getEunomiaConnectionDetails always downloads datasets even if they already exist

[ablack3]

It looks like getEunomiaConnectionDetails is downloading datasets even when they have already been downloaded.

library(Eunomia)

cd <- getEunomiaConnectionDetails()
#> attempting to download GiBleed
#> attempting to extract and load: /Users/ablack/eunomia_data/GiBleed_5.3.zip to: /Users/ablack/eunomia_data/GiBleed_5.3.sqlite

cd <- getEunomiaConnectionDetails()
#> attempting to download GiBleed
#> attempting to extract and load: /Users/ablack/eunomia_data/GiBleed_5.3.zip to: /Users/ablack/eunomia_data/GiBleed_5.3.sqlite

^{Created on 2024-09-17 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29)
#>  os       macOS Sonoma 14.1
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/Amsterdam
#>  date     2024-09-17
#>  pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version date (UTC) lib source
#>  backports           1.5.0   2024-05-23 [1] CRAN (R 4.3.3)
#>  bit                 4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
#>  bit64               4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
#>  blob                1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
#>  cachem              1.1.0   2024-05-16 [1] CRAN (R 4.3.3)
#>  checkmate           2.3.2   2024-07-29 [1] CRAN (R 4.3.3)
#>  cli                 3.6.3   2024-06-21 [1] CRAN (R 4.3.3)
#>  CommonDataModel     0.2.0   2024-02-07 [1] CRAN (R 4.3.1)
#>  crayon              1.5.3   2024-06-20 [1] CRAN (R 4.3.3)
#>  DatabaseConnector   6.3.2   2023-12-11 [1] CRAN (R 4.3.1)
#>  DBI                 1.2.3   2024-06-02 [1] CRAN (R 4.3.3)
#>  digest              0.6.37  2024-08-19 [1] CRAN (R 4.3.3)
#>  Eunomia           * 2.0.0   2024-09-17 [1] Github (ohdsi/eunomia@79c8944)
#>  evaluate            0.24.0  2024-06-10 [1] CRAN (R 4.3.3)
#>  fansi               1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
#>  fastmap             1.2.0   2024-05-15 [1] CRAN (R 4.3.3)
#>  fs                  1.6.4   2024-04-25 [1] CRAN (R 4.3.1)
#>  glue                1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
#>  hms                 1.1.3   2023-03-21 [1] CRAN (R 4.3.0)
#>  htmltools           0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
#>  knitr               1.48    2024-07-07 [1] CRAN (R 4.3.3)
#>  lifecycle           1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
#>  magrittr            2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise             2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  pillar              1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig           2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  R6                  2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  readr               2.1.5   2024-01-10 [1] CRAN (R 4.3.1)
#>  reprex              2.1.1   2024-07-06 [1] CRAN (R 4.3.3)
#>  rJava               1.0-11  2024-01-26 [1] CRAN (R 4.3.1)
#>  rlang               1.1.4   2024-06-04 [1] CRAN (R 4.3.3)
#>  rmarkdown           2.28    2024-08-17 [1] CRAN (R 4.3.3)
#>  RSQLite             2.3.7   2024-05-27 [1] CRAN (R 4.3.3)
#>  rstudioapi          0.16.0  2024-03-24 [1] CRAN (R 4.3.1)
#>  sessioninfo         1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  SqlRender           1.18.1  2024-08-21 [1] CRAN (R 4.3.3)
#>  tibble              3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect          1.2.1   2024-03-11 [1] CRAN (R 4.3.1)
#>  tzdb                0.4.0   2023-05-12 [1] CRAN (R 4.3.0)
#>  utf8                1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
#>  vctrs               0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
#>  vroom               1.6.5   2023-12-05 [1] CRAN (R 4.3.1)
#>  withr               3.0.1   2024-07-31 [1] CRAN (R 4.3.3)
#>  xfun                0.47    2024-08-17 [1] CRAN (R 4.3.3)
#>  yaml                2.3.10  2024-07-26 [1] CRAN (R 4.3.3)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

[ablack3]

Using the issue66 branch seems to work.

