ndex2

NDEx2 Python Client

.. _NDEx: http://ndexbio.org .. _NDEx REST Server API: http://home.ndexbio.org/using-the-ndex-server-api

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Overview

The NDEx2 Python Client provides methods to access NDEx_ via the NDEx REST Server API_. As well as methods for common operations on networks via the NiceCXNetwork class.

Dependencies

• six <https://pypi.org/project/six>__
• ijson <https://pypi.org/project/ijson>__
• requests <https://pypi.org/project/requests>__
• requests_toolbelt <https://pypi.org/project/requests_toolbelt>__
• networkx <https://pypi.org/project/networkx>__
• urllib3 <https://pypi.org/project/urllib3>__
• pandas <https://pypi.org/project/pandas>__
• enum34 <https://pypi.org/project/enum34>__ (Python < 3.4)
• numpy <https://pypi.org/project/numpy>__
• enum <https://pypi.org/project/enum>__ (Python 2.6 & 2.7)

Compatibility

Python 3.5+

.. note::

Python < 3.5 may have some issues

Installation

The NDEx2 Python Client module can be installed from the Python Package Index (PyPI) repository using PIP:

::

pip install ndex2

If you already have an older version of the ndex2 module installed, you can use this command instead:

::

pip install --upgrade ndex2

Resources

• The NDEx2 Python Client documentation <https://ndex2.readthedocs.io/en/latest/>_ is available on Read the Docs.
• Please refer to our Jupyter Notebook Tutorials <https://github.com/ndexbio/ndex-jupyter-notebooks>_ GitHub repository for code examples to work with networks using the NDEx2 Python Client and NiceCX object class.

License

See LICENSE.txt <https://github.com/ndexbio/ndex2-client/blob/master/LICENSE.txt>_

======= History

3.10.0 (2025-01-14)

• Enhancements

  • Added store_layout_in_pos argument in get_graph method of CX2NetworkXFactory that saves layout coordinates in G.pos (x and y) and G.zpos (z).
  • Added get_layout_from_pos argument in get_cx2network method of NetworkXToCX2NetworkFactory that determines the source of the layout coordinates. If True, the layout is derived from G.pos (x and y) and G.zpos. If False, the layout uses the (x, y, z) values specified as the node attributes.
  • Added interaction_col argument in get_cx2network of PandasDataFrameToCX2NetworkFactory that allows to specify the name of the column with edge interactions

• Bug fixes

  • Fix for string IDs in NetworkX networks - cast to integer if possible or add as name attribute.
  • Fix for DataFrames without column names

3.9.0 (2024-06-18)

• Enhancements

  • Added set_name(), remove_node_attribute(), remove_edge_attribute, get_opaque_aspect(), and set_opaque_aspect() to CX2Network class.

• Bug fixes

  • Fixed bug in type conversion. Datatypes in shorter form such as 'str', 'int' etc. are accepted.

3.8.0 (2024-02-07)

• Enhancements
  • Added add_network_attribute(), add_node_attribute(), add_edge_attribute(), lookup_node_id_by_name() to CX2Network class.
  • Added new parameters to get_cx2network in PandasDataFrameToCX2NetworkFactory to make it easier to convert Pandas Dataframe.
  • Added get_nodelist_table() to CX2NetworkPandasDataFrameFactory class.

3.7.0 (2024-01-03)

• Enhancements
  • Added CX2NetworkXFactory under cx2.py module to convert CX2Network object to NetworkX Graph <https://networkx.org>__
  • Added NetworkXToCX2NetworkFactory under cx2.py module to convert NetworkX Graph <https://networkx.org>__ to CX2Network object
  • Added PandasDataFrameToCX2NetworkFactory under cx2.py module to convert Pandas DataFrame <https://pandas.org>__ to CX2Network object
  • Added CX2NetworkPandasDataFrameFactory under cx2.py module to convert CX2Network object to Pandas DataFrame <https://pandas.org>__

3.6.0 (2023-11-14)

• Enhancements

  • Added CX2Network class under cx2.py module to represent networks CX2 format <https://cytoscape.org/cx/cx2/specification/cytoscape-exchange-format-specification-(version-2)/>__
  • Added RawCX2NetworkFactory class under cx2.py to create CX2Network objects
  • Added NoStyleCXToCX2NetworkFactory class under cx2.py to convert NiceCXNetwork to CX2Network

• Bug fixes

  • Fixed SyntaxWarnings Issue #92 <https://github.com/ndexbio/ndex2-client/issues/92>__

3.5.1 (2023-04-11)

