inst/hbcdtlfb/www/R/startup_redcap_aws.R

In ucsd-dsm/hbcd-tlfb: HBCD TLFB shiny app

query <- parseQueryString(session$clientData$url_search)
tlfb_id(query$id)
tlfb_v(query$v)

null_query <- (is.null(tlfb_id()) | is.null(tlfb_v()))

if (null_query) {
  
  if(local_development) {
    # tlfb_id("TEST_TLFBG_1")
    tlfb_id("TEST_TLFB0002")
    # tlfb_id("TEST_TLFB_NOSUBSTANCE")
    tlfb_v(2)
    null_query <- FALSE
  }
  
  if(! local_development) {
    
    # Stop if missing parameters in URL.
    shinyalert::shinyalert(
      title = "Missing Parameters in URL",
      text = 
        "No id and/or version provided in the URL.</br>
  Try again adding '?v=XXX&id=YYY' at the end of the URL</br>
  for example for v1:</br> 
  <a href = 'https://ucsd-cmig.shinyapps.io/hbcd-tlfb-dev/?v=1&id=TEST_TLFB0002'>https://ucsd-cmig.shinyapps.io/hbcd-tlfb-dev/?v=1&id=TEST_TLFB0002</a></br>
  or for v2:</br>
  <a href = 'https://ucsd-cmig.shinyapps.io/hbcd-tlfb-dev/?v=2&id=TEST_TLFB0002'>https://ucsd-cmig.shinyapps.io/hbcd-tlfb-dev/?v=2&id=TEST_TLFB0002</a>",
      size = "m",
      animation = FALSE,
      closeOnEsc = FALSE,
      closeOnClickOutside = FALSE,
      showConfirmButton = FALSE,
      html = TRUE,
      type = "error",
      immediate = TRUE
    )
    
    Sys.sleep(3)
    stopApp("Missing Parameters in URL")
  }
  
}

if (! null_query) {
  
  # Connect.
  shinyalert::shinyalert(
    title = "Connection in Progress...",
    text = "It might take a few seconds.",
    size = "m",
    animation = FALSE,
    closeOnEsc = FALSE,
    closeOnClickOutside = FALSE,
    showConfirmButton = FALSE,
    html = TRUE,
    type = "info",
  )
  
  redcap_dta <- try(REDCapR::redcap_read(
    redcap_uri = Sys.getenv("REDCAP_TLFB_URI"),
    fields = selection_names_redcap,
    token = Sys.getenv("REDCAP_TLFB_TOKEN"),
    records = tlfb_id())$data
  )
  
  # Exit app if no connection.
  connect_redcap_test <- ! inherits(redcap_dta, "try-error")
  
  if (! connect_redcap_test) {
    shinyalert::shinyalert(
      title = "Can't connect to REDCap",
      text = "Please check your internet connection, if the issue persist, report to the data team.",
      size = "m",
      animation = FALSE,
      closeOnEsc = FALSE,
      closeOnClickOutside = FALSE,
      showConfirmButton = FALSE,
      html = TRUE,
      type = "error",
      immediate = TRUE
    )
    
    Sys.sleep(3)
    stopApp("Can't connect to REDCap") 
  }
  
  # Test record existence and completeness.
  if (tlfb_v() == 1) {
    test_non_null <- redcap_dta |> nrow() > 0
    ifelse(test_non_null, 
           test_event <- "v01_arm_1" %in% redcap_dta$redcap_event_name, 
           { 
             test_event <- FALSE
             test_complete <- FALSE
             test_record <- FALSE
           })
    ifelse(test_event,
           test_complete <- redcap_dta[redcap_dta$redcap_event_name == "v01_arm_1", "assist_v1_complete"] == 2,
           {
             test_complete <- FALSE
             test_record <- FALSE
           })
    if(test_complete)  test_record <- TRUE
  }
  
  if (tlfb_v() == 2) {
    test_non_null <- redcap_dta |> nrow() > 0
    ifelse(test_non_null, 
           test_event <- "v02_arm_1" %in% redcap_dta$redcap_event_name, 
           { 
             test_event <- FALSE
             test_complete <- FALSE
             test_record <- FALSE
           })
    ifelse(test_event,
           test_complete <- redcap_dta[redcap_dta$redcap_event_name == "v02_arm_1", "assist_v2_complete"] == 2,
           {
             test_complete <- FALSE
             test_record <- FALSE
           })
    if(test_complete)  test_record <- TRUE
  }
  
  if (! test_record) {
    shinyalert::shinyalert(
      title = "ASSIST record not present/complete",
      text = "Please report to the data team.</br>
    You will be disconnected from the app.",
      size = "m",
      animation = FALSE,
      closeOnEsc = FALSE,
      closeOnClickOutside = FALSE,
      showConfirmButton = FALSE,
      html = TRUE,
      type = "error",
      immediate = TRUE
    )
    
