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Bug: Importing local gpml file doesn't work unless pathway is first imported from WikiPathways #113
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Update for Cytoscape 3.9: The error that shows up when trying to import a gpml via "File>Import Network from File" is now Pathway not available -- invalid gpml |
I think this issue is important. And it causes confusion when the Wikipathways team curates it as a mysterious copy. |
Hi Kozo, sorry about the confusion about the copied pathway at WikiPathways. This issue definitely needs to be resolved, but in your case I would recommend using the workaround solution, which doesn't involved WikiPathways at all. This works in Cytoscape 3.9, and also in the upcoming 3.10 version:
So as long as any pathway has been opened using the WP app, a local gpml can be opened without the import error. Let me know if you have any questions. Kristina |
Thanks @khanspers (+ I'm sorry for the late replay...), |
Note: This assumes that import of local gpmls is supposed to work, which it did previously.
Workflow:
From Task History:
Open any pathway from WikiPathways from Network Search tool, for example sandbox
File>Import Network from File, select gpml, choose "import as pathway". => pathway is imported successfully
Based on this, maybe there's a problem with finding the visual style, which is solved after a pathway is successfully imported from WP.org?
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