galaxyproject
Genome list page
@ElectronicBlueberry Add a client route /genome-list to display a list of available genomes, reusing components from the /datatypes page. Allows sorting and keyword filtering.
How to test the changes?
There is not really any logic worth testing here but can add a test if anyone disagrees.
License
- [x] I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.
Suggesting to rename this to something agnostic. Maybe dbkeys? In general we should avoid using the word genome in the user interface and go with dbkey or build instead.
Yes, imho opinion also the title, so e.g. use a title like Database Keys. The idea here is that metadata data specifying associated reference datasets can also be used in other context down the road and not just for genomes and biological applications.
After a chat with @bgruening I have refactored this similar to your suggestion, but we should aim to upgrade this to a "reference data" page which allows the user to click on a dbkey and view indices that have been built against it. We should also include reference data that are not built against a dbkey (e.g. Nr BLAST database) - for users, we could call the latter "Generic" and former "Subject" (as in, keyed to genomes/subjects via dbkey) reference data.
This looks good to me functionality-wise. I hesitate to bikeshed, but I think naming it something like reference data or similar would be another improvement over dbkey, which is niche nomenclature yet again.
@dannon I suggested this terminology but @bgruening points out that this is not a comprehensive list of reference data. It only describes the subjects (i.e. genomes) for which "keyed" (subject-oriented) reference data are available. A user might look at this page and assume that the Nr BLAST DB is not available on this Galaxy. They might also think that a STAR indexes do not exist. I agree that DB keys is nonsense language to a typical user, but can't think of a more intuitive name that is also accurate.
My expectation is that we won't promote the existence of this page to users until it clearly communicates the relationship between dbkeys (or subjects, or whatever we call them) and reference data.
Maybe "available references" or "available reference keys"? Or, is there terminology from the non-bio segments that we can leverage? What, if anything, is the equivalent for materials science or astronomy or one of the other new fields folks are using Galaxy for?
Yeah I like "reference data keys" with the short explanation of what that means. @bgruening @guerler any comments?
@neoformit yes that sounds good to me, thank you for putting the effort in to come up with an agnostic name which we now can use consistently moving forward!
If we want to get this in I think reference data keys makes a lot of sense. However, I do not know how useful this endpoint is and if we can easily remove it later.
Mid-term I would rather see a reference_data endpoint where all data is listed and the dbkey are used inside this page to aggregate and navigate the user (for the subset of data where it is useful).
@bgruening I don't think this page is so useful for users, perhaps somewhat for admins. I'd merge on the premise that it doesn't do much harm. Does it make sense to make the route /reference-data with the view that it can be updated to include reference data properly (as discussed) at a later date?