PathExplorer bug

[Yujin Kim]

Hello,

For my internship, i'm using Cytoscape 3.5 on Mac OS X 10.9.5 and i downloaded PathExplorer to get which nodes are linked to others via other nodes.
I installed successfully the app and it works from the get go but when i reload Cytoscape, the menu displayed when i right click on a node doesn't show up. And i uninstalled the app, and the menu shows up again.
I'm fairly new to Cytoscape and i don't know how to do what i described earlier from scratch.

Thanks,

Yujin

[Scooter Morris]

Hi Yujin,
   Definitely sounds like a PathExplorer bug.  One thing you can try is to use PathExplorer to get the path of interest, then just disable it in the AppManager (Apps->App Manager) rather than uninstalling it.  You can enable and disable it in the same session without having to restart Cytoscape.

-- scooter

[Yujin Kim]

Hi,

Thanks for the answer, for the moment i guess i'll do that but i need the paths of numerous nodes so it's going to be annoying to say the least.
Do you know if the developer is active in this group or should i contact him directly?

Yujin

[Alexander Pico]

Hi Yujin,

Sorry for the delayed response.  I’ve looked into errors and it appears something has changed in how “hidden” tables are accessed in Cytoscape. We will investigate this further. In the meantime, I’ve attached an custom “fixed” version of the PathExplorer app that you can install to replace your current one.

Note: in order to attach it to this email I had to rename the extension to .jarrr. Simply rename it .jar and then it should install and work fine in Cytoscape.

Let me know if you have any trouble.

Thanks!

 - Alex

[Yujin Kim]

Hello,

Thanks a lot, it works fine now!

Yujin

[Fletcher Barton]

I have a similar problem. When PathExplorer is enabled, right-click is often disabled (it doesn't appear), preventing any number of manual edits. In the past the reason was that nodes or edges had been manually added but the 'not in path' value was empty, so if I then manually entered "false" in any empty box, the dropdown reappeared. Another way of restoring it was to copy the network and paste it into a new, blank network (having already entered 'falses' in the original). Today I dutifully examined all 'in path' cells and found them non-null, but the dropdown was disabled anyhow. I had to disable PathExplorer in AppStore (I'm using 3.10.0), close and save the session, then reopen it. So: will the above jarrr solve my problem, and is it usable on Windows? Thanks.

[Alex Pico]

Yes, it works on all platforms. Please give it a try and let us know. Thanks!

 - Alex

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