From 8c2706e1468240ddb815b40a21bd5e952aef9d99 Mon Sep 17 00:00:00 2001
From: Guillaume Vernieres <guillaume.vernieres@noaa.gov>
Date: Tue, 9 May 2023 07:25:43 -0400
Subject: [PATCH] Adapt the marine DA to the new COM structure (#457)

* works but needs tidy

* adopted -new com for ctests

* code tidy

* working state, reverted yamls, started switching to FileHandler

* use filehandler for post

* fixed com naming

* removed module purge/load

* code tidy?

* first try # 127

* reverted stage.atmos stuff

* no module load

---------

Co-authored-by: Cory Martin <cory.r.martin@noaa.gov>
---
 .gitignore                                    |   1 +
 .../exgdas_global_marine_analysis_chkpt.sh    |   4 +-
 scripts/exgdas_global_marine_analysis_post.py |  96 +++++++------
 scripts/exgdas_global_marine_analysis_prep.py | 132 ++++++++++--------
 scripts/exgdas_global_marine_analysis_vrfy.py |  10 +-
 .../global-workflow/run_jedi_exe_3denvar.sh   |   8 +-
 .../global-workflow/run_jedi_exe_3dhofx.sh    |   8 +-
 .../atm/global-workflow/run_jedi_exe_3dvar.sh |   8 +-
 .../atm/global-workflow/run_jedi_exe_letkf.sh |   8 +-
 test/soca/CMakeLists.txt                      |  20 ---
 test/soca/gw/CMakeLists.txt                   |   7 +
 test/soca/gw/prep.sh                          |  40 ++++++
 test/soca/gw/run_jjobs.yaml.test              |   6 +-
 test/soca/{ => gw}/static.sh                  |   0
 test/soca/runtime_vars.sh                     |  52 -------
 test/soca/test_bmat.sh                        |  28 ----
 test/soca/test_bmat_vrfy.sh                   |  26 ----
 test/soca/test_prep.sh                        |  75 ----------
 test/soca/test_run.sh                         |  38 -----
 test/soca/test_utils.sh                       |  10 --
 ush/soca/run_jjobs.py                         |  83 +++++++----
 ush/ufsda/stage.py                            |  11 +-
 22 files changed, 264 insertions(+), 407 deletions(-)
 create mode 100755 test/soca/gw/prep.sh
 rename test/soca/{ => gw}/static.sh (100%)
 mode change 100644 => 100755
 delete mode 100644 test/soca/runtime_vars.sh
 delete mode 100755 test/soca/test_bmat.sh
 delete mode 100755 test/soca/test_bmat_vrfy.sh
 delete mode 100755 test/soca/test_prep.sh
 delete mode 100755 test/soca/test_run.sh
 delete mode 100644 test/soca/test_utils.sh

diff --git a/.gitignore b/.gitignore
index d11bd354c..4eff16035 100644
--- a/.gitignore
+++ b/.gitignore
@@ -159,6 +159,7 @@ fv3-jedi-data/
 fv3-jedi-lm/
 gsibec/
 gsw/
+icepack/
 /ioda/
 ioda-data/
 iodaconv/
diff --git a/scripts/exgdas_global_marine_analysis_chkpt.sh b/scripts/exgdas_global_marine_analysis_chkpt.sh
index 56bde64d4..6863a29a6 100755
--- a/scripts/exgdas_global_marine_analysis_chkpt.sh
+++ b/scripts/exgdas_global_marine_analysis_chkpt.sh
@@ -44,8 +44,8 @@ mom6_iau_incr=${DATA}/inc.nc
 # prepare nsst yaml
 if [ $DO_MERGENSST = "YES" ]; then
 cat > nsst.yaml << EOF
-sfc_fcst: ${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos/${GPREFIX}sfcf006.nc
-sfc_ana: ${COMOUT}/../atmos/${APREFIX}sfcanl.nc
+sfc_fcst: ${COM_ATMOS_HISTORY_PREV}/${GPREFIX}sfcf006.nc
+sfc_ana: ${COM_ATMOS_ANALYSIS}/${APREFIX}sfcanl.nc
 nlayers: 5
 EOF
 
