NDEx2 Python Client

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 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 is available on Read the Docs.
• Please refer to our Jupyter Notebook Tutorials GitHub repository for code examples to work with networks using the NDEx2 Python Client and NiceCX object class.

License

See LICENSE.txt

Installation

From Pypi

Stable release

To install NDEx2 Python Client, run this command in your terminal:

pip install ndex2

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources

The sources for NDEx2 Python Client can be downloaded from the Github repo.

You can either clone the public repository:

git clone git://github.com/ndexbio/ndex2-client

Or download the tarball:

curl  -OL https://github.com/ndexbio/ndex2-client/tarball/master

Once you have a copy of the source, you can install it with:

python setup.py install

Quick Tutorial

Below are some small, fully runnable, code blocks that show how to download, edit, and upload networks in NDEx

Note

For examples below, it is assumed that NDEx2 Python client is

Download network from NDEx

The code block below uses the NDEx2 Python client to download BioGRID: Protein-Protein Interactions (SARS-CoV) network from NDEx as a NiceCXNetwork.

The number of nodes and edges are then printed out and the network is converted to Networkx object.

import json
import ndex2


# Create NDEx2 python client
client = ndex2.client.Ndex2()

# Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx
# https://www.ndexbio.org/viewer/networks/669f30a3-cee6-11ea-aaef-0ac135e8bacf
client_resp = client.get_network_as_cx_stream('669f30a3-cee6-11ea-aaef-0ac135e8bacf')

# Convert downloaded network to NiceCXNetwork object
net_cx = ndex2.create_nice_cx_from_raw_cx(json.loads(client_resp.content))

# Display information about network and output 1st 100 characters of CX
print('Name: ' + net_cx.get_name())
print('Number of nodes: ' + str(len(list(net_cx.get_nodes()))))
print('Number of nodes: ' + str(len(list(net_cx.get_edges()))))
print(json.dumps(net_cx.to_cx())[0:100])

# Create Networkx network
g = net_cx.to_networkx(mode='default')

print('Name: ' + str(g))
print('Number of nodes: ' + str(g.number_of_nodes()))
print('Number of edges: ' + str(g.number_of_edges()))
print('Network annotations: ' + str(g.graph))

Upload new network to NDEx

The code block below shows how to upload a network that is a NiceCXNetwork object to NDEx.

import ndex2

# Create a test network
net_cx = ndex2.nice_cx_network.NiceCXNetwork()

# Set name of network
net_cx.set_name('Upload new network to NDEx')

# Create two nodes and one edge
node_one_id = net_cx.create_node(node_name='foo', node_represents='representing foo')
node_two_id = net_cx.create_node(node_name='bar', node_represents='representing bar')
net_cx.create_edge(edge_source=node_one_id, edge_target=node_two_id, edge_interaction='interacts')

# Create client, be sure to replace <USERNAME> and <PASSWORD> with NDEx username & password
client = ndex2.client.Ndex2(username='<USERNAME>', password='<PASSWORD>')

# Save network to NDEx, value returned is link to raw CX data on server.
client.save_new_network(net_cx.to_cx(), visibility='PRIVATE')

# Example return value: https://www.ndexbio.org/v2/network/4027bead-89f2-11ec-b3be-0ac135e8bacf
# To view network in NDEx replace 'v2' with 'viewer' and add 's' to 'network' like so:
# https://www.ndexbio.org/viewer/networks/4027bead-89f2-11ec-b3be-0ac135e8bacf

Note

To update an existing network replace save_new_network() in code block above with update_cx_network() and set first argument to net_cx.to_cx_stream() and the second argument to str UUID of network

Add nodes, edges, and attributes to network

The code block below shows how to add nodes, edges and attributes to a NiceCXNetwork object

import ndex2

# create an empty NiceCXNetwork object
# a NiceCXNetwork could also be downloaded from NDEx or created from CX data
net_cx = ndex2.nice_cx_network.NiceCXNetwork()

# create a node, id of node is returned
node_one_id = net_cx.create_node(node_name='foo', node_represents='representing foo')

# create another node
node_two_id = net_cx.create_node(node_name='bar', node_represents='representing bar')

# create an edge connecting the nodes, id of edge is returned
edge_id = net_cx.create_edge(edge_source=node_one_id, edge_target=node_two_id, edge_interaction='interacts')

# add attribute named 'altname' to 'foo' node, nothing is returned
net_cx.set_node_attribute(node_one_id, 'altname', 'alternate name for foo', type='string')

# add attribute to 'bar' node
net_cx.set_node_attribute(node_two_id, 'altname', 'alternate name for bar', type='string')

# add an edge attribute named 'weight' with value of 0.5. Set as string
# value and then set type.
net_cx.set_edge_attribute(edge_id, 'weight', '0.5', type='double')

# Create Networkx network
g = net_cx.to_networkx(mode='default')

print('Name: ' + str(g))
print('Number of nodes: ' + str(g.number_of_nodes()))
print('Number of edges: ' + str(g.number_of_edges()))
print('Node annotations: ' + str(g.nodes.data()))
print('Edge annotations: ' + str(g.edges.data()))

Build a lookup table for node names to node ids

The code block below shows how to iterate through nodes in a NiceCXNetwork object and build a dict of node names to node ids. The network downloaded below is Multi-Scale Integrated Cell (MuSIC) v1

import ndex2
import json

# Create NDEx2 python client
client = ndex2.client.Ndex2()

# Download MuSIC network from NDEx
client_resp = client.get_network_as_cx_stream('7fc70ab6-9fb1-11ea-aaef-0ac135e8bacf')

# Convert downloaded network to NiceCXNetwork object
net_cx = ndex2.create_nice_cx_from_raw_cx(json.loads(client_resp.content))

node_name_dict = {}

# Build dictionary and print out all the nodes
for node_id, node_obj in net_cx.get_nodes():
    print('node_id: ' + str(node_id) + ' node_obj: ' + str(node_obj))
    node_name_dict[node_obj['n']] = node_id


# Print out dictionary
print(str(node_name_dict))

More Tutorials and Examples

• Basic Use of the NDEx2 Python Client: NDEx2 Client v2.0 Tutorial
• Working with the NiceCX Network Class: NiceCX v2.0 Tutorial

To use these tutorials or if Github isn’t showing the above notebooks in the browser, clone the ndex-jupyter-notebooks repository to your local machine and start Jupyter Notebooks in the project directory.

For information on installing and using Jupyter Notebooks, go to jupyter.org

• Click here for example code to load content into NDEx

Reference

The NDEx2 Python Client can be broken into two main parts:

1. NiceCXNetwork provides a data model for working with NDEx networks stored in CX format
2. Ndex2 REST client provides provides methods to interact with NDEx REST Service

Creating NiceCXNetwork objects

ndex2.create_nice_cx_from_raw_cx(cx)

Create a NiceCXNetwork() from a as a list of dict objects in CX format

Example:

import json
import ndex2

# cx_as_str is a str containing JSON in CX format above
net_cx = ndex2.create_nice_cx_from_raw_cx(json.loads(cx_as_str))

Parameters:cx (list) – CX as a list of dict objects Returns:NiceCXNetwork Return type:NiceCXNetwork()

ndex2.create_nice_cx_from_file(path)

Create a NiceCXNetwork() from a file that is in the CX format

Parameters:

path (str) – the path of the CX file

Raises:

• Exception – if path is not a file
• OSError – if there is an error opening the path file
• JSONDecodeError – if there is an error parsing the path file with json.load()

Returns:

NiceCXNetwork

Return type:

NiceCXNetwork()

ndex2.create_nice_cx_from_server(server, username=None, password=None, uuid=None, ndex_client=None)

Create a NiceCXNetwork() based on a network retrieved from NDEx, specified by its UUID.

Changed in version 3.5.0: Code refactor and ndex_client parameter has been added

If the network is not public, then username and password arguments (or ndex_client with username and password set) for an account on the server with permission to access the network must be supplied.

Example usage:

import ndex2

# Download BioGRID: Protein-Protein Interactions (SARS-CoV) from NDEx
# https://www.ndexbio.org/viewer/networks/669f30a3-cee6-11ea-aaef-0ac135e8bacf
net_cx = ndex2.create_nice_cx_from_server(None, uuid='669f30a3-cee6-11ea-aaef-0ac135e8bacf')

Note

If ndex_client is not passed in, this function internally creates Ndex2 using values from parameters passed into this function.

