Comments (10)
tetron
commented on August 20, 2024
1
Yes I fixed that already the latest run should use different links that
work.
…On Sat, May 16, 2020, 12:04 Pjotr Prins ***@***.***> wrote:
Ideally fetch the data itself.
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pjotrp
commented on August 20, 2024
Ideally fetch the data itself.
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pjotrp
commented on August 20, 2024
Useful for #56
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pjotrp
commented on August 20, 2024
Does it include links for metadata files too?
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pjotrp
commented on August 20, 2024
Beautiful - already runs on http://covid19.genenetwork.org/. See http://collections.lugli.arvadosapi.com/c=00a6af865453564f6a59b3d2c81cc7c1+123/sequence.fasta
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tetron
commented on August 20, 2024
There are no links to metadata files because the metadata is loaded into
triples.
…On Sat, May 16, 2020, 12:07 Pjotr Prins ***@***.***> wrote:
Does it include links for metadata files too?
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pjotrp
commented on August 20, 2024
I am thinking backups and verification by the uploader. Can we store the metadata in the form of a file as it comes in and annotate that in a triple (I can do the latter)? We also need some annotation for the pipelines run, though that is a separate task.
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tetron
commented on August 20, 2024
Technically since they are stored in the same collection as the fasta you
already have a verifiable way to get the metadata yaml, by taking the fasta
URIs and replacing "sequence.fasta" with "metadata.yaml" at the end.
…On Sat, May 16, 2020, 12:13 Pjotr Prins ***@***.***> wrote:
I am thinking backups and verification by the uploader. Can we store the
metadata as it comes in and annotate that in a triple (I can do the
latter)? We also need some annotation for the pipelines run, though that is
a separate task.
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pjotrp
commented on August 20, 2024
Beautiful. http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/sequence.fasta has http://collections.lugli.arvadosapi.com/c=030bcb8fda7f19743157359f5855f7a6+126/metadata.yaml
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tetron
commented on August 20, 2024
Verifiable in this case does require having the keep manifest so a backup
plan would need to stash those somewhere.
We don't have an official way of mirroring data from keep that doesn't
involve running the Arvados infrastructure however it is not terribly
difficult either it would just involve storing/reading data with a well
defined directory layout instead of fetching from a service.
…On Sat, May 16, 2020, 12:27 Pjotr Prins ***@***.***> wrote:
Closed #58 <#58>.
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