ndex2 3.4.0

Nice CX Python includes a client and a data model.

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

• ijson

• requests

• requests_toolbelt

• networkx

• urllib3

• pandas

• enum34 (Python < 3.4)

• numpy

• enum (Python 2.6 & 2.7)

Compatibility

Python 2.7+

Note

Python 2.7 may have some issues, Python 3.6+ is preferred

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

License

See LICENSE.txt

History

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

• Switched NiceCXNetwork.upload_to() to named arguments and added client parameter. Issue #80

• Switched NiceCXNetwork.update_to() to named arguments and added client parameter. Issue #81

• Fixed documentation NiceCXNetwork.update_to() to correctly state method returns empty string upon success. Issue #82

• 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

• 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

3.3.2 (2021-04-13)

• Fixed bug where NiceCXNetwork.create_node() and .create_edge() overwrote existing nodes/edges. Issue #60

• Fixed bug where enum34 package would be unnecessarily installed on versions of Python 3.4 and newer. Issue #76

• Improved documentation for Ndex2.set_network_properties() method. Issue #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

• 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

• Fixed bug in NiceCXNetwork.add_network_attribute() method where type not properly reset when adding duplicate attribute Issue #50

• Added delete_networksets() method to Ndex2 client to allow deletion of networksets Issue #59

3.2.0 (2019-04-23)

• Verify consistent conversion of cx for networkx 1.11 and 2.0+ Issue #30

• NiceCXNetwork.get_nodes(), NiceCXNetwork.get_edges(), NiceCXNetwork.get_metadata() needs to make correct iterator call in Python 2 Issue #44

• Add NiceCXNetwork.get_network_attribute_names() function enhancement Issue #45

• NiceCXNetwork.create_edge fails to correctly create edge when node dict passed in Issue #46

3.1.0a1 (2019-03-20)

• Add method to ndex2 python client to apply style from one NiceCXNetwork to another NiceCXNetwork Issue #43

3.0.0a1 (2019-02-11)

• In NiceCXNetwork class ability to add to User-Agent for calls to NDEx service Issue #36

• Methods in ndex2/client.py should raise an NDExError for invalid credentials Issue #39

• Add timeout flag to all web request calls Issue #33

• Update User-Agent to reflect actual version of software Issue #35

• NiceCXNetwork.set_node_attribute() incorrectly handles duplicate attributes Issue #41

• NiceCXNetwork.set_node_attribute() fails if node object passed to it Issue #42

• Passing None to user_agent parameterin Ndex2() constructor raises TypeError Issue #34

• Ndex2() constructor does not properly handle invalid json from server Issue #28

• Eliminate circular import between ndex2 and ndex2cx/nice_cx_builder.py Issue #31

• Replace print statements with logging calls in ndex2/client.py Issue #32

2.0.1 (2019-01-03)

• Fixed bug where logs directory is created within the package installation directory. Issue #26