116 lines
2.8 KiB
Bash
Executable File
116 lines
2.8 KiB
Bash
Executable File
#!/bin/bash
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if [ "$1" == "-h" ] ; then
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echo "
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sdoi - search for doi guid on pubmed and append bibtex entry to bibtex db. Optionally import a downloaded pdf.
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usage:
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sdoi.sh 'doi'
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sdoi.sh 'doi' download.pdf
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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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set -e #exit if an error
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# set -v -x -e #debugging
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#Setup defaults
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doi=$1
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fn=$2
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styleSheet=${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 $pdfPathOut)
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#define functions
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import_bib() {
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#decide whether to process and move an associated pdf or just exit
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if [ -z "$fn" ]; then
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append_bibfile
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clean_up
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else
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extract_name
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append_pdf
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append_bibfile
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clean_up
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fi
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}
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fetchBib_pubmed() {
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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" > $tmpBib.xml
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xsltproc --novalid $styleSheet $tmpBib.xml > $tmpBib
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}
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fetchBib_doiDotOrg() {
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echo "pubmed id not found, trying doi.org.."
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curl -LH 'Accept: application/x-bibtex' "http//dx.doi.org/"$doi >> $tmpBib
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echo -e "\n" >> $tmpBib
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}
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extract_name() {
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#extract some strings to make a nice filename for the pdf
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key="LastName";
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author=$(grep $key --max-count=1 $tmpBib.xml | sed -E "s|\W*<$key>(.+)</$key>\W*|\1|" | tr -d " ")
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key="MedlineTA";
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journal=$(grep $key --max-count=1 $tmpBib.xml | sed -E "s|\W*<$key>(.+)</$key>\W*|\1|" | tr -d " ")
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key1="PubDate";
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key2="Year"; year=$(awk "/<$key1>/,/<\/$key1>/" $tmpBib.xml | grep $key2 | sed -E "s|\W*<$key2>(.+)</$key2>\W*|\1|")
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}
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append_bibfile() {
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#import bibtex
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#first grep for a uid (doi) in case its already in db
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if [[ -z $(rg $doi $bibdFileOut) ]]; then
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echo "importing $tmpBib"
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cat $tmpBib >> $bibdFileOut
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else
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echo "$doi already found in $bibdFileOut, exiting"
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fi
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}
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append_pdf() {
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fn2=${author}_${journal}$year-$uid.pdf
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#move pdf file to papers repository, add file name to bibtex url 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*url = \{).*(\}.*)|\1$relPath/$fn2\2|" $tmpBib
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}
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clean_up() {
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#clean up
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rm -f $tmpBib $tmpBib.xml
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exit 1
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}
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#main
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uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$doi&field=doi&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s|<Id>([0-9]+)</Id>|\1|")
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tmpBib=$(mktemp -p ./ --suffix=.bib)
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if [ -z "$uid" ]; then
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fetchBib_doiDotOrg
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else
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fetchBib_pubmed
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fi
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if [ -s "$tmpBib" ]; then
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import_bib
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else
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echo "sorry, doi not found.."
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clean_up
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fi
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