New upstream version 14.1.20201130+dfsg

1 files changed, 34 insertions, 3 deletions

diff --git a/elink b/elink
index 4797c1e..9e376ed 100755
--- a/elink
+++ b/elink
@@ -34,6 +34,15 @@
 
 pth=$( dirname "$0" )
 
+case ":$PATH:" in
+  *:"$pth":* )
+    ;;
+  * )
+    PATH="$PATH:$pth"
+    export PATH
+    ;;
+esac
+
 # conditionally execute original Perl implementation
 
 PERL=""
@@ -343,7 +352,7 @@ then
   needHistory=true
 fi
 
-# take database from WebEnv value or -db argument
+# take database from dbase value or -db argument
 
 if [ -z "$dbase" ]
 then
@@ -452,7 +461,7 @@ then
   fi
 fi
 
-# special case to lookup accessions in assembly
+# special case to lookup accessions in assembly database
 
 if [ "$dbase" = "assembly" ] && [ "$needHistory" = false ] && [ -n "$ids" ]
 then
@@ -464,8 +473,30 @@ then
   fi
 fi
 
+# special case to lookup accessions in protein database
+
+if [ "$dbase" = "protein" ] && [ "$needHistory" = false ] && [ -n "$ids" ]
+then
+  hasAccns=$( echo "$ids" | sed -e 's/[0-9,]//g' )
+  if [ -n "$hasAccns" ]
+  then
+    query=$( ProteinAccnQuery )
+    ids=$( esearch -db "$dbase" -query "$query" | efetch -format uid )
+  fi
+fi
+
 # -cited or -cites access the NIH Open Citation Collection dataset (see PMID 31600197)
 
+PostInIcite() {
+
+  if [ -n "$web_env" ]
+  then
+    epost -db pubmed -web "$web_env" -log "$log"
+  else
+    epost -db pubmed -log "$log"
+  fi
+}
+
 LinkInIcite() {
 
   iciteElement="$1"
@@ -479,7 +510,7 @@ LinkInIcite() {
   done |
   accn-at-a-time |
   sort -n | uniq |
-  epost -db pubmed -log "$log"
+  PostInIcite
 }
 
 QueryIcite() {