init lab bin

sdoi.sh

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