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Report summary of GWO ingest #627

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znatty22 opened this issue Apr 22, 2021 · 0 comments
Open

Report summary of GWO ingest #627

znatty22 opened this issue Apr 22, 2021 · 0 comments
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feature New functionality

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@znatty22
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znatty22 commented Apr 22, 2021

Our current process of ingesting the genomic workflow outputs doesn't include collection or reporting of the results. We should somehow report to the end user what happened in the process.

The result summary should include:

  • The before ingest gwo counts of: specimens for the study, gfs for the study, and seq exp for the study
  • The after ingest gwo counts of the above

At a minimum the results should be logged and put into a Study Creator event at the end of the ingest run.

And the short-term, ideal solution would be to produce a results file and upload it to the study creator. With the following information in the file, a user should be able to easily see which harmonized files were loaded or not, which harmonized files were linked to specimens or not, which harmonized files were linked to seq exp or not:

URL KF Genomic File ID KF Biospecimen ID KF Seq Experiment ID Result
s3://foo.cram GF_00001111 BS_00001111 SE_00001111
s3://bar.cram NA NA NA
s3://baz.cram GF_00002222 BS_00002222 NA
s3://boo.cram GF_00003333 NA NA
@znatty22 znatty22 added the feature New functionality label Apr 22, 2021
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