Parameters:

• server (str) – the URL of the NDEx server hosting the network
• username (str) – the user name of an account with permission to access the network
• password (str) – the password of an account with permission to access the network
• uuid (str) – the UUID of the network
• ndex_client (Ndex2) – Used as NDEx REST client overriding server, username and password parameters if set

Raises:

NDExError – If uuid is not specified

Returns:

NiceCXNetwork

Return type:

NiceCXNetwork()

Networkx

ndex2.create_nice_cx_from_networkx(G)

Creates a NiceCXNetwork based on a networkx.Graph graph.

Changed in version 3.5.0: Major refactor to fix multiple bugs #83, #84, #90

import ndex2
import networkx as nx

G = nx.Graph()
G.add_node(1, someval=1.5, name='node 1')
G.add_node(2, someval=2.5, name='node 2')
G.add_edge(1, 2, weight=5)

print(ndex2.create_nice_cx_from_networkx(G).to_cx())

The resulting NiceCXNetwork contains the nodes, edges and their attributes from the networkx.Graph graph and also preserves the graph ‘pos’ attribute as a CX cartesian coordinates aspect CARTESIAN_LAYOUT_ASPECT with the values of Y inverted

Description of how conversion is performed:

Network:

• Network name is set value of G.graph.get('name') or to created from networkx by ndex2.create_nice_cx_networkx() if name is None or not present

Nodes:

• Node id is value of n from this for loop: for n, d G.nodes(data=True): if n is NOT an int, new ids starting from 0 are used
• Node name is value of name attribute on the node or is set to id of node if name is not present.
• Node represents is value of represents attribute on the node or set is to node name if None or not present

Edges:

• Interaction is value of interaction attribute on the edge or is set to neighbor-of if None or not present

Note

Data types are inferred by using isinstance() and converted to corresponding CX data types. For list items, only the 1st item is examined to determine type

Parameters:G (networkx.Graph) – Graph to convert Raises:Exception – if G parameter is None or there is another error in conversion Returns:Converted network Return type:NiceCXNetwork

Pandas

ndex2.create_nice_cx_from_pandas(df, source_field=None, target_field=None, source_node_attr=[], target_node_attr=[], edge_attr=[], edge_interaction=None, source_represents=None, target_represents=None)

Create a NiceCXNetwork() from a pandas.DataFrame in which each row specifies one edge in the network.

Changed in version 3.5.0: Removed print statements showing progress and network name is now being set

If only the df argument is provided the pandas.DataFrame is treated as ‘SIF’ format, where the first two columns specify the source and target node ids of the edge and all other columns are ignored. The edge interaction is defaulted to “interacts-with”

If both the source_field and target_field arguments are provided, then those and any other arguments refer to headers in the pandas.DataFrame, controlling the mapping of columns to the attributes of nodes, and edges in the resulting NiceCXNetwork().

If a header is not mapped, the corresponding column is ignored.

If the edge_interaction is not specified, interaction is set to “interacts-with”

import ndex2
import pandas as pd

data = {'source': ['Node 1','Node 2'],
        'target': ['Node 2','Node 3'],
        'interaction': ['helps', 'hurts']}
df = pd.DataFrame.from_dict(data)

net = ndex2.create_nice_cx_from_pandas(df, source_field='source',
                                       target_field='target',
                                       edge_interaction='interaction')

print(net.get_nodes())
print(net.get_edges())

Note

The datatype for everything added to the network is the CX string type

Parameters:

• df (pandas.DataFrame) – Pandas dataframe to process
• source_field (str) – header name specifying the name of the source node.
• target_field (str) – header name specifying the name of the target node.
• source_node_attr (list) – list of header names specifying attributes of the source node.
• target_node_attr (list) – list of header names specifying attributes of the target node.
• edge_attr (list) – list of header names specifying attributes of the edge.
• edge_interaction (str) – the relationship between the source node and the target node, defaulting to “interacts-with”
• source_represents (str) –
• target_represents (str) –

Returns:

NiceCXNetwork

Return type:

NiceCXNetwork()

Converting NiceCXNetwork objects to other formats

Below are converters that facilitate conversion of NiceCXNetwork object to other types (such as NetworkX)

Networkx

class ndex2.nice_cx_network.DefaultNetworkXFactory(legacymode=False)

Converts NiceCXNetwork to networkx.Graph object or one of its subtypes

For details on implementation see get_graph()

Constructor

Note: the parameters in the constructor change behavior of get_graph()

Parameters:legacymode (bool) – If set to True then get_graph() behaves like NDEx2 Python client version 3.1 and earlier in that this method returns a networkx.Graph object. see get_graph() for more information Raises:NDExError – If invalid value is set in legacymode parameter

get_graph(nice_cx_network, networkx_graph=None)

Creates a networkx.Graph, or a subtype, object from nice_cx_network passed in.

Warning

Converting large networks (10,000+ edges or nodes) may take a long time and consume lots of memory.

The conversion is done as follows:

Any network attributes are copied to the networkx.Graph in manner described here: add_network_attributes_from_nice_cx_network()

For nodes:

All nodes are added with the node id set to the id or NODE_ID of input network nodes.

A node attribute named ‘name’ is set for each node with its value set to the value of the ‘name’ attribute from the input network.

If ‘r’ exists on node, the value is added as a node attribute named ‘represents’ (unless legacymode is set to True in constructor)

All other node attributes are added using the same attribute name as found in the input network. The value is directly set as it was found in input network (could be single object or list)

For edges:

Each edge is added setting the source to the value of EDGE_SOURCE attribute and target set as EDGE_TARGET attribute of input network.

Any edge attributes named EDGE_INTERACTION are renamed ‘interaction’ and stored as an attribute for the edge

Changed in version 3.5.0: If the value of an edge attribute is a list then the value is set directly in the graph as is as opposed to being converted into a comma delimited string

Coordinates are copied in manner described here: copy_cartesian_coords_into_graph()

Warning

If legacymode is set to True in constructor then:

• networkx.Graph created by this method does NOT support multiple edges between the same nodes. Extra edges encountered are ignored and not converted.
• In addition, the ‘r’ attribute in the node dict is NOT copied to the resulting networkx.Graph object.
• networkx_graph parameter is ignored

Parameters:

• nice_cx_network (NiceCXNetwork) – Network to extract graph from
• networkx_graph (networkx.Graph or subtype) – Empty networkx graph to populate which is IGNORED if legacymode is set to True in constructor. If unset and legacymode is False in constructor then a networkx.MultiDiGraph is created

Raises:

NDExError – if input network is None

Returns:

Input network converted to networkx Graph

Return type:

networkx.Graph if legacymode is set to True in constructor otherwise networkx.MultiDiGraph unless networkx_graph is set in which case networkx_graph is returned

This networkx converter is still callable, but has been deprecated

class ndex2.nice_cx_network.LegacyNetworkXVersionTwoPlusFactory

Deprecated since version 3.2.0: This implementation contains errors, but is left for backwards compatibility of NiceCXNetwork.to_networkx()

Converts NiceCXNetwork to networkx.Graph object following logic in legacy NDEx2 Python client when networkx 2.0+ is installed.

Warning

This implementation assumes networkx 2.0+ is installed and will fail with older versions.

For conversion details see get_graph()

Constructor

get_graph(nice_cx_network, networkx_graph=None)

Creates a networkx.Graph object from nice_cx_network passed in.

Deprecated since version 3.2.0: This implementation contains errors, but is left for backwards compatibility of NiceCXNetwork.to_networkx()

Warning

Converting large networks (10,000+ edges or nodes) may take a long time and consume lots of memory.

This implementation uses node name as ID for nodes, which is problematic if multiple nodes share the same name and results in invalid mapping of node positions

networkx.Graph created by this method does NOT support multiple edges between the same nodes. Extra edges encountered are ignored and not converted.

The conversion is done as follows:

Any network attributes are copied to the networkx.Graph in manner described here: add_network_attributes_from_nice_cx_network()

For nodes:

All nodes are added with the node id set to value of ‘n’ on node. For multiple nodes with same ‘n’ value behavior is unknown

A node attribute named ‘name’ is set for each node with its value set to the value of the ‘name’ attribute from the input network.

If ‘r’ exists on node, the value is added as a node attribute named ‘represents’

All other node attributes are added using the same attribute name as found in the input network. The value is directly set name as found in the input network. The value is directly set as it was found in input network (could be single object or list)

For edges:

Each edge is added setting the source to the value of ‘s’ attribute and target set as ‘t’ attribute of input network.

Any edge attributes named ‘i’ are renamed ‘interaction’ and stored as an attribute for the edge

If the value of an edge attribute is a list then the list values are turned into a string separated by a comma and then enclosed by double quotes.

