NiceCXNetwork
-------------

.. note::

    Using the newer data model :py:class:`~ndex2.cx2.CX2Network`
    is encouraged since all networks on NDEx_ can be retrieved in newer `CX2 format`_ via
    the `NDEx REST Service`_

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

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
:py:meth:`~ndex2.nice_cx_network.NiceCXNetwork.upload_to` to create a new network or
:py:meth:`~ndex2.nice_cx_network.NiceCXNetwork.update_to` to update an existing network.

Methods
===========================

Example usage of the methods below can be found in the Jupyter notebook links here:

`Tutorial Notebook <https://github.com/ndexbio/ndex-jupyter-notebooks/blob/master/notebooks/NiceCX%20v2.0%20Tutorial.ipynb>`__
`Navigating NiceCXNetwork Notebook <https://github.com/ndexbio/ndex-jupyter-notebooks/blob/master/notebooks/NiceCX%20v2.0%20navigating%20the%20network.ipynb>`__

Node methods
****************************
.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: create_node, get_nodes, get_node_attributes, get_node_attribute, get_node_attribute_value, set_node_attribute,

Edge methods
****************************
.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: create_edge, get_edges, get_edge_attributes, get_edge_attribute, get_edge_attribute_value, set_edge_attribute
    :noindex:

Network methods
****************************
.. autoclass:: ndex2.nice_cx_network.NiceCXNetwork
    :members: get_context, get_name, get_network_attribute, get_network_attribute_names, get_opaque_aspect, set_context, set_name, set_network_attribute, set_opaque_aspect
    :noindex:

Miscellaneous 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
    :noindex:

Supported data types
=====================

The following `CX Data Types <https://home.ndexbio.org/data-model/#data_types>`__
are supported in methods that accept **type**

    Example:

    .. code-block:: python

        import ndex2
        net = ndex2.nice_cx_network.NiceCXNetwork()
        node_id = net.create_node('hi')
        net.set_node_attribute(node_id, 'somevalue', 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`

.. _NDEx: https://www.ndexbio.org
.. _`CX format`: https://cytoscape.org/cx/specification/cytoscape-exchange-format-specification-(version-1)
.. _CX: https://cytoscape.org/cx/specification/cytoscape-exchange-format-specification-(version-1)
.. _`CX2 format`: https://cytoscape.org/cx/cx2/specification/cytoscape-exchange-format-specification-(version-2)
.. _`NDEx REST Service`: https://home.ndexbio.org/using-the-ndex-server-api