spring work

sdoi.sh

@@ -26,25 +26,7 @@ doi=$1
 fn=$2
 
 set -e #exit if an error
-
+# set -v -x -e #debugging
-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|")
-
-tmpBib=$(mktemp -p --suffix=.bib)
-
-if [ -z "$uid" ]; then
-  fetchBib_doiDotOrg
-else
-  fetchBib_pubmed
-fi
-
-if [ -s "$tmpBib" ]; then
-  import_bib
-else
-  echo "sorry, doi not found.."
-  clean_up
-fi
-
-  
 
 function import_bib {
   #decide whether to process and move an associated pdf or just exit
@@ -111,3 +93,21 @@ function clean_up {
   exit 1
 }
 
+
+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|")
+
+tmpBib=$(mktemp -p ./ --suffix=.bib)
+
+if [ -z "$uid" ]; then
+  fetchBib_doiDotOrg
+else
+  fetchBib_pubmed
+fi
+
+if [ -s "$tmpBib" ]; then
+  import_bib
+else
+  echo "sorry, doi not found.."
+  clean_up
+fi
+

spubmed.sh

@@ -30,7 +30,8 @@ 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#")
+#curl's option globoff needed for using brackets in a uri
+uid=$(curl -s --globoff "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=$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"