Coordinates are copied in manner described here: copy_cartesian_coords_into_graph()

Parameters:

• nice_cx_network (NiceCXNetwork) – Network to extract graph from
• networkx_graph (networkx.Graph or subtype) – ignored by this implementation

Returns:

Input network converted to networkx Graph

Return type:

networkx.Graph

Base class for `Networkx <https://networkx.org/>`__ converters above

class ndex2.nice_cx_network.NetworkXFactory

Base class for subclasses that implement a factory that creates networkx.Graph objects and contains a couple utility methods used by implementing factory classes

add_edge(networkx_graph, source_node, target_node, attribute_dict)

Adds edge to graph dealing with differences between networkx 1.x and 2.x+

Parameters:

• networkx_graph (networkx.Graph or one of its subtypes) – networkx graph to add node to
• source_node – id of source node
• target_node – id of target node
• attribute_dict (dict) – dictionary of edge attributes

Returns:

None

add_network_attributes_from_nice_cx_network(nice_cx_network, networkx_graph)

Iterates through network attributes of input nice_cx_network appending the attributes to the graph object passed in setting the values like so:

networkx_graph.graph[attribute_name] = attribute_value

If the value of a network attribute is of type list then the values are converted to strings and concatenated into a single string separated by commas.

Parameters:

• nice_cx_network (NiceCXNetwork) – Network to extract network attributes from
• networkx_graph (networkx.Graph) – networkx Graph object, should work with any of the types of Graphs ie MultiGraph etc..

Raises:

NDExError – If either input parameter is None

Returns:

None

add_node(networkx_graph, nodeid, node_attributes, name=None, represents=None)

Adds node to graph dealing with differences between networkx 1.x and 2.x+

Parameters:

• networkx_graph (networkx.Graph or one of its subtypes) – networkx graph to add node to
• nodeid – node identifier can be string, int etc.
• node_attributes (dict) – dictionary of key => value data to set set node attributes with
• name (string) – name of node that is set as attribute with key ‘name’ on node
• represents – represents value for node that is set as attribute with key ‘represents’ on node

Returns:

None

copy_cartesian_coords_into_graph(nice_cx_network, networkx_graph)

Examines the nice_cx_network extracting the content of the opaque aspect CARTESIAN_LAYOUT_ASPECT

Changed in version 3.5.0: code now inverts value of y coordinate so position is correct in networkx

If data is found in above aspect, then this method iterates through the list of values which is assumed to be a dictionary of node ids with coordinates as seen here:

[
 { 'node': <id>, 'x': <x coord>, 'y': <y coord},
 { 'node': <id>, 'x': <x coord>, 'y': <y coord},
 .
 .
]

These values (as seen in example above) are stored in the networkx_graph object as tuples with id of node set as key like so:

networkx_graph.pos[<id from above>] = (<x coord>, <y coord>)

Parameters:

• nice_cx_network (NiceCXNetwork) – Input network
• networkx_graph (networkx.Graph) – Network to append coordinates to

Raises:

NDExError – If either input parameter is None

Returns:

None

Pandas

For conversion to Pandas see to_pandas_dataframe()

NiceCXNetwork

The NiceCXNetwork class provides a data model for working with NDEx networks that are stored in 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 NiceCXNetwork object is populated it can be saved to the NDEx server by calling either upload_to() to create a new network or 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 Navigating NiceCXNetwork Notebook

Node methods

class ndex2.nice_cx_network.NiceCXNetwork(**attr)

create_node(node_name=None, node_represents=None)

Creates a new node with the corresponding name and represents (external id)

Warning

Version 3.3.1 and prior of this library had a bug that caused this method to behave incorrectly. Please upgrade to 3.3.2 or greater.

Example:

my_node = create_node(node_name='MAPK1, node_represents='1114208')

Parameters:

• node_name (str) – Name of the node
• node_represents (str) – Representation of the node (alternate identifier)

Returns:

Node ID

Return type:

int

get_node_attribute(node, attribute_name)

Get the node attribute of a node, where the node may be specified by its id or passed in as an object.

Example:

get_node_attribute(my_node, 'Pathway') # returns: {'@id': 0, 'n': 'diffusion-heat', 'v': 0.832, 'd': 'double'}

Parameters:

• node (int or node dict with @id attribute) – node object or node id
• attribute_name – attribute name

Returns:

the node attibute object or None if the attribute doesn’t exist

Return type:

dict

get_node_attribute_value(node, attribute_name)

Get the value(s) of an attribute of a node, where the node may be specified by its id or passed in as an object.

Example:

get_node_attribute_value(my_node, 'Pathway') # returns: 'Signal Transduction / Growth Regulation'

Parameters:

• node (int or node dict with @id attribute) – node object or node id
• attribute_name – attribute name

Returns:

the value of the attibute or None if the attribute doesn’t exist

Return type:

string

get_node_attributes(node)

Get the attribute objects of a node, where the node may be specified by its id or passed in as an object.

Example:

get_node_attributes(my_node) # returns: [{'po': 0, 'n': 'Pathway', 'v': 'Signal Transduction / Growth Regulation'}]

Parameters:node (int or node dict with @id attribute) – node object or node id Returns:node attributes Return type:list

get_nodes()

Returns an iterator over node ids as keys and node objects as values.

Example:

for id, node in nice_cx.get_nodes():

node_name = node.get('n')

node_represents = node.get('r')

Returns:iterator over nodes Return type:iterator

set_node_attribute(node, attribute_name, values, type=None, overwrite=False)

Set an attribute of a node, where the node may be specified by its id or passed in as a node dict.

Example:

set_node_attribute(my_node, 'Pathway', 'Signal Transduction / Growth Regulation')

or

set_node_attribute(my_node, 'Mutation Frequency', 0.007, type='double')

Parameters:

• node (int or node dict with @id attribute) – Node to add the attribute to
• attribute_name (string) – attribute name
• values (list, string, int or double) – A value or list of values of the attribute
• type (str) – The datatype of the attribute values, defaults is string. See Supported data types
• overwrite (bool True means to overwrite node attribute named attribute_name) – If True node attribute matching ‘attribute_name’ is removed first otherwise code blindly adds attribute

Returns:

None

Return type:

None

Edge methods

class ndex2.nice_cx_network.NiceCXNetwork(**attr)

create_edge(edge_source=None, edge_target=None, edge_interaction=None)

Create a new edge in the network by specifying source-interaction-target

Warning

Version 3.3.1 and prior of this library had a bug that caused this method to behave incorrectly. Please upgrade to 3.3.2 or greater.

Example:

my_edge = create_edge(edge_source=my_node, edge_target=my_node2, edge_interaction='up-regulates')

Parameters:

• edge_source (int, dict (with EDGE_ID property)) – The source node of this edge, either its id or the node object itself.
• edge_target (int, dict (with EDGE_ID property)) – The target node of this edge, either its id or the node object itself.
• edge_interaction (string) – The interaction that describes the relationship between the source and target nodes

Returns:

Edge ID

Return type:

int

get_edge_attribute(edge, attribute_name)

Get the edge attributes of an edge, where the edge may be specified by its id or passed in as an object.

Example:

get_edge_attribute(my_edge, 'weight')

# returns: {'@id': 0, 'n': 'weight', 'v': 0.849, 'd': 'double'}

Parameters:

• edge (int or edge dict with @id attribute) – Edge object or edge id
• attribute_name – Attribute name

Returns:

Edge attribute object

Return type:

list, string, int or double

get_edge_attribute_value(edge, attribute_name)

Get the value(s) of an attribute of an edge, where the edge may be specified by its id or passed in as an object.

Example:

get_edge_attribute_value(my_edge, 'weight')

# returns: 0.849

Parameters:

• edge (int or edge dict with @id attribute) – Edge object or edge id
• attribute_name – Attribute name

Returns:

Edge attribute value(s)

Return type:

list, string, int or double

get_edge_attributes(edge)

Get the attribute objects of an edge, where the edge may be specified by its id or passed in as an object.

Example:

get_edge_attributes(my_edge)

# returns: [{'@id': 0, 'n': 'weight', 'v': 0.849, 'd': 'double'}, {'@id': 0, 'n': 'Type', 'v': 'E1'}]

Parameters:edge (int or edge dict with @id attribute) – Edge object or edge id Returns:Edge attribute objects Return type:list of edge dict

get_edges()

Returns an iterator over edge ids as keys and edge objects as values.

Example:

for edge_id, edge_obj in nice_cx.get_edges():

print(edge_obj.get('i')) # print interaction

print(edge_obj.get('s')) # print source node id

Returns:Edge iterator Return type:iterator

set_edge_attribute(edge, attribute_name, values, type=None)

Set the value(s) of attribute of an edge, where the edge may be specified by its id or passed in an object.

