R/Connection.R

In OHDSI/Eunomia: A Standard Dataset in the OMOP Common Data Model

# Copyright 2020 Observational Health Data Sciences and Informatics
#
# This file is part of Eunomia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.


#' Get Eunomia Connection Details
#'
#' @description
#' Creates a copy of the Eunomia database, and provides details for connecting to that copy.
#'
#' @param databaseFile   The path where the database file will be copied to. By default, the database
#'                       will be copied to a temporary folder, and will be deleted at the end of the R
#'                       session.
#'
#' @return
#' A ConnectionDetails object, to be used with the \code{DatabaseConnector} package.
#'
#' @examples
#' connectionDetails <- getEunomiaConnectionDetails()
#' connection <- connect(connectionDetails)
#' querySql(connection, "SELECT COUNT(*) FROM person;")
#' disconnect(connection)
#'
#' @export
getEunomiaConnectionDetails <- function(databaseFile = tempfile(fileext = ".sqlite")) {
  extractFolder <- tempdir()
  file <- xzfile(system.file("sqlite", "cdm.tar.xz", package = "Eunomia"), open = "rb")
  untar(file, exdir = extractFolder)
  close(file)
  file.rename(from = file.path(extractFolder, "cdm.sqlite"), to = databaseFile)
  details <- DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = databaseFile)
  return(details)
}