Bulk Ingest #8301
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Bulk Ingest #8301
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Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8301 +/- ##
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Coverage ? 76.562%
Complexity ? 21800
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Files ? 1390
Lines ? 83084
Branches ? 13237
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Hits ? 63611
Misses ? 14308
Partials ? 5165 |
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koncheto-broad
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May 10, 2023
mcovarr
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| ## TODO I dont love that we are hardcoding them here and in the python--they need to be params! |
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why not just do that now with defaulted params?
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I want to update this whole python script in my next pr where I also address sample sets
scripts/variantstore/wdl/extract/bulk_ingest_test_files/shriners_columns_for_import.json
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* add Aarons changes * put terra token in python * id not bucket * hardcode for testing * do we need a new docker image? * set workspace info * pull in name from rawls * pass output locations * add back prepare * add GvsImportGenomes back * update python for grabbing cols * split methods for easier testing * set defaults, but allow optional overrides for sample table and id * add unit test for python column guessing * clean up python for testing * add proper docker * is this where the loop is coming from? * better names * remove testing artifact * add back problem lines to the test * throw out columns with values other than strings * set defaults in the right place
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Successful run here:
https://job-manager.dsde-prod.broadinstitute.org/jobs/41b11f26-9d55-45ad-b593-ddb5b8c78184
Bulk load data here:
https://console.cloud.google.com/bigquery?project=spec-ops-aou&ws=!1m25!1m4!4m3!1sgvs-internal!2sgg_quickstart1!3sgg-quickstart1_vat_12!1m4!1m3!1sspec-ops-aou!2sbquxjob_11f0b098_187d879575c!3sUS!1m4!4m3!1sspec-ops-aou!2sgg_quickstart!3svet_001!1m4!1m3!1sspec-ops-aou!2sbquxjob_aa2c57_187d8b92d34!3sUS!1m4!4m3!1sgvs-internal!2src_ingest_bulk_test_useability!3ssample_load_status
All that now needs to be input (assuming that we guess the additional parameters correctly)
this needs a new docker image and an interactive rebase lol
documentation attempt:
https://docs.google.com/document/d/1fxu0EnNp7ie42BtFQsSSN6QUESUiDl3fm8F5AnNkKhw/edit#heading=h.s5k25ipaom03