def test_infer_data_type_empty_list(self):
builder = NiceCXBuilder()
self.assertEqual(([], 'list_of_string'), builder._infer_data_type([]))
self.assertEqual(([], 'list_of_string'),
builder._infer_data_type([], split_string=True))
def test_infer_data_type_bool(self):
"""
Test added for bug: https://github.com/ndexbio/ndex2-client/issues/83
:return:
"""
builder = NiceCXBuilder()
self.assertEqual((True, 'boolean'), builder._infer_data_type(True))
self.assertEqual((True, 'boolean'),
builder._infer_data_type(True, split_string=True))
def test_infer_data_type_list_of_integer(self):
"""
Test added for bug: https://github.com/ndexbio/ndex2-client/issues/83
:return:
"""
builder = NiceCXBuilder()
self.assertEqual(([1], 'list_of_integer'),
builder._infer_data_type([1]))
self.assertEqual(([1], 'list_of_integer'),
builder._infer_data_type([1], split_string=True))
def test_infer_data_type_str_split_is_false(self):
builder = NiceCXBuilder()
# empty string
self.assertEqual(('', 'string'), builder._infer_data_type(''))
# string with space
self.assertEqual((' ', 'string'), builder._infer_data_type(' '))
# simple string
self.assertEqual(('foo', 'string'), builder._infer_data_type('foo'))
# simple string with double quote
self.assertEqual(('foo"', 'string'), builder._infer_data_type('foo"'))
# string with comma delimiter, but split_string is left
# to default which is False
self.assertEqual(('item1,item2', 'string'),
builder._infer_data_type('item1,item2'))
# string with comma delimiter, but split_string is left
# to default which is False
self.assertEqual(('item1;item2', 'string'),
builder._infer_data_type('item1;item2'))
# string with comma and semicolon delimiter and double quote,
# but split_string is left to default which is False
self.assertEqual(('item1;item2,item3"', 'string'),
builder._infer_data_type('item1;item2,item3"'))
def test_infer_data_type_int(self):
"""
Test added for bug: https://github.com/ndexbio/ndex2-client/issues/83
:return:
"""
builder = NiceCXBuilder()
self.assertEqual((1, 'integer'), builder._infer_data_type(1))
self.assertEqual((1, 'integer'),
builder._infer_data_type(1, split_string=True))
self.assertEqual((0, 'integer'), builder._infer_data_type(0))
self.assertEqual((0, 'integer'),
builder._infer_data_type(0, split_string=True))
self.assertEqual((-1, 'integer'), builder._infer_data_type(-1))
self.assertEqual((-1, 'integer'),
builder._infer_data_type(-1, split_string=True))
def create_nice_cx_from_networkx(G):
"""
Creates a :py:class:`~ndex2.nice_cx_network.NiceCXNetwork` based on a
networkx graph.
The resulting :py:class:`~ndex2.nice_cx_network.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.
