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NiceCXNetwork

The :class:`~ndex2.nice_cx_network.NiceCXNetwork` class provides a data model for working with NDEx networks that are stored in CX format.

Click here for more information about CX format.

Note

The term niceCX is CX with no duplicate aspects.

Methods are provided to add nodes, edges, node attributes, edge attributes, etc. Once a :class:`~ndex2.nice_cx_network.NiceCXNetwork` object is populated it can be saved to the NDEx server by calling either :func:`~ndex2.nice_cx_network.NiceCXNetwork.upload_to()` to create a new network or :func:`~ndex2.nice_cx_network.NiceCXNetwork.upload_to()` to update an existing network.

To see deprecated methods go to Deprecated NiceCXNetwork methods

Methods for building niceCX

see also this notebook

Node methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: create_node, set_node_attribute

Edge methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: create_edge, set_edge_attribute

Network methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: set_context, set_name, set_network_attribute, set_opaque_aspect

Methods for accessing niceCX properties

see also this notebook

Node methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: get_node_attribute, get_node_attribute_value, get_node_attributes, get_nodes

Edge methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: get_edge_attribute, get_edge_attribute_value, get_edge_attributes, get_edges

Network methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: get_context, get_name, get_network_attribute, get_network_attribute_names, get_opaque_aspect

Misc niceCX methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: apply_template, apply_style_from_network, print_summary, to_cx, to_cx_stream, to_networkx, to_pandas_dataframe, update_to, upload_to

Conversion of niceCX to other formats

There are several classes described below that facilitate conversion of :class:`~ndex2.nice_cx_network.NiceCXNetwork` object to other types (such as NetworkX)

Networkx

.. autoclass:: ndex2.nice_cx_network.DefaultNetworkXFactory
    :members: get_graph

Deprecated

These networkx converters are still callable, but have been deprecated

.. autoclass:: ndex2.nice_cx_network.LegacyNetworkXVersionTwoPlusFactory
    :members: get_graph

Deprecated NiceCXNetwork methods

.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: add_edge, add_node, get_edge_attribute_objects, get_node_attribute_objects, get_summary, set_provenance, get_provenance

Supported data types

The following data types are supported in methods that accept type

Example:

set_edge_attribute(0, 'weight', 0.5, type='double')
  • string
  • double
  • boolean
  • integer
  • long
  • list_of_string
  • list_of_double
  • list_of_boolean
  • list_of_integer
  • list_of_long

These constants are defined here: :py:const:`~ndex2.constants.VALID_ATTRIBUTE_DATATYPES`

Methods for creating niceCX from other data models

.. automodule:: ndex2
    :members: create_nice_cx_from_raw_cx, create_nice_cx_from_file, create_nice_cx_from_networkx, create_nice_cx_from_pandas, create_nice_cx_from_server

Client access to NDEx server API

The Ndex2 class provides methods to interface with the NDEx REST Server API The :py:class:`~ndex2.client.Ndex2` object can be used to access an NDEx server either anonymously or using a specific user account. For each NDEx server and user account that you want to use in your script or application, you create an :py:class:`~ndex2.client.Ndex2` instance.

Example creating anonymous connection:

import ndex2.client
anon_ndex=ndex2.client.Ndex2("http://public.ndexbio.org")

Example creating connection with username and password:

import ndex2.client
my_account="your account"
my_password="your password"
my_ndex=ndex2.client.Ndex2("http://public.ndexbio.org", my_account, my_password)
.. autoclass:: ndex2.client.Ndex2
    :members: add_networks_to_networkset, create_networkset, delete_network, delete_networks_from_networkset, get_neighborhood, get_neighborhood_as_cx_stream, get_network_as_cx_stream, get_network_ids_for_user, get_network_set, get_network_summary, get_sample_network, get_task_by_id, get_user_by_username, get_user_network_summaries, grant_network_to_user_by_username, grant_networks_to_group, grant_networks_to_user, make_network_private, make_network_public, save_cx_stream_as_new_network, save_new_network, search_networks, set_network_properties, set_network_system_properties, set_read_only, update_cx_network, update_network_group_permission, update_network_profile, update_network_user_permission

Constants

.. automodule:: ndex2.constants
    :members:

Exceptions

.. autoclass:: ndex2.exceptions.NDExError


.. autoclass:: ndex2.exceptions.NDExUnauthorizedError


.. autoclass:: ndex2.exceptions.NDExInvalidCXError