Adapt the marine DA to the new COM structure

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT

@@ -1,7 +1,7 @@
 #!/bin/bash
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
-WIPE_DATA="NO"
+export WIPE_DATA="NO"
 
 export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT_VRFY

@@ -1,7 +1,7 @@
 #!/bin/bash
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
-WIPE_DATA="NO"
+export WIPE_DATA="NO"
 export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
 

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT

@@ -7,9 +7,8 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalchkpt" -c "base ocnanal ocnana
 
 
 ##############################################
-# Begin JOB SPECIFIC work
+# Set variables used in the script
 ##############################################
-
 # Ignore possible spelling error (nothing is misspelled)
 # shellcheck disable=SC2153
 GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
@@ -23,7 +22,14 @@ export GPREFIX="${GDUMP}.t${gcyc}z."
 # shellcheck disable=SC2153
 export APREFIX="${CDUMP}.t${cyc}z."
 
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
+# Generate COM variables from templates
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_HISTORY:COM_ATMOS_HISTORY_TMPL
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
 
 ###############################################################
 # Run relevant script

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_POST

@@ -1,21 +1,28 @@
 #!/bin/bash
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
-WIPE_DATA="NO"
+export WIPE_DATA="NO"
 DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalpost" -c "base ocnanalpost"
 
 
 ##############################################
-# Begin JOB SPECIFIC work
+# Set variables used in the script
 ##############################################
-
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
-export COMOUTice=${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ice
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
 export CDATE=${CDATE:-${PDY}${cyc}}
+export GDUMP=${GDUMP:-"gdas"}
+
+# Generate COM variables from templates
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_ICE_RESTART
+
+mkdir -p "${COM_OCEAN_ANALYSIS}"
+mkdir -p "${COM_ICE_RESTART}"
 
-mkdir -p "${COMOUT}"
-mkdir -p "${COMOUTice}/RESTART"
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
 
 # Add UFSDA to PYTHONPATH
 ufsdaPATH="${HOMEgfs}/sorc/gdas.cd/ush/"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP

@@ -1,20 +1,16 @@
 #!/bin/bash
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
-DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
+export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanalprep"
 
 
 ##############################################
 # Set variables used in the script
 ##############################################
 export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT="ocean"
-
-##############################################
-# Begin JOB SPECIFIC work
-##############################################
-
+# Ignore possible spelling error (nothing is misspelled)
+# shellcheck disable=SC2153
 GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 export GDATE
 export gPDY=${GDATE:0:8}
@@ -25,12 +21,16 @@ export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
 export APREFIX="${CDUMP}.t${cyc}z."
 
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
+# Generate COM variables from templates
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_OCEAN_HISTORY:COM_OCEAN_HISTORY_TMPL
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_HISTORY:COM_ICE_HISTORY_TMPL
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_RESTART:COM_ICE_RESTART_TMPL
 
-mkdir -p "${COMOUT}"
 
-# COMIN_GES and COMIN_GES_ENS are used in script
-export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/ocean"
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
 
 # Add UFSDA to PYTHONPATH
 ufsdaPATH="${HOMEgfs}/sorc/gdas.cd/ush/"

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN

@@ -1,7 +1,7 @@
 #!/bin/bash
 export STRICT="NO"
 source "${HOMEgfs}/ush/preamble.sh"
-WIPE_DATA="NO"
+export WIPE_DATA="NO"
 export DATA="${DATAROOT}/${RUN}ocnanal_${cyc}"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
 

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY

@@ -7,14 +7,22 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanal
 ##############################################
 # Set variables used in the script
 ##############################################
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+export GDUMP=${GDUMP:-"gdas"}
+# Ignore possible spelling error (nothing is misspelled)
+# shellcheck disable=SC2153
+GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+export gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
 
+RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OCEAN_ANALYSIS
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_OCEAN_HISTORY:COM_OCEAN_HISTORY_TMPL
+RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx COM_ICE_HISTORY:COM_ICE_HISTORY_TMPL
 
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
-export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/ocean}
-
 # Add UFSDA to PYTHONPATH
 export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/:${HOMEgfs}/sorc/gdas.cd/ush/eva:${PYTHONPATH}