feat: Add ability to run tasks dataproc. #948
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bpblanken
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dev
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benb/create_dataproc_cluster_task
…s into benb/run_pipeline_on_dataproc_task
…s into benb/run_pipeline_on_dataproc_task
bpblanken
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jklugherz
reviewed
Jan 6, 2025
| ) | ||
| except google.api_core.exceptions.NotFound: | ||
| return False | ||
| else: |
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is this else needed here? won't the following lines be executed anyway if no exception is thrown in the try block?
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yeah... I was getting a lint error if I had the return within the try. I don't think the rule properly accounts for the return in the expect block. I can lift them out of the "else" no problem though.
jklugherz
reviewed
Jan 6, 2025
| request={ | ||
| 'project_id': Env.GCLOUD_PROJECT, | ||
| 'region': Env.GCLOUD_REGION, | ||
| 'job_id': f'{self.task_name}-{self.run_id}', |
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nit, but you could make job_id an instance attribute self.job_id = f'{self.task_name}-{self.run_id}' so that you do it in just 1 spot instead of 4
jklugherz
reviewed
Jan 6, 2025
| @@ -166,11 +175,13 @@ def run(self): | |||
| 'cluster': get_cluster_config(self.reference_genome, self.run_id), | |||
| }, | |||
| ) | |||
| while True: | |||
| wait_s = 0 | |||
| while wait_s < TIMEOUT_S: | |||
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do we also want this waiting behavior in BaseRunJobOnDataprocTask?
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I left it out because I couldn't think of a good timeout... there's going to be wide variability depending on who's using it and how much compute they as for. Setting an extreme timout (like 48 hours) might be better though.
jklugherz
approved these changes
Jan 6, 2025
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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