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clinicalml / omop-learn

Python package for machine learning for healthcare using a OMOP common data model
MIT License
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new cohort sql file for v5.3.1. support and a cdm version field in the config file #5

Closed egillax closed 3 years ago

egillax commented 3 years ago

Hi everyone,

My name is Egill, a postdoc from Erasmus MC in Rotterdam and I was testing your package against some synthetic data. I will eventually also test it on real data.

I needed to make some slight changes to the sql code so it would run on v5.3.1 of the cdm. I think the most common version in use is v5.3.1 so it would be good to support that. The only relevant difference from v5.3.1 to v6 is that the death_dates are not in the person table but in a death table. So I added a new cohort sql file to support that. Then I added a cdm version field in the config.

Then when running the notebooks I just added something like:

if config.CDM_VERSION == 'v5.3.1': 
    cohort_script_path = config.SQL_PATH_COHORTS + '/gen_EOL_cohort_v531.sql'  
else:  
    cohort_script_path = config.SQL_PATH_COHORTS + '/gen_EOL_cohort.sql'

I didn't include the notebooks in the pull request since then I would overwrite the figures which are there, and since the data I used was synthetic my figures were not so good to have as an example.

Cheers, Egill

justinlimkz commented 3 years ago

Hi Egill, thank you very much for testing out the package and adding v5.3.1 compatibility! I'm merging your pull request, and will edit the notebook to include the config.CDM_VERSION check you mentioned.