Example:

set_edge_attribute(0, 'weight', 0.5, type='double')

or

set_edge_attribute(my_edge, 'Disease', 'Atherosclerosis')

Parameters:

• edge (int or edge dict with @id attribute) – Edge to add the attribute to
• attribute_name (str) – Attribute name
• values (list) – A value or list of values of the attribute
• type (str) – The datatype of the attribute values, defaults to the python datatype of the values. See Supported data types

Returns:

None

Return type:

None

Network methods

class ndex2.nice_cx_network.NiceCXNetwork(**attr)

get_context()

Get the @context information of the network. This information maps namespace prefixes to their defining URIs

Example:

{'pmid': 'https://www.ncbi.nlm.nih.gov/pubmed/'}

Returns:context object Return type:dict

get_name()

Get the network name

Returns:Network name Return type:string

get_network_attribute(attribute_name)

Get the value of a network attribute

Parameters:attribute_name (string) – Attribute name Returns:Network attribute object Return type:dict

get_network_attribute_names()

Creates a a generator that gets network attribute names.

Returns:attribute name via a generator Return type:string

get_opaque_aspect(aspect_name)

Get the elements of the aspect specified by aspect_name

Parameters:aspect_name (string) – the name of the aspect to retrieve. Returns:Opaque aspect Return type:list of aspect elements

set_context(context)

Set the @context information of the network. This information maps namespace prefixes to their defining URIs

Example:

from ndex2.nice_cx_network import NiceCXNetwork

net = NiceCXNetwork()
net.set_context({'pmid': 'https://www.ncbi.nlm.nih.gov/pubmed/'})

Parameters:context (dict or list) – dict where key is name and value is URI or list of those dict objects Raises:NDExError – If context is not of type list or dict Returns:None Return type:none

set_name(network_name)

Set the network name

Example:

set_name('P38 Signaling')

Parameters:network_name (string) – Network name Returns:None Return type:None

set_network_attribute(name, values=None, type=None)

Set an attribute of the network

from ndex2.nice_cx_network import NiceCXNetwork

net = NiceCXNetwork()
net.set_network_attribute(name='networkType', values='Genetic interactions')

Parameters:

• name (str) – Attribute name
• values (list, str, float, or int) – The values of the attribute
• type (str) – The datatype of the attribute values. See Supported data types

Returns:

None

Return type:

none

set_opaque_aspect(aspect_name, aspect_elements)

Set the aspect specified by aspect_name to the list of aspect elements. If aspect_elements is None, the aspect is removed.

Changed in version 3.5.0: Fixed bug where passing None in aspect_elements did NOT remove aspect. Code also now raises NDExError if input values are invalid

from ndex2.nice_cx_network import NiceCXNetwork
net = NiceCXNetwork()

# to set an opaque aspect
net.set_opaque_aspect('foo', [{'data': 'val'}])

# to remove an opaque aspect named 'foo'
net.set_opaque_aspect('foo', None)

Parameters:

• aspect_name (str) – Name of the aspect
• aspect_elements (list of dict or dict) – Aspect element

Raises:

NDExError – If aspect_name is None, or if aspect_elements is not None, dict, or list

Returns:

None

Return type:

none

Miscellaneous methods

class ndex2.nice_cx_network.NiceCXNetwork(**attr)

apply_style_from_network(nicecxnetwork)

Applies Cytoscape visual properties from the network passed into this method. The style is pulled from VISUAL_PROPERTIES or CY_VISUAL_PROPERTIES

Parameters:

nicecxnetwork (NiceCXNetwork) – Network to extract style from

Raises:

• TypeError – If object passed in is NOT a NiceCXNetwork object or if object is None
• NDExError – If NiceCXNetwork does not have any visual styles

Returns:

None

Return type:

None

apply_template(server, uuid, username=None, password=None)

Applies the Cytoscape visual properties of a network from the provided uuid to this network.

This allows the use of networks formatted in Cytoscape as templates to apply visual styles to other networks.

Changed in version 3.5.0: Fixed bug where style from template was appended instead of replacing the existing style. In most cases, method now raises NDExError and subclasses instead of more generic Exception

from ndex2.nice_cx_network import NiceCXNetwork

nice_cx = NiceCXNetwork()
nice_cx.apply_template('public.ndexbio.org',
                       '51247435-1e5f-11e8-b939-0ac135e8bacf')

Parameters:

• server (str) – server host name (i.e. public.ndexbio.org)
• username (str) – username (optional - used when accessing private networks)
• password (str) – password (optional - used when accessing private networks)
• uuid (str) – uuid of the styled network

Raises:

• NDExError – Raised if server or uuid not set or if metaData is not found in the network specified by uuid or some other server error
• NDExUnauthorizedError – If credentials not authorized to access network specified by uuid
• NDExNotFoundError – If network with uuid not found

Returns:

None

Return type:

None

print_summary()

Print a network summary

Returns:Network summary Return type:string

to_cx(log_to_stdout=True)

Return the CX corresponding to the network.

Changed in version 3.5.0: Added log_to_stdout param which lets caller silence print statement Generating CX

Parameters:log_to_stdout (bool) – If True then code will output to standard out Generating CX Returns:CX representation of the network Return type:CX (list of dict aspects)

to_cx_stream()

Returns a stream of the CX corresponding to the network. Can be used to post to endpoints that can accept streaming inputs

Returns:The CX stream representation of this network. Return type:io.BytesIO

to_networkx(mode='legacy')

Returns a NetworkX Graph() object or one of its subclasses based on the network. The mode parameter dictates how the translation occurs.

This method currently supports the following mode values:

Warning

legacy mode has known bugs when networkx 2.0+ or greater is installed.

See the description on legacy mode below for more information.

Modes:

legacy:

If mode set to legacy then this method will behave as it has for all versions of NDEx2 Python Client 3.1.0 and earlier which varies depending on version of networkx installed as described here:

For networkx 2.0 and greater: (see LegacyNetworkXVersionTwoPlusFactory)

For older versions of networkx the following class is used with the legacymode parameter set to True: (see DefaultNetworkXFactory)

default:

If mode is default or None then this method uses DefaultNetworkXFactory regardless of networkx installed with legacymode set to False

Note

default mode is the preferred mode to use

Examples:

# returns networkx graph using improved converter
graph = nice_cx.to_networkx(mode='default')

# returns networkx graph using legacy implementation
graph = nice_cx.to_networkx(mode='legacy)

Parameters:mode (string) – Since translation to networkx can be done in many ways this mode lets the caller dictate the method. Raises:NDExError – If mode is not None, ‘legacy’, or ‘default’ Returns:Networkx graph Return type:networkx.Graph or networkx.MultiGraph

to_pandas_dataframe(dataconverter=<ndex2.util.PandasDataConverter object>, include_attributes=False)

Network edges exported as a pandas.DataFrame

Changed in version 3.5.0: Added include_attributes and dataconverter parameters

The following columns will be added to the pandas.DataFrame:

• source - Name of edge source node
• interaction - Interaction between source and target node
• target - Name of edge target node

If include_attributes parameter is set to True then:

All edge attributes will be also added as separate columns with same name.

Attributes on source node will be added as a columns with source_ prefixed to name.

Attributes on target node will be added as columns with target_ prefixed to name.

Note

Values will converted based on CX data types. See PandasDataConverter for information on how conversion is performed

from ndex2.nice_cx_network import NiceCXNetwork

net = NiceCXNetwork()
node_one = net.create_node('node1')
node_two = net.create_node('node2')

net.set_node_attribute(node_one, 'weight', 0.5, type='double')
net.set_node_attribute(node_two, 'weight', 0.2, type='double')

edge_one = net.create_edge(edge_source=node_one, edge_target=node_two,
                           edge_interaction='binds')

net.set_edge_attribute(edge_one, 'edgelabel', 'an edge')
df = net.to_pandas_dataframe(include_attributes=True) # df is now a pandas dataframe

print(df.head())

Output from above code block:

   source interaction target edgelabel  target_weight  source_weight
0  node1       binds  node2   an edge            0.2            0.5

Note

This method only processes nodes, edges, node attributes and edge attributes, but not network attributes or other aspects

Parameters:

• dataconverter (DataConverter) – Object that converts CX data values to native data types. Default is PandasDataConverter
• include_attributes (bool) – If True then edge attributes are added to pandas.DataFrame, otherwise only source, target, and interaction are added

Raises:

NDExInvalidParameterError – If include_attributes is not None or a bool

Returns:

Edge table with attributes

Return type:

pandas.DataFrame

update_to(uuid, server=None, username=None, password=None, user_agent='', client=None)

Replace the network on NDEx server with matching NDEx uuid with this network.

Changed in version 3.4.0: This method was switched to named arguments and the server and account credentials can be passed in one of two ways.

