70 lines
2.0 KiB
Bash
70 lines
2.0 KiB
Bash
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#!/bin/bash
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#sdoi - search for doi and append bibtex entry to db
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# usage:
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# sdoi.sh 'doi.string'
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#Setup defaults
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styleSheet="$HOME/bin/pubmed2bibtex.xsl"
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bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
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pdfPathOut="$HOME/projects/bibd/papers"
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relPath=$(basename $pdfPathOut)
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doi=$1
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fn=$2
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set -e #exit if an error
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uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
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if [ -z "$uid" ]; then
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echo "pubmed id not found"
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exit 1
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fi
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#request pubmed xml and transform into bibtex
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curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $uid.xml
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xsltproc --novalid $styleSheet $uid.xml > $uid.bib
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#decide whether to process and move an associated pdf or just exit
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if [ -z "$fn" ]; then
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if [[ -z $(rg $uid $bibdFileOut) ]]; then
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#import bibtex
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echo "importing $uid.bib"
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cat $uid.bib >> $bibdFileOut
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else
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echo "$uid already found in $bibdFileOut, exiting"
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fi
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#clean up
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rm $uid.xml $uid.bib
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exit 1
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else
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#extract some strings to make a nice filename for the pdf
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key="LastName";
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author=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#")
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key="MedlineTA";
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journal=$(grep $key --max-count=1 $uid.xml | sed -E "s#\W*<$key>(.+)</$key>\W*#\1#" | tr -d " ")
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key1="PubDate";
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key2="Year"; year=$(awk "/<$key1>/,/<\/$key1>/" $uid.xml | grep $key2 | sed -E "s#\W*<$key2>(.+)</$key2>\W*#\1#")
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fn2=${author}_${journal}$year-$uid.pdf
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#move pdf file to papers repository, add file name to bibtex file field
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mv $fn $pdfPathOut/$fn2
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echo "moved to $pdfPathOut/$fn2"
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sed -i -E "s|(\W*file = \{).*(\}.*)|\1$relPath/$fn2\2|" $uid.bib
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if [[ -z $(rg $uid $bibdFileOut) ]]; then
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#import bibtex
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echo "importing $uid.bib"
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cat $uid.bib >> $bibdFileOut
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else
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echo "$uid already found in $bibdFileOut, exiting"
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fi
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#clean up
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rm $uid.xml $uid.bib
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fi
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