• Bug fixes
  • Fixed bug where ndex2.create_nice_cx_from_networkx() fails with numpy version 1.24 Issue #96 <https://github.com/ndexbio/ndex2-client/issues/96>__
  • Updated post and put calls in client.py to only pass credentials if they are set. This change is to accommodate changes in upcoming version 3 of requests library

3.5.0 (2022-06-28)

• Enhancements

  • Added skip_version_check parameter to Ndex2() constructor to let caller optionally bypass NDEx server call to see if v2 endpoint is supported

  • Added the following CX2 methods to Ndex2() client: get_network_as_cx2_stream(), get_network_aspect_as_cx2_stream(), save_cx2_stream_as_new_network(), save_new_cx2_network(), and update_cx2_network() Issue #87 <https://github.com/ndexbio/ndex2-client/issues/87>__

  • In Ndex2() client, methods that raise NDExError exceptions from calls to NDEx server will now raise the more specific NDExUnauthorizedError subclass when the response from NDEx server is a 401 aka unauthorized.

  • Added new parameters dataconverter and include_attributes to NiceCXNetwork.to_pandas_dataframe(). dataconverter parameter specifies data type conversion and include_attributes parameter lets caller specify whether all node/edge attributes are added to the resulting DataFrame

  • Added new parameter to ndex2.create_nice_cx_from_server() named ndex_client that lets caller specify NDex2() client object to use.

  • Passing None for the server positional parameter into ndex2.create_nice_cx_from_server(None, uuid='XXXX') will default to the production NDEx server

• Bug fixes

  • Fixed bug where creation of NiceCXNetwork from networkx via ndex2.create_nice_cx_from_networkx() incorrectly set the data type for boolean values to integer. Issue #83 <https://github.com/ndexbio/ndex2-client/issues/83>__

  • Fixed bug where converting NiceCXNetwork to networkx and back does not handle name attribute correctly. Issue #84 <https://github.com/ndexbio/ndex2-client/issues/84>__

  • Fixed bug where @context was lost if it was set as aspect in CX format and loaded into NiceCXNetwork object. Issue #88 <https://github.com/ndexbio/ndex2-client/issues/88>__

  • Fixed bug where creation of NiceCXNetwork from networkx via ndex2.create_nice_cx_from_networkx() incorrectly set the data type for empty list to string. Issue #90 <https://github.com/ndexbio/ndex2-client/issues/90>__

  • Fixed bug where Y coordinates of nodes would be inverted when converting to/from networkx from NiceCXNetwork. This was due to differences in coordinate systems between networkx and NiceCXNetwork

  • DefaultNetworkXFactory networkx converter (used by NiceCXNetwork.to_networkx(mode='default')) no longer converts edge attributes that are of type list into strings delimited by commas

  • Fixed bug where ndex2.create_nice_cx_from_server() failed on networks with provenanceHistory aspect

• Removals

  • Removed unused test methods from internal class NiceCXBuilder: load_aspect(), stream_aspect(), stream_aspect_raw()

  • Removed the following deprecated methods from NiceCXNetwork: add_node(), add_edge(), get_edge_attribute_object(), get_node_attribute_objects(), get_edge_attribute_objects(), add_metadata(), get_provenance(), set_provenance(), __merge_node_attributes(), create_from_pandas(), create_from_networkx(), create_from_server(), upload_new_network_stream(), & create_from_cx()

3.4.0 (2021-05-06)

• Added offset and limit parameters to Ndex2.get_network_ids_for_user() to enable retrieval of all networks for a user. Issue #78 <https://github.com/ndexbio/ndex2-client/issues/78>__

• Switched NiceCXNetwork.upload_to() to named arguments and added client parameter. Issue #80 <https://github.com/ndexbio/ndex2-client/issues/80>__

• Switched NiceCXNetwork.update_to() to named arguments and added client parameter. Issue #81 <https://github.com/ndexbio/ndex2-client/issues/81>__

• Fixed documentation NiceCXNetwork.update_to() to correctly state method returns empty string upon success. Issue #82 <https://github.com/ndexbio/ndex2-client/issues/82>__

• Fixed bug in NiceCXNetwork.set_opaque_aspect() where passing None in the aspect_elements parameter raised an error instead of removing the aspect

• Added Ndex2.get_user_by_id() method to get user information by NDEx user Id.

• Added Ndex2.get_id_for_user() method to get NDEx user Id by username.

• Added Ndex2.get_networksets_for_user_id() to get Network Sets for a given user Id. Issue #61 <https://github.com/ndexbio/ndex2-client/issues/61>__

• Improved documentation by adding intersphinx to provide links to python documentation for python objects.

