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OHDSI / Eunomia

An R package that facilitates access to a variety of OMOP CDM sample data sets.
https://ohdsi.github.io/Eunomia/
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V2.0 release candidate #52

Closed ablack3 closed 5 months ago

ginberg commented 1 year ago

hi @fdefalco, I am wondering if you already had a look at this PR?

fdefalco commented 1 year ago

I've pushed a number of new changes to this branch so it now has support for duckdb, sqlite, with csv and parquet files. It is failing in the runner due to an issue with a remotes dependency which I'll try and figure out. If you can each give this a test it would be much appreciated! @ablack3 @ginberg

ginberg commented 1 year ago

hi @fdefalco, thanks for the updates! Overall it's working well for me. But, we have a 'Remotes' section in the Description now for the CommonDataModel, which means that we can't submit it to CRAN. This is a pity because we would also like to put other packages depending on Eunomia, like FeatureExtraction, on CRAN. We are just using one method from CommonDataModel it seems (writeDdl). Maybe we can include this function (for now) into this package and have a long term goal of also putting the CommonDataModel on CRAN?

fdefalco commented 12 months ago

Ok. I'm going to work on getting CommonDataModel into CRAN, then it won't be a remotes dependency.

anthonysena commented 9 months ago

Just wanted to follow up here to see if there has been any progress towards getting the CommonDataModel package into CRAN @fdefalco? I also wanted to ask why we've introduced this dependency into Eunomia? With Eunomia 2.0, we've externalized the data sets and have versioned them according to the CDM specification (i.e. v5.3, v.5.4) so the DDL that is created can be implied from the .csv files in that data. If Eunomia is geared towards providing a lightweight testing DB, is this not sufficient?

fdefalco commented 7 months ago

Happy to report that CommonDataModel has now been approved to CRAN so re-initiating work on this thread.

https://cran.r-project.org/web/packages/CommonDataModel/index.html

anthonysena commented 6 months ago

Following up here @fdefalco - just let me know if I can help to resolve these conflicts so we can test & release Eunomia 2.0.

anthonysena commented 5 months ago

Noticed the activity here - thanks for pushing this along @fdefalco. I also noticed the test failure on MacOS and it may be related to this issue: https://github.com/apache/arrow/issues/41050.