#' @name read.xlsx
#' @title  Read from an Excel file or Workbook object
#' @description Read data from an Excel file or Workbook object into a data.frame
#' @param xlsxFile An xlsx file, Workbook object or URL to xlsx file.
#' @param sheet The name or index of the sheet to read data from.
#' @param startRow first row to begin looking for data.  Empty rows at the top of a file are always skipped,
#' regardless of the value of startRow.
#' @param colNames If `TRUE`, the first row of data will be used as column names.
#' @param skipEmptyRows If `TRUE`, empty rows are skipped else empty rows after the first row containing data
#' will return a row of NAs.
#' @param rowNames If `TRUE`, first column of data will be used as row names.
#' @param detectDates If `TRUE`, attempt to recognise dates and perform conversion.
#' @param cols A numeric vector specifying which columns in the Excel file to read.
#' If NULL, all columns are read.
#' @param rows A numeric vector specifying which rows in the Excel file to read.
#' If NULL, all rows are read.
#' @param check.names logical. If TRUE then the names of the variables in the data frame
#' are checked to ensure that they are syntactically valid variable names
#' @param sep.names One character which substitutes blanks in column names. By default, "."
#' @param namedRegion A named region in the Workbook. If not NULL startRow, rows and cols parameters are ignored.
#' @param na.strings A character vector of strings which are to be interpreted as NA. Blank cells will be returned as NA.
#' @param fillMergedCells If TRUE, the value in a merged cell is given to all cells within the merge.
#' @param skipEmptyCols If `TRUE`, empty columns are skipped.
#' @seealso [getNamedRegions()]
#' @details Formulae written using writeFormula to a Workbook object will not get picked up by read.xlsx().
#' This is because only the formula is written and left to be evaluated when the file is opened in Excel.
#' Opening, saving and closing the file with Excel will resolve this.
#' @author Alexander Walker
#' @return data.frame
#' @export
#' @examples
#'
#' xlsxFile <- system.file("extdata", "readTest.xlsx", package = "openxlsx")
#' df1 <- read.xlsx(xlsxFile = xlsxFile, sheet = 1, skipEmptyRows = FALSE)
#' sapply(df1, class)
#'
#' df2 <- read.xlsx(xlsxFile = xlsxFile, sheet = 3, skipEmptyRows = TRUE)
#' df2$Date <- convertToDate(df2$Date)
#' sapply(df2, class)
#' head(df2)
#'
#' df2 <- read.xlsx(
#'   xlsxFile = xlsxFile, sheet = 3, skipEmptyRows = TRUE,
#'   detectDates = TRUE
#' )
#' sapply(df2, class)
#' head(df2)
#'
#' wb <- loadWorkbook(system.file("extdata", "readTest.xlsx", package = "openxlsx"))
#' df3 <- read.xlsx(wb, sheet = 2, skipEmptyRows = FALSE, colNames = TRUE)
#' df4 <- read.xlsx(xlsxFile, sheet = 2, skipEmptyRows = FALSE, colNames = TRUE)
#' all.equal(df3, df4)
#'
#' wb <- loadWorkbook(system.file("extdata", "readTest.xlsx", package = "openxlsx"))
#' df3 <- read.xlsx(wb,
#'   sheet = 2, skipEmptyRows = FALSE,
#'   cols = c(1, 4), rows = c(1, 3, 4)
#' )
#'
#' ## URL
#' ##
#' \dontrun{
#' xlsxFile <- "https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx"
#' head(read.xlsx(xlsxFile))
#' }
#'
#' @export
read.xlsx <- function(
  xlsxFile,
  sheet,
  startRow        = 1,
  colNames        = TRUE,
  rowNames        = FALSE,
  detectDates     = FALSE,
  skipEmptyRows   = TRUE,
  skipEmptyCols   = TRUE,
  rows            = NULL,
  cols            = NULL,
  check.names     = FALSE,
  sep.names       = ".",
  namedRegion     = NULL,
  na.strings      = "NA",
  fillMergedCells = FALSE
) {
  UseMethod("read.xlsx", xlsxFile)
}

