From 188bfc16cceafb195e534cd5d8dfc2c8b715aacf Mon Sep 17 00:00:00 2001
From: "Judy.K.Henderson" <Judy.K.Henderson@noaa.gov>
Date: Wed, 23 Aug 2023 21:00:57 +0000
Subject: [PATCH]  Clean up getic scripts     jet xml file calls
 getic_gsl_fv3gfsv16.sh     hera xml file calls getic.sh  (includes EMCDIR)

---
 jobs/rocoto/getic.sh               | 11 ++++--
 jobs/rocoto/getic_gsl.sh           | 60 ------------------------------
 jobs/rocoto/getic_gsl_fv3gfsv15.sh |  3 +-
 jobs/rocoto/getic_gsl_fv3gfsv16.sh |  2 +-
 4 files changed, 10 insertions(+), 66 deletions(-)
 delete mode 100755 jobs/rocoto/getic_gsl.sh

diff --git a/jobs/rocoto/getic.sh b/jobs/rocoto/getic.sh
index 050b0dbe6d..469fdc921c 100755
--- a/jobs/rocoto/getic.sh
+++ b/jobs/rocoto/getic.sh
@@ -2,7 +2,7 @@
 
 source "$HOMEgfs/ush/preamble.sh"
 
-## this script makes links to FV3GFS netcdf files under /public and copies over GFS analysis file for verification
+## this script makes links to FV3GFS netcdf files under /public 
 ##   /home/rtfim/UFS_CAMSUITE/FV3GFSrun/FV3ICS/YYYYMMDDHH/gfs
 ##     gfs.tHHz.sfcanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.sfcanl.nc
 ##     gfs.tHHz.atmanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.atmanl.nc
@@ -13,7 +13,6 @@ echo "CDUMP = $CDUMP"
 echo "COMPONENT = $COMPONENT"
 echo "ICSDIR = $ICSDIR"
 echo "PUBDIR = $PUBDIR"
-echo "GFSDIR = $GFSDIR"
 echo "RETRODIR = $RETRODIR"
 echo "ROTDIR = $ROTDIR"
 echo "PSLOT = $PSLOT"
@@ -23,7 +22,7 @@ echo
 yyyymmdd=`echo $CDATE | cut -c1-8`
 hh=`echo $CDATE | cut -c9-10`
 yyddd=`date +%y%j -u -d $yyyymmdd`
-fv3ic_dir=${ROTDIR}/${CDUMP}.${yyyymmdd}/${hh}/model_data/${COMPONENT}
+fv3ic_dir=${ROTDIR}/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}
 
