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databio / bedboss

Python pipeline for processing BED files for BEDbase
https://docs.bedbase.org
BSD 2-Clause "Simplified" License
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Use pephubclient to upload bed metadata as PEP sample #31

Closed khoroshevskyi closed 6 months ago

khoroshevskyi commented 7 months ago

Bedboss should utilize PEPHubClient to add bed metadata. For example:

phc.sample.add({
    "sample_name": bed_id,
    "genome": "hg38",
    # Add other metadata fields here
})

This metadata should be retrieved from the provided PEP to Bedboss. Additionally, this line of code should be integrated into bedstat, as all processing occurs there."

donaldcampbelljr commented 7 months ago

Made a PEP to capture this information (it is unclear which PEP the pipeline should report his information to): databio/allbeds:bedbase

donaldcampbelljr commented 7 months ago

Ok, I've done a first pass on adding this functionality to Bedstat with the caveats:

  1. The pephubclient does not exist yet
  2. Given our test failures, I did not bother writing a test for this either.
donaldcampbelljr commented 7 months ago

Ok, I've made the discussed changes. We will still need to validate input as well as remove items from the pep_sample_dict as it will contain attributes that we don't consider metadata. But for now, this would allow for uploading sample to https://pephub.databio.org/databio/allbeds?tag=bedbase

khoroshevskyi commented 6 months ago

This issue was solved in v0.1.0