#' @export
read.xlsx.default <- function(
  xlsxFile,
  sheet,
  startRow        = 1,
  colNames        = TRUE,
  rowNames        = FALSE,
  detectDates     = FALSE,
  skipEmptyRows   = TRUE,
  skipEmptyCols   = TRUE,
  rows            = NULL,
  cols            = NULL,
  check.names     = FALSE,
  sep.names       = ".",
  namedRegion     = NULL,
  na.strings      = "NA",
  fillMergedCells = FALSE
) {
  ## Validate inputs and get files
  xlsxFile <- getFile(xlsxFile)
  
  if (!file.exists(xlsxFile)) {
    stop("File does not exist.")
  }
  
  sheetselected <- TRUE
  if (missing(sheet)) {
    sheet <- 1
    sheetselected <- FALSE
  }
  
  if (!grepl("\\.xlsx|\\.xlsm$", xlsxFile)) {
    stop("openxlsx can only read .xlsx or .xlsm files", call. = FALSE)
  }
  
  assert_true_false1(colNames)
  assert_true_false1(rowNames)
  assert_true_false1(detectDates)
  assert_true_false1(skipEmptyRows)
  assert_true_false1(check.names)
  assert_character1(sep.names, scalar = TRUE)
  assert_length(sheet, 1L)
  assert_length(startRow, 1L)
  
  if (is.null(rows)) {
    rows <- NA
  } else if (length(rows) > 1L) {
    rows <- as.integer(sort(rows))
  }
  
  xmlDir <- paste0(tempfile(), "_excelXMLRead")
  xmlFiles <- unzip(xlsxFile, exdir = xmlDir)
  on.exit(unlink(xmlDir, recursive = TRUE), add = TRUE)
  
  sharedStringsFile <- grep("sharedStrings.xml$", xmlFiles, perl = TRUE, value = TRUE)
  workbook <- grep("workbook.xml$", xmlFiles, perl = TRUE, value = TRUE)
  workbookRelsXML <- grep("workbook.xml.rels$", xmlFiles, perl = TRUE, value = TRUE)
  
  ## get workbook names
  workbookRelsXML <- paste(readUTF8(workbookRelsXML), collapse = "")
  workbookRelsXML <- getChildlessNode(xml = workbookRelsXML, tag = "Relationship")
  
  workbook <- unlist(readUTF8(workbook))
  workbook <- removeHeadTag(workbook)
  
  sheets <- unlist(regmatches(
    workbook,
    gregexpr("(?<=<sheets>).*(?=</sheets>)", workbook, perl = TRUE)
  ))
  sheets <- unlist(regmatches(
    sheets, 
    gregexpr("<sheet[^>]*>", sheets, perl = TRUE)
  ))
  ## Some veryHidden sheets do not have a sheet content and their rId is empty.
  ## Such sheets need to be filtered out because otherwise their sheet names
  ## occur in the list of all sheet names, leading to a wrong association
  ## of sheet names with sheet indeces.
  sheets <- grep('r:id="[[:blank:]]*"', sheets, invert = TRUE, value = TRUE)
  
  
  ## make sure sheetId is 1 based
  sheetrId <- unlist(getRId(sheets))
  sheetNames <- unlist(regmatches(
    sheets, 
    gregexpr('(?<=name=")[^"]+', sheets, perl = TRUE)
  ))
  sheetNames <- replaceXMLEntities(sheetNames)
  
  
  nSheets <- length(sheetrId)
  if (nSheets == 0) {
    stop("Workbook has no worksheets")
  }
  
  ## Named region logic
  reading_named_region <- FALSE
  if (!is.null(namedRegion)) {
    dn <- getNodes(xml = workbook, tagIn = "<definedNames>")
    dn <- unlist(regmatches(dn, gregexpr("<definedName [^<]*", dn, perl = TRUE)))
    
