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bigomics
Dead links in OPG
on geneset enrichment, some of the links are directing to "gene set not found" on GSEA website
see user feedback
Assuming you mean the Enrichment analysis table in the Geneset enrichment page:
I'm marking this issue as uncloseable, since we can never know when "some of the links" are fixed. I would recommend that we either get a list of the specific links that were broken for the user, or we repurpose this issue to creating a catalogue all of the links that are broken for a specific dataset or two. But going through 2000+ links manually sounds tough.
I agree, we could have a report form for when people find deadlinks in the table itself... there will be future challenges as API changes, websites down, renaming of genesets, etc...
so we need to activelly fix these things, as it seems they are important to the users!
Ah that's a beautiful idea. It would be possible to extend this idea to include a caution icon or report icon in all plotmodules that would dropdown to a textareainput so that users could easily submit an issue for any given plot. then the report could get emailed to us.
would be useful for bugs and suggestions in general, we can discuss with Ivo and see how to move forward. I would love see this implemented.
I will reopen this, as we might have a solution that applies to many cases:
One solution would be for the user to be able to report broken links (or plots, tables) directly in the plot or table. What do you think?
User reply: Yes that would be a nice way implement noting dead links.
Should we use this approach @ivokwee?
Should the "report" icon be added to the plotmodule / tablemodule in general so that it's on every plot/table? Then if a user reports something as not working, we can pull info from the environment / settings that caused it?
I think that would be great, both for suggestions and issues. For example, certain datasets might create plot problems, and would be nice if the user could report to us.
Let's get the ok from @ivokwee as this is a big change.
I don't like the reporting thing. Before that we should investigate why the links are not working. You do not need to check 2000 links manually, you can create a simple loop and do a curl to check them all. In any case, if you get them from external DB there must be a link.
I don't like asking users to actively debug dead links. Looks like we ship broken stuff. Better disable the link. Again, we could just test each link in a loop if needed.
No, maybe asking users to report dead links for us is a bit much. They should just work. @mauromiguelm mentioned that it wasn't as simple as running curl because the links do return something but just not the right info? Is that right?
correct, the link works, but the database cannot find the entry, as image below, and returns a standard page. I dont see any easy solution other than Beautiful Soup or some report button.
on geneset enrichment, some of the links are directing to "gene set not found" on GSEA website
see user feedback
So you can grep on 'geneset not found'... But again I think we should find out why a certain gene set is not found: any extra spaces? Newline? Non UTF8 chars? Can you give me an example of a geneset that is not there?
Did some research, looks like all C5 genesets links are broken, have not found any other broken link on different genesets.
