# initially only interfacing 4D data

# TODO loggen zoveel mogelijk over ontvangen data (nieuwe GLIMS data)
# TODO pushen R scripts naar git server waar Gerhard en Kornelis bij kunnen

# require(stringr)
require(tidyverse)
require(AMR)

dataFolder = './data'

get_most_recent_4D_file = function(path, prefix) {
  files = list.files(dataFolder, paste0('^', prefix, '*'))
  tFiles = tibble(name = files, 
                  mtime = file.mtime(file.path(dataFolder, files))) %>%
    arrange(desc(mtime))
  
  tmpFilename = tFiles$name[1]
  
  return(tmpFilename)
}

read_4D_file = function(path) {
  tFile = read_tsv(path, col_types = paste0(rep('c', 30), collapse = ''))
  
  # remove comment lines
  if (nrow(tFile) > 0) {
    tFile = tFile %>%
      slice( seq(4, nrow(tFile)) ) %>% 
      filter(str_sub(ID, 1, 3) != '___')
  }
  
  if (colnames(tFile)[1] == 'X1') {
    if (str_detect(path, 'AB-')) {
      tFile = tibble(ID = '0', 
                     Monsternummer = '', 
                     IsolNr = '', 
                     AB = '', 
                     V = '',
                     PrefMIC ='',
                     MIC = '',
                     D = '',
                     DIF = '',
                     PrefEtest = '',
                     E = '',
                     ETEST = '',
                     RIS = '',
                     RAP = '',
                     ...15 = '')
    } else if (str_detect(path, 'MS-')) {
      tFile = tibble(UMCG.Monster= '0',
                     PIN.Lot= '0',
                     TypeObject= '0',
                     Lot= '0',Echtgenoot= '0',
                     AchternNaam= '0',
                     Geboortedatum= '0',
                     Geslacht= '0',
                     OntvOLabDatum= '0',
                     Tijdstip.materiaal.afgenomen= '0',
                     PC= '0',
                     Aanvrager= '0',
                     ligafdeling= '0',
                     A= '0',
                     B= '0',
                     C= '0',
                     Materiaal= '0',
                     Materiaal.variabelen= '0',
                     X = F)
      } else if (str_detect(path, 'ST-')) {
      tFile = tibble(ID = '0', 
                     Monsternummer = '', 
                     MMBProc = '',
                     Isolnr = '', 
                     MO = '', 
                     Waarde = '', 
                     Pos = '',
                     Rap = '')
    } else if (str_detect(path, 'TM-')) {
      tFile = tibble(ID = '0', 
                     Monsternummer = '', 
                     Test = '',
                     Uitslag = '')
    } else if (str_detect(path, 'TS-')) {
      tFile = tibble(ID = '0', 
                     Monsternummer = '', 
                     Isolnr = '', 
                     Test = '', 
                     Waarde = '', 
                     Rapport = '')
    }
  }
  if ('ID' %in% colnames(tFile)) {
    tFile = tFile %>%
      filter(ID != '0')
  } else if ('UMCG.Monster' %in% colnames(tFile)) {
    tFile = tFile %>%
      filter(UMCG.Monster != '0')
  }
  
  return(tFile)
}

read_4D_TM_file = function(path) {
  tmFilename = str_remove(path, paste0(dirname(path), '/'))
  tmFileL = readLines(path)
  tmFileL = tmFileL[c(5:length(tmFileL))]
  for (l in 1:length(tmFileL)) {
    if (str_count(tmFileL[l], '\t') == 3) {
      tmFileL = paste0(tmFileL, '\t')
    }
  }
  newTmFilename = file.path(dirname(path), 
                            tmFilename %>% str_replace('TM', 'bTM'))
  if (file.exists(newTmFilename)) file.remove(newTmFilename)
  writeLines(tmFileL, newTmFilename)
  
  tFile = read_tsv(newTmFilename, 
                   col_names = c('ID','Monsternummer','Test','Status.test.tm','Uitslag'), 
                   col_types = 'ccccc')
  
  # remove comment lines
  tFile = tFile %>%
    slice(c(5:(tFile %>% nrow()))) %>%
    mutate(
      Monsternummer = as.character(Monsternummer)
    )
  return(tFile)
}

get_most_recent_4D_MS_file = function(path) {
  # get files
  msFiles = list.files(path, '^MS*')
  # create table with modification datetimes, for selection of the most recent one
  tmsFiles = tibble(name = msFiles,
                    mtime = file.mtime(file.path(path, msFiles))) %>%
    arrange(desc(mtime))
  # get the name of the most recently modified file
  msFilename = tmsFiles$name[1]
  