    # search for sheetNames in list of named_region
    # sheet in between '>' and '!'
    dn_sheetNames <- gsub(".*[>]([^.]+)[!].*", "\\1", dn)
    
    # Check if there are any whitespaces in dn_sheetNames.
    # Hint: sheet names must not contain: \ / ? * [ ]
    wsp <- grepl(pattern = "'", dn_sheetNames)
    if (any(wsp)) {
      # sheetNames in between ''' and '''. If there is a whitespace in a sheet
      # name, the name will be "'sheet 1'" instead of "sheet 1.
      dn_sheetNames[wsp] <- gsub("^'+|'+$", "\\1", dn_sheetNames[wsp])
    }
    # namedRegion in between 'name="' and '"'
    dn_namedRegion <- gsub(".*name=\"([[:graph:]_]+)\".*", "\\1", dn)
    
    if (length(dn) == 0) {
      warning("Workbook has no named region.")
      return(invisible(NULL))
    }
    
    if (all(dn_namedRegion != namedRegion)) {
      warning("Workbook has no such named region.")
      return(invisible(NULL))
    }
    
    idx <- match(dn_namedRegion, namedRegion)
    
    # make sure that the length of both vectors is identical
    dn <- dn[!is.na(idx)]
    dn_namedRegion <- dn_namedRegion[!is.na(idx)]
    dn_sheetNames  <- dn_sheetNames[!is.na(idx)]
    
    # a sheet was selected
    if (sheetselected) {
      idx <- match(dn_sheetNames, sheetNames)
      if (is.numeric(sheet)) {
        idx <- which(idx == sheet)
        
      } else {
        idx <- which(dn_sheetNames == sheet)
      }
      dn <- dn[idx]
      
      if (length(dn) > 1) {
        warning("unexpectedly found more than one dn.")
        print(dn)
        return(invisible(NULL))
      }
      
      if ( identical(dn, character(0)) ) {
        warning("Workbook has no such named region on this sheet.")
        return(invisible(NULL))
      }
    }
    
    # Do not print warning if a specific sheet is requested
    if ((length(dn) > 1) && (!sheetselected)) {
      msg <- c(sprintf("Region '%s' found on multiple sheets: \n", namedRegion),
        paste(dn_sheetNames, collapse = "\n"),
        "\nUsing the first appearance.")
      message(msg)
      
      dn <- dn[1]
      dn_namedRegion <- dn_namedRegion[1]
      dn_sheetNames  <- dn_sheetNames[1]
    }
    
    # region is redefined later
    region <- regmatches(dn, regexpr("(?<=>)[^\\<]+", dn, perl = TRUE))
    sheet <- sheetNames[vapply(sheetNames, grepl, NA, dn)]
    
    if (length(sheet) > 1) {
      sheet <- sheet[which.max(nchar(sheet))]
    }
    
    region <- gsub("[^A-Z0-9:]", "", gsub(sheet, "", region, fixed = TRUE))
    
    if (grepl(":", region, fixed = TRUE)) {
      cols <- unlist(lapply(
        strsplit(region, split = ":", fixed = TRUE),
        convertFromExcelRef
      ))
      rows <- unlist(lapply(strsplit(region, split = ":", fixed = TRUE), function(x) {
        as.integer(gsub("[A-Z]", "", x, perl = TRUE))
      }))
      cols <- seq.int(min(cols), max(cols))
      rows <- seq.int(min(rows), max(rows))
    } else {
      cols <- convertFromExcelRef(region)
      rows <- as.integer(gsub("[A-Z]", "", region, perl = TRUE))
    }
    
    startRow <- 1
    reading_named_region <- TRUE
  }
  
  ## get the file_name for each sheetrId
  file_name <- sapply(sheetrId, function(rId) {
    txt <- grep(sprintf('Id="%s"', rId), workbookRelsXML, fixed = TRUE, value = TRUE)
    regmatches(txt, regexpr('(?<=Target=").+xml(?=")', txt, perl = TRUE))
  })
  
