Rc vs 778 spike import limit #8197
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RoriCremer
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Feb 22, 2023
1. We do NOT want to assume that the sample ids we want are in the name field. Pass that through as a parameter. 2. We want to explicitly pause every 500 samples, as that's our page size. It slows our requests down enough to not spam the backend server and hit 503 errors, although it does slow down the rate at which we can write the files if the dataset is too big. Which shouldn't be a concern, because as long as it doesn't cause errors it is still a hands off process. 3. We want to account to heterogenous data. In AoU Delta, for instance, the control samples keep their vcf and vcf_index data in a different field. This would cause the whole thing to fail if we weren't accounting for that explicitly, and now we generate an errors.txt file that will hold the row that we couldn't find the correct columns for so they can be examined later
… data table and being slightly more informative in the output of the python script
…ficiency (and handling larger callsets)
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Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8197 +/- ##
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Coverage ? 83.979%
Complexity ? 34803
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Files ? 2194
Lines ? 167039
Branches ? 18005
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Hits ? 140278
Misses ? 20534
Partials ? 6227 |
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Github actions tests reported job failures from actions build 4358183003
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mcovarr
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Mar 15, 2023
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| docker: "us.gcr.io/broad-dsde-methods/variantstore:2023-1-20-FOFN" |
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ISO 8601 nit, names should be like YYYY-MM-DD, i.e. always two digits for month and day. Nice for sorting things chronologically and lexically at the same time. 🙂
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The goal of this PR is to adjust the ingest in two ways:
There is still work to do around making the bulk ingest process significantly more user-friendly