Uploading interactome and hierarchy to NDEx

To properly make use of Cell View and subnetworks vizualization in Cytoscape Web, it is necessary to upload both interactome and hierarchy. It is important to properly switch network annotations, which is detailed in HCX format documentation. Cell Maps Utils package provides a class NDExHierarchyUploader to simplify the process.

This code block below uses the hierarchy and interactome from `Example 2`_ above.

import os
import ndex2
from cellmaps_utils.ndexupload import NDExHierarchyUploader

#Specify NDEx server
ndexserver = 'www.ndexbio.org''
ndexuser = '<USER>'
ndexpassword = '<PASSWORD>'

# Initialize NDExHierarchyUploader with the specified NDEx server and credentials
uploader = NDExHierarchyUploader(ndexserver, ndexuser, ndexpassword, visibility=True)

# Upload the hierarchy and parent network to NDEx
parent_uuid, parenturl, hierarchy_uuid, hierarchyurl = uploader.save_hierarchy_and_parent_network(hierarchy, interactome)

print(f"Parent network UUID is {parent_uuid} and its URL in NDEx is {parenturl}")
print(f"Hierarchy network UUID is {hierarchy_uuid} and its URL in NDEx is {hierarchyurl}")

It is possible to also directly upload from files (this will replace the HCX::interactionNetworkName network annotation with HCX::interactionNetworkUUID):

import os
import ndex2
from cellmaps_utils.ndexupload import NDExHierarchyUploader

#Specify NDEx server
ndexserver = 'www.ndexbio.org''
ndexuser = '<USER>'
ndexpassword = '<PASSWORD>'

# Initialize NDExHierarchyUploader with the specified NDEx server and credentials
uploader = NDExHierarchyUploader(ndexserver, ndexuser, ndexpassword, visibility=True)

# Upload the hierarchy and parent network to NDEx
parent_uuid, parenturl, hierarchy_uuid, hierarchyurl = uploader.upload_hierarchy_and_parent_network_from_files(hierarchy_path='path/to/output/hierarchy.cx2', parent_path='path/to/interactome.cx2')

print(f"Parent network UUID is {parent_uuid} and its URL in NDEx is {parenturl}")
print(f"Hierarchy network UUID is {hierarchy_uuid} and its URL in NDEx is {hierarchyurl}")

If your hierarchy already has HCX::interactionNetworkUUID annotation, there is no need to use NDExHierarchyUploader and it can be directly saved to NDEx:

import os
import ndex2

#Specify NDEx server
ndexserver = 'www.ndexbio.org''
ndexuser = '<USER>'
ndexpassword = '<PASSWORD>'

ndexclient = ndex2.client.Ndex2(host=ndexserver, username=ndexuser, password=ndexpassword)
ndexclient.save_new_cx2_network(hierarchy.to_cx2(), visibility=self._visibility)