 ## create links in FV3ICS directory
 mkdir -p $fv3ic_dir
@@ -48,6 +47,12 @@ elif [[ -f $PUBDIR/${pubatm_file} ]]; then
   echo "linking $PUBDIR...."
   ln -fs $PUBDIR/${pubsfc_file} $sfc_file
   ln -fs $PUBDIR/${pubatm_file} $atm_file
+elif  [[ -f $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file} ]]; then
+  echo "linking $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}..."
+  echo "sfc_file:  $sfc_file"
+  echo "atm_file:  $atm_file"
+  ln -s $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${sfc_file}
+  ln -s $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file}
 elif  [[ -f $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file} ]]; then
   echo "linking $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}..."
   echo "sfc_file:  $sfc_file"
diff --git a/jobs/rocoto/getic_gsl.sh b/jobs/rocoto/getic_gsl.sh
deleted file mode 100755
index 050b0dbe6d..0000000000
--- a/jobs/rocoto/getic_gsl.sh
+++ /dev/null
@@ -1,60 +0,0 @@
-#! /usr/bin/env bash
-
-source "$HOMEgfs/ush/preamble.sh"
-
-## this script makes links to FV3GFS netcdf files under /public and copies over GFS analysis file for verification
-##   /home/rtfim/UFS_CAMSUITE/FV3GFSrun/FV3ICS/YYYYMMDDHH/gfs
-##     gfs.tHHz.sfcanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.sfcanl.nc
-##     gfs.tHHz.atmanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.atmanl.nc
-
-echo
-echo "CDATE = $CDATE"
-echo "CDUMP = $CDUMP"
-echo "COMPONENT = $COMPONENT"
-echo "ICSDIR = $ICSDIR"
-echo "PUBDIR = $PUBDIR"
-echo "GFSDIR = $GFSDIR"
-echo "RETRODIR = $RETRODIR"
-echo "ROTDIR = $ROTDIR"
-echo "PSLOT = $PSLOT"
-echo
-
-## initialize
-yyyymmdd=`echo $CDATE | cut -c1-8`
-hh=`echo $CDATE | cut -c9-10`
-yyddd=`date +%y%j -u -d $yyyymmdd`
-fv3ic_dir=${ROTDIR}/${CDUMP}.${yyyymmdd}/${hh}/model_data/${COMPONENT}
-
-## create links in FV3ICS directory
-mkdir -p $fv3ic_dir
-cd $fv3ic_dir
-echo "making link to netcdf files under $fv3ic_dir"
-
-pubsfc_file=${yyddd}${hh}00.${CDUMP}.t${hh}z.sfcanl.nc
-sfc_file=`echo $pubsfc_file | cut -d. -f2-`
-pubatm_file=${yyddd}${hh}00.${CDUMP}.t${hh}z.atmanl.nc
-atm_file=`echo $pubatm_file | cut -d. -f2-`
-
-echo "pubsfc_file:  $pubsfc_file"
-echo "pubatm_file:  $pubatm_file"
-
-if  [[ -f $RETRODIR/${pubatm_file} ]]; then
-  echo "linking $RETRODIR...."
-  echo "pubsfc_file:  $pubsfc_file"
-  echo "pubatm_file:  $pubatm_file"
-  ln -fs $RETRODIR/${pubsfc_file} $sfc_file
-  ln -fs $RETRODIR/${pubatm_file} $atm_file 
-elif [[ -f $PUBDIR/${pubatm_file} ]]; then
-  echo "linking $PUBDIR...."
-  ln -fs $PUBDIR/${pubsfc_file} $sfc_file
-  ln -fs $PUBDIR/${pubatm_file} $atm_file
-elif  [[ -f $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file} ]]; then
-  echo "linking $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}..."
-  echo "sfc_file:  $sfc_file"
-  echo "atm_file:  $atm_file"
-  ln -s $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${sfc_file}
-  ln -s $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file}
-else
-  echo "missing input files!"
-  exit 1
-fi
diff --git a/jobs/rocoto/getic_gsl_fv3gfsv15.sh b/jobs/rocoto/getic_gsl_fv3gfsv15.sh
index f28e6c5ab9..1bbb985d15 100755
--- a/jobs/rocoto/getic_gsl_fv3gfsv15.sh
+++ b/jobs/rocoto/getic_gsl_fv3gfsv15.sh
@@ -2,7 +2,7 @@
 
 source "$HOMEgfs/ush/preamble.sh"
 
-## this script makes links to FV3GFS (GFSv15.1) nemsio files under /public and copies over GFS analysis file for verification
+## this script makes links to FV3GFS (GFSv15.1) nemsio files under /public 
 ##   /scratch4/BMC/rtfim/rtfuns/FV3GFS/FV3ICS/YYYYMMDDHH/gfs
 ##     gfs.tHHz.sfcanl.nemsio -> /public/data/grids/gfs/nemsio/YYDDDHH00.gfs.tHHz.sfcanl.nemsio
 ##     gfs.tHHz.atmanl.nemsio -> /public/data/grids/gfs/nemsio/YYDDDHH00.gfs.tHHz.atmanl.nemsio
@@ -14,7 +14,6 @@ echo "CDUMP = $CDUMP"
 echo "COMPONENT = $COMPONENT"
 echo "ICSDIR = $ICSDIR"
 echo "PUBDIR = $PUBDIR"
-echo "GFSDIR = $GFSDIR"
 echo "RETRODIR = $RETRODIR"
 echo "ROTDIR = $ROTDIR"
 echo "PSLOT = $PSLOT"
diff --git a/jobs/rocoto/getic_gsl_fv3gfsv16.sh b/jobs/rocoto/getic_gsl_fv3gfsv16.sh
index ec5c3dcef2..4e25e48716 100755
--- a/jobs/rocoto/getic_gsl_fv3gfsv16.sh
+++ b/jobs/rocoto/getic_gsl_fv3gfsv16.sh
@@ -2,7 +2,7 @@
 
 source "$HOMEgfs/ush/preamble.sh"
 
-## this script makes links to FV3GFS netcdf files under /public and copies over GFS analysis file for verification
+## this script makes links to FV3GFS netcdf files under /public 
 ##   /home/rtfim/UFS_CAMSUITE/FV3GFSrun/FV3ICS/YYYYMMDDHH/gfs
 ##     gfs.tHHz.sfcanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.sfcanl.nc
 ##     gfs.tHHz.atmanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.atmanl.nc