1. correct handling of ps and tau variable in the exclude_variable check scripts.

2. remove ps from excl_cmip6.
3. correct mapfile paths in the three publication phase files.
4. correct the argument handling in the esgpublish wrapper script.

20200319_exclvarcheck_cmip6.sh

@@ -36,10 +36,8 @@ if [ $? -ne 0 ]; then
 fi
 grep -w $varname $excllist >/dev/null;
 if [ $? -eq 0 ]; then
-    if [ "$varname" != "ps" ]; then
-        echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile";
-        echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile" >>$warnings;
-    fi
+    echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile";
+    echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile" >>$warnings;
 fi
 timefound=0;
 bog=`for i in $blah; do if [ "$i" = "$varname" ]; then continue; fi;  echo $i; done`
@@ -55,11 +53,13 @@ if [ "$bog" != "" ]; then
 		fi
 		grep -w $ln $excllist >/dev/null;
 		if [ $? -ne 0 ]; then
-			#echo "contents of file in question"
-			#cat $tmpfiletwo
-			echo "line in question: $ln"
-			echo "Found variable $ln in file $ncfile";
-			echo "Found variable $ln in file $ncfile" >>$suspects;
+                        if [ "$varname" != "ps" -a "$varname" != "tau" ]; then
+			    #echo "contents of file in question"
+			    #cat $tmpfiletwo
+			    echo "line in question: $ln"
+			    echo "Found variable $ln in file $ncfile";
+			    echo "Found variable $ln in file $ncfile" >>$suspects;
+                        fi
 		fi
 		
 	done ;

esgf_publish_cmip6_phase_09.sh

@@ -59,7 +59,7 @@ fi
 while read filename; do 
     mapname=`basename ${filename}`;
     logfile="${process_dir}/${phase}_publish1_01_${mapname}_${timestamp}.log";
-    args="--map ${mapname} --project ${experiment} --service fileservice --no-create-cim"
+    args="--map mapfiles/${mapname} --project ${experiment} --service fileservice --no-create-cim"
     bash ${ESGF_PUBLISHING_ESGPUB_WRAPPER} ${phase} ${ESGF_VENV_DIR} ${ESGF_VENV_NAME} ${script_dir} "${args}" ${logfile}
     if [ $? -ne 0 ]; then
         echo "Error during publication. Aborting.";

esgf_publish_cmip6_phase_10.sh

@@ -58,7 +58,7 @@ fi
 while read filename; do 
     mapname=`basename ${filename}`;
     logfile="${process_dir}/${phase}_publish2_01_${mapname}_${timestamp}.log";
-    args="--map ${mapname} --project ${experiment} --noscan --thredds --service fileservice --no-create-cim"
+    args="--map mapfiles/${mapname} --project ${experiment} --noscan --thredds --service fileservice --no-create-cim"
     bash ${ESGF_PUBLISHING_ESGPUB_WRAPPER} ${phase} ${ESGF_VENV_DIR} ${ESGF_VENV_NAME} ${script_dir} "${args}" ${logfile}
     if [ $? -ne 0 ]; then
         echo "Error during publication. Aborting.";

esgf_publish_cmip6_phase_11.sh

@@ -59,7 +59,7 @@ fi
 while read filename; do
     mapname=`basename ${filename}`;
     logfile="${process_dir}/${phase}_publish3_01_${mapname}_${timestamp}.log";
-    args="--map ${mapname} --project ${experiment} --noscan --publish --service fileservice --no-create-cim"
+    args="--map mapfiles/${mapname} --project ${experiment} --noscan --publish --service fileservice --no-create-cim"
     bash ${ESGF_PUBLISHING_ESGPUB_WRAPPER} ${phase} ${ESGF_VENV_DIR} ${ESGF_VENV_NAME} ${script_dir} "${args}" ${logfile}
     if [ $? -ne 0 ]; then
         echo "Error during publication. Aborting.";

esgf_publish_esgpublishwrapper.sh

@@ -11,6 +11,6 @@ source ${ESGF_VENV_DIR}/bin/activate ${ESGF_VENV_NAME}
 
 cd ${script_dir};
 echo "PHASE${phase}: working in '`pwd`'";
-esgpublish "$args" > ${result_log} 2>&1 || exit 1
+esgpublish `echo "$args"` > ${result_log} 2>&1 || exit 1
 conda deactivate
 exit 0

excl_cmip6

 wavelength
 ap
 ap_bnds
-ps
 a
 a_bnds
 alev1

local_exclvarcheck_cmip6.sh

@@ -26,10 +26,8 @@ if [ $? -ne 0 ]; then
 fi
 grep -w $varname $excllist >/dev/null;
 if [ $? -eq 0 ]; then
-    if [ "$varname" != "ps" ]; then
-        echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile";
-        echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile" >>$warnings;
-    fi
+    echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile";
+    echo "Warning: a variable $varname you need to publish is listed in the excludes file; ref $ncfile" >>$warnings;
 fi
 timefound=0
 bog=`for i in $blah; do if [ "$i" = "$varname" ]; then continue; fi;  echo $i; done`
@@ -45,10 +43,12 @@ if [ "$bog" != "" ]; then
 		fi
 		grep -w $ln $excllist >/dev/null;
 		if [ $? -ne 0 ]; then
-			#echo "contents of file in question"
-			echo "line in question: $ln"
-			echo "Found variable $ln in file $ncfile";
-			echo "Found variable $ln in file $ncfile" >>$suspects;
+                	if [ "$varname" != "ps" -a "$varname" != "tau" ]; then
+				#echo "contents of file in question"
+				echo "line in question: $ln"
+				echo "Found variable $ln in file $ncfile";
+				echo "Found variable $ln in file $ncfile" >>$suspects;
+			fi
 		fi
 		
 	done ;