  
  ## get the correct sheets
  if (is.character(sheet)) {
    sheetNames <- replaceXMLEntities(sheetNames)
    sheetInd <- which(sheetNames == sheet)
    if (length(sheetInd) == 0) {
      stop(sprintf('Cannot find sheet named "%s"', sheet))
    }
    sheet <- file_name[sheetInd]
  } else {
    if (nSheets < sheet) {
      stop(sprintf("sheet %s does not exist.", sheet))
    }
    sheet <- file_name[sheet]
  }
  
  if (length(sheet) == 0) {
    stop("Length of sheet is 0", call. = FALSE)
  }
  
  ## get file
  worksheet <- xmlFiles[grepl(tolower(sheet), tolower(xmlFiles), fixed = TRUE)]
  if (length(worksheet) == 0) {
    stop("Length of worksheet is 0", call. = FALSE)
  }
  
  ## read in sharedStrings
  if (length(sharedStringsFile) > 0) {
    sharedStrings <-
      getSharedStringsFromFile(sharedStringsFile = sharedStringsFile, isFile = TRUE)
    if (!is.null(na.strings)) {
      sharedStrings[is.na(sharedStrings) | sharedStrings %in% na.strings] <- "openxlsx_na_vlu"
    }
  } else {
    sharedStrings <- ""
  }
  
  if (is.character(startRow)) {
    startRowStr <- startRow
    startRow <- 1
  } else {
    startRowStr <- NULL
  }
  
  ## single function get all r, s (if detect dates is TRUE), t, v
  cell_info <- getCellInfo(
    xmlFile = worksheet,
    sharedStrings = sharedStrings,
    skipEmptyRows = skipEmptyRows,
    startRow = startRow,
    rows = rows,
    getDates = detectDates
  )
  
  if (fillMergedCells && length(cell_info$cellMerge) > 0) {
    # stop("Not implemented")
    
    merge_mapping <- mergeCell2mapping(cell_info$cellMerge)
    
    ## remove any elements from  r, string_refs, b, s that existing in merge_mapping
    ## insert all missing refs into r
    
    to_remove_inds <- cell_info$r %in% merge_mapping$ref
    to_remove_elems <- cell_info$r[to_remove_inds]
    
    if (any(to_remove_inds)) {
      cell_info$r <- cell_info$r[!to_remove_inds]
      cell_info$s <- cell_info$s[!to_remove_inds]
      cell_info$v <- cell_info$v[!to_remove_inds]
      cell_info$string_refs <-
        cell_info$string_refs[!cell_info$string_refs %in% to_remove_elems]
    }
    
    ## Now insert
    inds <- match(merge_mapping$anchor_cell, cell_info$r)
    
    ## String refs (must sort)
    new_string_refs <-
      merge_mapping$ref[merge_mapping$anchor_cell %in% cell_info$string_refs]
    cell_info$string_refs <-
      c(cell_info$string_refs, new_string_refs)
    cell_info$string_refs <-
      cell_info$string_refs[order(
        as.integer(gsub("[A-Z]", "", cell_info$string_refs, perl = TRUE)),
        nchar(cell_info$string_refs),
        cell_info$string_refs
      )]
    
    ## r
    cell_info$r <- c(cell_info$r, merge_mapping$ref)
    cell_info$v <- c(cell_info$v, cell_info$v[inds])
    
    ord <- order(
      as.integer(gsub("[A-Z]", "", cell_info$r, perl = TRUE)),
      nchar(cell_info$r),
      cell_info$r
    )
    
    cell_info$r <- cell_info$r[ord]
    cell_info$v <- cell_info$v[ord]
    
    if (length(cell_info$s) > 0) {
      cell_info$s <- c(cell_info$s, cell_info$s[inds])[ord]
    }
    
    cell_info$nRows <- calc_number_rows(x = cell_info$r, skipEmptyRows = skipEmptyRows)
  }
  
  cell_rows <- as.integer(gsub("[A-Z]", "", cell_info$r, perl = TRUE))
  cell_cols <- convert_from_excel_ref(x = cell_info$r)
  
