Dev #1014
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Dev #1014
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* Add service account credentialing * ruff
* Add service account credentialing * ruff * First pass * tests passing * add coverage of bigquery test * change function names * use generators everywhere * bq requirement * resolver * Update sample id name * Build Sex Check Table from TDR Metrics (#999)
* refactor: Move feature flags out of environment to their own dataclass * lint: ruff * ruff
…nt in the expected loadable samples (#1003) * bugfix: exclude samples from relationship checking that are not present in the expected loadable samples * cleanup
#1005) * feat: add remap and family loading failures as validation exceptions rather than runtime errors * move on * Update write_remapped_and_subsetted_callset_test.py * ruff
* Support gcs dirs in rsync * ws * Add create dataproc cluster task * add dataproc * ruff * requirements * still struggling * Gencode refactor to remove gcs * bump reqs * Run dataproc job * lib * running * merge requirements * Flip'em * Better exception handling * Cleaner approach if less generalizable * write a test * Fix tests * lint * Add test for success * refactor to use a base class... better for adding support for multiple jobs * cleanup * ruff * Fix missing mock * Fix flapping test * pr comments
…n gcs and on local disk. (#1006) * Support gcs dirs in rsync * ws * Add create dataproc cluster task * add dataproc * ruff * requirements * still struggling * Gencode refactor to remove gcs * bump reqs * Run dataproc job * lib * running * merge requirements * Flip'em * Better exception handling * Cleaner approach if less generalizable * write a test * Fix tests * lint * Add test for success * refactor to use a base class... better for adding support for multiple jobs * cleanup * ruff * Fix missing mock * Fix flapping test * first commit * Finish test and cleanup * Allow any order
…r local users (#1009) * Support gcs dirs in rsync * ws * Add create dataproc cluster task * add dataproc * ruff * requirements * still struggling * Gencode refactor to remove gcs * bump reqs * Run dataproc job * lib * running * merge requirements * Flip'em * Better exception handling * Cleaner approach if less generalizable * write a test * Fix tests * lint * Add test for success * refactor to use a base class... better for adding support for multiple jobs * cleanup * ruff * Fix missing mock * Fix flapping test * first commit * Finish test and cleanup * Allow any order * First commit * ruff * ruff * finish off * A few minor tweaks
* Misaligned ploidy samples * regex * Make sure s is a key in tests, update validation errors to support body * unnecessary key * Update v03_pipeline/lib/misc/validation.py Co-authored-by: Daniel Marten <78616802+matren395@users.noreply.github.com> * Update validation_test.py * validation * fix test --------- Co-authored-by: Daniel Marten <78616802+matren395@users.noreply.github.com>
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