data-raw/R/read_pdf_tables.R

In danimedi/residentado_peru: What the Package Does (One Line, Title Case)

#' Save tables from raw PDF data as CSV files
#'
#' @param path_input_pdf relative path in the project to the folder where the PDF files are located
#' @param path_output_csv relative path in the project to the folder where the CSV files will be saved
read_pdf_tables <- function(path_input_pdf, path_output_csv) {

  # obtain files to extract tables from
  pdfs <- list.files(path_input_pdf, pattern = "[.]pdf$", full.names = TRUE)

  # loop to extract the tables and write csv files
  for (pdf in pdfs) {

    # obtain the name of the output file
    file <- gsub("[.]pdf$", ".csv", basename(pdf))
    file <- file.path(path_output_csv, file)

    # check if it exists to avoid running something more than once
    if (!basename(file) %in% list.files(path_output_csv)) {

      tryCatch({
        print(paste("working with", basename(pdf), "..."))

        # extract the tables from PDF file
        dat <- tabulizer::extract_tables(pdf, output = "matrix", encoding = "UTF-8")

        # check that there is no problems with the first page (same number of columns)
        # otherwise, fix the first page first, and then join it with the rest
        if (ncol(dat[[1]]) == ncol(dat[[2]])) {
          # bind the rows
          dat <- do.call(rbind, dat)
          # name the columns from the first row and transform it to a data frame
          colnames(dat) <- dat[1,]
          dat <- dat[-1,]
          dat <- as.data.frame(dat)
        } else {
          # remove empty values of the first page and save the names from the first
          # row in `col_names`, `table1` contains the data of the "clean" table/matrix
          # of the first page (by removing the last empty columns)
          i <- sapply(dat[[1]][1,], function(x) nchar(x) > 0)
          col_names <- dat[[1]][1, i]
          i <- seq_len(ncol(dat[[2]]))
          table1 <- dat[[1]][-1, i]
          # join everything
          dat <- do.call(rbind, dat[-1])
          dat <- rbind(table1, dat)
          # name columns
          colnames(dat) <- col_names
          dat <- as.data.frame(dat)
        }

        # save data as CSV
        readr::write_csv(dat, file)

      }, error = function(e) e, warning = function(w) w)
    }

  }

  # check the missing transformed files
  raws <- list.files(path_input_pdf, pattern = "[.]pdf$")
  raws <- gsub("[.]pdf$", "", raws)
  cleans <- list.files(path_output_csv, pattern = "[.]csv$")
  cleans <- gsub("[.]csv$", "", cleans)
  missing <- raws[!raws %in% cleans]
  if (length(missing) == 0) {
    "There are no missing files"
  } else if (length(missing) > 0) {
    paste("there are", missing, "missing files in the output folder")
  }

}