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PathVisio / pathvisio

PathVisio - pathway editor, visualization and analysis software
http://www.pathvisio.org
Apache License 2.0
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HTTP response 404: server has not found anything matching the request URI. Error when using statistics function on downloaded from Wikipathways pathways #184

Open punter-funter opened 2 years ago

punter-funter commented 2 years ago

To whom it may concern,

When running the statistics function over Wikipathways downloaded pathways, it throws the following error

pastedImage

I found out that problem is in the particular pathways itself. 27 pathways out of 738 from the WikiPathways database (version 20220510) caused this mistake. When deleted, everything worked fine. Here are identifiers of the 27 pathways: WP4657, WP5113, WP4718, WP4719, WP3850, WP4328, WP4536, WP3958, WP4880, WP4863, WP3635, WP3634, WP5044, WP4853, WP4010, WP4944, WP2509, WP2507, WP5115, WP5027, WP4341, WP5043, WP4900, WP4846, WP5098, WP4725, WP4726

With kind regards,

mkutmon commented 2 years ago

thanks for your report! are you using the may 2022 release of pathways? do you have any plugins installed in pathvisio?

mkutmon commented 2 years ago

based on the error message, this looks like a BridgeDb plugin issue. If you have the plugin installed, can you try to uninstall it, restart PathVisio, connect a local identifier mapping database and then perform the statistics again?

punter-funter commented 2 years ago

Thank you for your responses!

I have used the following release wikipathways-20220510-gpml-Homo_sapiens. But i have checked the earlier releases as well - it still produces this mistake no matter what.

I did not install BridgeDb plugin to my knowledge, but I used the following file to import the expression data Hs_Derby_Ensembl_91.bridge

So far I have solved this mistake by taking out these 27 pathways. It provided the statistic. Basically, I just wanted to inform you of this bug