# Use the data from Menke 2020 (DOI:10.1101/2020.01.15.908111) as a
# demonstration analysis for this paper. This is a relevant paper because
# it provides good statistics about the status of reproducibility in
# scientific publications.
#
# Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
#
# This Makefile is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version.
#
# This Makefile is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
# Public License for more details. See <http://www.gnu.org/licenses/>.




# Save the "Table 3" spreadsheet from the downloaded `.xlsx' file into a
# simple plain-text file that is easy to use.
mk20dir = $(BDIR)/menke2020
mk20tab3 = $(mk20dir)/table-3.txt
$(mk20dir):; mkdir $@
$(mk20tab3): $(indir)/menke-etal-2020.xlsx | $(mk20dir)

        # Set a base-name for the table-3 data.
	base=$(basename $(notdir $<))-table-3

        # Unfortunately XLSX I/O only works when the input and output are
        # in the directory it is running. So first, we need to switch to
        # the input directory, run it, then put our desired output where we
        # want and delete the extra files.
	topdir=$$(pwd)
	cd $(indir)
	xlsxio_xlsx2csv $(notdir $<)
	cp $(notdir $<)."Table 3 All by journal by year".csv $$base.csv
	rm $(notdir $<).*.csv
	cd $$topdir

        # Read the necessary information. Note that we are dealing with a
        # CSV (comma-separated value) file. But when there are commas in a
        # string, quotation signs are put around it. The `FPAT' values is
        # fully described in the GNU AWK manual. In short, it ensures that
        # if there is a comma in the middle of double-quotes, it doesn't
        # count as a delimter.
	echo "# Column 1: YEAR [counter, i16] Year of journal's publication." > $@.tmp
	echo "# Column 2: NUM_PAPERS [counter, i16] Number of studied papers in that journal." >> $@.tmp
	echo "# Column 3: NUM_ID_TOOLS [counter, i16] Number of software/tools that were identified." >> $@.tmp
	awk 'NR>1{printf("%-6d%-5d%d\n", $$2, $$3, $$(NF-1)*$$NF)}' \
	    FPAT='([^,]+)|("[^"]+")' $(indir)/$$base.csv >> $@.tmp

        # Set the temporary file as the final target. This was done so if
        # there is any possible crash in the steps above, this rule is
        # re-run (its final target isn't rebuilt).
	mv $@.tmp $@





# Main LaTeX macro file
$(mtexdir)/menke2020.tex: $(mk20tab3) | $(mtexdir)
	touch $@