Failed to open wikipathways after upgrading to cytoscape 6

[ax...@case.edu]

Good morning. I just upgraded to cytoscape 6 (windows 7 64 bit enviroment) and I no longer can use wikipathways in this versionor the older ones. First error that I got is below:
Retrieve list of organisms from WikiPathways sun.security.validator.ValidatorException: PKIX path building failed: ...
Searching for that error, somebody fixed it installign the latest version of java 8.
Prior to installing cytoscape 6, I did ran the script that you provide to make sure I could ran it, and it passed, so I installed the program.
After having the above error and solution provided, realized that my version jave 8 was a tad behind in ptaches, so I instaleld the latest. And reinstalled wikipathways. Error above dissapeared, but now when I try to open a pathway, it looks like is goign to work, but it freezes as soon as it gets to the cy:command_documentation_generation.
I have not been able to find any information about this.

[Alex Pico]

Hi Axp8,

Thanks for the thorough issue report. It looks like you solved the WikiPathways-specific issue on your own. Nice work! The last error you report (cy:command_documentation_generation) is related to CyREST. Can you let us know which version of the CyREST app you have installed. For core apps, like CyREST, you’ll want to look in ‘apps’ dir in the Cytoscape installation dir (not Cytoscape Configuration).

Also, can you provide a stack trace? Ideally, if you could launch Cytoscape from command line, then you can copy/paste the errors that show up there.

These system-specific errors are hard for others to reproduce obviously (since it works on our machines), so these extra details are essential.

I’m cc’ing the primary author of CyREST to help as well.
- Alex

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[David Otasek]

Hi Axp8, in addition to the information Alex requested, sending us your cytoscape framework log would be very helpful. It's normally located in your configuration directory as: /CytoscapeConfiguration/3/framework-cytoscape.log

On Thu, Mar 15, 2018 at 1:05 PM, Alex Pico <alex...@gladstone.ucsf.edu> wrote:

Hi Axp8,

Thanks for the thorough issue report.  It looks like you solved the WikiPathways-specific issue on your own. Nice work! The last error you report (cy:command_documentation_generation) is related to CyREST. Can you let us know which version of the CyREST app you have installed.  For core apps, like CyREST, you’ll want to look in ‘apps’ dir in the Cytoscape installation dir (not Cytoscape Configuration).

Also, can you provide a stack trace? Ideally, if you could launch Cytoscape from command line, then you can copy/paste the errors that show up there.

These system-specific errors are hard for others to reproduce obviously (since it works on our machines), so these extra details are essential.

I’m cc’ing the primary author of CyREST to help as well.
 - Alex

> On Mar 14, 2018, at 6:55 AM, ax...@case.edu wrote:
>
> Good morning. I just upgraded to cytoscape 6 (windows 7 64 bit enviroment) and I no longer can use wikipathways in this versionor the older ones. First error that I got is below:
> Retrieve list of organisms from WikiPathways sun.security.validator.ValidatorException: PKIX path building failed: ...
> Searching for that error, somebody fixed it installign the latest version of java 8.
> Prior to installing cytoscape 6, I did ran the script that you provide to make sure I could ran it, and it passed, so I installed the program.
> After having the above error and solution provided, realized that my version jave 8 was a tad behind in ptaches, so I instaleld the latest. And reinstalled wikipathways. Error above dissapeared, but now when I try to open a pathway, it looks like is goign to work, but it freezes as soon as it gets to the cy:command_documentation_generation.
> I have not been able to find any information about this.
>
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> To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.
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