tests/testthat/_snaps/tb_vigibase.md

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

basic use and here package works

Code
  options(cli.progress_show_after = 0)
  options(cli.progress_clear = FALSE)
  tb_vigibase(path_base = path_base, path_sub = path_sub, force = TRUE)
Message

  -- tb_vigibase() ---------------------------------------------------------------
  i Creating vigibase tables.
  This process must only be done once per database version.
  It can take up to 30minutes.
  =>----------------------------- percent, seconds | Read DEMO.txt 
  ==>---------------------------- percent, seconds | Split demo 
  ====>-------------------------- percent, seconds | Write demo.parquet 
  =====>------------------------- percent, seconds | Read DRUG.txt 
  ======>------------------------ percent, seconds | Split drug 
  ========>---------------------- percent, seconds | Write drug.parquet 
  =========>--------------------- percent, seconds | Read FOLLOWUP.txt 
  ==========>-------------------- percent, seconds | Split followup 
  ==========>-------------------- percent, seconds | Write followup.parquet 
  ===========>------------------- percent, seconds | Read ADR.txt 
  ============>------------------ percent, seconds | Split adr 
  =============>----------------- percent, seconds | Write adr.parquet 
  =============>----------------- percent, seconds | Read OUT.txt 
  ==============>---------------- percent, seconds | Split out 
  ==============>---------------- percent, seconds | Write out.parquet 
  ==============>---------------- percent, seconds | Read SRCE.txt 
  ==============>---------------- percent, seconds | Split srce 
  ===============>--------------- percent, seconds | Write srce.parquet 
  ===============>--------------- percent, seconds | Read LINK.txt 
  ================>-------------- percent, seconds | Split link (longest step) 
  ====================>---------- percent, seconds | Write link.parquet 
  =====================>--------- percent, seconds | Read IND.txt 
  ======================>-------- percent, seconds | Split ind 
  =======================>------- percent, seconds | Write ind.parquet 
  ========================>------ percent, seconds | Read SUSPECTEDDUPLICATES.txt 
  =========================>----- percent, seconds | Split suspdup 
  =========================>----- percent, seconds | Write suspdup.parquet 
  ============================>-- percent, seconds | Process Subsidiary files 
  ==============================> percent, seconds | Done

Code
  tb_vigibase(path_base = here_path_base, path_sub = here_path_sub, force = TRUE)
Message

  -- tb_vigibase() ---------------------------------------------------------------
  i Creating vigibase tables.
  This process must only be done once per database version.
  It can take up to 30minutes.
  =>----------------------------- percent, seconds | Read DEMO.txt 
  ==>---------------------------- percent, seconds | Split demo 
  ====>-------------------------- percent, seconds | Write demo.parquet 
  =====>------------------------- percent, seconds | Read DRUG.txt 
  ======>------------------------ percent, seconds | Split drug 
  ========>---------------------- percent, seconds | Write drug.parquet 
  =========>--------------------- percent, seconds | Read FOLLOWUP.txt 
  ==========>-------------------- percent, seconds | Split followup 
  ==========>-------------------- percent, seconds | Write followup.parquet 
  ===========>------------------- percent, seconds | Read ADR.txt 
  ============>------------------ percent, seconds | Split adr 
  =============>----------------- percent, seconds | Write adr.parquet 
  =============>----------------- percent, seconds | Read OUT.txt 
  ==============>---------------- percent, seconds | Split out 
  ==============>---------------- percent, seconds | Write out.parquet 
  ==============>---------------- percent, seconds | Read SRCE.txt 
  ==============>---------------- percent, seconds | Split srce 
  ===============>--------------- percent, seconds | Write srce.parquet 
  ===============>--------------- percent, seconds | Read LINK.txt 
  ================>-------------- percent, seconds | Split link (longest step) 
  ====================>---------- percent, seconds | Write link.parquet 
  =====================>--------- percent, seconds | Read IND.txt 
  ======================>-------- percent, seconds | Split ind 
  =======================>------- percent, seconds | Write ind.parquet 
  ========================>------ percent, seconds | Read SUSPECTEDDUPLICATES.txt 
  =========================>----- percent, seconds | Split suspdup 
  =========================>----- percent, seconds | Write suspdup.parquet 
  ============================>-- percent, seconds | Process Subsidiary files 
  ==============================> percent, seconds | Done

Code
  tb_vigibase(path_base = path_base, path_sub = here_path_sub, force = TRUE)
Message

