V2.0 release candidate #52
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Add test for exportToCsv
skip tests when Java 8 is not available
…supportsJava8() function during tests.
…supportsJava8() function during tests. (#15) Co-authored-by: Adam Black <adam.black@odysseusinc.com>
…on, add installation of libcurl and libssh to github actions workflow.
Remove dependency on rcmdcheck, remove test of supportsJava8() function, add installation of libcurl and libssh to github actions workflow.
* removed drat installation instructions, CRAN only * Update README.md * updates and fixes switched to readr for csv writing fixes #13 added gender concepts to concept table fixes #21 fixes #19 Co-authored-by: Frank DeFalco <fdefalco@ohdsi.org> Co-authored-by: Martijn Schuemie <schuemie@ohdsi.org> Co-authored-by: Frank DeFalco <fdefalco@its.jnj.com>
Fix GiBleed.sql
… translate calls because it causes cryptic errors when devtools::test() is called.
…8 function and RSQLite is actually not used by this package directly so it is removed from Description to avoid the R check NOTE.
Reads the environment variable to get the github base url to EunomiaDatasets. Downloads and specified dataset and version as a zip file. Reads in all the CSVs.
Decaffeinate Eunomia
make getEunomiaConnectionDetails backwards compatible
convert dates to numbers when loading data to sqlite
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hi @fdefalco, I am wondering if you already had a look at this PR? |
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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 |
| #' @param overwrite Remove and replace an existing data set. | ||
| #' @export | ||
| loadDataFiles <- function(dataPath, | ||
| dbPath, |
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the function parameters are not properly aligned
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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? |
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Ok. I'm going to work on getting CommonDataModel into CRAN, then it won't be a remotes dependency. |
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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? |
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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 |
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Following up here @fdefalco - just let me know if I can help to resolve these conflicts so we can test & release Eunomia 2.0. |
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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: apache/arrow#41050. |
remediate macos github actions limitation
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