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I haven't looked into this in any detail, but I opened a random GitHub Actions log for a random project just to copy some example log output and spotted this:
2022-12-19 09:18:33 [info ] cohortextractor-stats [cohortextractor.log_utils] description=generate_cohort execution_time=0:00:00.159524 execution_time_secs=0.1595239189999802 index_date=all state=error study_definition=study_definition_controlfinal time=679.542627243 timing=stop timing_id=0
Exception at 2022-12-19 09:18:33 UTC
Traceback (most recent call last):
File "/opt/venv/bin/cohortextractor", line 8, in <module>
sys.exit(main())
File "/app/cohortextractor/cohortextractor.py", line 891, in main
generate_cohort(
File "/app/cohortextractor/cohortextractor.py", line 167, in generate_cohort
_generate_cohort(
File "/app/cohortextractor/cohortextractor.py", line 240, in _generate_cohort
study.to_file(
File "/app/cohortextractor/study_definition.py", line 114, in to_file
dataframe_to_file(df, filename)
File "/app/cohortextractor/pandas_utils.py", line 17, in dataframe_to_file
df.to_feather(filename, compression="zstd")
File "/opt/venv/lib/python3.8/site-packages/pandas/util/_decorators.py", line 207, in wrapper
return func(*args, **kwargs)
File "/opt/venv/lib/python3.8/site-packages/pandas/core/frame.py", line 2681, in to_feather
to_feather(self, path, **kwargs)
File "/opt/venv/lib/python3.8/site-packages/pandas/io/feather_format.py", line 67, in to_feather
raise ValueError(
ValueError: feather does not support serializing <class 'pandas.core.indexes.base.Index'> for the index; you can .reset_index() to make the index into column(s)
I haven't looked into this in any detail, but I opened a random GitHub Actions log for a random project just to copy some example log output and spotted this:
That's from:
https://github.com/opensafely/covid-vaccine-effectiveness-seqtrial/actions/runs/3729963891/jobs/6326466775#step:3:6251
Which was running this action:
https://github.com/opensafely/covid-vaccine-effectiveness-seqtrial/blob/11c1d8381b1d3b3ffef643429315baa2df2de13b/project.yaml#L308-L317
With this version of Cohort Extractor:
https://github.com/opensafely-core/cohort-extractor/pkgs/container/cohortextractor/57403067?tag=1.80.10
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