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pubseq / bh20-seq-resource

Tool to upload SARS-CoV-2 sequences to BH20 Arvados instance and orchestrate analysis
Apache License 2.0
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submitterShap error #91

Closed tetron closed 3 years ago

tetron commented 4 years ago

I'm seeing this error running import

[2020-07-07 20:43:19] WARNING 'MT385461.1 uploaded by unknown@50f4c4f28070 from 3.89.224.155' (lugli-4zz18-nb1luabe2d62v9k) has valid
ation errors:   Testing <http://arvados.org/keep:67ad83a2d78ebaa3142fda891604051d+126/metadata.yaml> against shape https://raw.github
usercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape
    Testing _:b1 against shape https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submitterShape
    _:b1 context:
      <http://arvados.org/keep:67ad83a2d78ebaa3142fda891604051d+126/metadata.yaml> MainSchema:submitter _:b1 .
         _:b1 sio:SIO_000116 "Data Science" .
         _:b1 sio:SIO_000172 "Chan-Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA" .

         No matching triples found for predicate obo:NCIT_C42781
AndreaGuarracino commented 4 years ago

Looking at the YAML file, there is an empty authors field that I should avoid to write. Could you try to remove that field and re-import it?

pjotrp commented 4 years ago

Is this working?