New upstream version 14.8.20210324+dfsg

1 files changed, 24 insertions, 22 deletions

diff --git a/elink b/elink
index 2e8f184..8a137da 100755
--- a/elink
+++ b/elink
@@ -206,7 +206,7 @@ do
         db="$1"
         shift
       else
-        echo "ERROR: Missing -db argument" >&2
+        echo "${red_fg}ERROR: Missing -db argument${reset_colors}" >&2
         exit 1
       fi
       ;;
@@ -217,7 +217,7 @@ do
         ids="$1"
         shift
       else
-        echo "ERROR: Missing -id argument" >&2
+        echo "${red_fg}ERROR: Missing -id argument${reset_colors}" >&2
         exit 1
       fi
       while [ $# -gt 0 ]
@@ -244,7 +244,7 @@ do
           idtype=acc
         fi
       else
-        echo "ERROR: Missing -format argument" >&2
+        echo "${red_fg}ERROR: Missing -format argument${reset_colors}" >&2
         exit 1
       fi
       ;;
@@ -255,7 +255,7 @@ do
         target="$1"
         shift
       else
-        echo "ERROR: Missing -target argument" >&2
+        echo "${red_fg}ERROR: Missing -target argument${reset_colors}" >&2
         exit 1
       fi
       ;;
@@ -266,7 +266,7 @@ do
         name="$1"
         shift
       else
-        echo "ERROR: Missing -name argument" >&2
+        echo "${red_fg}ERROR: Missing -name argument${reset_colors}" >&2
         exit 1
       fi
       ;;
@@ -277,7 +277,7 @@ do
         cmmd="$1"
         shift
       else
-        echo "ERROR: Missing -cmd argument" >&2
+        echo "${red_fg}ERROR: Missing -cmd argument${reset_colors}" >&2
         exit 1
       fi
       ;;
@@ -288,7 +288,7 @@ do
         mode="$1"
         shift
       else
-        echo "ERROR: Missing -mode argument" >&2
+        echo "${red_fg}ERROR: Missing -mode argument${reset_colors}" >&2
         exit 1
       fi
       ;;
@@ -322,7 +322,7 @@ do
       then
         shift "$argsConsumed"
       else
-        echo "ERROR: Unrecognized option $1" >&2
+        echo "${red_fg}ERROR: Unrecognized option $1${reset_colors}" >&2
         exit 1
       fi
       ;;
@@ -363,7 +363,7 @@ fi
 
 if [ -z "$dbase" ]
 then
-  echo "ERROR: Missing -db argument" >&2
+  echo "${red_fg}ERROR: Missing -db argument${reset_colors}" >&2
   exit 1
 fi
 
@@ -400,7 +400,7 @@ case "$cmmd" in
   * )
     if [ -z "$target" ] && [ "$related" = false ] && [ "$cited" = false ] && [ "$cites" = false ]
     then
-      echo "ERROR: Must supply -target or -related on command line" >&2
+      echo "${red_fg}ERROR: Must supply -target or -related on command line${reset_colors}" >&2
       exit 1
     fi
     if [ -z "$target" ]
@@ -428,7 +428,7 @@ fi
 
 if [ "$dbase" = "nlmcatalog" ]
 then
-  echo "ERROR: Entrez Direct does not support links for the nlmcatalog database" >&2
+  echo "${red_fg}ERROR: Entrez Direct does not support links for the nlmcatalog database${reset_colors}" >&2
   exit 1
 fi
 
@@ -438,22 +438,23 @@ if [ "$needHistory" = true ]
 then
   if [ -t 0 ]
   then
-    echo "ERROR: ENTREZ_DIRECT message not piped from stdin" >&2
+    echo "${red_fg}ERROR: ENTREZ_DIRECT message not piped from stdin${reset_colors}" >&2
     exit 1
   fi
   if [ -z "$web_env" ]
   then
-    echo "ERROR: WebEnv value not found in elink input" >&2
+    echo "${red_fg}ERROR: WebEnv value not found in elink input${reset_colors}" >&2
     exit 1
   fi
   if [ -z "$qry_key" ]
   then
-    echo "ERROR: QueryKey value not found in elink input" >&2
+    echo "${red_fg}ERROR: QueryKey value not found in elink input${reset_colors}" >&2
     exit 1
   fi
   if [ "$num" -lt 1 ]
   then
-    # silently exit if no results to process
+    # print message with count of 0 if no results to process
+    WriteEDirect "$target" "$web_env" "$qry_key" "0" "$stp" "$err"
     exit 0
   fi
 fi
@@ -462,7 +463,7 @@ if [ "$cited" = true ] || [ "$cites" = true ]
 then
   if [ "$dbase" != "pubmed" ]
   then
-    echo "ERROR: -cited or -cites can only be used with -db pubmed" >&2
+    echo "${red_fg}ERROR: -cited or -cites can only be used with -db pubmed${reset_colors}" >&2
     exit 1
   fi
 fi
@@ -603,7 +604,7 @@ LinkInGroups() {
 
       if [ -n "$err" ]
       then
-        echo "ERROR: elink failed - $err" >&2
+        echo "${red_fg}ERROR: elink failed - $err${reset_colors}" >&2
         exit 1
       fi
       if [ -z "$web_env" ]
@@ -660,8 +661,9 @@ then
 
   if [ -n "$num" ] && [ "$num" -lt 1 ]
   then
-    res=$( RunWithCommonArgs nquire -url "$base" elink.fcgi -dbfrom "$target" \
-           -query_key "$qry_key" -WebEnv "$wbnv" -cmd "acheck" )
+    uids=$( GenerateUidList "$dbase" | head -n 500 | join-into-groups-of 500 )
+    res=$( RunWithCommonArgs nquire -url "$base" elink.fcgi \
+           -dbfrom "$dbase" -id "$uids" -cmd "acheck" )
 
     if [ -n "$res" ]
     then
@@ -672,10 +674,10 @@ then
         tst=$( echo "$res" | xtract -pattern LinkInfo -if LinkName -equals "$name" -element LinkName )
         if [ -n "$tst" ]
         then
-          echo "ERROR: acheck test indicates non-zero count expected" >&2
+          echo "${red_fg}ERROR: acheck test indicates non-zero count expected${reset_colors}" >&2
         fi
       else
-        echo "ERROR: acheck test failed - $err" >&2
+        echo "${red_fg}ERROR: acheck test failed - $err${reset_colors}" >&2
       fi
     fi
   fi
@@ -687,5 +689,5 @@ fi
 
 # warn on error
 
-echo "ERROR: ELink failure" >&2
+echo "${red_fg}ERROR: ELink failure${reset_colors}" >&2
 exit 1