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ndexbio / gsoc_llm

GSOC 2024 LLM Project
MIT License
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Provide a diagnosis of the CX2 output problem #19

Closed dexterpratt closed 2 months ago

dexterpratt commented 5 months ago

Dexter will work with the Ideker Lab software team to diagnose the problem and give feedback on the CX2 generation method

dexterpratt commented 5 months ago

Jing's response:

@dexter , this is not a valid cx2 file. There are many problems in this file. It is missing the cx2 descriptor, attributeDeclaration, and status aspects. Looks like it is trying to generate a cx1 file. The file extension is .json. Cytoscape will trying to load it as a CytoscapeJS object I think.

And here is the documentation for CX2 in the ndex2 package:

https://ndex2.readthedocs.io/en/latest/cx2.html

It provides examples of using a CX2Network object to build CX2 networks.

Here is the documentation for generating CX2 json from the object and then saving the CX2 to NDEx:

https://ndex2.readthedocs.io/en/latest/cx2.html#ndex2.cx2.CX2Network.to_cx2 https://ndex2.readthedocs.io/en/latest/ndex2client.html#ndex2.client.Ndex2.save_new_cx2_network

Favourj-bit commented 4 months ago

@dexterpratt This is noted