  ## subsetting ----
  ## Remove cells where cell is NA (na.strings or empty sharedString '<si><t/></si>')
  
  if (length(cell_info$v) == 0) {
    warning("No data found on worksheet.\n", call. = FALSE)
    return(NULL)
  }
  
  keep <- !is.na(cell_info$v)
  if (!is.null(cols)) {
    keep <- keep & (cell_cols %in% cols)
  }
  
  ## End of subsetting
  
  ## Subset
  cell_rows <- cell_rows[keep]
  cell_cols <- cell_cols[keep]
  
  v <- cell_info$v[keep]
  s <- cell_info$s[keep]
  
  string_refs <- match(cell_info$string_refs, cell_info$r[keep])
  string_refs <- string_refs[!is.na(string_refs)]
  
  if (skipEmptyRows) {
    nRows <- length(unique(cell_rows))
  } else if (reading_named_region) {
    ## keep region the correct size
    nRows <- max(rows) - min(rows) + 1
  } else {
    nRows <- max(cell_rows) - min(cell_rows) + 1
  }
  
  if (nRows == 0 || length(cell_rows) == 0) {
    warning("No data found on worksheet.", call. = FALSE)
    return(NULL)
  }
  
  Encoding(v) <- "UTF-8" ## only works if length(v) > 0
  
  if (!is.null(startRowStr)) {
    stop("startRowStr not implemented")
    ind <- grep(startRowStr, v, ignore.case = TRUE)
    if (length(ind) > 0) {
      startRow <- as.numeric(gsub("[A-Z]", "", r[ind[[1]]]))
      toKeep <- grep(sprintf("[A-Z]%s$", startRow), r)[[1]]
      if (toKeep > 1) {
        toRemove <- 1:(toKeep - 1)
        string_refs <- string_refs[!string_refs %in% r[toRemove]]
        v <- v[-toRemove]
        r <- r[-toRemove]
        nRows <-
          calc_number_rows(x = r, skipEmptyRows = skipEmptyRows)
      }
    }
  }
  
  ## Determine date cells (if required)
  origin <- 25569L
  if (detectDates) {
    ## get date origin
    if (grepl('date1904="1"|date1904="true"', workbook, ignore.case = TRUE)) {
      origin <- 24107L
    }
    
    stylesXML <- grep("styles.xml", xmlFiles, value = TRUE)
    styles <- readUTF8(stylesXML)
    styles <- removeHeadTag(styles)
    
    ## Number formats
    numFmts <- getChildlessNode(xml = styles, tag = "numFmt")
    
    dateIds <- NULL
    if (length(numFmts) > 0) {
      numFmtsIds <- sapply(numFmts, getAttr, tag = 'numFmtId="', USE.NAMES = FALSE)
      formatCodes <- sapply(numFmts, getAttr, tag = 'formatCode="', USE.NAMES = FALSE)
      formatCodes <- gsub(".*(?<=\\])|@", "", formatCodes, perl = TRUE)
      
      ## this regex defines what "looks" like a date
      dateIds <- numFmtsIds[!grepl("[^mdyhsapAMP[:punct:] ]", formatCodes) &
          nchar(formatCodes > 3)]
    }
    
    dateIds <- c(dateIds, 14)
    