    Sys.sleep(3)
    stopApp("ASSIST record not present/complete")
  }
  
  # Test connection to AWS.
  connect_server <- try(
    aws.s3::bucket_exists(
      bucket = "hbcd-tlfb", 
      base_url = "storjshare.io", 
      region = "gateway.us1"),
    silent = TRUE)
  
  connect_server_test <- ! inherits(connect_server, "try-error")
  
  if (! connect_server_test) {
    
    shinyalert::shinyalert(
      title = "Can't connect to AWS",
      text = "Please check your internet connection, if the issue persist, report to data team.",
      size = "m",
      animation = FALSE,
      closeOnEsc = FALSE,
      closeOnClickOutside = FALSE,
      showConfirmButton = FALSE,
      html = TRUE,
      type = "error",
      immediate = TRUE
    )
  }
  
  if(connect_redcap_test & test_record & connect_server_test)  {
    redcap_dta(redcap_dta)
    
    # Test if a record exist on AWS.
    test_existing_record <- list(
      complete = aws.s3::head_object(
        object = glue("{tlfb_id()}_v{tlfb_v()}_COMPLETE.rds"), 
        bucket = "hbcd-tlfb", 
        base_url = "storjshare.io", 
        region = "gateway.us1"
      ),
      partial = aws.s3::head_object(
        object = glue("{tlfb_id()}_v{tlfb_v()}_PARTIAL.rds"), 
        bucket = "hbcd-tlfb", 
        base_url = "storjshare.io", 
        region = "gateway.us1"
      )
    )
    
    if (test_existing_record$complete) {
      aws_file <- aws.s3::get_object(
        object = glue("{tlfb_id()}_v{tlfb_v()}_COMPLETE.rds"), 
        bucket = "hbcd-tlfb", 
        base_url = "storjshare.io", 
        region = "gateway.us1"
      )
      
      tlfb_data_session <- readRDS(file = gzcon(rawConnection(aws_file)))
      existing_record(tlfb_data_session)
      text_exisiting_record <- "There is already a 
      <strong>COMPLETE record</strong> for this ID</br>
      Previousely entered substances (not events) have been loaded."
    }
    
    if (! test_existing_record$complete & test_existing_record$partial) {
      aws_file <- aws.s3::get_object(
        object = glue("{tlfb_id()}_v{tlfb_v()}_PARTIAL.rds"), 
        bucket = "hbcd-tlfb", 
        base_url = "storjshare.io", 
        region = "gateway.us1"
      )
      tlfb_data_session <- readRDS(file = gzcon(rawConnection(aws_file)))
      existing_record(tlfb_data_session)
      text_exisiting_record <- "There is already a 
      <strong>PARTIAL record</strong> for this ID</br>
      Previousely entered substances (not events) have been loaded."
    }
    
    if (! test_existing_record$complete & ! test_existing_record$partial) {
      text_exisiting_record <- "There is no exisiting record for this ID. You can start entering data"
    }
    
    # Ask user to start sesssion.
    shinyalert::shinyalert(
      inputId = "start_session",
      title = "Welcome to the Timeline Followback App!",
      text = glue(
        "{icon('check')}{text_exisiting_record}</br>
         {icon('check')}ID {tlfb_id()}</br>
         {icon('check')}ASSIST Version {tlfb_v()}</br>
         {icon('check')}Connection to AWS server established"
      ),
      size = "m",
      animation = FALSE,
      closeOnEsc = FALSE,
      closeOnClickOutside = FALSE,
      html = TRUE,
      type = "success",
      confirmButtonText = "Start Session",
      immediate = TRUE
    )
  }
}