R/create_ir.R

In Public-Health-Scotland/qifunctions: Quality Indicator functions

#
#' @title Create IR folder and templates
#'
#' @description \code{create_ir} Creates folder, code and output template for an
#' information request.
#'
#' @details Everything is created in cl-out.
#'
#' @param ir_number A \code{character} string specifying the name of the IR,
#' including the year, e.g. IR2022-5555.
#'
#' @param title An optional \code{character} string specifying the title of the IR.
#'
#' @param source An optional \code{character} string specifying the source of the data.
#'
#' @return Creates a series of directories in cl-out, a script that can be used
#' as a template for the IR, and an Excel file for the final output
#'
#' @examples create_ir("IR2022-55555")
#'
#' create_ir("IR2022-55555", title = "Number of admissions", source = "SMR01")
#'
#' @importFrom magrittr %>%
#' @importFrom magrittr %<>%
#'
#' @export


create_ir <- function(ir_number, title = NULL, source = NULL) {

  ir_year <- sub("-.*", "", ir_number)

  Sys.umask("000") # to set permissions right

  ###############################################.
  ## Creating directories ----
  ###############################################.


  # Filepath changes depending on Desktop/Server
  platform <- dplyr::case_when(sessionInfo()$platform %in% c("x86_64-redhat-linux-gnu (64-bit)",
                                                             "x86_64-pc-linux-gnu (64-bit)") ~ "/conf/",
                               T ~ "//Isdsf00d03/")


  cl_out <- paste0(platform, "linkage/output/") # cl-out
  ir_folder <- paste0(cl_out, ir_year, "/", ir_number) # folder for IR

  # Function fails in directory already exists.
  if (dir.exists(ir_folder)) {
    stop(paste0("Folder ", ir_folder, " already exists."))
  }


  # Creating folder and subfolders
  dir.create(ir_folder, showWarnings = TRUE, recursive = TRUE, mode = "770")
  dir.create(paste0(ir_folder, "/data"), showWarnings = TRUE, recursive = TRUE, mode = "770")
  dir.create(paste0(ir_folder, "/emails"), showWarnings = TRUE, recursive = TRUE, mode = "770")
  dir.create(paste0(ir_folder, "/code"), showWarnings = TRUE, recursive = TRUE, mode = "770")
  # dir.create(paste0(ir_folder, "/.Rproj.user"), showWarnings = TRUE, recursive = TRUE, mode = "770")

  ###############################################.
  ## Creating template IR script ----
  ###############################################.

  # Creating script for code
  ir_script <- paste0(ir_folder, "/code/", ir_number , ".R")
  if (file.exists(ir_script) == F) {

    file.create(ir_script, overwrite = FALSE)

    # Writing IR template code in script
    ir_template <- "# Code for

    ###############################################.
    ## Packages ----
    ###############################################.
    library(odbc)          # For accessing SMRA databases
    library(dplyr)         # For data manipulation in the tidy way
    library(readr)         # For reading/writing CSVs
    library(tidyr)         # for pivoting data
    library(magrittr)      # for more pipe operators
    library(lubridate)     # for date operations

    #SMRA connection
    channel <- suppressWarnings(dbConnect(odbc(),  dsn='SMRA',
    uid=.rs.askForPassword('SMRA Username:'),
    pwd=.rs.askForPassword('SMRA Password:')))


    ###############################################.
    ## Extracting data ----
    ###############################################.
    # extracting cases from SMRA
    dataset <- as_tibble(dbGetQuery(channel, statement = paste0(
    'SELECT link_no, cis_marker, admission_date,
          main_condition, other_condition_1, other_condition_2, other_condition_3,
          other_condition_4, other_condition_5, hbtreat_currentdate
        FROM ANALYSIS.SMR01_PI  z
        WHERE admission_date between \"1 January 2016\" and \"31 December 2021\" '))) %>%
    setNames(tolower(names(.)))

    write_csv(output, 'data/output.csv') # saving file

    ###END"

    writeLines(ir_template, ir_script)

  } else {
    print("Script for this IR already exists")
  }

  ###############################################.
  ## Bringing IR template ----
  ###############################################.

  ir_excel <- openxlsx::loadWorkbook(system.file("extdata", "ir-template.xlsx",
                                                   package = "qifunctions"))

  # Writing reference number in function
  openxlsx::writeData(ir_excel, "Notes", paste("Ref:", ir_number),
                      startCol = 2, startRow = 3)

  # Writing month of extract based on current date
  openxlsx::writeData(ir_excel, "Notes",
                      paste("Date extracted: ", format(Sys.Date(), "%B %Y")),
                      startCol = 2, startRow = 4)

  # Adding title if specified in the function call
  if (!is.null(title) ) {
    openxlsx::writeData(ir_excel, "Notes", title,
                        startCol = 2, startRow = 1)
  }

  # Adding source if specified in the function call
  if (!is.null(source) ) {
    openxlsx::writeData(ir_excel, "Notes",
                        paste("Source:", source, "- Public Health Scotland"),
                        startCol = 2, startRow = 2)
  }

  openxlsx::saveWorkbook(ir_excel, paste0(ir_folder, "/", ir_number , ".xlsx"))

  ###############################################.
  ## Creating new project ----
  ###############################################.

  # Creating R project and opens in new window
  # rstudioapi::openProject(ir_folder, newSession = TRUE)
  # system(paste0("chmod -R 775 ", ir_folder))
}