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