3.3.3 (2021-04-22)

• Fixed bug where NiceCXNetwork.to_networkx() fails with ValueError when installed networkx version has X.Y.Z format (example: 2.5.1) Issue #79 <https://github.com/ndexbio/ndex2-client/issues/79>_

3.3.2 (2021-04-13)

• Fixed bug where NiceCXNetwork.create_node() and .create_edge() overwrote existing nodes/edges. Issue #60 <https://github.com/ndexbio/ndex2-client/issues/60>_

• Fixed bug where enum34 package would be unnecessarily installed on versions of Python 3.4 and newer. Issue #76 <https://github.com/ndexbio/ndex2-client/issues/76>_

• Improved documentation for Ndex2.set_network_properties() method. Issue #77 <https://github.com/ndexbio/ndex2-client/issues/77>_

3.3.1 (2019-09-23)

• Added MANIFEST.in file to include README.rst, HISTORY.rst, and LICENSE.txt files as well as documentation and tests so python setup.py install will work properly on distribution of this client on PyPI. Thanks to Ben G. for catching this. Issue #62 <https://github.com/ndexbio/ndex2-client/pull/62>_

• Minor updates to README.rst

3.3.0 (2019-09-11)

• Fixed bug where if server version is not 2.0 exactly then Ndex2() object incorrectly falls back to version of 1.3 of REST calls Issue #40 <https://github.com/ndexbio/ndex2-client/issues/40>_

• Fixed bug in NiceCXNetwork.add_network_attribute() method where type not properly reset when adding duplicate attribute Issue #50 <https://github.com/ndexbio/ndex2-client/issues/50>_

• Added delete_networksets() method to Ndex2 client to allow deletion of networksets Issue #59 <https://github.com/ndexbio/ndex2-client/issues/59>_

3.2.0 (2019-04-23)

• Verify consistent conversion of CX for networkx 1.11 and 2.0+ Issue #30 <https://github.com/ndexbio/ndex2-client/issues/30>_

• NiceCXNetwork.get_nodes(), NiceCXNetwork.get_edges(), NiceCXNetwork.get_metadata() needs to make correct iterator call in Python 2 Issue #44 <https://github.com/ndexbio/ndex2-client/issues/44>_

• Add NiceCXNetwork.get_network_attribute_names() function enhancement Issue #45 <https://github.com/ndexbio/ndex2-client/issues/45>_

• NiceCXNetwork.create_edge() fails to correctly create edge when node dict passed in Issue #46 <https://github.com/ndexbio/ndex2-client/issues/46>_

3.1.0a1 (2019-03-20)

• Add method to ndex2 python client to apply style from one NiceCXNetwork to another NiceCXNetwork Issue #43 <https://github.com/ndexbio/ndex2-client/issues/43>_

3.0.0a1 (2019-02-11)

• In NiceCXNetwork class ability to add to User-Agent for calls to NDEx service Issue #36 <https://github.com/ndexbio/ndex2-client/issues/36>_

• Methods in ndex2/client.py should raise an NDExError for invalid credentials Issue #39 <https://github.com/ndexbio/ndex2-client/issues/39>_

• Add timeout flag to all web request calls Issue #33 <https://github.com/ndexbio/ndex2-client/issues/33>_

• Update User-Agent to reflect actual version of software Issue #35 <https://github.com/ndexbio/ndex2-client/issues/35>_

• NiceCXNetwork.set_node_attribute() incorrectly handles duplicate attributes Issue #41 <https://github.com/ndexbio/ndex2-client/issues/41>_

• NiceCXNetwork.set_node_attribute() fails if node object passed to it Issue #42 <https://github.com/ndexbio/ndex2-client/issues/42>_

• Passing None to user_agent parameterin Ndex2() constructor raises TypeError Issue #34 <https://github.com/ndexbio/ndex2-client/issues/34>_

• Ndex2() constructor does not properly handle invalid json from server Issue #28 <https://github.com/ndexbio/ndex2-client/issues/28>_

• Eliminate circular import between ndex2 and ndex2cx/nice_cx_builder.py Issue #31 <https://github.com/ndexbio/ndex2-client/issues/31>_

• Replace print statements with logging calls in ndex2/client.py Issue #32 <https://github.com/ndexbio/ndex2-client/issues/32>_

2.0.1 (2019-01-03)

• Fixed bug where logs directory is created within the package installation directory. Issue #26 <https://github.com/ndexbio/ndex2-client/issues/26>_