Package 'TestGenerator'

Check if a given remote file is available for download

Description

Check if a given remote file is available for download

Usage

checkRemoteFileAvailable(remoteFile)

Arguments

remoteFile

a remote resource

Value

NULL if the remote resource is not available, other "success"

---

Check if the given tables and columns are valid and return the loaded data.

Description

Check if the given tables and columns are valid and return the loaded data.

Usage

checkTablesColumns(cdmVersion, filePath, extraTable = FALSE)

Arguments

cdmVersion	cdm version
filePath	Path to the test patient data in xlsx format
extraTable	if extra tables are provided or not, default FALSE

Value

a named list containing the loaded data

---

Clean up a test CDM on a remote database

Description

Drops the schema containing the test CDM and disconnects from the database.

Usage

cleanupTestCdm(cdm)

Arguments

cdm	A CDM reference object created by patientsCDM() with a remote database backend.

Value

Invisibly returns NULL.

---

Download Test Data Files

Description

Download Test Data Files

Usage

downloadTestData(
  datasetName = "mimicIV",
  cdmVersion = "5.3",
  pathToData = Sys.getenv("STUDY_DATASETS"),
  overwrite = FALSE
)

Arguments

datasetName	The data set name as found on https://github.com/darwin-eu/EunomiaDatasets. The data set name corresponds to the folder with the data set ZIP files
cdmVersion	The OMOP CDM version. This version will appear in the suffix of the data file, for example: synpuf_5.3.zip. Default: '5.3'
pathToData	The path where the Eunomia data is stored on the file system., By default the value of the environment variable "EUNOMIA_DATA_FOLDER" is used.
overwrite	Control whether the existing archive file will be overwritten should it already exist.

Value

Invisibly returns the destination if the download was successful.

Examples

downloadTestData(pathToData = tempdir())

---

Generates an Excel file with sheets that correspond to an OMOP-CDM tables.

Description

Generates an Excel file with sheets that correspond to an OMOP-CDM tables.

Usage

generateTestTables(
  tableNames = c("person", "observation_period", "visit_occurrence", "visit_detail",
    "condition_occurrence", "drug_exposure", "procedure_occurrence", "measurement",
    "observation", "death", "drug_era", "condition_era", "dose_era", "location",
    "care_site", "provider"),
  cdmVersion,
  outputFolder,
  filename = paste0("test_cdm_", cdmVersion)
)

Arguments

tableNames	A list specifying the table names to include in the Excel file.
cdmVersion	The CDM version to use for creating the requested tables (either 5.3 or 5.4).
outputFolder	The folder where the Excel file will be saved.
filename	The name of the Excel file. It does not include the extension .xlsx.

Value

An Excel file with the tables requested.

---

Deprecated cohort timeline visualisation

Description

graphCohort() is deprecated and will be removed in a future release.

Usage

graphCohort(subject_id, cohorts = list())

Arguments

subject_id	Deprecated.
cohorts	Deprecated.

Value

Invisibly returns NULL.

---

Pushes test population into a blank CDM.

Description

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", "databricks", "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

filePath <- system.file("extdata", "testPatientsRSV.xlsx", package = "TestGenerator")
TestGenerator::readPatients(filePath = filePath, outputPath = tempdir())
cdm <- TestGenerator::patientsCDM(pathJson = tempdir(), testName = "test")
duckdb::duckdb_shutdown(duckdb::duckdb())

---

Converts a sample of patients into Unit Testing Definition JSON file.

Description

Converts a sample of patients into Unit Testing Definition JSON file.

Usage

readPatients(
  filePath = NULL,
  testName = "test",
  outputPath = NULL,
  cdmVersion = "5.4",
  extraTable = FALSE
)

Arguments

filePath	Path to the test patient data in Excel format. The Excel has sheets that represent tables from the OMOP-CDM, e.g. person, drug_exposure, condition_ocurrence, etc.
testName	A name of the test population in character.
outputPath	Path of the output file, if NULL, a folder will be created in the project folder inst/testCases.
cdmVersion	cdm version, default "5.4".
extraTable	Name of non-standard tables to be included in the test CDM.

Value

A JSON file with sample patients inside the project directory.

Examples

filePath <- system.file("extdata", "testPatientsRSV.xlsx", package = "TestGenerator")
readPatients(filePath = filePath, outputPath = tempdir())

---

Converts a sample of patients in CSV format into a Unit Testing Definition JSON file.

Description

Converts a sample of patients in CSV format into a Unit Testing Definition JSON file.

Usage

readPatients.csv(
  filePath = NULL,
  testName = "test",
  outputPath = NULL,
  cdmVersion = "5.4",
  reduceLargeIds = FALSE
)

Arguments

filePath	Path to the test patient data in CSV format. Multiple CSV files representing tables tables from the OMOP-CDM must be provided, e.g. person.csv, drug_exposure.csv, condition_ocurrence.csv, etc.
testName	Name for the test population file in character.
outputPath	Path of the output file, if NULL, a folder will be created in the project folder inst/testCases.
cdmVersion	cdm version, default "5.4".
reduceLargeIds	Reduces the length of very long ids generally in int64 format, such as those found in the MIMIC-IV database.

Value

A JSON file with sample patients inside the project directory.

Examples

filePath <- system.file("extdata", "mimic_sample", package = "TestGenerator")
readPatients.csv(
  filePath = filePath,
  outputPath = tempdir(),
  cdmVersion = "5.3"
  )

---

Converts a sample of patients in XLSX format into Unit Testing Definition JSON file.

Description

Converts a sample of patients in XLSX format into Unit Testing Definition JSON file.

Usage

readPatients.xl(
  filePath = NULL,
  testName = "test",
  outputPath = NULL,
  cdmVersion = "5.4",
  extraTable = FALSE
)

Arguments

filePath	Path to the test patient data in Excel format. The Excel has sheets that represent tables from the OMOP-CDM, e.g. person, drug_exposure, condition_ocurrence, etc.
testName	A name of the test population in character.
outputPath	Path to write the test JSON files. If NULL, the files will be written at the project's testthat folder, i.e. tests/testthat/testCases.
cdmVersion	cdm version, default "5.4".
extraTable	TRUE or FALSE. If TRUE, non-standard tables will be included in the test CDM.

Value

A directory with the test JSON files with sample patients inside the project directory.

Examples

filePath <- system.file("extdata", "testPatientsRSV.xlsx", package = "TestGenerator")
readPatients.xl(filePath = filePath, outputPath = tempdir())

---

Create GitHub Action workflows for specific DBMS

Description

Copies GitHub Action workflow templates from the package's inst/workflows directory to the .github/workflows directory of the current project. The copied workflows can be used to run backend-specific tests for PostgreSQL, SQL Server, and Databricks.

Usage

useGithubAction(
  dbms_type = c("postgresql", "sqlserver", "databricks"),
  overwrite = FALSE
)

Arguments

dbms_type	A character vector of supported DBMS types to process. Supported values are "postgresql", "sqlserver", and "databricks".
overwrite	A logical value indicating whether to overwrite existing workflow files in the .github/workflows directory. Defaults to FALSE.

Value

Invisibly returns TRUE when the selected workflow files are copied successfully.

Examples

## Not run: 
useGithubAction(dbms_type = "postgresql")
useGithubAction(
  dbms_type = c("postgresql", "sqlserver", "databricks"),
  overwrite = TRUE
)

## End(Not run)

---