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Enable search #169

Open mattmaurano opened 4 years ago

mattmaurano commented 4 years ago

https://genome.ucsc.edu/goldenPath/help/hubQuickStartSearch.html

There is some sort of metadata support for ENCODE http://genome.ucsc.edu/goldenPath/help/trackSearch.html

mattmaurano commented 4 years ago

John, can you investigate what sort of metadata we can provide, its exact format, and how it manifests in the browser search box?

cadley-nyulangone commented 4 years ago

OK

On Mon, Mar 23, 2020 at 10:50 AM mattmaurano notifications@github.com wrote:

John, can you investigate what sort of metadata we can provide, its exact format, and how it manifests in the browser search box?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/mauranolab/mapping/issues/169#issuecomment-602645582, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKY4NJQRTMBM4N2U3332OZ3RI5ZKJANCNFSM4LNL65KQ .

cadley-nyulangone commented 4 years ago

I get the same problems. I've sent in an inquiry to UCSC asking why the simple search tab does not work. I also notice that when you are working from the cegsvectors assembly, then go to the search tab, you get a database error message rather than the search input screen. I've asked about that as well. hg38, mm10, and rn6 all seem to work with the advanced tab.

The elements are not in a place that the search tool looks in. It just looks in track names, descriptions, groups, and metadata.

I'll work on finding a way to use the metadata feature.

cadley-nyulangone commented 4 years ago

The database error that comes up when trying to search the cegsvectors assembly has been replicated by UCSC. Search (both simple and advanced) doesn't work for custom assemblies. This is a bug in the browser, and they will try to get it fixed in a future release.

cadley-nyulangone commented 4 years ago

Just received some feedback from UCSC:

Basic Search:  Works only for native browser tracks.  This is intended.

Advanced Search:  Works for both native browser tracks and for hubs.
                  In the hubs, it's supposed to work for both custom genomes and for the native UCSC genomes.
                  However, due to a browser bug, it currently only works for the native UCSC genomes.

In Advanced Search, items you put in the Track Name field are matched against track short and long labels, not 
against the track name field in the track stanza. The Description field is supposed to be used to scan the html
file for the track, if it exists, but this also is buggy.

They are working on these issues, "but that may take some time".