CX2

The CX2Network class represents the CX2 (Cytoscape Exchange) network format.

The class provides structured access, manipulation, reading, processing, and writing of network data elements including nodes, edges, attributes, visual properties, and other features of the network.

New in version 3.6.0.

CX2Network methods

class ndex2.cx2.CX2Network[source]

A representation of the CX2 (Cytoscape Exchange) network format.

This class provides functionality to read, process, and write data in the CX2 format. It facilitates the structured access and manipulation of network data elements such as nodes, edges, attributes, and visual properties.

The class maintains internal data structures that hold network data and provides methods to:

Load data from raw CX2 files.
Generate the CX2 representation of the current state.
Write the current state to a CX2 formatted file.

Attributes:

attribute_declarations
A dictionary representing the declarations of attributes for network elements.
network_attribute
A dictionary storing global attributes of the network.
nodes
A dictionary of nodes.
edges
A dictionary of edges.
aliases
A dictionary that maps aspect names (like “nodes” or “edges”) to their alias declarations.
default_values
A dictionary that maps aspect names to their default attribute values.
visual_properties
A list storing visual properties of the network.
node_bypasses
A dictionary of node-specific visual properties that bypass default styles.
edge_bypasses
A dictionary of edge-specific visual properties that bypass default styles.
opaque_aspects
A list of other aspects in the CX2 format which don’t have a defined structure in this class.
status
A dictionary representing the network’s status.

New in version 3.6.0.

add_edge(edge_id=None, source=None, target=None, attributes=None)[source]

Adds an edge to the network.

Parameters:

edge_id (int or str) – ID of the edge to add.
source (int or str) – Source node of the edge.
target (int or str) – Target node of the edge.
attributes (dict, optional) – Attributes of the edge.

add_edge_bypass(edge_id, value)[source]

Adds an edge-specific visual property bypass.

Parameters:

edge_id (str) – ID of the edge.
value (Any) – Visual property bypass value.

add_node(node_id=None, attributes=None, x=None, y=None, z=None)[source]

Adds a node to the network.

Parameters:

node_id (int or str) – ID of the node to add.
attributes (dict, optional) – Attributes of the node.
x (float, optional) – X-coordinate of the node.
y (float, optional) – Y-coordinate of the node.
z (float, optional) – Z-coordinate of the node.

Raises:

NDExAlreadyExists – If node with node_id already exists

add_node_bypass(node_id, value)[source]

Adds a node-specific visual property bypass.

Parameters:

node_id (str) – ID of the node.
value (Any) – Visual property bypass value.

add_opaque_aspect(aspect)[source]

Adds an opaque aspect to the list of opaque aspects.

Parameters:: aspect (dict) – The opaque aspect to add.

create_from_raw_cx2(cx2_data)[source]

Loads and processes a raw CX2 data into structured data within the instance.

Parameters:

cx2_data (str or list) – Path to the CX2 file or a list representing CX2 data to be processed.

Raises:

NDExError – If cx2_data is None
NDExInvalidCX2Error – If there is an error parsing cx2_data

get_alias(aspect_name, attribute_name)[source]

Retrieves alias for a given aspect’s attribute.

Parameters:

aspect_name (str) – The name of the aspect (e.g., ‘nodes’, ‘edges’).
attribute_name (str) – The attribute whose declared data type needs to be retrieved.

Returns:

The alias or None if not found.

Return type:

str

get_aliases(aspect)[source]

Retrieves aliases for a given aspect’s attributes.

Parameters:: aspect (str) – The name of the aspect (e.g., ‘nodes’, ‘edges’).
Returns:: Dictionary mapping aliases to attribute names.
Return type:: dict

get_attribute_declarations()[source]

Retrieves the attribute declarations.

Returns:: The attribute declarations.
Return type:: dict

get_declared_type(aspect_name, attribute_name, attribute_value=None)[source]

Retrieves the declared data type for a given aspect’s attribute.

Parameters:

aspect_name (str) – The name of the aspect (e.g., ‘nodes’, ‘edges’).
attribute_name (str) – The attribute whose declared data type needs to be retrieved.
attribute_value (str, int, bool, float, list) – Actual value that will be used to infer data type if data type has not yet been defined for attribute

Returns:

The declared data type or ‘string’ if not found.

Return type:

str

get_default_value(aspect_name, attribute_name)[source]

Retrieves default value for a given aspect’s attribute.

Parameters:

aspect_name (str) – The name of the aspect (e.g., ‘nodes’, ‘edges’).
attribute_name (str) – The attribute whose declared data type needs to be retrieved.

Returns:

The default value or None if not found.

Return type:

str

get_default_values(aspect)[source]

Retrieves default values for a given aspect’s attributes.

Parameters:: aspect (str) – The name of the aspect (e.g., ‘nodes’, ‘edges’).
Returns:: Dictionary mapping attribute names to their default values.
Return type:: dict

get_edge(edge_id)[source]

Retrieves an edge based on its ID.

Parameters:: edge_id (int or str) – ID of the edge to retrieve.
Returns:: Edge with the given ID or None if not found.
Return type:: dict or None

get_edge_bypasses()[source]

Retrieves the edge-specific visual property bypasses.

