68 lines
2.0 KiB
Bash
Executable File
68 lines
2.0 KiB
Bash
Executable File
#!/bin/bash
|
|
#pdf2bib
|
|
# usage:
|
|
# pdf2bib.sh file.pdf
|
|
# depends:
|
|
# xsltproc - xml processor, from GNOME project
|
|
# pubmed2bibtex.xsl - xml processor stylesheet
|
|
#James Ackman 2018-11-07T14:41:53-08:00
|
|
|
|
#Setup defaults
|
|
styleSheet="$HOME/bin/pubmed2bibtex.xsl"
|
|
bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
|
|
pdfPathOut="$HOME/projects/bibd/papers"
|
|
relPath=$(basename $pdfPathOut)
|
|
fn=$1
|
|
|
|
set -e #exit if an error
|
|
echo "using $pdfPathOut"
|
|
echo "using $bibdFileOut"
|
|
|
|
#try to extract doi from pdf and retrieve a pubmed id
|
|
doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i doi: --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#doi:(.+)#\1#")
|
|
|
|
if [ -z "$doi" ]; then
|
|
echo "doi not found"
|
|
exit 1
|
|
fi
|
|
|
|
## TODO: dedupe this with sdoi.sh
|
|
uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
|
|
|
|
if [ -z "$uid" ]; then
|
|
echo "pubmed id not found"
|
|
exit 1
|
|
fi
|
|
|
|
#request pubmed xml and transform into bibtex
|
|
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $uid.xml
|
|
xsltproc --novalid $styleSheet $uid.xml > $uid.bib
|
|
|
|
#extract some strings to make a nice filename for the pdf
|
|
key="LastName";
|
|
author=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#")
|
|
|
|
key="MedlineTA";
|
|
journal=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#" | tr -d " ")
|
|
|
|
key1="PubDate";
|
|
key2="Year"; year=$(awk "/<$key1>/,/<\/$key1>/" $uid.xml | grep $key2 | sed -E "s#\W*<$key2>(.+)</$key2>\W*#\1#")
|
|
|
|
fn2=${author}_${journal}$year-$uid.pdf
|
|
|
|
#move pdf file to papers repository, add file name to bibtex file field
|
|
mv $fn $pdfPathOut/$fn2
|
|
echo "moved to $pdfPathOut/$fn2"
|
|
sed -i -E "s|(\W*file = \{).*(\}.*)|\1$relPath/$fn2\2|" $uid.bib
|
|
|
|
if [[ -z $(rg $uid $bibdFileOut) ]]; then
|
|
#import bibtex
|
|
echo "importing $uid.bib"
|
|
cat $uid.bib >> $bibdFileOut
|
|
else
|
|
echo "$uid already found in $bibdFileOut, exiting"
|
|
fi
|
|
|
|
#clean up
|
|
rm $uid.xml $uid.bib
|