Option 1) Set username and password parameters.

Option 2) Set client parameter with valid Ndex2 object

Note

If client parameter is set, username, password, and server parameters are ignored.

Example:

import ndex2
nice_cx = ndex2.nice_cx_network.NiceCXNetwork()
nice_cx.create_node('foo')

# using production NDEx server
nice_cx.update_to('2ec87c51-c349-11e8-90ac-525400c25d22',
                  username=user_var,
                  password=password_var)

# if one needs to use alternate NDEx server
nice_cx.update_to('2ec87c51-c349-11e8-90ac-525400c25d22',
                  server='public.ndexbio.org',
                  username=username_var,
                  password=password_var)

# Option 2, create Ndex2 client object
ndex_client = ndex2.client.Ndex2(username=username_var,
                                 password=password_var)

# using NDEx client object for connection
nice_cx.update_to('2ec87c51-c349-11e8-90ac-525400c25d22',
                  client=ndex_client)

Parameters:

• uuid (str) – UUID of the network on NDEx.
• server (str) – The NDEx server to upload the network to. Leaving unset or None will use production.
• username (str) – The username of the account to store the network.
• password (str) – The password for the account.
• user_agent (str) – String to append to User-Agent field sent to NDEx REST service
• client (Ndex2) – NDEx2 object with valid credentials. If set server, username, and password parameters will be ignored.

Returns:

Empty string

Return type:

str

upload_to(server=None, username=None, password=None, user_agent='', client=None)

Upload this network as a new network on NDEx server.

Changed in version 3.4.0: This method was switched to named arguments and the server and account credentials can be passed in one of two ways.

Option 1) Set username and password parameters.

Option 2) Set client parameter with valid Ndex2 object

Note

If client parameter is set, username, password, and server parameters are ignored

Example:

import ndex2
nice_cx = ndex2.nice_cx_network.NiceCXNetwork()
nice_cx.create_node('foo')

# using production NDEx server
nice_cx.update_to(username=user_var,
                  password=password_var)

# if one needs to use alternate NDEx server
nice_cx.update_to(server='public.ndexbio.org',
                  username=username_var,
                  password=password_var)

# Option 2, create Ndex2 client object
ndex_client = ndex2.client.Ndex2(username=username_var,
                                 password=password_var)

# using NDEx client object for connection
nice_cx.update_to(client=ndex_client)

Parameters:

• server (str) – The NDEx server to upload the network to. Leaving unset or None will use production
• username (str) – The username of the account to store the network.
• password (str) – The password for the account.
• user_agent (str) – String to append to User-Agent field sent to NDEx REST service
• client (Ndex2) – NDEx2 object with valid credentials. If set server, username, and password parameters will be ignored.

Returns:

The UUID of the network on NDEx.

Return type:

str

Supported data types

The following CX Data Types are supported in methods that accept type

Example:

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: VALID_ATTRIBUTE_DATATYPES

Ndex2 REST client

The Ndex2 class provides methods to interface with the NDEx REST Server API The 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 Ndex2 instance.

Example creating anonymous connection:

import ndex2.client
anon_ndex=ndex2.client.Ndex2()

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)

class ndex2.client.Ndex2(host=None, username=None, password=None, update_status=False, debug=False, user_agent='', timeout=30, skip_version_check=False)

A class to facilitate communication with an NDEx server.

If host is not provided it will default to the NDEx public server. UUID is required

Creates a connection to a particular NDEx server.

New in version 3.5.0: skip_version_check parameter added

Parameters:

• host (str) – The URL of the server.
• username (str) – The username of the NDEx account to use. (Optional)
• password (str) – The account password. (Optional)
• update_status (bool) – If set to True tells constructor to query service for status
• user_agent (str) – String to append to User-Agent header sent with all requests to server
• timeout (float or tuple(float, float)) – The timeout in seconds value for requests to server. This value is passed to Request calls Click here for more information
• skip_version_check (bool) – If True, it is assumed NDEx server supports v2 endpoints, otherwise NDEx server is queried to see if v2 endpoints are supported

add_networks_to_networkset(set_id, networks)

Add networks to a network set. User must have visibility of all networks being added

Parameters:

• set_id (str) – network set id
• networks (list) – networks (ids as str) that will be added to the set

Returns:

None

Return type:

None

create_networkset(name, description)

Creates a new network set

Parameters:

• name (str) – Network set name
• description (str) – Network set description

Returns:

URI of the newly created network set

Return type:

str

delete_network(network_id, retry=5)

Deletes the specified network from the server

Parameters:

• network_id (str) – Network id
• retry (int) – Number of times to retry if deleting fails

Raises:

NDExUnauthorizedError – If credentials are invalid or not set

Returns:

Error json if there is an error. Blank

Return type:

str

delete_networks_from_networkset(set_id, networks, retry=5)

Removes network(s) from a network set.

Parameters:

• set_id (str) – network set id
• networks (list) – networks (ids as str) that will be removed from the set
• retry (int) – Number of times to retry

Returns:

None

Return type:

None

delete_networkset(networkset_id)

Deletes the network set, requires credentials

Parameters:

networkset_id (str) – networkset UUID id

Raises:

• NDExInvalidParameterError – for invalid networkset id parameter
• NDExUnauthorizedError – If no credentials or user is not authorized
• NDExNotFoundError – If no networkset with id passed in found
• NDExError – For any other error with contents of error in message

Returns:

None upon success

get_id_for_user(username)

Gets NDEx user Id for user

New in version 3.4.0.

import ndex2.client
my_ndex = ndex2.client.Ndex2()
my_ndex.get_id_for_user('nci-pid')

Parameters:

username (str) – Name of user on NDEx. If None user set in constructor of this client will be used.

Raises:

• NDExError – If there was an error on the server.
• NDExInvalidParameterError – If username is empty string or is of type other then str.

Returns:

Id of user on NDEx server.

Return type:

str

get_neighborhood(network_id, search_string, search_depth=1, edge_limit=2500)

Get the CX for a subnetwork of the network specified by UUID network_id and a traversal of search_depth steps around the nodes found by search_string.

Parameters:

• network_id (str) – The UUID of the network.
• search_string (str) – The search string used to identify the network neighborhood.
• search_depth (int) – The depth of the neighborhood from the core nodes identified.
• edge_limit (int) – The maximum size of the neighborhood.

Returns:

The CX json object.

Return type:

response object

get_neighborhood_as_cx_stream(network_id, search_string, search_depth=1, edge_limit=2500, error_when_limit=True)

Get a CX stream for a subnetwork of the network specified by UUID network_id and a traversal of search_depth steps around the nodes found by search_string.

Parameters:

• network_id (str) – The UUID of the network.
• search_string (str) – The search string used to identify the network neighborhood.
• search_depth (int) – The depth of the neighborhood from the core nodes identified.
• edge_limit (int) – The maximum size of the neighborhood.
• error_when_limit (bool) – Default value is true. If this value is true the server will stop streaming the network when it hits the edgeLimit, add success: false and error: “EdgeLimitExceeded” in the status aspect and close the CX stream. If this value is set to false the server will return a subnetwork with edge count up to edgeLimit. The status aspect will be a success, and a network attribute {“EdgeLimitExceeded”: “true”} will be added to the returned network only if the server hits the edgeLimit..

Returns:

The response.

Return type:

response object

get_network_as_cx2_stream(network_id, access_key=None)

Get the existing network with UUID network_id from the NDEx connection as CX2 stream contained within a requests.Response object

New in version 3.5.0.

Example usage:

from ndex2.client import Ndex2
client = Ndex2(skip_version_check=True)

# 7fc.. is UUID MuSIC v1 network: http://doi.org/10.1038/s41586-021-04115-9
client_resp = client.get_network_as_cx2_stream('7fc70ab6-9fb1-11ea-aaef-0ac135e8bacf')

# for HTTP status code, 200 means success
print(client_resp.status_code)

# for smaller networks one can get the CX2 by calling:
print(client_resp.json())

Note

For retrieving larger networks see requests.Response.iter_content()

This method sets stream=True in the request to avoid loading response into memory.

Parameters:

• network_id – The UUID of the network
• access_key – Optional access key UUID

Raises:

NDExError – If there was an error

Returns:

Requests library response with CX2 in content and status code of 200 upon success

Return type:

requests.Response

get_network_as_cx_stream(network_id)

Get the existing network with UUID network_id from the NDEx connection as a CX stream.

Parameters:network_id (str) – The UUID of the network. Returns:The response. Return type:response object

get_network_aspect_as_cx_stream(network_id, aspect_name)

Get the specified aspect of the existing network with UUID network_id from the NDEx connection as a CX stream.

