Eunomia
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OHDSI
A new GiBleed dataset is always downloaded breaking unittests on R 4.4.0
A new GiBleed dataset is always downloaded when getting the Eunomia ConnectionDetails with Eunomia::getEunomiaConnectionDetails(), even though both the zip,- and sqlite-file exist already.
When running the the function it will also throw an additional error, when ran in an enclose environment (unittest, GitHub Actions, reprex).
#> Error: table person already exists
as it is trying to overwrite the existing CDM.
file.exists(file.path(Sys.getenv("EUNOMIA_DATA_FOLDER"), "GiBleed_5.3.sqlite"))
#> [1] TRUE
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
#> attempting to download GiBleed
#> attempting to extract and load: D:/Users/mvankessel/Documents/EunomiaCache/GiBleed_5.3.zip to: D:/Users/mvankessel/Documents/EunomiaCache/GiBleed_5.3.sqlite
#> Error: table person already exists
Created on 2024-05-22 with reprex v2.1.0
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.0 (2024-04-24 ucrt)
#> os Windows 11 x64 (build 22631)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate Dutch_Netherlands.utf8
#> ctype Dutch_Netherlands.utf8
#> tz Europe/Amsterdam
#> date 2024-05-22
#> pandoc 3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [1] CRAN (R 4.4.0)
#> bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0)
#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0)
#> blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0)
#> cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
#> checkmate 2.3.1 2023-12-04 [1] CRAN (R 4.4.0)
#> cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0)
#> CommonDataModel 0.2.0 2024-02-07 [1] CRAN (R 4.4.0)
#> DatabaseConnector 6.3.2 2023-12-11 [1] CRAN (R 4.4.0)
#> DBI 1.2.2 2024-02-16 [1] CRAN (R 4.4.0)
#> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0)
#> Eunomia 2.0.0 2024-04-23 [1] CRAN (R 4.4.0)
#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0)
#> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
#> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
#> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> knitr 1.46 2024-04-06 [1] CRAN (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
#> readr 2.1.5 2024-01-10 [1] CRAN (R 4.4.0)
#> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.4.0)
#> D rJava 1.0-11 2024-01-26 [1] CRAN (R 4.4.0)
#> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0)
#> rmarkdown 2.27 2024-05-17 [1] CRAN (R 4.4.0)
#> RSQLite 2.3.6 2024-03-31 [1] CRAN (R 4.4.0)
#> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> SqlRender 1.17.0 2024-03-20 [1] CRAN (R 4.4.0)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
#> tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.4.0)
#> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
#> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
#> xfun 0.44 2024-05-15 [1] CRAN (R 4.4.0)
#> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.4.0)
#>
#> [1] C:/R/R-4.4.0/library
#>
#> D ── DLL MD5 mismatch, broken installation.
#>
#> ──────────────────────────────────────────────────────────────────────────────
The following code should resolve this:
getEunomiaConnectionDetails <- function(databaseFile = tempfile(fileext = ".sqlite"), dbms = "sqlite") {
if (interactive() & !("DatabaseConnector" %in% rownames(utils::installed.packages()))) {
message("The DatabaseConnector package is required but not installed.")
if (!isTRUE(utils::askYesNo("Would you like to install DatabaseConnector?"))) {
return(invisible(NULL))
} else {
utils::install.packages("DatabaseConnector")
}
}
if (!file.exists(file.path(Sys.getenv("EUNOMIA_DATA_FOLDER"), "GiBleed_5.3.sqlite"))) {
datasetLocation <- getDatabaseFile(datasetName = "GiBleed", dbms = dbms, databaseFile = databaseFile)
}
DatabaseConnector::createConnectionDetails(dbms = dbms, server = datasetLocation)
}
file.exists(file.path(Sys.getenv("EUNOMIA_DATA_FOLDER"), "GiBleed_5.3.sqlite"))
#> [1] TRUE
connectionDetails <- getEunomiaConnectionDetails()
Created on 2024-05-22 with reprex v2.1.0
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.0 (2024-04-24 ucrt)
#> os Windows 11 x64 (build 22631)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate Dutch_Netherlands.utf8
#> ctype Dutch_Netherlands.utf8
#> tz Europe/Amsterdam
#> date 2024-05-22
#> pandoc 3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0)
#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0)
#> cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0)
#> DatabaseConnector 6.3.2 2023-12-11 [1] CRAN (R 4.4.0)
#> DBI 1.2.2 2024-02-16 [1] CRAN (R 4.4.0)
#> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0)
#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
#> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> knitr 1.46 2024-04-06 [1] CRAN (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.4.0)
#> D rJava 1.0-11 2024-01-26 [1] CRAN (R 4.4.0)
#> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0)
#> rmarkdown 2.27 2024-05-17 [1] CRAN (R 4.4.0)
#> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
#> xfun 0.44 2024-05-15 [1] CRAN (R 4.4.0)
#> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.4.0)
#>
#> [1] C:/R/R-4.4.0/library
#>
#> D ── DLL MD5 mismatch, broken installation.
