Add helper functions for querying Terra Data Repository
#998
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bpblanken
changed the title
Terra Data Repository
bpblanken
changed the title
Terra Data RepositoryTerra Data Repository
jklugherz
reviewed
Dec 12, 2024
| status_forcelist=[500, 502, 503, 504], | ||
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| s.mount('https://', HTTPAdapter(max_retries=retries)) | ||
| s = requests_retry_session() |
jklugherz
reviewed
Dec 12, 2024
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| def gen_bq_table_names() -> Generator[str]: | ||
| with ThreadPoolExecutor(max_workers=5) as executor: |
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How did you chose 5 max_workers?
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I believe ai was responsible for this choice 🍭.
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I'll make it a constant on the downstream pr.
jklugherz
reviewed
Dec 12, 2024
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| def _get_dataset_ids() -> list[str]: |
Contributor
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Are we calling this on every pipeline run? It fetches all of the datasets in the TDR, is there a way to filter it first by dataset name perhaps?
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Yes! This should be called every pipeline run, but it's only a single API request. The plan was to use the result of this request + a persisted list of dataset ids that we've seen before to create a "new dataset ids" list that would be passed into gen_bq_sample_metrics.
Base automatically changed from
benb/add_service_account_credentialing
to
dev
December 13, 2024 14:41
…s into benb/fetch_predicted_sex_from_tdr
bpblanken
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Dec 13, 2024
* Add service account credentialing (#997) * Add service account credentialing * ruff * feat: Handle parsing empty predicted sex into Unknown (#1000) * Add helper functions for querying `Terra Data Repository` (#998) * 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)
bpblanken
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Jan 7, 2025
* Add service account credentialing (#997) * Add service account credentialing * ruff * feat: Handle parsing empty predicted sex into Unknown (#1000) * Add helper functions for querying `Terra Data Repository` (#998) * 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 to FeatureFlag enum. (#1002) * refactor: Move feature flags out of environment to their own dataclass * lint: ruff * ruff * bugfix: exclude samples from relationship checking that are not present in the expected loadable samples (#1003) * bugfix: exclude samples from relationship checking that are not present in the expected loadable samples * cleanup * feat: add remap and family loading failures as validation exceptions … (#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 * feat: Add ability to run tasks dataproc. (#948) * 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
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Adds helper functions for querying
tdrand the underlyingbig querystores. Does not manage the persistence of these into the pipeline!