The node name is taken from the networkx node id. Node 'represents' is
taken from the networkx node attribute 'represents'
:param G: networkx graph
:type G: networkx graph
:return: NiceCXNetwork
:rtype: :py:class:`~ndex2.nice_cx_network.NiceCXNetwork`
"""
niceCxBuilder = NiceCXBuilder()
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')
#=========================================
# Check to see if the node label is same
# (case insensitive) as 'name' attribute
#=========================================
#use_node_label = False
#for n, d in G.nodes_iter(data=True):
# if not isinstance(n, int) and d and d.get('name'):
# if n.lower() == d.get('name').lower():
# use_node_label = True
# break
for n, d in G.nodes(data=True):
# =============
# ADD NODES
# =============
#if d and d.get('name'):
# if isinstance(n, int):
# node_id = niceCxBuilder.add_node(name=d.get('name'),represents=d.get('name'), id=n, map_node_ids=True)
# else:
# # If networkx node is of type string then maybe the 'name' atribute is no longer accurate
# if use_node_label:
# node_id = niceCxBuilder.add_node(name=n,represents=n, map_node_ids=True)
# else:
# node_id = niceCxBuilder.add_node(name=d.get('name'),represents=d.get('name'), map_node_ids=True)
#else:
if isinstance(n, int):
node_id = niceCxBuilder.add_node(name=n,
represents=d.get('represents'),
id=n,
map_node_ids=True)
else:
node_id = niceCxBuilder.add_node(name=n,
represents=d.get('represents'),
map_node_ids=True)
# ======================
# ADD NODE ATTRIBUTES
# ======================
for k, v in d.items():
use_this_value, attr_type = niceCxBuilder._infer_data_type(
v, split_string=True)
if k == 'citation' and not isinstance(use_this_value, list):
use_this_value = [use_this_value]
attr_type = 'list_of_string'
if use_this_value is not None:
niceCxBuilder.add_node_attribute(node_id,
k,
use_this_value,
type=attr_type)
index = 0
for u, v, d in G.edges(data=True):
# =============
# ADD EDGES
# =============
if d.get('interaction') is None or d.get('interaction') == 'null':
interaction = 'neighbor-of'
else:
interaction = d.get('interaction')
if isinstance(u, int):
niceCxBuilder.add_edge(source=u,
target=v,
interaction=interaction,
id=index)
else:
niceCxBuilder.add_edge(source=niceCxBuilder.node_id_lookup.get(u),
target=niceCxBuilder.node_id_lookup.get(v),
interaction=interaction,
id=index)
# ==============================
# ADD EDGE ATTRIBUTES
# ==============================
for k, val in d.items():
if k != 'interaction':
use_this_value, attr_type = niceCxBuilder._infer_data_type(
val, split_string=True)
if k == 'citation' and not isinstance(use_this_value, list):
use_this_value = [use_this_value]
attr_type = 'list_of_string'
if use_this_value is not None:
niceCxBuilder.add_edge_attribute(property_of=index,
name=k,
values=use_this_value,
type=attr_type)
index += 1
if hasattr(G, 'pos'):
aspect = _create_cartesian_coordinates_aspect_from_networkx(G)
niceCxBuilder.add_opaque_aspect('cartesianLayout', aspect)
return niceCxBuilder.get_nice_cx()
def test_infer_data_type_double(self):
"""
Test added for bug: https://github.com/ndexbio/ndex2-client/issues/83
:return:
"""
builder = NiceCXBuilder()
self.assertEqual((1.5, 'double'), builder._infer_data_type(1.5))
self.assertEqual((1.5, 'double'),
builder._infer_data_type(1.5, split_string=True))
self.assertEqual((0.0, 'double'), builder._infer_data_type(0.0))
self.assertEqual((0.0, 'double'),
builder._infer_data_type(0.0, split_string=True))
self.assertEqual((-1.0, 'double'), builder._infer_data_type(-1.0))
self.assertEqual((-1.0, 'double'),
builder._infer_data_type(-1.0, split_string=True))
self.assertEqual((-1.0, 'double'), builder._infer_data_type(-1.0))
self.assertEqual((-1.0, 'double'),
builder._infer_data_type(-1.0, split_string=True))
self.assertEqual((None, 'double'), builder._infer_data_type(math.nan))
self.assertEqual((None, 'double'),
builder._infer_data_type(math.nan, split_string=True))
self.assertEqual(('INFINITY', 'double'),
builder._infer_data_type(math.inf))
self.assertEqual(('INFINITY', 'double'),
builder._infer_data_type(math.inf, split_string=True))
def test_infer_data_type_none_val(self):
builder = NiceCXBuilder()
self.assertEqual((None, None), builder._infer_data_type(None))
def create_nice_cx_from_networkx(G):
"""
Creates 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.