diff --git a/scripts/exgdas_global_marine_analysis_post.py b/scripts/exgdas_global_marine_analysis_post.py
index 1055d9135..8e375d9b2 100755
--- a/scripts/exgdas_global_marine_analysis_post.py
+++ b/scripts/exgdas_global_marine_analysis_post.py
@@ -23,71 +23,85 @@
 import shutil
 import logging
 from datetime import datetime, timedelta
-import ufsda
+from pygw.file_utils import FileHandler
+
+
+# TODO: Move this somewhere else?
+def list_all_files(dir_in, dir_out, wc='*', fh_list=[]):
+    files = glob.glob(os.path.join(dir_in, wc))
+    for file_src in files:
+        file_dst = os.path.join(dir_out, os.path.basename(file_src))
+        fh_list.append([file_src, file_dst])
+    return fh_list
+
 
 # set up logger
 logging.basicConfig(format='%(asctime)s:%(levelname)s:%(message)s', level=logging.INFO, datefmt='%Y-%m-%d %H:%M:%S')
 logging.info(f"---------------- Copy from RUNDIR to COMOUT")
 
-comout = os.getenv('COMOUT')
-comoutice = os.getenv('COMOUTice')
+com_ocean_analysis = os.getenv('COM_OCEAN_ANALYSIS')
+com_ice_restart = os.getenv('COM_ICE_RESTART')
 anl_dir = os.getenv('DATA')
 cdate = os.getenv('CDATE')
 pdy = os.getenv('PDY')
 staticsoca_dir = os.getenv('SOCA_INPUT_FIX_DIR')
-cdump = os.getenv('CDUMP')
-# TODO: this cycle math does the job, but datetime might be safer
+RUN = os.getenv('CDUMP')
 cyc = str(os.getenv('cyc')).zfill(2)
 bcyc = str((int(cyc) - 3) % 24).zfill(2)
 gcyc = str((int(cyc) - 6) % 24).zfill(2)  # previous cycle
 bdatedt = datetime.strptime(cdate, '%Y%m%d%H') - timedelta(hours=3)
 bdate = datetime.strftime(bdatedt, '%Y-%m-%dT%H:00:00Z')
 
-# Make a copy the IAU increment
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'inc.nc'),
-                          os.path.join(comout, cdump + '.t' + cyc + 'z.ocninc.nc'))
+post_file_list = []
 
-# Copy of the ioda output files, as is for now
-ufsda.disk_utils.copytree(os.path.join(anl_dir, 'diags'),
-                          os.path.join(comout, 'diags'))
+# Make a copy the IAU increment
+post_file_list.append([os.path.join(anl_dir, 'inc.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocninc.nc')])
 
 # Copy of the diagonal of the background error for the cycle
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'ocn.bkgerr_stddev.incr.' + bdate + '.nc'),
-                          os.path.join(comout, cdump + '.t' + cyc + 'z.ocn.bkgerr_stddev.nc'))
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'ice.bkgerr_stddev.incr.' + bdate + '.nc'),
-                          os.path.join(comout, cdump + '.t' + cyc + 'z.ice.bkgerr_stddev.nc'))
+post_file_list.append([os.path.join(anl_dir, f'ocn.bkgerr_stddev.incr.{bdate}.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocn.bkgerr_stddev.nc')])
+post_file_list.append([os.path.join(anl_dir, f'ice.bkgerr_stddev.incr.{bdate}.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ice.bkgerr_stddev.nc')])
 
 # Copy the ice and ocean increments
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'Data', 'ocn.3dvarfgat_pseudo.incr.' + bdate + '.nc'),
-                          os.path.join(comout, cdump + '.t' + cyc + 'z.ocn.incr.nc'))
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'Data', 'ice.3dvarfgat_pseudo.incr.' + bdate + '.nc'),
-                          os.path.join(comout, cdump + '.t' + cyc + 'z.ice.incr.nc'))
-
-# Copy the localization and correlation operators
-ufsda.disk_utils.copytree(os.path.join(anl_dir, 'bump'),
-                          os.path.join(comout, 'bump'))
+post_file_list.append([os.path.join(anl_dir, 'Data', f'ocn.3dvarfgat_pseudo.incr.{bdate}.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocn.incr.nc')])
+post_file_list.append([os.path.join(anl_dir, 'Data', f'ice.3dvarfgat_pseudo.incr.{bdate}.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ice.incr.nc')])
 
