Welcome to ndex2’s documentation!¶

Contents:

NiceCXNetwork module¶

The NiceCXNetwork class provides a data model for working with NDEx networks. Methods are provided to add nodes, edges, node attributes, edge attributes, etc. Once a NiceCXNetwork data 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.

To see deprecated methods go to Deprecated NiceCXNetwork methods

Methods for building niceCX¶

Node methods¶

Edge methods¶

Network methods¶

Methods for accessing niceCX properties¶

Node methods¶

Edge methods¶

Network methods¶

Misc niceCX methods¶

Deprecated NiceCXNetwork methods¶

Supported data types¶

The following data types are supported in methods that accept type

Example:

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

string
double
boolean
integer
long
list_of_string
list_of_double
list_of_boolean
list_of_integer
list_of_long

Methods for creating niceCX from other data models¶

ndex2.create_nice_cx_from_raw_cx(cx)¶

Create a NiceCXNetwork from a CX json object. (see http://www.home.ndexbio.org/data-model)

Parameters:	cx – a valid CX document
Returns:	NiceCXNetwork

ndex2.create_nice_cx_from_file(path)¶

Create a NiceCXNetwork from a file that is in the CX format.

Parameters:	path – the path of the CX file
Returns:	NiceCXNetwork

ndex2.create_nice_cx_from_networkx(G)¶

Creates a NiceCXNetwork based on a networkx graph. The resulting NiceCXNetwork contains the nodes edges and their attributes from the networkx graph and also preserves the graph ‘pos’ attribute as a CX cartesian coordinates aspect. Node name is taken from the networkx node id. Node ‘represents’ is taken from the networkx node attribute ‘represents’

Parameters:	G (networkx graph) – networkx graph
Returns:	NiceCXNetwork
Return type:	NiceCXNetwork

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.

If only the df argument is provided the 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, the those and any other arguments refer to headers in the 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 it defaults to “interacts-with”

Parameters:

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

Returns:

NiceCXNetwork

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

Create a NiceCXNetwork based on a network retrieved from NDEx, specified by its UUID. If the network is not public, then username and password arguments for an account on the server with permission to access the network must be supplied.

Parameters:	server – the URL of the NDEx server hosting the network. username – the user name of an account with permission to access the network. password – the password of an account with permission to access the network. uuid – the UUID of the network.
Returns:	NiceCXNetwork

Client access to NDEx server API¶

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

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

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 (basestring) – network set id networks (list of strings) – networks that will be added to the set
Returns:	None
Return type:	None

create_networkset(name, description)¶

Creates a new network set

Parameters:	name (string) – Network set name description (string) – Network set description
Returns:	URI of the newly created network set
Return type:	string

delete_network(network_id, retry=5)¶

Deletes the specified network from the server

Parameters:	network_id (string) – Network id retry (int) – Number of times to retry if deleting fails
Returns:	Error json if there is an error. Blank
Return type:	string

delete_networks_from_networkset(set_id, networks, retry=5)¶

Removes network(s) from a network set.

Parameters:	set_id (basestring) – network set id networks (list of strings) – networks that will be removed from the set retry (int) – Number of times to retry
Returns:	None
Return type:	None

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 (boolean) – 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_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_ids_for_user(username)¶

Get the network uuids owned by the user

Parameters:	username (str) – users NDEx username
Returns:	list of uuids

get_network_set(set_id)¶

Gets the network set information including the list of networks

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

get_network_summary(network_id)¶

Gets information about a network.

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

get_sample_network(network_id)¶

Gets the sample network

Parameters:	network_id (string) – Network id
Returns:	Sample network
Return type:	list of dicts in cx format

get_task_by_id(task_id)¶

Retrieves a task by id

Parameters:	task_id (string) – Task id
Returns:	Task
Return type:	dict

get_user_by_username(username)¶

Gets the user id by user name

Parameters:	username (string) – User name
Returns:	User id
Return type:	string

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.

Parameters:	username (str) – the username of the network owner offset (int) – the starting position of the network search limit –
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 (string) – User name network_id (string) – Network id permission (string) – 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 (string) – Group id networkids (list) – List of network ids permission (string) – 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 (string) – User id networkids (list of strings) – Network ids permission (string (default is READ)) – Network permissions
Returns:	none
Return type:	none

make_network_private(network_id)¶

Makes the network specified by the network_id private.

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

make_network_public(network_id)¶

Makes the network specified by the network_id public.

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

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 (string) – Sets the visibility (PUBLIC or PRIVATE)
Returns:	Response data
Return type:	string or dict

save_new_network(cx, visibility=None)¶

Create a new network (cx) on the server

Parameters:	cx (list of dicts) – Network cx visibility (string) – Sets the visibility (PUBLIC or PRIVATE)
Returns:	Response data
Return type:	string 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)¶

Sets network properties

Parameters:	network_id (string) – Network id network_properties (list) – List of NDEx property value pairs
Returns:
Return type:

set_network_system_properties(network_id, network_properties)¶

Set network system properties

Parameters:	network_id (string) – Network id network_properties (dict of NDEx network property value pairs) – Network properties
Returns:	Result
Return type:	dict

set_read_only(network_id, value)¶

Sets the read only flag on the specified network

Parameters:	network_id (string) – Network id value (bool) – Read only value
Returns:	Result
Return type:	dict

update_cx_network(cx_stream, network_id)¶

Update the network specified by UUID network_id using the CX stream cx_stream.

Parameters:

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

Returns:

The response.

Return type:

response object

update_network_group_permission(groupid, networkid, permission)¶

Updated group permissions

Parameters:	groupid (string) – Group id networkid (string) – Network id permission (string) – 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’.

Parameters:	network_id (string) – Network id network_profile (dict) – Network profile
Returns:
Return type:

update_network_user_permission(userid, networkid, permission)¶

Updated network user permission

Parameters:	userid (string) – User id networkid (string) – Network id permission (string) – Network permission
Returns:	Result
Return type:	dict

Welcome to ndex2’s documentation!¶

NiceCXNetwork module¶

Methods for building niceCX¶

Node methods¶

Edge methods¶

Network methods¶

Methods for accessing niceCX properties¶

Node methods¶

Edge methods¶

Network methods¶

Misc niceCX methods¶

Deprecated NiceCXNetwork methods¶

Supported data types¶

Methods for creating niceCX from other data models¶

Client access to NDEx server API¶

ndex2¶

Indices and tables¶