ndex package

ndex.client module

class ndex.client.Ndex(host='http://public.ndexbio.org', username=None, password=None)

A class to facilitate communication with an NDEx server.

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

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.
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_summary(network_id)

Gets information about a network.

Parameters:network_id (str) – The UUID of the network.
Returns:The response.
Return type:response object
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, provenance=None)

Create a new network from a CX stream, optionally providing a provenance history object to be included in the new network.

Parameters:
  • cx_stream – The network stream.
  • provenance – The desired provenance history associated with the network.
Returns:

The response.
Return type:

response object
search_networks(search_string='', account_name=None, skip_blocks=0, block_size=100)

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
  • skip_blocks (int) – The number of blocks to skip. Usually zero, but may be used to page results.
  • block_size (int) – The size of the block.
Returns:

The response.
Return type:

response object
update_cx_network(cx_stream, network_id, provenance=None)

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.
  • provenance – The desired provenance history associated with the network.
Returns:

The response.
Return type:

response object

ndex.networkn module

class ndex.networkn.NdexGraph(cx=None, server=None, username=None, password=None, uuid=None, networkx_G=None, data=None, **attr)

Bases: networkx.classes.multidigraph.MultiDiGraph

A graph compatible with NDEx

add_edge_between(source_node_id, target_node_id, interaction='interacts_with', attr_dict=None, **attr)

Add an edge between two nodes in this network specified by source_node_id and target_node_id, optionally specifying the type of interaction.

Parameters:
  • source_node_id (int) – The node id of the source node.
  • target_node_id (int) – The node id of the target node.
  • interaction (str) – The type of interaction specified by the newly added edge.
  • attr_dict (dict) – Dictionary of node attributes. Key/value pairs will update existing data associated with the node.
  • attr – Set or change attributes using key=value.
add_new_node(name=None, attr_dict=None, **attr)

Add a cx node, possibly with a particular name, to the graph.

Parameters:
  • name (str) – The name of the node. (Optional).
  • attr_dict (dict) – Dictionary of node attributes. Key/value pairs will update existing data associated with the node.
  • attr – Set or change attributes using key=value.
clear()

Eliminate all graph data in this network. The network will then be empty and can be filled with data starting “from scratch”.

create_from_edge_list(edge_list, interaction='interacts with')

Create a network from a list of tuples that represent edges. Each tuple consists of two nodes names that are to be connected. This operation will first clear ALL data already in the network.

Parameters:
  • edge_list (list) – A list of tuples containing node names that are connected.
  • interaction (str or list) – Either a list of interactions that is the same length as the edge_list a single string with an interaction to be applied to all edges.
get_all_edge_attribute_keys()

Get the unique list of all attribute keys used in at least one edge in the network.

Returns:A list of edge attribute keys.
Return type:list
get_all_node_attribute_keys()

Get the unique list of all attribute keys used in at least one node in the network.

Returns:A list of attribute keys.
Return type:list
get_edge_attribute_value_by_id(edge_id, query_key)

Get the value for attribute of the edge specified by edge_id.

Parameters:
  • edge_id – The id of the edge.
  • query_key – The name of the attribute whose value should be retrieved.
Returns:

The attribute value. If the value is a list, this returns the entire list.
Return type:

any
get_edge_attribute_values_by_id_list(edge_id_list, query_key)

Given a list of edge ids and particular attribute key, return a list of corresponding attribute values.’

Parameters:
  • edge_id_list – A list of edge ids whose attribute values we wish to retrieve
  • query_key – The name of the attribute whose corresponding values should be retrieved.
Returns:

A list of attribute values corresponding to the edge keys input.
Return type:

list
get_edge_ids_by_node_attribute(source_node_value, target_node_value, query_key='name')

Returns a list of edge ids of all edges where both the source node and target node have the specified values for query_key.

Parameters:
  • source_node_value – The value we want in the source node.
  • target_node_value – The value we want in the target node.
  • query_key – The name of the attribute where we should look for the value.
Returns:

A list of edge ids.
Return type:

list
get_name()

Get the name of this graph

Returns:The descriptive name for this network.
Return type:str
get_node_attribute_value_by_id(node_id, query_key='name')

Get the value of a particular node attribute based on the id.

Parameters:
  • node_id (int) – A node id.
  • query_key (str) – The name of the attribute whose value we desire.
Returns:

The attribute value.
Return type:

any
get_node_attribute_values_by_id_list(id_list, query_key='name')

Returns a list of attribute values that correspond with the attribute key using the nodes in id_list.

Parameters:
  • id_list – A list of node ids whose attribute values we wish to retrieve.
  • query_key – The name of the attribute whose corresponding values should be retrieved.
Returns:

A list of attribute values.
Return type:

list
get_node_ids(value, query_key='name')

Returns a list of node ids of all nodes in which query_key has the specified value.

Parameters:
  • value – The value we want.
  • query_key – The name of the attribute where we should look for the value.
Returns:

A list of node ids.
Return type:

list
get_node_name_by_id(id)

Given a node id, return the name of the node.

Parameters:id (int) – The cx id of the node.
Returns:The name of the node.
Return type:str
get_node_names_by_id_list(id_list)

Given a list of node ids, return a list of node names.

Parameters:id_list (list) – A list of node ids whose attribute values we wish to retrieve.
Returns:A list of node names.
Return type:list
remove_nodes_from(nbunch)
set_edge_attribute(id, attribute_key, attribute_value)

Set the value of a particular edge attribute.

Parameters:
  • id (int) – The edge id we wish to set an attribute on.
  • attribute_key (string) – The name of the attribute we wish to set.
  • attribute_value (any) – The value we wish to set the attribute to.
set_name(name)

Set the name of this graph

Parameters:name (str) – A descriptive name for the network which will show up on NDEx.
show_stats()

Show the number of nodes and edges.

to_cx()

Convert this network to a CX dictionary

Returns:The cx dictionary that represents this network.
Return type:dict
to_cx_stream()

Convert this network to a CX stream

Returns:The CX stream representation of this network.
Return type:io.BytesIO
upload_to(server, username, password)

Upload this network to the specified server to the account specified by username and password.

Parameters:
  • server (str) – The NDEx server to upload the network to.
  • username (str) – The username of the account to store the network.
  • password (str) – The password for the account.
Returns:

The UUID of the network on NDEx.
Return type:

str
Example:
ndexGraph.upload_to(‘http://test.ndexbio.org‘, ‘myusername’, ‘mypassword’)
write_to(filename)

Write this network as a CX file to the specified filename.

Parameters:filename (str) – The name of the file to write to.