#>
#> ──────────────────────────────────────────────────────────────────────────────
Is this only happening for the default dataset or is it also occurring on other datasets specified by name?
So far I have only noticed it when using getEunomiaConnectionDetails(), where the GiBleed dataset is hardcoded.
Thanks, yes, I can confirm I'm seeing the same behavior. I think the root of this is that getEunomiaConnectionDetails uses getDatabaseFile which defaults overwrite to TRUE. getEunomiaConnectionDetails doesn't provide any way to specify a different behavior. I think the desired behavior would be to use an existing copy unless otherwise specified. So I can add a overwrite parameter to getEunomiaConnectionDetails with a default of FALSE and then pass that along to getDatabaseFile in the getEunomiaConnectionDetails. Does that work for you?
Fix is now in the develop branch if you would like to test that would be great.
Seems to work, thank you.
# Install OHDSI/Eunomia@develop
# remotes::install_github("OHDSI/Eunomia@develop")
file.exists(file.path(Sys.getenv("EUNOMIA_DATA_FOLDER"), "GiBleed_5.3.sqlite"))
#> [1] TRUE
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
Created on 2024-05-30 with reprex v2.1.0
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.0 (2024-04-24 ucrt)
#> os Windows 11 x64 (build 22631)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate Dutch_Netherlands.utf8
#> ctype Dutch_Netherlands.utf8
#> tz Europe/Amsterdam
#> date 2024-05-30
#> pandoc 3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0)
#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0)
#> blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0)
#> cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
#> callr 3.7.6 2024-03-25 [1] CRAN (R 4.4.0)
#> cli 3.6.2 2023-12-11 [1] CRAN (R 4.4.0)
#> curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0)
#> DatabaseConnector 6.3.2 2023-12-11 [1] CRAN (R 4.4.0)
#> DBI 1.2.2 2024-02-16 [1] CRAN (R 4.4.0)
#> desc 1.4.3 2023-12-10 [1] CRAN (R 4.4.0)
#> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0)
#> Eunomia 2.0.0 2024-05-30 [1] Github (OHDSI/Eunomia@f016f27)
#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0)
#> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
#> fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0)
#> glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0)
#> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> V knitr 1.46 2024-05-29 [1] CRAN (R 4.4.0) (on disk 1.47)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
#> memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.4.0)
#> pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
#> processx 3.8.4 2024-03-16 [1] CRAN (R 4.4.0)
#> ps 1.7.6 2024-01-18 [1] CRAN (R 4.4.0)
#> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.0)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.4.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.4.0)
#> R.oo 1.26.0 2024-01-24 [1] CRAN (R 4.4.0)
#> R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.4.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
#> readr 2.1.5 2024-01-10 [1] CRAN (R 4.4.0)
#> remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.0)
#> reprex 2.1.0 2024-01-11 [1] CRAN (R 4.4.0)
#> D rJava 1.0-11 2024-01-26 [1] CRAN (R 4.4.0)
#> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0)
#> rmarkdown 2.27 2024-05-17 [1] CRAN (R 4.4.0)
#> RSQLite 2.3.7 2024-05-27 [1] CRAN (R 4.4.0)
#> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> styler 1.10.3 2024-04-07 [1] CRAN (R 4.4.0)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
#> tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.4.0)
#> utf8 1.2.4 2023-10-22 [1] CRAN (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
#> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0)
#> xfun 0.44 2024-05-15 [1] CRAN (R 4.4.0)
#> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.4.0)
#>
#> [1] C:/R/R-4.4.0/library
#>
#> V ── Loaded and on-disk version mismatch.
#> D ── DLL MD5 mismatch, broken installation.
#>
#> ──────────────────────────────────────────────────────────────────────────────
Also the previously failing unit tests in my code, also pass now.