56 lines
1.6 KiB
Bash
Executable File
56 lines
1.6 KiB
Bash
Executable File
#!/bin/bash
|
|
if [ "$1" == "-h" ] ; then
|
|
echo "
|
|
pdf2bib - search for a doi within a pdf, query pubmed, and append bibtex entry with pdf to your local bib database file. Last two steps are identical to sdoi.sh
|
|
|
|
usage:
|
|
pdf2bib.sh file.pdf
|
|
|
|
depends:
|
|
pdftotext - from ghostscript or poppler or texlive ?
|
|
xsltproc - xml processor, from GNOME project
|
|
pubmed2bibtex.xsl - xml processor stylesheet
|
|
|
|
defaults:
|
|
Set the three required default file locations (xsl file, bib file, pdf directory)
|
|
"
|
|
exit 0
|
|
fi
|
|
|
|
set -e #exit if an error
|
|
# set -v -x -e #debugging
|
|
|
|
#Setup defaults
|
|
fn=$1
|
|
|
|
|
|
#try to extract doi from pdf and retrieve a pubmed id
|
|
#for 'DOI:' syntax
|
|
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi:" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|doi:(.+)|\1|")
|
|
|
|
# search for doi string between first page last page 10
|
|
doi=$(pdftotext -q -f 1 -l 10 $fn - | grep -iE "doi:? ?/?10\." --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|.*doi:? ?/?(10.+)|\1|")
|
|
|
|
|
|
#for 'https://doi.org' syntax
|
|
if [ -z "$doi" ]; then
|
|
doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi\.org/10\." --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|.+doi\.org/(10.+)|\1|")
|
|
fi
|
|
|
|
# for 'https://doi.org' syntax
|
|
# if [ -z "$doi" ]; then
|
|
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi.org/" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|.+doi\.org\/(.+)|\1|")
|
|
# fi
|
|
#
|
|
# if [ -z "$doi" ]; then
|
|
# doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -iE "doi ?" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s|doi ?(.+)|\1|")
|
|
# fi
|
|
|
|
if [ -z "$doi" ]; then
|
|
echo "doi not found"
|
|
exit 1
|
|
fi
|
|
|
|
sdoi.sh $doi $fn
|
|
|