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[16.04] fix/replace biomart data source #2149
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More info at http://www.biomart.org/notice.html . |
@nsoranzo I just noticed that ensembl is probably providing only a subset of former biomart data? :/ |
@martenson I suspected that too, but I am no expert. |
Better than nothing for the moment. We could put a warning message in the tool explaining the situation, perhaps? You can use an rST warning class for it, e.g.
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@natefoo the tool form is never visible on our side; it just opens a new tab for you - so I am not sure we have a good place where to put a warning |
Oh, right. |
@martenson Yeah, my reading of the notice and understanding of how this works leads me to think that this change would reduce the set of available stuff pretty dramatically (and somewhat arbitrarily -- I don't know how many more users would complain if stuff vanished than if it was just temporarily disabled). Should we just temporarily disable it? |
I say subset is better than nothing. |
How'd you pick the ensembl subset over one of the other ones? |
I picked fairly randomly (browsed a few and this one had the most data). I would be interested in knowing whether the original biomart encompassed all the data from the community servers listed at http://www.biomart.org/notice.html |
That's what I was afraid of. And, yeah, my understanding just based on how they phrased the notice leads me to think they did. |
Alternatively we can create a new section where we would list all these data sources. However I am not sure whether all support the GALAXY_URL redirect...but they might. |
Eh, we could make it explicit. PR inc, which if it seems good to you, I'll merge this. martenson#14 seem good? |
(I'm totally fine with a temporarily reduced subset, as long as it's clear to users that's what they're getting) |
I went through some more URL listed at the notice and they are surprisingly often dead. |
moving to WIP until we figure out what to do |
Specify Ensembl biomart server in descriptions.
back to review state; lets fix this with just ensembl and decide later if we want more |
LGTM, then. Thanks! |
closes #2148