OHDSI / OHDSI/DatabaseConnector

DBI::dbIsValid does not seem to work with postgres

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Dominant language
R
Stars
57
Forks
93
Avg merge
10d 12h
Merged PRs (30d)
1

Description

Expectation:
DBI::dbIsValid(connection) should return false if the connection is closed.

Actual behavior: DBI::dbIsValid(connection) returns true when the connection is closed in this postgres example.

con <- DBI::dbConnect(DatabaseConnector::DatabaseConnectorDriver(),
               dbms = "postgresql",
               server = Sys.getenv("CDM5_POSTGRESQL_SERVER"),
               user = Sys.getenv("CDM5_POSTGRESQL_USER"),
               password = Sys.getenv("CDM5_POSTGRESQL_PASSWORD"))


DBI::dbIsValid(con)
#> TRUE
DBI::dbDisconnect(con)
# this returns true
DBI::dbIsValid(con)
#> TRUE
# even though the connection is closed
DBI::dbListTables(con)
#> Error in rJava::.jcall(conn@jConnection, "Ljava/sql/DatabaseMetaData;",  : 
  org.postgresql.util.PSQLException: This connection has been closed.

I can run this code interactively but when I run it using the reprex package it crashes R on my machine which is why I'm not able to provide an actual reprex.

image
> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.0

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Amsterdam
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shiny_1.7.5             DatabaseConnector_6.3.2 usethis_2.2.2           testthat_3.2.0         

loaded via a namespace (and not attached):
 [1] xfun_0.40         bslib_0.5.1       processx_3.8.2    rJava_1.0-6       gargle_1.5.2     
 [6] callr_3.7.3       vctrs_0.6.5       odbc_1.3.5        tools_4.3.1       ps_1.7.5         
[11] generics_0.1.3    tibble_3.2.1      fansi_1.0.6       RSQLite_2.3.2     blob_1.2.4       
[16] pkgconfig_2.0.3   R.oo_1.25.0       checkmate_2.3.0   dbplyr_2.4.0      assertthat_0.2.1 
[21] lifecycle_1.0.4   R.cache_0.16.0    compiler_4.3.1    brio_1.1.3        bigrquery_1.4.2  
[26] httpuv_1.6.11     sass_0.4.7        htmltools_0.5.6   yaml_2.3.7        jquerylib_0.1.4  
[31] pillar_1.9.0      later_1.3.1       ellipsis_0.3.2    R.utils_2.12.2    cachem_1.0.8     
[36] RPostgres_1.4.6   mime_0.12         styler_1.10.2     tidyselect_1.2.0  digest_0.6.33    
[41] dplyr_1.1.4       duckdb_0.8.1-3    purrr_1.0.2       fastmap_1.1.1     cli_3.6.2        
[46] magrittr_2.0.3    triebeard_0.4.1   utf8_1.2.4        clipr_0.8.0       withr_2.5.2      
[51] promises_1.2.1    backports_1.4.1   bit64_4.0.5       rmarkdown_2.24    httr_1.4.7       
[56] bit_4.0.5         R.methodsS3_1.8.2 hms_1.1.3         memoise_2.0.1     evaluate_0.23    
[61] knitr_1.44        miniUI_0.1.1.1    rlang_1.1.2       urltools_1.7.3    Rcpp_1.0.11      
[66] xtable_1.8-4      glue_1.6.2        DBI_1.2.0         reprex_2.0.2      rstudioapi_0.15.0
[71] jsonlite_1.8.7    R6_2.5.1          fs_1.6.3   

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

No source file or test is named. Start by reproducing the example with DBI::dbIsValid(), DBI::dbDisconnect(), and DBI::dbListTables() against PostgreSQL, then trace how DatabaseConnector handles the JDBC connection state. Done means dbIsValid(con) returns FALSE after dbDisconnect(con) without causing a crash.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, postgresql, r
Domain
databases
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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