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#' @title
#' exportResultsToCSV
#'
#' @description
#' \code{exportResultsToCSV} exports all results to a CSV file
#'
#' @details
#' \code{exportResultsToCSV} writes a CSV file with all results to the export folder.
#'
#' @param connectionDetails An R object of type \code{connectionDetails} created using the
#' function \code{createConnectionDetails} in the
#' \code{DatabaseConnector} package.
#' @param resultsDatabaseSchema Fully qualified name of database schema that we can write final
#' results to. Default is cdmDatabaseSchema. On SQL Server, this should
#' specifiy both the database and the schema, so for example, on SQL
#' Server, 'cdm_results.dbo'.
#' @param analysisIds (OPTIONAL) A vector containing the set of Achilles analysisIds for
#' which results will be generated. If not specified, all analyses will
#' be executed. Use \code{\link{getAnalysisDetails}} to get a list of
#' all Achilles analyses and their Ids.
#' @param minCellCount To avoid patient identification, cells with small counts (<=
#' minCellCount) are deleted. Set to 0 for complete summary without
#' small cell count restrictions.
#' @param exportFolder Path to store results
#' @returns
#' No return value. Called to export CSV file to the file system.
#' @export
exportResultsToCSV <- function(connectionDetails,
resultsDatabaseSchema,
analysisIds = c(),
minCellCount = 5,
exportFolder) {
# Ensure the export folder exists
if (!file.exists(exportFolder)) {
dir.create(exportFolder, recursive = TRUE)
}
# Connect to the database
connection <- DatabaseConnector::connect(connectionDetails)
on.exit(DatabaseConnector::disconnect(connection))
# Obtain the data from the achilles tables
sql <- SqlRender::loadRenderTranslateSql(sqlFilename = "export/raw/export_raw_achilles_results.sql",
packageName = "Achilles", dbms = connectionDetails$dbms, warnOnMissingParameters = FALSE, results_database_schema = resultsDatabaseSchema,
min_cell_count = minCellCount, analysis_ids = analysisIds)
ParallelLogger::logInfo("Querying achilles_results")
results <- DatabaseConnector::querySql(connection = connection, sql = sql)
# Save the data to the export folder
readr::write_csv(results, file.path(exportFolder, "achilles_results.csv"))
}
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