  -- tb_vigibase() ---------------------------------------------------------------
  i Creating vigibase tables.
  This process must only be done once per database version.
  It can take up to 30minutes.
  =>----------------------------- percent, seconds | Read DEMO.txt 
  ==>---------------------------- percent, seconds | Split demo 
  ====>-------------------------- percent, seconds | Write demo.parquet 
  =====>------------------------- percent, seconds | Read DRUG.txt 
  ======>------------------------ percent, seconds | Split drug 
  ========>---------------------- percent, seconds | Write drug.parquet 
  =========>--------------------- percent, seconds | Read FOLLOWUP.txt 
  ==========>-------------------- percent, seconds | Split followup 
  ==========>-------------------- percent, seconds | Write followup.parquet 
  ===========>------------------- percent, seconds | Read ADR.txt 
  ============>------------------ percent, seconds | Split adr 
  =============>----------------- percent, seconds | Write adr.parquet 
  =============>----------------- percent, seconds | Read OUT.txt 
  ==============>---------------- percent, seconds | Split out 
  ==============>---------------- percent, seconds | Write out.parquet 
  ==============>---------------- percent, seconds | Read SRCE.txt 
  ==============>---------------- percent, seconds | Split srce 
  ===============>--------------- percent, seconds | Write srce.parquet 
  ===============>--------------- percent, seconds | Read LINK.txt 
  ================>-------------- percent, seconds | Split link (longest step) 
  ====================>---------- percent, seconds | Write link.parquet 
  =====================>--------- percent, seconds | Read IND.txt 
  ======================>-------- percent, seconds | Split ind 
  =======================>------- percent, seconds | Write ind.parquet 
  ========================>------ percent, seconds | Read SUSPECTEDDUPLICATES.txt 
  =========================>----- percent, seconds | Split suspdup 
  =========================>----- percent, seconds | Write suspdup.parquet 
  ============================>-- percent, seconds | Process Subsidiary files 
  ==============================> percent, seconds | Done

Code
  tb_vigibase(path_base = here_path_base, path_sub = path_sub, force = TRUE)
Message

  -- tb_vigibase() ---------------------------------------------------------------
  i Creating vigibase tables.
  This process must only be done once per database version.
  It can take up to 30minutes.
  =>----------------------------- percent, seconds | Read DEMO.txt 
  ==>---------------------------- percent, seconds | Split demo 
  ====>-------------------------- percent, seconds | Write demo.parquet 
  =====>------------------------- percent, seconds | Read DRUG.txt 
  ======>------------------------ percent, seconds | Split drug 
  ========>---------------------- percent, seconds | Write drug.parquet 
  =========>--------------------- percent, seconds | Read FOLLOWUP.txt 
  ==========>-------------------- percent, seconds | Split followup 
  ==========>-------------------- percent, seconds | Write followup.parquet 
  ===========>------------------- percent, seconds | Read ADR.txt 
  ============>------------------ percent, seconds | Split adr 
  =============>----------------- percent, seconds | Write adr.parquet 
  =============>----------------- percent, seconds | Read OUT.txt 
  ==============>---------------- percent, seconds | Split out 
  ==============>---------------- percent, seconds | Write out.parquet 
  ==============>---------------- percent, seconds | Read SRCE.txt 
  ==============>---------------- percent, seconds | Split srce 
  ===============>--------------- percent, seconds | Write srce.parquet 
  ===============>--------------- percent, seconds | Read LINK.txt 
  ================>-------------- percent, seconds | Split link (longest step) 
  ====================>---------- percent, seconds | Write link.parquet 
  =====================>--------- percent, seconds | Read IND.txt 
  ======================>-------- percent, seconds | Split ind 
  =======================>------- percent, seconds | Write ind.parquet 
  ========================>------ percent, seconds | Read SUSPECTEDDUPLICATES.txt 
  =========================>----- percent, seconds | Split suspdup 
  =========================>----- percent, seconds | Write suspdup.parquet 
  ============================>-- percent, seconds | Process Subsidiary files 
  ==============================> percent, seconds | Done

path_base and path_sub exist before working on tables

Code
  tb_vigibase(path_base = wrong_path, path_sub = wrong_path, force = TRUE)
Condition <no_dir>
  Error in `tb_vigibase()`:
  ! `path_base` must exist.
  x "/a/wrong/filepath/" does not exist.

vigicaen documentation built on April 3, 2025, 8:55 p.m.