init lab bin

spubmed.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+#spubmed.sh - search for pubmed for author, journal, year
+# usage:
+#  spubmed.sh 'kaas' 'trends+neurosci' '1995'
+#  spubmed.sh 'rakic' 'j+comp+neurol' '1972'
+
+#Setup defaults
+styleSheet="$HOME/bin/pubmed2bibtex.xsl"
+bibdFileOut="$HOME/projects/bibd/OMEGA.bib"
+pdfPathOut="$HOME/projects/bibd/papers"
+relPath=$(basename $pdfPathOut)
+author=$1
+journal=$2
+year=$3
+
+set -e #exit if an error
+
+uid=$(curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$author[au]+AND+$journal[ta]+AND+$year[dp]&retmode=xml" | grep -E "<Id>[0-9]+</Id>" | sed -E "s#<Id>([0-9]+)</Id>#\1#")
+
+if [ -z "$uid" ]; then
+  echo "pubmed id not found"
+  exit 1
+fi
+
+if [[ $(echo $uid | wc -w) -gt 1 ]]; then
+  echo 'more than one pmid found, going to pubmed'
+  exturl="https://www.ncbi.nlm.nih.gov/pubmed/?term=$author[au]+AND+$journal[ta]+AND+$year[dp]"
+  xdg-open $exturl
+  exit 1
+fi
+
+echo $uid | xclip -selection clipboard
+echo $uid
+
+# #request pubmed xml and transform into bibtex
+# curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=$uid&retmode=xml" > $uid.xml
+# xsltproc --novalid $styleSheet $uid.xml > $uid.bib
+# 
+# #import bibtex
+# echo "importing $uid.bib"
+# cat $uid.bib >> $bibdFileOut
+# 
+# #clean up
+# rm $uid.xml $uid.bib