helpFound

pdf2bib.sh

@@ -1,31 +1,49 @@
 #!/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
+if [ "$1" == "-h" ] ; then
+    echo "
+        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
+
+         usage:
+          pdf2bib.sh file.pdf
+
+         depends:
+          pdftotext - from ghostscript or poppler or texlive ?
+          xsltproc - xml processor, from GNOME project
+          pubmed2bibtex.xsl - xml processor stylesheet
+
+         defaults:
+          Set the three required default file locations (xsl file, bib file, pdf directory)
+          "
+    exit 0
+fi
 
 #Setup defaults
-styleSheet="$HOME/bin/pubmed2bibtex.xsl"
-bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
-pdfPathOut="$HOME/projects/bibd/papers"
+styleSheet=${pubmedStyleSheet:-$HOME/bin/pubmed2bibtex.xsl}
+bibdFileOut=${bibdFileOut:-$HOME/projects/bibd/OMEGA.bib}
+pdfPathOut=${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
+#for 'DOI:' syntax
 doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i doi: --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#doi:(.+)#\1#")
 
+#for 'https://doi.org' syntax
+if [ -z "$doi" ]; then
+  doi=$(pdftotext -q -f 1 -l 1 $fn - | grep -i "doi.org/" --max-count=1 | tr [:upper:] [:lower:] | sed -E "s#.+doi\.org\/(.+)#\1#")
+fi
+
 if [ -z "$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#")