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Cellular Overview Glitch in web version of tools

asked 2018-06-27 09:42:17 -0500

gpharhay gravatar image

In the web version of ptools, it used to be possible to click on a Pathway Class ( Fatty Acid and Lipids Biosynthesis) in the cellular overview so that the details Pathway Class would be displayed -- Parent Class, Child Classes, and Instances. This doesn't not happen any longer. Output in the lisp window complains about No Unique Object ID. This occurs for my and the E coli PGDB that comes with ptools.

Thankfully, the desktop version of ptools does not exhibit this behavior, that is, the desktop version still works properly

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answered 2018-06-27 19:09:23 -0500

Richard gravatar image

You can get to the information you desire in the web version by hovering over a reaction in a pathway of the class you want to get this information about, select the pathway from the tooltip that appears, and then, on the pathway page, there's a list of superclasses of that pathway, and selecting one of those will give you the summary you're looking for.

However, I'm confused by your report. First, I'm unaware of it ever being a feature of the web version. Second, what lisp window? Are you running a web server locally? What version of Pathway Tools are you running? I can't reproduce this behavior (including anything appearing on the server console) in 21.5, 22.0, or beta when running a webserver. The desktop does indeed seem to do as you desire.

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It is certainly possible that I am not correctly remembering the behavior of the web version of ptools when mousing over the cellular overview. I am using version 22.0. I can confirm that the behavior that you describe when selecting a pathway with the tooltip, and resulting list of superclasses of the pathway. The lisp window I referred to is the window that is fired off when starting up the web version of ptools locally. The errors that I see in that window does not coincide with clicking on the cellular overview, but rather, appear when the pgdb is manually selected by clicking on “change organism database”. If you wish, I can send you a screenshot of the lisp window that shows the errors that appear when the E coli PGDB is loaded.

gpharhay gravatar imagegpharhay ( 2018-07-05 17:42:33 -0500 )edit

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Asked: 2018-06-27 09:42:17 -0500

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Last updated: Jun 27