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get_study_samples downloads incorrect file #24

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SandyRogers opened this issue Aug 11, 2022 · 0 comments
Open

get_study_samples downloads incorrect file #24

SandyRogers opened this issue Aug 11, 2022 · 0 comments
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@SandyRogers
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Possibly related to #6


Reproduce

get_study_samples('MTBLS297')

does not return the samples list shown on the website.
(This is probably the case for other studies too, I just happened to check this one.)

It looks like get_study_samples assumes a samples file will be at /files/samples, rather than some other filename.

Possible fix

Something like this seems to work (to find the actual filename):

files <- get_study_files('MTBLS297')
samples_file <- files[which(files$type=='metadata_sample'),'file']
download_study_file('MTBLS297', samples_file)

If this is the right approach I can submit a PR with a change to this effect?

@wilsontom wilsontom self-assigned this Aug 15, 2022
@wilsontom wilsontom added the bug Something isn't working label Aug 15, 2022
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