    ## which styles are using these dateIds
    cellXfs <- getNodes(xml = styles, tagIn = "<cellXfs")
    xf <- getChildlessNode(xml = cellXfs, tag = "xf")
    lookingFor <- paste(sprintf('numFmtId="%s"', dateIds), collapse = "|")
    dateStyleIds <- which(sapply(xf, function(x) grepl(lookingFor, x), USE.NAMES = FALSE)) - 1L
    
    isDate <- s %in% dateStyleIds
    
    ## set to false if in string_refs
    isDate[seq_along(s) %in% string_refs] <- FALSE
    
    # check numbers are also integers
    not_an_integer <- numeric(length(v))
    not_an_integer[isDate] <- suppressWarnings(as.numeric(v[isDate]))
    not_an_integer <- (not_an_integer %% 1L != 0) & !is.na(not_an_integer)
    isDate[not_an_integer] <- FALSE
    if (origin == 25569L) {
      earlyDates <- suppressWarnings(as.integer(v) < 60)
      v[earlyDates & isDate] <- as.integer(v[earlyDates & isDate]) + 1L
    }
    
    ## perform int to date to character conversion (way too slow)
    v[isDate] <- format(
      as.Date(as.integer(v[isDate]) - origin, origin = "1970-01-01"),
      "%Y-%m-%d"
    )
  } else {
    isDate <- as.logical(NA)
  }
  
  ## Build data.frame
  m <- read_workbook(
    cols_in       = cell_cols,
    rows_in       = cell_rows,
    v             = v,
    string_inds   = string_refs,
    is_date       = isDate,
    hasColNames   = colNames,
    hasSepNames   = sep.names,
    skipEmptyRows = skipEmptyRows,
    skipEmptyCols = skipEmptyCols,
    nRows         = nRows,
    clean_names   = clean_names
  )
  
  if (rowNames) {
    # set the first column as the rownames
    rownames(m) <- m[[1]]
    m[[1]] <- NULL
  }
  
  if (colNames) {
    if (check.names) {
      colnames(m) <- make.names(colnames(m), unique = TRUE)
    }
  } else {
    # Need to reset column names
    if (rowNames) {
      colnames(m) <- make.names(seq_along(m))
    }
  }
  
  m
}

#' @name readWorkbook
#' @title  Read from an Excel file or Workbook object
#' @description Read data from an Excel file or Workbook object into a data.frame
#' @inheritParams read.xlsx
#' @details Creates a data.frame of all data in worksheet.
#' @author Alexander Walker
#' @return data.frame
#' @seealso [getNamedRegions()]
#' @seealso [read.xlsx()]
#' @export
#' @examples
#' xlsxFile <- system.file("extdata", "readTest.xlsx", package = "openxlsx")
#' df1 <- readWorkbook(xlsxFile = xlsxFile, sheet = 1)
#'
#' xlsxFile <- system.file("extdata", "readTest.xlsx", package = "openxlsx")
#' df1 <- readWorkbook(xlsxFile = xlsxFile, sheet = 1, rows = c(1, 3, 5), cols = 1:3)
readWorkbook <- function(
  xlsxFile,
  sheet           = 1,
  startRow        = 1,
  colNames        = TRUE,
  rowNames        = FALSE,
  detectDates     = FALSE,
  skipEmptyRows   = TRUE,
  skipEmptyCols   = TRUE,
  rows            = NULL,
  cols            = NULL,
  check.names     = FALSE,
  sep.names       = ".",
  namedRegion     = NULL,
  na.strings      = "NA",
  fillMergedCells = FALSE
) {
  read.xlsx(
    xlsxFile        = xlsxFile,
    sheet           = sheet,
    startRow        = startRow,
    colNames        = colNames,
    rowNames        = rowNames,
    detectDates     = detectDates,
    skipEmptyRows   = skipEmptyRows,
    skipEmptyCols   = skipEmptyCols,
    rows            = rows,
    cols            = cols,
    check.names     = check.names,
    sep.names       = sep.names,
    namedRegion     = namedRegion,
    na.strings      = na.strings,
    fillMergedCells = fillMergedCells
  )
}