remotes::install_github("ohdsi/Eunomia", ref = "issue66")
#> Skipping install of 'Eunomia' from a github remote, the SHA1 (2da16697) has not changed since last install.
#>   Use `force = TRUE` to force installation

library(Eunomia)

cd <- getEunomiaConnectionDetails()

cd <- getEunomiaConnectionDetails()

library(DatabaseConnector)

con <- connect(cd)
#> Connecting using SQLite driver
getTableNames(con)
#>  [1] "attribute_definition"  "care_site"             "cdm_source"           
#>  [4] "cohort"                "cohort_attribute"      "cohort_definition"    
#>  [7] "concept"               "concept_ancestor"      "concept_class"        
#> [10] "concept_relationship"  "concept_synonym"       "condition_era"        
#> [13] "condition_occurrence"  "cost"                  "death"                
#> [16] "device_exposure"       "domain"                "dose_era"             
#> [19] "drug_era"              "drug_exposure"         "drug_strength"        
#> [22] "fact_relationship"     "location"              "measurement"          
#> [25] "metadata"              "note"                  "note_nlp"             
#> [28] "observation"           "observation_period"    "payer_plan_period"    
#> [31] "person"                "procedure_occurrence"  "provider"             
#> [34] "relationship"          "source_to_concept_map" "specimen"             
#> [37] "visit_detail"          "visit_occurrence"      "vocabulary"
disconnect(con)

^{Created on 2024-09-17 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29)
#>  os       macOS Sonoma 14.1
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/Amsterdam
#>  date     2024-09-17
#>  pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version date (UTC) lib source
#>  backports           1.5.0   2024-05-23 [1] CRAN (R 4.3.3)
#>  bit                 4.0.5   2022-11-15 [1] CRAN (R 4.3.0)
#>  bit64               4.0.5   2020-08-30 [1] CRAN (R 4.3.0)
#>  blob                1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
#>  cachem              1.1.0   2024-05-16 [1] CRAN (R 4.3.3)
#>  checkmate           2.3.2   2024-07-29 [1] CRAN (R 4.3.3)
#>  cli                 3.6.3   2024-06-21 [1] CRAN (R 4.3.3)
#>  curl                5.2.2   2024-08-26 [1] CRAN (R 4.3.3)
#>  DatabaseConnector * 6.3.2   2023-12-11 [1] CRAN (R 4.3.1)
#>  DBI                 1.2.3   2024-06-02 [1] CRAN (R 4.3.3)
#>  digest              0.6.37  2024-08-19 [1] CRAN (R 4.3.3)
#>  Eunomia           * 2.0.0   2024-09-17 [1] Github (ohdsi/Eunomia@2da1669)
#>  evaluate            0.24.0  2024-06-10 [1] CRAN (R 4.3.3)
#>  fansi               1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
#>  fastmap             1.2.0   2024-05-15 [1] CRAN (R 4.3.3)
#>  fs                  1.6.4   2024-04-25 [1] CRAN (R 4.3.1)
#>  glue                1.7.0   2024-01-09 [1] CRAN (R 4.3.1)
#>  hms                 1.1.3   2023-03-21 [1] CRAN (R 4.3.0)
#>  htmltools           0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
#>  knitr               1.48    2024-07-07 [1] CRAN (R 4.3.3)
#>  lifecycle           1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
#>  magrittr            2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise             2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  pillar              1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig           2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  R6                  2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  readr               2.1.5   2024-01-10 [1] CRAN (R 4.3.1)
#>  remotes             2.5.0   2024-03-17 [1] CRAN (R 4.3.1)
#>  reprex              2.1.1   2024-07-06 [1] CRAN (R 4.3.3)
#>  rJava               1.0-11  2024-01-26 [1] CRAN (R 4.3.1)
#>  rlang               1.1.4   2024-06-04 [1] CRAN (R 4.3.3)
#>  rmarkdown           2.28    2024-08-17 [1] CRAN (R 4.3.3)
#>  RSQLite             2.3.7   2024-05-27 [1] CRAN (R 4.3.3)
#>  rstudioapi          0.16.0  2024-03-24 [1] CRAN (R 4.3.1)
#>  sessioninfo         1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  tibble              3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tzdb                0.4.0   2023-05-12 [1] CRAN (R 4.3.0)
#>  utf8                1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
#>  vctrs               0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
#>  withr               3.0.1   2024-07-31 [1] CRAN (R 4.3.3)
#>  xfun                0.47    2024-08-17 [1] CRAN (R 4.3.3)
#>  yaml                2.3.10  2024-07-26 [1] CRAN (R 4.3.3)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

[fdefalco]

I believe this is already fixed in develop?

https://github.com/OHDSI/Eunomia/blob/develop/R/Connection.R

[ginberg]

@fdefalco maybe it's good to make a new release for that fix (in develop branch)? That saves a lot of downloads

[fdefalco]

@ginberg Agreed, there are a few coordinated releases we are attempting to have including Eunomia / Achilles / DataQualityDashboard / AresIndexer / Ares so we are in the middle of testing across the packages.

