R/Sharing.R

In ohdsi-studies/IbdCharacterization: Characterization of Inflammatory Bowel Disease Patient Cohorts

# Copyright 2022 Observational Health Data Sciences and Informatics
#
# This file is part of IbdCharacterization
#
# 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.

rootFTPFolder <- function() {
  return("/IbdCharacterization/")
}

#' @export
uploadDiagnosticsResults <- function(outputFolder, privateKeyFileName, userName) {
  uploadResults(file.path(outputFolder, "diagnostics"), privateKeyFileName, userName, remoteFolder = paste0(rootFTPFolder(), "CohortDiagnostics"))
}

#' @export
uploadStudyResults <- function(outputFolder, privateKeyFileName, userName) {
  uploadResults(outputFolder, privateKeyFileName, userName, remoteFolder = paste0(rootFTPFolder(), "StudyResults"))
}

#' Upload results to OHDSI server
#' 
#' @details
#' This function uploads 'Results_\<databaseId\>.zip' to the OHDSI SFTP server. Before sending, you can inspect the zip file,
#' which contains (zipped) CSV files. You can send the zip file from a different computer than the one on which is was created.

#' @param privateKeyFileName   A character string denoting the path to the RSA private key provided by the study coordinator.
#' @param userName             A character string containing the user name provided by the study coordinator.
#' @param outputFolder         Name of local folder to place results; make sure to use forward slashes
#'                             (/). Do not use a folder on a network drive since this greatly impacts
#'                             performance.
#'                             
uploadResults <- function(outputFolder, privateKeyFileName, userName, remoteFolder) {
  fileName <- list.files(outputFolder, "^Results_.*.zip$", full.names = TRUE)
  if (length(fileName) == 0) {
    stop("Could find results file in folder. Did you run (and complete) execute?") 
  }
  if (length(fileName) == 0) {
    stop("Multiple results files found. Don't know which one to upload") 
  }
  OhdsiSharing::sftpUploadFile(privateKeyFileName = privateKeyFileName, 
                               userName = userName,
                               remoteFolder = remoteFolder,
                               fileName = fileName)
  ParallelLogger::logInfo("Finished uploading")
}