Problem importing pathway as pathway in cytoscape 3.7.1

[IreneHemel]

For my internship with @DeniseSl22 I want to import several pathways into cytoscape as a pathway, however when I try this on my computer (Windows 10 version 1803) in cytoscape 3.7.1 with version 3.3.7 of the WikiPathways app all the nodes are stacked.

Image is an example based on WP4225, but it is the same for all pathways I tried

When I try the same thing in cytoscape 3.6.1, with the same Wikipathways app version, it does work, but not in 3.7.1

[mkutmon]

@IreneHemel I just tried it with 3.7.1 and app version 3.3.7 and it worked fine. Can you retry after restarting Cytoscape?

[IreneHemel]

When I restarted it yesterday and earlier today it didn't work (I worked in a saved session with other pathways that were imported as a network). I just tried it in a new session and then it does work, however when I open a pathway as a network and try to open one as a pathway after, the nodes are stacked again

[mkutmon]

ah okay, so it happens if you have multiple pathways open in one session? Does this also happen for other pathways?

[IreneHemel]

Yes, as soon as I open 1 pathway as a network I cannot open any as a pathway. So far this has happend for all the pathways I tried to open (WP4225, 4571, 4583, 4584 and 4595)

[AdamStuart]

Irene,

Sorry, I can’t reproduce it here. It sounds like some variable is getting stuck in the wrong state. You can probably uninstall and reinstall the app to clear it (faster than a restart), but it that’s not a very satisfying solution.

Check your default layout setting. After importing as a network, Cytoscape would apply a layout, and maybe it is encountering a problem there. For the sake of testing, I’d set Grid layout to be my default. That will at least spread them out from a single spot.

I assume you are doing this via the user interface, as opposed to sending CyRest commands. If you are using commands then please send me the script.

Adam

On May 14, 2019, at 4:54 AM, IreneHemel notifications@github.com wrote:

For my internship with @DeniseSl22 https://github.com/DeniseSl22 I want to import several pathways into cytoscape as a pathway, however when I try this on my computer (Windows 10 version 1803) in cytoscape 3.7.1 with version 3.3.7 of the WikiPathways app all the nodes are stacked.

https://user-images.githubusercontent.com/49555069/57693969-ca960e80-764a-11e9-9e30-229040246356.png Image is an example based on WP4225, but it is the same for all pathways I tried

When I try the same thing in cytoscape 3.6.1, with the same Wikipathways app version, it does work, but not in 3.7.1 https://user-images.githubusercontent.com/49555069/57695527-c9ff7700-764e-11e9-955f-d42cc3c797cc.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/wikipathways/cytoscape-wikipathways-app/issues/106?email_source=notifications&email_token=AB2K73KIL657QPVKY67EJZLPVKR5TA5CNFSM4HMZEZIKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GTU6LGQ, or mute the thread https://github.com/notifications/unsubscribe-auth/AB2K73J5YMAPUBCHD7CQG23PVKR5TANCNFSM4HMZEZIA.

[IreneHemel]

My default layout is set to perfused force directed layout, when I change it to a grid layout the problem still appears. I can apply the layout after the stacked nodes appear and then it does apply the layout, however I cannot go back from that to the pathway layout I want.

Disabeling and enabeling the app does work, so I will use that for now and I indeed work with the user interface, not with commands

[AlexanderPico]

This same thing happened to me yesterday. I could consistently reproduce it with these steps:

1. Fresh launch of Cytoscape (must be a fresh start; not just a "close session")
2. Search for WP179
3. Open as network
4. Repeat search for WP179
5. Open as pathway

Obs: overlapping nodes Exp: pathway layout

Same thing happens when steps 2-5 are done with automation calls:

2. 'wikipathways import-as-network id=WP179'
3. 'wikipathways import-as-pathway id=WP179'

Once this has occured, then all pathway imports are affected, even upon restart. The only fix is to disable/enable the WP app.

[AdamStuart]

I was able to "fix" this by changing the declaration of the BasicVizPropStore class in GpmlToPathway. (see Line 758) It was previously static, but now we re-declare the objects with each instance. Interface removed.

Note that BasicVizTableStore has the same static declaration.

[yihangx]

Reopen because of 3.3.9.

[AlexanderPico]

Fixed in 3.3.10

[BrandonMurugan]

I'm currently having this issue with WP v3.3.10 in Cytoscape 3.9.1; 3.10.0; and 3.10.1 It stacks the nodes when I open another WP pathway, and if I save and reopen a session file with just one WP pathway loaded

[BrandonMurugan]

Hi there. So I did figure out what happened. When I load a WP pathway, it loads two Views. One is formatted properly, and the other one is stacked and has the KGML_style applied. Deleting the offending View fixes it. The appearance of the "2" in the network list made me suspicious. See attachments below. It does seem to be a Cytoscape issue, since it does this for iGraph imports from R. I have no idea if it's just happening to me (maybe some setting/app) or is a more widespread issue.

Cheers!

[AlexanderPico]

Wow. That's interesting. Haven't seen that before. You mention the "KGML_style". That's coming from a KEGG app, I presume. Have you tried disabling that (and other apps)? Sometimes apps can collide.