New upstream version 14.0.20201030+dfsg

1 files changed, 53 insertions, 31 deletions

diff --git a/elink b/elink
index ff4761f..3a625e9 100755
--- a/elink
+++ b/elink
@@ -32,31 +32,50 @@
 #
 # ==========================================================================
 
-for x in "$@"
-do
-  if [ "x$x" = "x-newmode" ]
-  then
-    USE_NEW_EDIRECT=1
-    break
-  fi
-done
-
 pth=$( dirname "$0" )
 
+# conditionally execute original Perl implementation
+
 PERL=""
 
+internal=no
+while [ "$#" -ne 0 ]
+do
+  case "$1" in
+    -internal )
+      internal=yes
+      shift
+      ;;
+    -newmode )
+      USE_NEW_EDIRECT=1
+      shift
+      ;;
+    -oldmode )
+      USE_NEW_EDIRECT=0
+      shift
+      ;;
+    * )
+      break
+      ;;
+  esac
+done
+if [ "$internal" = yes ]
+then
+  set _ -internal "$@"
+  shift
+fi
+
 if [ ! -f "$pth"/ecommon.sh ]
 then
   USE_NEW_EDIRECT=false
 fi
 
-# set PERL path if using old EDirect
-
 case "${USE_NEW_EDIRECT}" in
   "" | [FfNn]* | 0 | [Oo][Ff][Ff] )
+    # set PERL path if using old EDirect
     PERL=perl
     case "$( uname -s )" in
-      CYGWIN_NT*)
+      CYGWIN_NT* )
         # Use a negative match here because the shell treats 0 as success.
         if perl -e 'exit $^O !~ /^MSWin/'; then
            pth=$( cygpath -w "$pth" )
@@ -71,8 +90,6 @@ case "${USE_NEW_EDIRECT}" in
     ;;
 esac
 
-# conditionally execute original Perl implementation
-
 if [ -n "${PERL}" ]
 then
   exec "${PERL}" "$pth"/edirect.pl -link "$@"
@@ -286,6 +303,10 @@ do
       cites=true
       shift
       ;;
+    -batch )
+      # accept -batch flag from old scripts - now standard behavior
+      shift
+      ;;
     -h | -help | --help )
       PrintHelp
       exit 0
@@ -437,22 +458,9 @@ fi
 
 # -cited or -cites access the NIH Open Citation Collection dataset (see PMID 31600197)
 
-iciteElement=""
-
-if [ "$cited" = true ]
-then
-  # equivalent of -name pubmed_pubmed_citedin (for pubmed records also in pmc)
-  iciteElement="cited_by"
-fi
-
-if [ "$cites" = true ]
-then
-  # equivalent of -name pubmed_pubmed_refs (for pubmed records also in pmc)
-  iciteElement="references"
-fi
-
 LinkInIcite() {
 
+  iciteElement="$1"
   GenerateUidList "$dbase" |
   join-into-groups-of 100 |
   while read uids
@@ -466,9 +474,9 @@ LinkInIcite() {
   epost -db pubmed -log "$log"
 }
 
-if [ -n "$iciteElement" ]
-then
-  cits=$( LinkInIcite )
+QueryIcite() {
+
+  cits=$( LinkInIcite "$1" )
 
   if [ -n "$cits" ]
   then
@@ -478,6 +486,20 @@ then
   fi
 
   WriteEDirect "$dbase" "$web_env" "$qry_key" "$num" "$stp" "$err"
+}
+
+if [ "$cited" = true ]
+then
+  # equivalent of -name pubmed_pubmed_citedin (for pubmed records also in pmc)
+  QueryIcite "cited_by"
+
+  exit 0
+fi
+
+if [ "$cites" = true ]
+then
+  # equivalent of -name pubmed_pubmed_refs (for pubmed records also in pmc)
+  QueryIcite "references"
 
   exit 0
 fi