  return(msFilename)
}

read_4D_MS_file = function(path) {
  # print(path)
  msFilename = str_remove(path, paste0(dirname(path), '/'))
  # read content
  msFileL = readLines(path)
  # remove lines with repeated '_', useful for the human eye only
  msFileL = msFileL[str_sub(msFileL, 1, 5) != '_____']
  # replace (real) header
  msHeader = readLines(file.path(dataFolder, 'headerMS.txt'))
  msFileL[1] = paste0(msHeader, '\t')
  # replace tabs within a date time combination with a space in line 2 and further,
  # for example: replace '29/09/2021	14:05' by '29/09/2021 14:05'
  #                                 ↑ = '\t'               ↑ = ' '
  for (i in 2:length(msFileL)) {
    msFileL[i] = msFileL[i] %>% str_replace_all('(?<=[:digit:]{4})\t(?=[:digit:]{2}:[:digit:]{2})', ' ')
  }
  # write to new machine readable file
  newMsFilename = file.path(dirname(path), 
                            msFilename %>% str_replace('MS', 'bMS'))
  if (file.exists(newMsFilename)) file.remove(newMsFilename)
  writeLines(msFileL, newMsFilename)
  # finally: read the machine readable file
  result = read.delim(file = newMsFilename, sep = '\t') %>%
    as_tibble() %>%
    mutate(
      UMCG.Monster = as.character(UMCG.Monster),
      PIN.Lot = as.character(PIN.Lot),
      Aanvrager = as.character(Aanvrager),
      C = as.character(C)
    )
  # Hurray!
  return(result)
}

# abFile = read_4D_file(dataFolder, 'AB')
# msFile = read_4D_MS_file(dataFolder)
# stFile = read_4D_file(dataFolder, 'ST')
# tmFile = read_4D_file(dataFolder, 'TM')
# tsFile = read_4D_file(dataFolder, 'TS')

ProcessAndMergeDailyFiles = function(abFile, msFile, stFile, tmFile, tsFile) {
  if (!is.null(abFile))
    abFile = abFile %>%
      filter(!is.na(RAP)) #%>%
  # mutate(
  #   #Monsternummer = as.character(Monsternummer)
  #   AB.amr = AMR::ab_property(AB, 'ab') %>% as.character()
  # )
  
  if (!is.null(stFile))
    stFile = stFile %>%
      filter(!is.na(Rap)) %>%
      # mutate(Monsternummer = as.character(Monsternummer) %>% str_trim()) %>%
      rename(IsolNr = Isolnr)
  
  if (!is.null(msFile))
    msFile = msFile %>%
      rename(Monsternummer = UMCG.Monster) %>%
      # mutate(Monsternummer = as.character(Monsternummer) %>% str_trim()) %>%
      select(-X)
  
  # if (!is.null(tmFile))
  # tmFile = tmFile %>%
  #   mutate(Monsternummer = as.character(Monsternummer) %>% str_trim())
  
  if (!is.null(tsFile))
    tsFile = tsFile %>%
      filter(!is.na(Rapport))
  #   mutate(Monsternummer = as.character(Monsternummer) %>% str_trim())
  
  if (!is.null(abFile) & !is.null(stFile))
    t_ab_st = abFile %>%
      full_join(stFile, 
                by = c('Monsternummer', 'IsolNr'), 
                suffix = c('.ab', '.st'))
  
  if (exists('t_ab_st')) {
    if (!is.null(t_ab_st) & !is.null(msFile)) {
      t_ab_st_ms = t_ab_st %>%
        full_join(msFile, by = 'Monsternummer') %>%
        rename(Waarde.st = Waarde)
      
      return(
        list(
          merged = t_ab_st_ms,
          abFile = abFile,
          stFile = stFile,
          msFile = msFile,
          tsFile = tsFile,
          tmFile = tmFile
        )
      )
      
      # t_ab_st_ms_ts = t_ab_st_ms %>%
      #   full_join(tsFile, by =  c('Monsternummer', 'IsolNr' = 'Isolnr'))
      # 
      # t_ab_st_ms_ts_tm = t_ab_st_ms_ts %>%
      #   add_column(Uitslag = NA,
      #              is_sampleResult = F) %>%
      #   add_row(Monsternummer = tmFile$Monsternummer,
      #           Test = tmFile$Test,
      #           Uitslag = tmFile$Uitslag,
      #           is_sampleResult = T)
      # 
      # t_ab_st_ms_ts_tm = t_ab_st_ms_ts_tm %>%
      #   rename(Waarde.ts = Waarde) %>%
      #   filter(!Test %in% c('no_filter_yet'))
      # 
      # # if ('X' %in% colnames(t_ab_st_ms_ts_tm)) {
      # #   t_ab_st_ms_ts_tm = t_ab_st_ms_ts_tm %>%
      # #     select(-'X')
      # #   print('Dit statement is voor debugging')
      # # }
    }
  }
  return(
    list(
      merged = NULL,
      abFile = abFile,
      stFile = stFile,
      msFile = msFile,
      tsFile = tsFile,
      tmFile = tmFile
    )
  )
}