Pushes test population into a blank CDM.

Usage

patientsCDM(
  pathJson = NULL,
  testName = NULL,
  cdmVersion = "5.4",
  cdmName = NULL,
  dbms = "duckdb",
  writeSchema = NULL
)

Arguments

pathJson: Directory where the sample populations in json are located. If NULL, gets the default inst/testCases directory.
testName: Name of the sample population JSON file. If NULL it will push the first sample population in the testCases directory.
cdmVersion: cdm version, default "5.4".
cdmName: Name of the cdm, default NULL.
dbms: Database management system to use. One of "duckdb", "spark", "sqlserver" or "postgresql". Default is "duckdb" which creates a local DuckDB CDM. For remote databases the function creates the CDM locally, trims the vocabulary, uploads to a new schema on the remote database, and returns the remote CDM reference. Remote databases require environment variables to be set. Call usethis::edit_r_environ() to set them.
writeSchema: Optional schema name to use on the remote database. If NULL (default), a unique schema is created automatically. Only used when dbms is not "duckdb".

Value

A CDM reference object with a sample population.

Examples

# \donttest{
filePath <- system.file("extdata", "testPatientsRSV.xlsx", package = "TestGenerator")
TestGenerator::readPatients(filePath = filePath, outputPath = tempdir())
#> ✔ All tables are valid
#> ✔ Unit Test Definition Created Successfully: 'test'
cdm <- TestGenerator::patientsCDM(pathJson = tempdir(), testName = "test")
#> 
#> Download completed!
#> Creating CDM database /tmp/RtmpC5568s/empty_cdm_5.4.zip
#> ■■■■■■■■■■■■■■■■■■■■■             65% | ETA:  3s
#> ■■■■■■■■■■■■■■■■■■■■■■■■■         81% | ETA:  4s
#> ■■■■■■■■■■■■■■■■■■■■■■■■■■■       86% | ETA:  3s
#> ! cdm name not specified and could not be inferred from the cdm source table
#> ✔ Standard table(s) in test data: person, observation_period, condition_occurrence, visit_occurrence, visit_detail and death
#> ✔ Patients pushed to blank CDM successfully
duckdb::duckdb_shutdown(duckdb::duckdb())
# }