inst/shiny/PLPViewer/modules/download.R

In quinterpriest/PatientLevelPrediction: Developing patient level prediction using data in the OMOP Common Data Model

downloadViewer <- function(id) {
  
  ns <- shiny::NS(id)
  
  shiny::div(
    
    shinydashboard::box(
      title = "Development R Package", 
      status = 'info', 
      solidHeader = T,
      shiny::p("Click here to download an R package that contains all the settings requires to replicate the model development using any OMOP CDM database."),
      shiny::actionButton(
        inputId = ns('downloadPackageDev'), 
        label = "Download Development"
      )
    ),
    
    shinydashboard::box(
      title = "Validation R Package", 
      status = 'info', 
      solidHeader = T,
      shiny::p("Click here to download an R package that contains all the settings requires to validate the existing model using any OMOP CDM database."),
      shiny::actionButton(
        inputId = ns('downloadPackageVal'), 
        label = "Download Validation"
      )
      
    )
  )
}

downloadServer <- function(id) {
  shiny::moduleServer(
    id,
    function(input, output, session) {
      
      shiny::observeEvent(
        input$downloadPackageDev, 
        {
        dir.create(file.path('/Users/jreps/Downloads', 'devPackage'), recursive = T)
        #Hydra::hydrate(specifications = specifications, outputFolder = outputPackageLocation)
          createPackage <- tryCatch(
            {downLoadSkeleton(
              outputFolder = file.path('/Users/jreps/Downloads'),
              packageName = 'devPackage',
              skeletonType = 'SkeletonPredictionStudy'
            )#'SkeletonPredictionValidationStudy'
            }, error = function(e){return(NULL)}
          )
        
        if(!is.null(createPackage)){
          createPackage <- tryCatch(
            {replaceName(
              packageLocation = file.path('/Users/jreps/Downloads', 'devPackage'),
              packageName = 'devPackage',
              skeletonType = 'SkeletonPredictionStudy')
            },
            error = function(e){return(NULL)}
          )
        }
        
        
      })
      
    }
  )
}

### DOWNLOAD

downLoadSkeleton <- function(
  outputFolder,
  packageName,
  skeletonType = 'SkeletonPredictionStudy'
){
  utils::download.file(
    url = paste0("https://github.com/ohdsi/",skeletonType,"/archive/master.zip"), 
    destfile = file.path(outputFolder, "package.zip")
  )
  # unzip the .zip file
  utils::unzip(
    zipfile = file.path(outputFolder, "package.zip"), 
    exdir = outputFolder
  )
  file.rename( 
    from = file.path(outputFolder, paste0(skeletonType, '-master')),
    to = file.path(outputFolder,  packageName)
  )
  unlink(file.path(outputFolder, "package.zip"))
  return(file.path(outputFolder, packageName))
}

# change name
replaceName <- function(
  packageLocation = getwd(),
  packageName = 'ValidateRCRI',
  skeletonType = 'SkeletonPredictionValidationStudy'
){
  
  filesToRename <- c(paste0(skeletonType,".Rproj"),paste0("R/",skeletonType,".R"))
  for(f in filesToRename){
    ParallelLogger::logInfo(paste0('Renaming ', f))
    fnew <- gsub(skeletonType, packageName, f)
    file.rename(from = file.path(packageLocation,f), to = file.path(packageLocation,fnew))
  }
  
  filesToEdit <- c(
    file.path(packageLocation,"DESCRIPTION"),
    file.path(packageLocation,"README.md"),
    file.path(packageLocation,"extras/CodeToRun.R"),
    dir(file.path(packageLocation,"R"), full.names = T)
  )
  for( f in filesToEdit ){
    ParallelLogger::logInfo(paste0('Editing ', f))
    x <- readLines(f)
    y <- gsub( skeletonType, packageName, x )
    cat(y, file=f, sep="\n")
    
  }
  
  return(packageName)
}