Returns:: The edge-specific visual property bypasses.
Return type:: dict

get_edges()[source]

Retrieves the edges in the network.

Returns:: Edges in the network.
Return type:: dict

get_name()[source]

Retrieves the network name.

Returns:: Network name
Return type:: str

get_network_attributes()[source]

Retrieves the network attributes.

Returns:: The network attributes.
Return type:: dict

get_node(node_id)[source]

Retrieves a node based on its ID.

Parameters:: node_id (int or str) – ID of the node to retrieve.
Returns:: Node with the given ID or None if not found.
Return type:: dict or None

get_node_bypasses()[source]

Retrieves the node-specific visual property bypasses.

Returns:: The node-specific visual property bypasses.
Return type:: dict

get_nodes()[source]

Retrieves the nodes in the network.

Returns:: Nodes in the network.
Return type:: dict

get_opaque_aspects()[source]

Retrieves the opaque aspects of the network.

Returns:: The opaque aspects of the network.
Return type:: list

get_status()[source]

Retrieves the status of the network.

Returns:: The status of the network.
Return type:: list

get_visual_properties()[source]

Retrieves the visual properties of the network.

Returns:: The visual properties of the network.
Return type:: dict

remove_edge(edge_id)[source]

Removes an edge from the network based on its ID.

Parameters:: edge_id (int or str) – ID of the edge to remove.

remove_node(node_id)[source]

Removes a node and checks for dangling edges (edges without both source and target).

Parameters:: node_id (int or str) – ID of the node to remove.

set_attribute_declarations(value)[source]

Sets the attribute declarations.

Parameters:: value (dict) – The attribute declarations to set.

set_network_attributes(network_attrs)[source]

Sets the network attributes after processing them using declared types in attribute declarations.

Parameters:: network_attrs (dict) – The network attributes to set.

set_opaque_aspects(value)[source]

Sets the opaque aspects for the network.

Parameters:: value (list) – New opaque aspects for the network.

set_status(value)[source]

Sets the status for the network.

Parameters:: value (dict) – New status for the network.

set_visual_properties(value)[source]

Sets the visual properties for the network.

Parameters:: value (dict) – New visual properties for the network.

to_cx2()[source]

Generates the CX2 representation of the current state of the instance.

This method constructs a list structure representing the current state of the network in the CX2 format.

Returns:: A list representing the CX2 formatted data of the current network state.
Return type:: list

update_edge(edge_id, attributes=None)[source]

Updates the attributes of an edge.

Parameters:

edge_id (int or str) – ID of the edge to update.
attributes (dict, optional) – New attributes for the edge.

update_node(node_id, attributes=None, x=None, y=None, z=None)[source]

Updates the attributes of a node.

Parameters:

node_id (int or str) – ID of the node to update.
attributes (dict, optional) – Attributes to update.
x (float, optional) – X-coordinate to update.
y (float, optional) – Y-coordinate to update.
z (float, optional) – Z-coordinate to update.

Raises:

NDExError – if node with node_id passed in does not exist

write_as_raw_cx2(output_path)[source]

Writes data from CX2Network object to a raw CX2 formatted JSON file.

Parameters:: output_path (str) – Destination file path for the CX2 formatted output.

CX2NetworkFactory classes and methods

class ndex2.cx2.CX2NetworkFactory[source]

Base class for Factory classes that create CX2Network objects

New in version 3.6.0.

get_cx2network(input_data=None) → CX2Network[source]

Defines method that creates CX2Network

Warning

Subclasses should implement, this method always raises NotImplementedError

Parameters:: input_data – Optional input data for used to generate network
Raises:: NotImplementedError – Always raised. Subclasses should implement
Returns:: Generated network
Return type:: CX2Network

class ndex2.cx2.NoStyleCXToCX2NetworkFactory[source]

Creates CX2Network network from CX data or NiceCXNetwork

New in version 3.6.0.

get_cx2network(input_data=None) → CX2Network[source]

Creates CX2Network from CX data or NiceCXNetwork but does NOT convert the style associated with input network

Note

Style is NOT converted by this call

Parameters:: input_data (str, list or NiceCXNetwork) – Optional input data used to generate network
Returns:: Generated network
Return type:: CX2Network

class ndex2.cx2.RawCX2NetworkFactory[source]

Factory class responsible for creating CX2Network instances directly from raw CX2.

New in version 3.6.0.

get_cx2network(input_data=None) → CX2Network[source]

Converts the provided raw CX2 into a CX2Network object.

Parameters:: input_data (dict or similar mapping type) – Raw CX2 to be converted.
Returns:: A constructed CX2Network object from the input data.
Return type:: CX2Network

Supported data types for attributes

string
double
boolean
integer
long
list_of_string
list_of_double
list_of_boolean
list_of_integer
list_of_long

Example

import json
from ndex2.cx2 import CX2Network

net = CX2Network()
net.create_from_raw_cx2('path_to_your_cx2_file.cx2')
net.write_as_raw_cx2('output_path.cx2')