[ablack3]

yep it is fixed in develop

remotes::install_github("ohdsi/eunomia", "develop")
#> Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead.
#> Skipping install of 'Eunomia' from a github remote, the SHA1 (f016f272) has not changed since last install.
#>   Use `force = TRUE` to force installation
library(Eunomia)

cd <- getEunomiaConnectionDetails()
cd <- getEunomiaConnectionDetails()

^{Created on 2024-10-07 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29)
#>  os       macOS Sonoma 14.1
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/Amsterdam
#>  date     2024-10-07
#>  pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version date (UTC) lib source
#>  bit                 4.5.0   2024-09-20 [1] CRAN (R 4.3.3)
#>  bit64               4.5.2   2024-09-22 [1] CRAN (R 4.3.3)
#>  blob                1.2.4   2023-03-17 [1] CRAN (R 4.3.0)
#>  cachem              1.1.0   2024-05-16 [1] CRAN (R 4.3.3)
#>  cli                 3.6.3   2024-06-21 [1] CRAN (R 4.3.3)
#>  curl                5.2.2   2024-08-26 [1] CRAN (R 4.3.3)
#>  DatabaseConnector   6.3.2   2023-12-11 [1] CRAN (R 4.3.1)
#>  DBI                 1.2.3   2024-06-02 [1] CRAN (R 4.3.3)
#>  digest              0.6.37  2024-08-19 [1] CRAN (R 4.3.3)
#>  Eunomia           * 2.0.0   2024-10-07 [1] Github (ohdsi/eunomia@f016f27)
#>  evaluate            1.0.0   2024-09-17 [1] CRAN (R 4.3.3)
#>  fansi               1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
#>  fastmap             1.2.0   2024-05-15 [1] CRAN (R 4.3.3)
#>  fs                  1.6.4   2024-04-25 [1] CRAN (R 4.3.1)
#>  glue                1.8.0   2024-09-30 [1] CRAN (R 4.3.3)
#>  hms                 1.1.3   2023-03-21 [1] CRAN (R 4.3.0)
#>  htmltools           0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1)
#>  knitr               1.48    2024-07-07 [1] CRAN (R 4.3.3)
#>  lifecycle           1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
#>  magrittr            2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise             2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  pillar              1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig           2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  R6                  2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  readr               2.1.5   2024-01-10 [1] CRAN (R 4.3.1)
#>  remotes             2.5.0   2024-03-17 [1] CRAN (R 4.3.1)
#>  reprex              2.1.1   2024-07-06 [1] CRAN (R 4.3.3)
#>  rJava               1.0-11  2024-01-26 [1] CRAN (R 4.3.1)
#>  rlang               1.1.4   2024-06-04 [1] CRAN (R 4.3.3)
#>  rmarkdown           2.28    2024-08-17 [1] CRAN (R 4.3.3)
#>  RSQLite             2.3.7   2024-05-27 [1] CRAN (R 4.3.3)
#>  rstudioapi          0.16.0  2024-03-24 [1] CRAN (R 4.3.1)
#>  sessioninfo         1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  tibble              3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tzdb                0.4.0   2023-05-12 [1] CRAN (R 4.3.0)
#>  utf8                1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
#>  vctrs               0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
#>  withr               3.0.1   2024-07-31 [1] CRAN (R 4.3.3)
#>  xfun                0.48    2024-10-03 [1] CRAN (R 4.3.3)
#>  yaml                2.3.10  2024-07-26 [1] CRAN (R 4.3.3)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

[anthonysena]

@fdefalco I'm re-opening this issue to see if we can get a new release of Eunomia on CRAN so that we can avoid the multi-download of the data set? Thanks!

[schuemie]

+1 on creating a release with this fix