
#==========================
for oa in self.opaque_aspect_inventory:
for k, v in oa.items():
self.nice_cx.add_opaque_aspect(k, v)
return self.nice_cx
def get_frag_from_list_by_key(self, cx, key):
return_list = []
for aspect in cx:
if key in aspect:
if isinstance(aspect[key], list):
for a_item in aspect[key]:
return_list.append(a_item)
else:
return_list.append(aspect[key])
return return_list
def load_aspect(self, aspect_name):
#with open('Signal1.cx', mode='r') as cx_f:
with open('network1.cx', mode='r') as cx_f:
aspect_json = json.loads(cx_f.read())
for aspect in aspect_json:
if aspect.get(aspect_name) is not None:
return aspect.get(aspect_name)
def stream_all_aspects(self, uuid):
return ijson.items(
urlopen('http://dev2.ndexbio.org/v2/network/' + uuid), 'item')
def stream_aspect(self, uuid, aspect_name):
if aspect_name == 'metaData':
print('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect')
md_response = requests.get('http://dev2.ndexbio.org/v2/network/' +
uuid + '/aspect')
json_respone = md_response.json()
return json_respone.get('metaData')
else:
#password_mgr = HTTPPasswordMgrWithDefaultRealm()
#top_level_url = 'http://dev2.ndexbio.org'
#password_mgr.add_password(None, top_level_url, self.username, self.password)
#handler = HTTPBasicAuthHandler(password_mgr)
#opener = build_opener(handler)
#install_opener(opener)
# Create an OpenerDirector with support for Basic HTTP Authentication...
#auth_handler = HTTPBasicAuthHandler()
#auth_handler.add_password(None, 'http://dev2.ndexbio.org', 'scratch', 'scratch')
#opener = build_opener(auth_handler)
# ...and install it globally so it can be used with urlopen.
#install_opener(opener)
request = Request('http://dev2.ndexbio.org/v2/network/' + uuid +
'/aspect/' + aspect_name)
base64string = base64.b64encode('%s:%s' % ('scratch', 'scratch'))
request.add_header("Authorization", "Basic %s" % base64string)
#result = urllib2.urlopen(request)
urlopen_result = None
try:
urlopen_result = urlopen(
request
) #'http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/' + aspect_name)
except HTTPError as e:
print(e.code)
return []
except URLError as e:
print('Other error')
print('URL Error %s' % e.message())
return []
return ijson.items(urlopen_result, 'item')
def stream_aspect_raw(self, uuid, aspect_name):
return ijson.parse(
urlopen('http://dev2.ndexbio.org/v2/network/' + uuid + '/aspect/' +
aspect_name))
def _infer_data_type(self, val, split_string=False):
if val is None:
return None, None
attr_type = 'string'
if split_string:
if isinstance(val, str):
val = val.replace('"', '')
if ',' in val:
val = val.split(',')
elif ';' in val:
val = val.split(';')
processed_value = val
if isinstance(val, float) or isinstance(val, np.float) or isinstance(
val, np.double):
if math.isnan(val):
# do something (skip?)
processed_value = None
elif math.isinf(val):
processed_value = 'INFINITY'
attr_type = 'double' # CX spec dropped support for float and instead uses double precision
elif isinstance(val, int) or isinstance(val, np.int):
attr_type = 'integer'
elif isinstance(val, list):
if len(val) > 0:
if isinstance(val[0], float) or isinstance(
val[0], np.float) or isinstance(val[0], np.double):
attr_type = 'list_of_double'
elif isinstance(val[0], int) or isinstance(val[0], np.int):
attr_type = 'list_of_integer'
else:
attr_type = 'list_of_string'
return processed_value, attr_type