60 lines
1.6 KiB
Bash
Executable File
60 lines
1.6 KiB
Bash
Executable File
#!/bin/bash
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if [ "$1" == "-h" ] ; then
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echo "
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spubmed.sh - search for pubmed for author, journal, year
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usage:
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spubmed.sh 'kaas' 'trends+neurosci' '1995'
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spubmed.sh 'rakic' 'j+comp+neurol' '1972'
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depends:
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xsltproc - xml processor, from GNOME project
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pubmed2bibtex.xsl - xml processor stylesheet
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defaults:
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Set the three required default file locations (xsl file, bib file, pdf directory)
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"
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exit 0
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fi
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#Setup defaults
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styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl}
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bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib}
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pdfPathOut=${pdfPathOut:-$HOME/projects/bibd/papers}
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relPath=$(basename $pdfPathOut)
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author=$1
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journal=$2
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year=$3
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set -e #exit if an error
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uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$author[au]+AND+$journal[ta]+AND+$year[dp]&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
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if [ -z "$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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if [[ $(echo $uid | wc -w) -gt 1 ]]; then
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echo 'more than one pmid found, going to pubmed'
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exturl="https://www.ncbi.nlm.nih.gov/pubmed/?term=$author[au]+AND+$journal[ta]+AND+$year[dp]"
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xdg-open $exturl
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exit 1
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fi
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echo $uid | xclip -selection clipboard
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echo $uid
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# #request pubmed xml and transform into bibtex
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# curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $uid.xml
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# xsltproc --novalid $styleSheet $uid.xml > $uid.bib
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#
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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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#
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# #clean up
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# rm $uid.xml $uid.bib
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