For a list of aspect names look at Core Aspects section of CX Data Model Documentation

Parameters:

• network_id (str) – The UUID of the network.
• aspect_name – The aspect NAME.

Returns:

The response.

Return type:

response object

get_network_ids_for_user(username, offset=0, limit=1000)

Get the network UUIDs owned by the user as well as any networks shared with the user. As set via limit parameter only the first 1,000 ids are returned. The offset parameter combined with limit provides pagination support.

Changed in version 3.4.0: offset and limit parameters added.

Parameters:

• username (str) – NDEx username
• offset (int) – Starting position of the query. If set, limit parameter must be set to a positive value.
• limit (int) – Number of summaries to return starting from offset If set to None or 0 all summaries will be returned.

Raises:

NDExInvalidParameterError – If offset/limit parameters are not of type int. If offset parameter is set to positive number and limit is 0 or negative.

Returns:

List of uuids as str

Return type:

list

get_network_set(set_id)

Gets the network set information including the list of networks

Deprecated since version 3.2.0: Use get_networkset() instead.

Parameters:set_id (str) – network set id Returns:network set information Return type:dict

get_network_summary(network_id)

Gets information and status of a network

Example usage:

from ndex2.client import Ndex2
client = Ndex2(skip_version_check=True)

# 7fc.. is UUID MuSIC v1 network: http://doi.org/10.1038/s41586-021-04115-9
net_sum = client.get_network_summary('7fc70ab6-9fb1-11ea-aaef-0ac135e8bacf')

print(net_sum)

Example result:

{
  "ownerUUID": "daa09f36-8cdd-11e7-a10d-0ac135e8bacf",
  "isReadOnly": true,
  "subnetworkIds": [],
  "isValid": true,
  "warnings": [],
  "isShowcase": true,
  "doi": "10.18119/N9188W",
  "isCertified": true,
  "indexLevel": "ALL",
  "hasLayout": true,
  "hasSample": false,
  "cxFileSize": 82656,
  "cx2FileSize": 68979,
  "visibility": "PUBLIC",
  "nodeCount": 70,
  "edgeCount": 87,
  "completed": true,
  "version": "1.0",
  "owner": "yue",
  "description": "<div><br/></div><div>Two central approaches for mapping cellular structure – protein fluorescent imaging and protein biophysical association – each generate extensive datasets but of distinct qualities and resolutions that are typically treated separately. The MuSIC map is designed to address this challenge, by integrating immunofluorescent images in the Human Protein Atlas with ongoing affinity purification experiments from the BioPlex resource. The result is a unified hierarchical map of eukaryotic cell architecture. In the MuSIC hierarchy, nodes represent systems and arrows indicate containment of the lower system by the upper. Node color indicates known (gold) or putative novel (purple) systems. The size of each circle is based on the number of proteins in the system. The relative height of each system in the layout is determined based on the predicted diameter of the system in MuSIC.<br/></div>",
  "name": "Multi-Scale Integrated Cell (MuSIC) v1",
  "properties": [
    {
      "subNetworkId": null,
      "predicateString": "author",
      "dataType": "string",
      "value": "Yue Qin"
    },
    {
      "subNetworkId": null,
      "predicateString": "rights",
      "dataType": "string",
      "value": "MIT license (MIT)"
    },
    {
      "subNetworkId": null,
      "predicateString": "rightsHolder",
      "dataType": "string",
      "value": "Yue Qin"
    },
    {
      "subNetworkId": null,
      "predicateString": "reference",
      "dataType": "string",
      "value": "Yue Qin, Edward L. Huttlin, Casper F. Winsnes, Maya L. Gosztyla, Ludivine Wacheul, Marcus R. Kelly, Steven M. Blue, Fan Zheng, Michael Chen, Leah V. Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John J. Lee, Wei Ouyang, Sophie N. Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F. Kreisberg, Steven P. Gygi, Jianzhu Ma, J. Wade Harper, Gene W. Yeo, Denis L. J. Lafontaine, Emma Lundberg, Trey Ideker<br><strong>A multi-scale map of cell structure fusing protein images and interactions</strong><br><i>Nature 600, 536–542 (2021).</i>, (2021)<br><a href="http://doi.org/10.1038/s41586-021-04115-9"  target="_blank">10.1038/s41586-021-04115-9</a>"
    }
  ],
  "externalId": "7fc70ab6-9fb1-11ea-aaef-0ac135e8bacf",
  "isDeleted": false,
  "modificationTime": 1630270298717,
  "creationTime": 1590539529001
}

Note

isvalid is a boolean to denote that the network was inspected, not that it is actually valid.

errorMessage Will be in result if there was an error parsing network

completed is set to True after all server tasks have completed and network is ready to be used

Parameters:network_id (str) – The UUID of the network Returns:Summary information about network Return type:dict

get_networkset(set_id)

Gets the network set information including the list of networks

Parameters:set_id (str) – network set id Returns:network set information Return type:dict

get_networksets_for_user_id(user_id, summary_only=True, showcase=False, offset=0, limit=0)

Gets a list of Network Set objects owned by the user identified by user_id

New in version 3.4.0.

Example when summary_only is True or if Network Set does not contain any networks:

[
 {'name': 'test networkset',
  'description': ' ',
  'ownerId': '4f0a6356-ed4a-49df-bd81-098fee90b448',
  'showcased': False,
  'properties': {},
  'externalId': '956e31e8-f25c-471f-8596-2cae8348dcad',
  'isDeleted': False,
  'modificationTime': 1568844043868,
  'creationTime': 1568844043868
 }
]

When summary_only is False and Network Set does contain networks there will be an additional property named networks:

'networks': ['face63b6-aba7-11eb-9e72-0ac135e8bacf',
             'fae4d1e8-aba7-11eb-9e72-0ac135e8bacf']

Parameters:

• user_id (str) – Id of user on NDEx. To get Id of user see get_id_for_user()
• summary_only (bool) – When True, the server will not return the list of network IDs in this Network Set
• showcase (bool) – When True, only showcased Network Sets are returned
• offset (int) – Index to first object to return. If 0/None no offset will be applied. If this parameter is set to a positive value then limit parameter must be set to a positive value or this offset will be ignored.
• limit (int) – Number of objects to retrieve. If 0, None, or negative all results will be returned.

Raises:

• NDExInvalidParameterError – If user_id parameter is not of type str. If offset/limit parameters are not None or of type int. If offset parameter is set to positive number and limit is 0, None, or negative.
• NDExError – If there is an error from server

Returns:

list with dict objects containing Network Sets

Return type:

list

get_sample_network(network_id)

Gets the sample network

Parameters:network_id (str) – Network id Raises:NDExUnauthorizedError – If credentials are invalid or not set Returns:Sample network in CX format Return type:list

get_task_by_id(task_id)

Retrieves a task by id

Parameters:task_id (str) – Task id Raises:NDExUnauthorizedError – If credentials are invalid or not set Returns:Task Return type:dict

get_user_by_id(user_id)

Gets user matching id from NDEx server.

New in version 3.4.0.

Result is a dict in format:

{'properties': {},
 'isIndividual': True,
 'userName': 'bsmith',
 'isVerified': True,
 'firstName': 'bob',
 'lastName': 'smith',
 'emailAddress': 'bob.smith@ndexbio.org',
 'diskQuota': 10000000000,
 'diskUsed': 3971183103,
 'externalId': 'f2c3a7ef-b0d9-4c61-bf31-4c9fcabe4173',
 'isDeleted': False,
 'modificationTime': 1554410147104,
 'creationTime': 1554410138498
}

Parameters:

user_id (str) – Id of user on NDEx server

Raises:

• NDExError – If there was an error on the server
• NDExInvalidParameterError – If user_id is not of type str or if empty str

Returns:

user object. externalId is Id of user on NDEx server

Return type:

dict

get_user_by_username(username)

Gets user information from NDEx.

Example user information:

{'properties': {},
 'isIndividual': True,
 'userName': 'bsmith',
 'isVerified': True,
 'firstName': 'bob',
 'lastName': 'smith',
 'emailAddress': 'bob.smith@ndexbio.org',
 'diskQuota': 10000000000,
 'diskUsed': 3971183103,
 'externalId': 'f2c3a7ef-b0d9-4c61-bf31-4c9fcabe4173',
 'isDeleted': False,
 'modificationTime': 1554410147104,
 'creationTime': 1554410138498
}

Parameters:username (str) – User name Returns:User information as dict Return type:dict

get_user_network_summaries(username, offset=0, limit=1000)

Get a list of network summaries for networks owned by specified user. It returns not only the networks that the user owns but also the networks that are shared with them directly. As set via limit parameter only the first 1,000 ids are returned. The offset parameter combined with limit parameter provides pagination support.

