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try moving clinvar submitter tmp file to gcs before importing (#742)
* try moving tmp file to gcs first * Oops
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v03_pipeline/lib/reference_data/clinvar.py

Lines changed: 6 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -177,8 +177,13 @@ def download_and_import_clinvar_submission_summary() -> hl.Table:
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delete=False,
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) as tmp_file:
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urllib.request.urlretrieve(CLINVAR_SUBMISSION_SUMMARY_URL, tmp_file.name) # noqa: S310
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gcs_tmp_file_name = os.path.join(
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Env.HAIL_TMPDIR,
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os.path.basename(tmp_file.name),
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)
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safely_move_to_gcs(tmp_file.name, gcs_tmp_file_name)
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return hl.import_table(
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tmp_file.name,
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gcs_tmp_file_name,
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force=True,
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filter='^(#[^:]*:|^##).*$', # removes all comments except for the header line
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types={

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