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Ensure only imaging studies are processed from OMOP ES parquet files #212 #271

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merged 3 commits into from
Jan 31, 2024
Merged

Ensure only imaging studies are processed from OMOP ES parquet files #212 #271

merged 3 commits into from
Jan 31, 2024

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peshence
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  • filter on accession number not none
  • remove accession number from test parquet files for all but expected two xray images

Talked about switching to e.g. csv but pandas was struggling with converting datetimes and I thought it was more trouble than ti was worth

@peshence peshence linked an issue Jan 31, 2024 that may be closed by this pull request
Ensure only imaging studies are processed from OMOP ES parquet files #212
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@peshence peshence requested a review from stefpiatek January 31, 2024 14:17
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stefpiatek approved these changes Jan 31, 2024
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Yeah that seems fair, I think something like json/toml might be easier but also happy with this. Looks like system tests are still failing CI. I think there's the same parquet file duplicated in the system tests resources (in top level test dir)

@peshence peshence enabled auto-merge (squash) January 31, 2024 17:49
@peshence peshence merged commit 8324363 into main Jan 31, 2024
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@peshence peshence deleted the 212-ensure-only-imaging-studies-are-processed-from-omop-es-parquet-files branch January 31, 2024 17:54
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Ensure only imaging studies are processed from OMOP ES parquet files
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@peshence @stefpiatek