Parameters:

• username (str) – Username of the network owner
• offset (int) – Starting position of the network search
• limit (int) – Number of summaries to return starting from offset

Returns:

List of uuids

Return type:

list

grant_network_to_user_by_username(username, network_id, permission)

Grants permission to network for the given user name

Parameters:

• username (str) – User name
• network_id (str) – Network id
• permission (str) – Network permission

Returns:

Result

Return type:

dict

grant_networks_to_group(groupid, networkids, permission='READ')

Set group permission for a set of networks

Parameters:

• groupid (str) – Group id
• networkids (list) – List of network ids
• permission (str) – Network permission

Returns:

Result

Return type:

dict

grant_networks_to_user(userid, networkids, permission='READ')

Gives read permission to specified networks for the provided user

Parameters:

• userid (str) – User id
• networkids (list) – Network ids as str
• permission (str (default is READ)) – Network permissions

Returns:

None

Return type:

None

make_network_private(network_id)

Makes the network specified by the network_id private by invoking set_network_system_properties() with

{'visibility': 'PRIVATE'}

Parameters:

network_id (str) – The UUID of the network.

Raises:

• NDExUnauthorizedError – If credentials are invalid or not set
• requests.exception.HTTPError – If there is some other error

Returns:

empty string upon success

Return type:

str

make_network_public(network_id)

Makes the network specified by the network_id public by invoking set_network_system_properties() with

{'visibility': 'PUBLIC'}

Parameters:

network_id (str) – The UUID of the network.

Raises:

• NDExUnauthorizedError – If credentials are invalid or not set
• requests.exception.HTTPError – If there is some other error

Returns:

empty string upon success

Return type:

str

save_cx2_stream_as_new_network(cx_stream, visibility=None)

Create a new network from a CX2 stream

New in version 3.5.0.

import io
import json
from ndex2.client import Ndex2
from ndex2.exceptions import NDExError

client = Ndex2(username=<NDEx USER NAME>,
               password=<NDEx PASSWORD>,
               skip_version_check=True)

# cx is set to an empty CX2 network
cx = [{"CXVersion":"2.0","hasFragments":false},
      {"status":[{"success":true}]}]

try:
    cx_stream = io.BytesIO(json.dumps(cx,
                                      cls=DecimalEncoder).encode('utf-8'))
    net_url = client.save_cx2_stream_as_new_network(cx_stream,
                                                    visibility='PUBLIC')
    print('Network URL: ' + str(net_url))
except NDExError as ne:
    print('Caught error: ' + str(ne))

Parameters:

• cx_stream (BytesIO like object) – IO stream of cx2
• visibility (str) – Sets the visibility (PUBLIC or PRIVATE)

Raises:

• NDExUnauthorizedError – If credentials are invalid or not set
• NDExError – if there is an error saving the network

Returns:

Full URL to newly created network (ie http://ndexbio.org/v3/networks/XXXX)

Return type:

str

save_cx_stream_as_new_network(cx_stream, visibility=None)

Create a new network from a CX stream.

Parameters:

• cx_stream (BytesIO) – IO stream of cx
• visibility (str) – Sets the visibility (PUBLIC or PRIVATE)

Raises:

NDExUnauthorizedError – If credentials are invalid or not set

Returns:

Response data

Return type:

str or dict

save_new_cx2_network(cx, visibility=None)

Create a new network (CX2) on the server

New in version 3.5.0.

from ndex2.client import Ndex2
from ndex2.exceptions import NDExError

client = Ndex2(username=<NDEx USER NAME>,
               password=<NDEx PASSWORD>,
               skip_version_check=True)

# cx is set to an empty CX2 network
cx = [{"CXVersion":"2.0","hasFragments":false},
      {"status":[{"success":true}]}]

try:
    net_url = client.save_new_cx2_network(cx, visibility='PRIVATE')
    print('URL of new network: ' + str(net_url))
except NDExError as ne:
    print('Caught error: ' + str(ne))

Parameters:

• cx (list) – Network CX2 which is a list of dict objects
• visibility (str) – Sets the visibility (PUBLIC or PRIVATE) If None sets visibility to PRIVATE

Raises:

• NDExUnauthorizedError – If credentials are invalid or not set
• NDExInvalidCXError – if cx is None, not a list, or is an empty list
• NDExError – if there is an error saving the network

Returns:

Full URL to newly created network (ie http://ndexbio.org/v3/networks/XXXX)

Return type:

str

save_new_network(cx, visibility=None)

Create a new network (CX) on the server

Parameters:

• cx (list) – Network CX which is a list of dict objects
• visibility (str) – Sets the visibility (PUBLIC or PRIVATE)

Raises:

NDExInvalidCXError – For invalid CX data

Returns:

Response data

Return type:

str or dict

search_networks(search_string='', account_name=None, start=0, size=100, include_groups=False)

Search for networks based on the search_text, optionally limited to networks owned by the specified account_name.

Parameters:

• search_string (str) – The text to search for.
• account_name (str) – The account to search
• start (int) – The number of blocks to skip. Usually zero, but may be used to page results.
• size (int) – The size of the block.
• include_groups –

Returns:

The response.

Return type:

response object

set_network_properties(network_id, network_properties)

Updates properties of network

Starting with version 2.5 of NDEx, any network properties not in the network_properties parameter are left unchanged.

Warning

name, description, version network attributes/properties cannot be updated by this method. Please use update_network_profile() to update these values.

The format of network_properties should be a list() of dict() objects in this format:

The predicateString field above is the network attribute/property name.

The dataType field above must be one of the following types

Regardless of dataType, value should be converted to str() or list() of str()

For more information please visit the underlying REST call documentation

Example to add two network properties (foo, bar):

Parameters:

• network_id (str) – Network id
• network_properties (list or str) – List of NDEx property value pairs aka network properties to set on the network. This can also be a str() in JSON format

Raises:

• Exception – If network_properties is not a str() or list()
• NDExUnauthorizedError – If credentials are invalid or not set
• requests.HTTPError – If there is an error with the request or if name, version, description is set in network_properties as a value to predicateString

Returns:

Empty string or 1

Return type:

str or int

set_network_system_properties(network_id, network_properties, skipvalidation=False)

Set network system properties on network with UUID specified by network_id

The network properties should be a dict() or a json string of a dict() in this format:

{'showcase': (boolean True or False),
 'visibility': (str 'PUBLIC' or 'PRIVATE'),
 'index_level': (str  'NONE', 'META', or 'ALL'),
 'readOnly': (boolean True or False)
}

Note

Omit any values from dict() that you do NOT want changed

Definition of showcase values:

True - means network will display in her home page for other users and False hides the network for other users. where other users includes anonymous users

Definition of visibility values:

‘PUBLIC’ - means it can be found or read by anyone, including anonymous users

‘PRIVATE’ - is the default, means that it can only be found or read by users according to their permissions

Definition of index_level values:

‘NONE’ - no index

‘META’ - only index network attributes

‘ALL’ - full index on the network

Definition of readOnly values:

True - means network is only readonly, False is NOT readonly

This method will validate network_properties matches above dict() unless skipvalidation is set to True in which case the code only verifies the network_properties is valid JSON

Parameters:

• network_id (str) – Network id
• network_properties (dict or str) – Network properties as dict() or a JSON string of dict() adhering to structure above.
• skipvalidation – If True, only verify network_properties can be parsed/converted to valid JSON

Raises:

• NDExUnsupportedCallError – If version of NDEx server is < 2
• NDExUnauthorizedError – If credentials are invalid or not set
• NDExInvalidParameterError – If invalid data is set in network_properties parameter
• requests.exception.HTTPError – If there is some other error

Returns:

empty string upon success

Return type:

str

set_read_only(network_id, value)

Sets the read only flag to value on the network specified by network_id

Parameters:

• network_id (str) – Network id
• value (bool) – Must True for read only, False otherwise

Raises:

• NDExUnauthorizedError – If credentials are invalid or not set
• NDExInvalidParameterError – If non bool is set in valid parameter
• requests.exception.HTTPError – If there is some other error

Returns:

empty string upon success

Return type:

str

update_cx2_network(cx_stream, network_id)

Update the network specified by UUID network_id using the CX2 stream cx_stream passed in

New in version 3.5.0.

import io
import json
from ndex2.client import Ndex2
from ndex2.exceptions import NDExError

client = Ndex2(username=<NDEx USER NAME>,
               password=<NDEx PASSWORD>,
               skip_version_check=True)

# cx is set to an empty CX2 network
cx = [{"CXVersion":"2.0","hasFragments":false},
      {"status":[{"success":true}]}]

try:
    cx_stream = io.BytesIO(json.dumps(cx,
                                      cls=DecimalEncoder).encode('utf-8'))
    client.update_cx2_network(cx_stream, <UUID OF NETWORK TO UPDATE>)
    print('Success')
except NDExError as ne:
    print('Caught error: ' + str(ne))

Parameters:

• cx_stream – The network stream.
• network_id (str) – The UUID of the network.