Node name is taken from the networkx node id. Node 'represents' is
taken from the networkx node attribute 'represents'
:param G: networkx graph
:type G: networkx graph
:return: NiceCXNetwork
:rtype: NiceCXNetwork
"""
niceCxBuilder = NiceCXBuilder()
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')
#=========================================
# Check to see if the node label is same
# (case insensitive) as 'name' attribute
#=========================================
#use_node_label = False
#for n, d in G.nodes_iter(data=True):
# if not isinstance(n, int) and d and d.get('name'):
# if n.lower() == d.get('name').lower():
# use_node_label = True
# break
for n, d in G.nodes(data=True):
# =============
# ADD NODES
# =============
#if d and d.get('name'):
# if isinstance(n, int):
# node_id = niceCxBuilder.add_node(name=d.get('name'),represents=d.get('name'), id=n, map_node_ids=True)
# else:
# # If networkx node is of type string then maybe the 'name' atribute is no longer accurate
# if use_node_label:
# node_id = niceCxBuilder.add_node(name=n,represents=n, map_node_ids=True)
# else:
# node_id = niceCxBuilder.add_node(name=d.get('name'),represents=d.get('name'), map_node_ids=True)
#else:
if isinstance(n, int):
node_id = niceCxBuilder.add_node(name=n,represents=d.get('represents'), id=n, map_node_ids=True)
else:
node_id = niceCxBuilder.add_node(name=n, represents=d.get('represents'), map_node_ids=True)
# ======================
# ADD NODE ATTRIBUTES
# ======================
for k, v in d.items():
use_this_value, attr_type = niceCxBuilder._infer_data_type(v, split_string=True)
if k == 'citation' and not isinstance(use_this_value, list):
use_this_value = [use_this_value]
attr_type = 'list_of_string'
if use_this_value is not None:
niceCxBuilder.add_node_attribute(node_id, k, use_this_value, type=attr_type)
index = 0
for u, v, d in G.edges(data=True):
# =============
# ADD EDGES
# =============
if d.get('interaction') is None or d.get('interaction') == 'null':
interaction = 'neighbor-of'
else:
interaction = d.get('interaction')
if isinstance(u, int):
niceCxBuilder.add_edge(source=u, target=v, interaction=interaction, id=index)
else:
niceCxBuilder.add_edge(source=niceCxBuilder.node_id_lookup.get(u), target=niceCxBuilder.node_id_lookup.get(v),
interaction=interaction, id=index)
# ==============================
# ADD EDGE ATTRIBUTES
# ==============================
for k, val in d.items():
if k != 'interaction':
use_this_value, attr_type = niceCxBuilder._infer_data_type(val, split_string=True)
if k == 'citation' and not isinstance(use_this_value, list):
use_this_value = [use_this_value]
attr_type = 'list_of_string'
if use_this_value is not None:
niceCxBuilder.add_edge_attribute(property_of=index, name=k, values=use_this_value, type=attr_type)
index += 1
if hasattr(G, 'pos'):
aspect = _create_cartesian_coordinates_aspect_from_networkx(G)
niceCxBuilder.add_opaque_aspect('cartesianLayout', aspect)
return niceCxBuilder.get_nice_cx()
def create_nice_cx_from_networkx(G):
"""
Creates a :py:class:`~ndex2.nice_cx_network.NiceCXNetwork` based on a
:class:`networkx.Graph` graph.
.. versionchanged:: 3.5.0
Major refactor to fix multiple bugs #83, #84, #90
.. code-block:: python
import ndex2
import networkx as nx
G = nx.Graph()
G.add_node(1, someval=1.5, name='node 1')
G.add_node(2, someval=2.5, name='node 2')
G.add_edge(1, 2, weight=5)
print(ndex2.create_nice_cx_from_networkx(G).to_cx())
The resulting :py:class:`~ndex2.nice_cx_network.NiceCXNetwork`
contains the nodes, edges and their attributes from the
:class:`networkx.Graph`
graph and also preserves the graph 'pos' attribute as a CX
cartesian coordinates aspect
:py:const:`~ndex2.constants.CARTESIAN_LAYOUT_ASPECT`
with the values of `Y` inverted
Description of how conversion is performed:
**Network:**
* Network name is set value of ``G.graph.get('name')`` or to
``created from networkx by ndex2.create_nice_cx_networkx()`` if
`name` is ``None`` or not present
**Nodes:**
* Node id is value of ``n`` from this for loop:
``for n, d G.nodes(data=True):`` if ``n`` is **NOT** an
:py:class:`int`, new ids starting from ``0`` are used
* Node name is value of `name` attribute on the node or is
set to id of node if `name` is not present.