 # Copy DA grid (computed for the start of the window)
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'soca_gridspec.nc'),
-                          os.path.join(comout, cdump + '.t' + bcyc + 'z.ocngrid.nc'))
+post_file_list.append([os.path.join(anl_dir, 'soca_gridspec.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{bcyc}z.ocngrid.nc')])
 
 # Copy the analysis at the start of the window
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'Data', 'ocn.3dvarfgat_pseudo.an.' + bdate + '.nc'),
-                          os.path.join(comout, cdump + '.t' + cyc + 'z.ocnana.nc'))
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'Data', 'ice.3dvarfgat_pseudo.an.' + bdate + '.nc'),
-                          os.path.join(comout, cdump + '.t' + cyc + 'z.iceana.nc'))
+post_file_list.append([os.path.join(anl_dir, 'Data', f'ocn.3dvarfgat_pseudo.an.{bdate}.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.ocnana.nc')])
+post_file_list.append([os.path.join(anl_dir, 'Data', f'ice.3dvarfgat_pseudo.an.{bdate}.nc'),
+                       os.path.join(com_ocean_analysis, f'{RUN}.t{cyc}z.iceana.nc')])
 
 # Copy the CICE analysis restart
 cdateice = pdy + '.' + cyc + '0000'
-ufsda.disk_utils.copyfile(os.path.join(anl_dir, 'Data', cdateice + '.cice_model.res.nc'),
-                          os.path.join(comoutice, 'RESTART', cdate + '.cice_model_anl.res.nc'))
-
-# Copy logs
-ufsda.mkdir(os.path.join(comout, 'logs'))
-for file in glob.glob(os.path.join(anl_dir, '*.out')):
-    ufsda.disk_utils.copyfile(file, os.path.join(comout, 'logs'))
-
-# Copy var.yaml
-ufsda.mkdir(os.path.join(comout, 'yaml'))
-for file in glob.glob(os.path.join(anl_dir, '*.yaml')):
-    ufsda.disk_utils.copyfile(file, os.path.join(comout, 'yaml'))
+post_file_list.append([os.path.join(anl_dir, 'Data', f'{cdateice}.cice_model.res.nc'),
+                       os.path.join(com_ice_restart, f'{cdate}.cice_model_anl.res.nc')])
+
+FileHandler({'copy': post_file_list}).sync()
+
+# create COM sub-directories
+FileHandler({'mkdir': [os.path.join(com_ocean_analysis, 'diags'),
+                       os.path.join(com_ocean_analysis, 'bump'),
+                       os.path.join(com_ocean_analysis, 'yaml')]}).sync()
+
+# ioda output files
+fh_list = list_all_files(os.path.join(anl_dir, 'diags'),
+                         os.path.join(com_ocean_analysis, 'diags'))
+
+# localization and correlation operators
+fh_list = list_all_files(os.path.join(anl_dir, 'bump'),
+                         os.path.join(com_ocean_analysis, 'bump'), fh_list=fh_list)
+
+# yaml configurations
+fh_list = list_all_files(os.path.join(anl_dir),
+                         os.path.join(com_ocean_analysis, 'yaml'), wc='*.yaml', fh_list=fh_list)
+
+FileHandler({'copy': fh_list}).sync()
diff --git a/scripts/exgdas_global_marine_analysis_prep.py b/scripts/exgdas_global_marine_analysis_prep.py
index 53545dc47..c52bd362a 100755
--- a/scripts/exgdas_global_marine_analysis_prep.py
+++ b/scripts/exgdas_global_marine_analysis_prep.py
@@ -35,7 +35,7 @@
 from pygw.attrdict import AttrDict
 from pygw.template import Template, TemplateConstants
 from pygw.yaml_file import YAMLFile
-
+from pygw.file_utils import FileHandler
 