Raises:

• NDExUnauthorizedError – If credentials are invalid or not set
• NDExError – If there is an error updating the network

Returns:

Nothing is returned. To check status call get_network_summary()

update_cx_network(cx_stream, network_id)

Update the network specified by UUID network_id using the CX stream cx_stream passed in

Parameters:

• cx_stream – The network stream.
• network_id (str) – The UUID of the network.

Raises:

NDExUnauthorizedError – If credentials are invalid or not set

Returns:

The response.

Return type:

response object

update_network_group_permission(groupid, networkid, permission)

Updated group permissions

Parameters:

• groupid (str) – Group id
• networkid (str) – Network id
• permission (str) – Network permission

Returns:

Result

Return type:

dict

update_network_profile(network_id, network_profile)

Updates the network profile Any profile attributes specified will be updated but attributes that are not specified will have no effect - omission of an attribute does not mean deletion of that attribute. The network profile attributes that can be updated by this method are: ‘name’, ‘description’ and ‘version’.

{
  "name": "string",
  "description": "string",
  "version": "string",
  "visibility": "string",
  "properties": [
    {
      "subNetworkId": "",
      "predicateString": "string",
      "dataType": "string",
      "value": "string"
    }
  ]
}

Parameters:

• network_id (str) – Network id
• network_profile (dict) – Network profile

Raises:

NDExUnauthorizedError – If credentials are invalid or not set

Returns:

Return type:

update_network_user_permission(userid, networkid, permission)

Updated network user permission

Parameters:

• userid (str) – User id
• networkid (str) – Network id
• permission (str) – Network permission

Returns:

Result

Return type:

dict

Constants

Contains constants used by the NDEx2 Python Client

ndex2.constants.BOOLEAN_DATATYPE = 'boolean'

Boolean data type for CX

ndex2.constants.CARTESIAN_LAYOUT_ASPECT = 'cartesianLayout'

Name of opaque aspect containing coordinates of nodes

"cartesianLayout": [ 
    {
        "node": 0,
        "x": 25.0,
        "y": 50.0
    }, {
        "node": 1,
        "x": -10.0,
        "y": -200.0
    }
]

Note

Although the name implies a cartesian coordinate system, that is actually wrong. The Y access is inverted so lower values of Y are rendered higher on a graph. 0,0 is considered upper left corner, but negative values are allowed

ndex2.constants.DOUBLE_DATATYPE = 'double'

Double data type for CX

ndex2.constants.EDGE_ID = '@id'

Key for id of edge

ndex2.constants.EDGE_INTERACTION = 'i'

Key for edge interaction

ndex2.constants.EDGE_SOURCE = 's'

Key for edge source

ndex2.constants.EDGE_TARGET = 't'

Key for edge target

ndex2.constants.INTEGER_DATATYPE = 'integer'

Integer data type for CX

ndex2.constants.LAYOUT_NODE = 'node'

Key for node id in CARTESIAN_LAYOUT_ASPECT opaque aspect

ndex2.constants.LAYOUT_X = 'x'

Key for X coordinate in CARTESIAN_LAYOUT_ASPECT opaque aspect

ndex2.constants.LAYOUT_Y = 'y'

Key for Y coordinate in CARTESIAN_LAYOUT_ASPECT opaque aspect

ndex2.constants.LIST_OF_BOOLEAN = 'list_of_boolean'

List of Boolean data type for CX

ndex2.constants.LIST_OF_DOUBLE = 'list_of_double'

List of Double data type for CX

ndex2.constants.LIST_OF_INTEGER = 'list_of_integer'

List of Integer data type for CX

ndex2.constants.LIST_OF_LONG = 'list_of_long'

List of Long data type for CX

ndex2.constants.LIST_OF_STRING = 'list_of_string'

List of String data type for CX

ndex2.constants.LONG_DATATYPE = 'long'

Long data type for CX

ndex2.constants.NET_ATTR_NAME = 'n'

Key for network attribute name

ndex2.constants.NET_ATTR_VALUE = 'v'

Key for network attribute value

ndex2.constants.NODE_ATTR_DATATYPE = 'd'

Key for node attribute data type

ndex2.constants.NODE_ATTR_NAME = 'n'

Key for node attribute name

ndex2.constants.NODE_ATTR_PROPERTYOF = 'po'

Key for node property of

ndex2.constants.NODE_ATTR_VALUE = 'v'

Key for node attribute value

ndex2.constants.NODE_ID = '@id'

Key for id of node

ndex2.constants.NODE_NAME = 'n'

Key for node name

ndex2.constants.NODE_REPRESENTS = 'r'

Key for node represents

ndex2.constants.STRING_DATATYPE = 'string'

String data type for CX

ndex2.constants.VALID_ATTRIBUTE_DATATYPES = ['boolean', 'double', 'integer', 'long', 'string', 'list_of_boolean', 'list_of_double', 'list_of_integer', 'list_of_long', 'list_of_string']

List of valid attribute data types

Miscellaneous

class ndex2.util.DataConverter

Base class for subclasses that convert CX data types to/from native data types

convert_value(value=None, datatype=None)

Defines method to converts value from CX to native data type using datatype as a guide

Parameters:

• value (object) – Value to convert
• datatype (str) – CX data type which is one of the following: ndex2.constants.VALID_ATTRIBUTE_DATATYPES

Raises:

NotImplementedError – Always raises this error cause subclasses should implement

Returns:

Always raises NotImplementedError

class ndex2.util.PandasDataConverter

Converts CX values to native Python data types via PandasDataConverter.convert_value() method

New in version 3.5.0.

convert_value(value=None, datatype=None)

Converts value parameter passed in to type based on value of datatype parameter passed in. This is used in data conversion by to_pandas_dataframe()

New in version 3.5.0.

Conversion rules for different values of datatype parameter:

• STRING_DATATYPE or None

  • value is converted by str and returned

• BOOLEAN_DATATYPE

  • If value is of type bool it is just returned. If value is of type str and equals true (ignore case) or 1 then True is returned and if value equals false (ignore case) or 0 is then False is returned. Otherwise value is converted by bool and returned. If conversion fails NDExError is raised

• DOUBLE_DATATYPE

  • value is converted by float and returned. If conversion fails NDExError is raised

• INTEGER_DATATYPE or LONG_DATATYPE

  • value is converted by int and returned. If conversion fails NDExError is raised

• LIST_OF_STRING, LIST_OF_BOOLEAN LIST_OF_DOUBLE, LIST_OF_INTEGER, LIST_OF_LONG

  • If value is NOT of type list then the value converted as if it’s datatype is STRING_DATATYPE. If value is a list, each element is converted as if it’s datatype is STRING_DATATYPE and values of list are converted to a comma delimited str

Example usage:

from ndex2.util import PandasDataConverter

converter = PandasDataConverter()

# converts number to type str
res = converter.convert_value(123, 'string')

# would output <class 'str'>
print(type(res))

Parameters:

• value (object) – Value to convert
• datatype (str) – CX data type which is one of the following: ndex2.constants.VALID_ATTRIBUTE_DATATYPES

Raises:

NDExError – If there is an error with conversion

Returns:

Converted value

Return type:

list, str, int, float, or bool

Exceptions

class ndex2.exceptions.NDExError

Base Exception for all NDEx2 Python Client Exceptions

Warning

Many methods in this code base still incorrectly raise errors not derived from this base class

class ndex2.exceptions.NDExNotFoundError

Raised if resource requested was not found

class ndex2.exceptions.NDExUnauthorizedError

Raised if unable to authenticate, either due to lack of or invalid credentials.

class ndex2.exceptions.NDExInvalidParameterError

Raised if invalid parameter is passed in

class ndex2.exceptions.NDExInvalidCXError

Raised due to invalid CX

class ndex2.exceptions.NDExUnsupportedCallError

Raised if call is unsupported, for example a method that is only supported in 2.0+ of NDEx server is attempted against a server running 1.0

License

Copyright © 2013-2022, The Regents of the University of California, The Cytoscape Consortium. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

History

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
  • 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
  • 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
  • Fixed bug where converting NiceCXNetwork to networkx and back does not handle name attribute correctly. Issue #84
  • Fixed bug where @context was lost if it was set as aspect in CX format and loaded into NiceCXNetwork object. Issue #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
  • 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
• 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
• 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
• 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

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