search

wikipathways / cytoscape-wikipathways-app

WikiPathways app for Cytoscape to open and access pathways from WikiPathways
Apache License 2.0
5 stars 7 forks source link

Bug: Importing local gpml file doesn't work unless pathway is first imported from WikiPathways #113

Open khanspers opened 3 years ago

khanspers commented 3 years ago

Note: This assumes that import of local gpmls is supposed to work, which it did previously.

Workflow:

  1. File>Import Network from File, select gpml, choose "import as pathway" => "Pathway not available -- invalid gpml" From Task History:

    • Task (org.cytoscape.task.internal.vizmap.LoadVizmapFileTask$AddVisualStylesTask@417b3b9f) progress: 100%
    • Caught exception executing task.

  2. Open any pathway from WikiPathways from Network Search tool, for example sandbox

  3. 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?

khanspers commented 2 years ago

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

kozo2 commented 1 year ago

I think this issue is important. If this issue is not resolved, Cytoscape users who want to import a local GPML (that has been slightly modified from Wikipathways) will have to create a new copy of the pathway on Wikipathways and update it.

And it causes confusion when the Wikipathways team curates it as a mysterious copy.

khanspers commented 1 year ago

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:

  1. Import ANY pathway from WikiPathways using the WP app in Cytoscape.
  2. Go to File > Import > Network from file and find your local gpml.

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

kozo2 commented 1 year ago

Thanks @khanspers (+ I'm sorry for the late replay...), As you said, after step 1 and 2, I was able to import my local GPML into Cytoscape without any problems!