Sync merge with develop

Merge remote-tracking branch 'origin/develop' into feature/monitor_jobs_separate

* origin/develop:
  Updates to prep ocean obs task (#1870)
  No longer write archive lists COM (#2000)

jobs/JGLOBAL_PREP_OCEAN_OBS

@@ -7,15 +7,23 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "prepoceanobs" -c "base prepoceanobs"
 # Set variables used in the script
 ##############################################
 
+export COMIN_OBS="${DATA}"
+
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
+# Add prep_marine_obs.py to PYTHONPATH
+export PYTHONPATH=${HOMEgfs}/sorc/gdas.cd/ush/soca:${PYTHONPATH}
 
 ###############################################################
 # Run relevant script
 
-# the relevant script goes here
+EXSCRIPT=${GDASPREPPY:-${HOMEgfs}/ush/exglobal_prep_ocean_obs.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
 
 ##############################################
 # End JOB SPECIFIC work

parm/config/gfs/config.prepoceanobs

@@ -1,9 +1,13 @@
 #!/bin/bash
 
 ########## config.prepoceanobs ##########
-# Pre Ocn Analysis specific
 
-echo "BEGIN: config.config.prepoceanobs"
+echo "BEGIN: config.prepoceanobs"
+
+export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
+export OBS_LIST=@SOCA_OBS_LIST@
+[[ -n "${OBS_LIST}" ]] || export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
+export OBS_YAML=${OBS_LIST}
 
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepoceanobs

scripts/exglobal_archive.sh

@@ -154,11 +154,7 @@ if [[ ${HPSSARCH} = "YES" || ${LOCALARCH} = "YES" ]]; then
     mod=$((nday % ARCH_FCSTICFREQ))
     if [[ "${mod}" -eq 0 ]] || [[ "${PDY}${cyc}" -eq "${firstday}" ]]; then SAVEFCSTIC="YES" ; fi
 
-
-    ARCH_LIST="${DATA}/archlist"
-    [[ -d ${ARCH_LIST} ]] && rm -rf "${ARCH_LIST}"
-    mkdir -p "${ARCH_LIST}"
-    cd "${ARCH_LIST}" || exit 2
+    cd "${DATA}" || exit 2
 
     "${HOMEgfs}/ush/hpssarch_gen.sh" "${RUN}"
     status=$?
@@ -196,7 +192,7 @@ if [[ ${HPSSARCH} = "YES" || ${LOCALARCH} = "YES" ]]; then
         if [ "${DO_AERO}" = "YES" ]; then
             for targrp in chem; do
                 # TODO: Why is this tar being done here instead of being added to the list?
-                ${TARCMD} -P -cvf "${ATARDIR}/${PDY}${cyc}/${targrp}.tar" $(cat "${ARCH_LIST}/${targrp}.txt")
+                ${TARCMD} -P -cvf "${ATARDIR}/${PDY}${cyc}/${targrp}.tar" $(cat "${DATA}/${targrp}.txt")
                 status=$?
                 if [[ "${status}" -ne 0 ]] && [[ "${PDY}${cyc}" -ge "${firstday}" ]]; then
                     echo "HTAR ${PDY}${cyc} ${targrp}.tar failed"
@@ -276,15 +272,15 @@ if [[ ${HPSSARCH} = "YES" || ${LOCALARCH} = "YES" ]]; then
                             break
                         fi
                     fi
-                done < "${ARCH_LIST}/${targrp}.txt"
+                done < "${DATA}/${targrp}.txt"
 
                 ;;
             *) ;;
         esac
 
         # Create the tarball
         tar_fl="${ATARDIR}/${PDY}${cyc}/${targrp}.tar"
-        ${TARCMD} -P -cvf "${tar_fl}" $(cat "${ARCH_LIST}/${targrp}.txt")
+        ${TARCMD} -P -cvf "${tar_fl}" $(cat "${DATA}/${targrp}.txt")
         status=$?
 
         # Change group to rstprod if it was found even if htar/tar failed in case of partial creation

sorc/link_workflow.sh

@@ -205,6 +205,7 @@ if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/jediinc2fv3.py"                     .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/ush/ioda/bufr2ioda/run_bufr2ioda.py"    .
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/build/bin/imsfv3_scf2ioda.py"           .
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/gdas.cd/scripts/exglobal_prep_ocean_obs.py"           .
 fi