* Node `represents` is value of `represents` attribute on the
node or set is to node `name` if ``None`` or not present
**Edges:**
* Interaction is value of `interaction` attribute on the edge
or is set to ``neighbor-of`` if ``None`` or not present
.. note::
Data types are inferred by using :py:func:`isinstance` and
converted to corresponding CX data types. For list items,
only the 1st item is examined to determine type
:param G: Graph to convert
:type G: :class:`networkx.Graph`
:raises Exception: if **G** parameter is ``None`` or there is another error
in conversion
:return: Converted network
:rtype: :py:class:`~ndex2.nice_cx_network.NiceCXNetwork`
"""
cx_builder = NiceCXBuilder()
if G is None:
raise Exception('Networkx input is empty')
network_name = G.graph.get('name')
if network_name is not None:
cx_builder.set_name(network_name)
else:
cx_builder.set_name('created from networkx by '
'ndex2.create_nice_cx_networkx()')
for n, d in G.nodes(data=True):
if isinstance(n, int):
n_name = d.get('name')
if n_name is None:
n_name = str(n)
node_id = cx_builder.add_node(name=n_name,
represents=d.get('represents'),
id=n,
map_node_ids=True)
else:
node_id = cx_builder.add_node(name=n,
represents=d.get('represents'),
map_node_ids=True)
# ======================
# ADD NODE ATTRIBUTES
# ======================
for k, v in d.items():
# if node attribute is 'name' skip it cause that will be used
# for name of node, also skip 'represents'
# fix for https://github.com/ndexbio/ndex2-client/issues/84
if k == 'name' or k == 'represents':
continue
use_this_value, attr_type = cx_builder._infer_data_type(
v, split_string=False)
# This might go away, waiting on response to
# https://ndexbio.atlassian.net/browse/UD-2181
if k == 'citation' and not isinstance(use_this_value, list):
use_this_value = [str(use_this_value)]
attr_type = constants.LIST_OF_STRING
if use_this_value is not None:
cx_builder.add_node_attribute(node_id,
k,
use_this_value,
type=attr_type)
index = 0
for u, v, d in G.edges(data=True):
# =============
# ADD EDGES
# =============
if d.get('interaction') is None or d.get('interaction') == 'null':
interaction = 'neighbor-of'
else:
interaction = d.get('interaction')
if isinstance(u, int):
cx_builder.add_edge(source=u,
target=v,
interaction=interaction,
id=index)
else:
cx_builder.add_edge(source=cx_builder.node_id_lookup.get(u),
target=cx_builder.node_id_lookup.get(v),
interaction=interaction,
id=index)
# ==============================
# ADD EDGE ATTRIBUTES
# ==============================
for k, val in d.items():
if k == 'interaction':
continue
use_this_value, attr_type = cx_builder._infer_data_type(
val, split_string=False)
# This might go away, waiting on response to
# https://ndexbio.atlassian.net/browse/UD-2181
if k == 'citation' and not isinstance(use_this_value, list):
use_this_value = [str(use_this_value)]
attr_type = constants.LIST_OF_STRING
if use_this_value is not None:
cx_builder.add_edge_attribute(property_of=index,
name=k,
values=use_this_value,
type=attr_type)
index += 1
if hasattr(G, 'pos'):
aspect = _create_cartesian_coordinates_aspect_from_networkx(G)
cx_builder.add_opaque_aspect(constants.CARTESIAN_LAYOUT_ASPECT, aspect)
return cx_builder.get_nice_cx()