 # set up logger
 logging.basicConfig(format='%(asctime)s:%(levelname)s:%(message)s', level=logging.INFO, datefmt='%Y-%m-%d %H:%M:%S')
@@ -138,6 +138,7 @@ def gen_bkg_list(bkg_path, out_path, window_begin=' ', yaml_name='bkg.yaml', ice
     test_hist_date(os.path.join(bkg_path, ocn_filename_ic), bkg_date)  # assert date of the history file is correct
 
     # Copy/process backgrounds and generate background yaml list
+    bkg_list_src_dst = []
     bkg_list = []
     for bkg in files:
 
@@ -158,12 +159,12 @@ def gen_bkg_list(bkg_path, out_path, window_begin=' ', yaml_name='bkg.yaml', ice
             # Process the CICE history file so they can be read by soca/fms
             # TODO: Add date check of the cice history
             # TODO: bkg_path should be 1 level up
-            cice_hist2fms(os.path.join(bkg_path, '..', 'ice', ice_filename),
+            cice_hist2fms(os.path.join(os.getenv('COM_ICE_HISTORY_PREV'), ice_filename),
                           os.path.join(out_path, agg_ice_filename))
 
-        # copy ocean bkg to out_path
-        ufsda.disk_utils.copyfile(os.path.join(bkg_path, ocn_filename),
-                                  os.path.join(out_path, ocn_filename))
+        # prepare list of ocean bkg to be copied to RUNDIR
+        bkg_list_src_dst.append([os.path.join(bkg_path, ocn_filename),
+                                 os.path.join(out_path, ocn_filename)])
 
         bkg_dict = {'date': bkg_date.strftime('%Y-%m-%dT%H:%M:%SZ'),
                     'basename': './bkg/',
@@ -173,9 +174,14 @@ def gen_bkg_list(bkg_path, out_path, window_begin=' ', yaml_name='bkg.yaml', ice
                     'remap_filename': './bkg/'+ocn_filename_ic}
         bkg_date = bkg_date + timedelta(hours=dt_pseudo)  # TODO: make the bkg interval a configurable
         bkg_list.append(bkg_dict)
+
+    # save pseudo model yaml configuration
     f = open(yaml_name, 'w')
     yaml.dump(bkg_list[1:], f, sort_keys=False, default_flow_style=False)
 
+    # copy ocean backgrounds to RUNDIR
+    FileHandler({'copy': bkg_list_src_dst}).sync()
+
 
 def find_bkgerr(input_date, domain):
     """
@@ -200,31 +206,25 @@ def find_bkgerr(input_date, domain):
 
 logging.info(f"---------------- Setup runtime environement")
 
-comout = os.getenv('COMOUT')
-comin_obs = os.getenv('COMIN_OBS')
+comin_obs = os.getenv('COMIN_OBS')  # R2D2 DB for now
 anl_dir = os.getenv('DATA')
 staticsoca_dir = os.getenv('SOCA_INPUT_FIX_DIR')
 
-# create analysis directory for files
-ufsda.mkdir(anl_dir)
-
-# create output directory for obs
-diags = os.path.join(anl_dir, 'diags')
-ufsda.mkdir(diags)
-
-# create output directory for obs
-bkg_dir = os.path.join(anl_dir, 'bkg')
-ufsda.mkdir(bkg_dir)
-
-# create output directory for soca DA
-anl_out = os.path.join(anl_dir, 'Data')
-ufsda.mkdir(anl_out)
+# create analysis directories
+diags = os.path.join(anl_dir, 'diags')   # output dir for soca DA obs space
+obs_in = os.path.join(anl_dir, 'obs')    # input      "           "
+bkg_dir = os.path.join(anl_dir, 'bkg')   # ice and ocean backgrounds
+anl_out = os.path.join(anl_dir, 'Data')  # output dir for soca DA
+FileHandler({'mkdir': [anl_dir, diags, obs_in, bkg_dir, anl_out]}).sync()
 
 # Variables of convenience
 half_assim_freq = timedelta(hours=int(os.getenv('assim_freq'))/2)
 window_begin = datetime.strptime(os.getenv('PDY')+os.getenv('cyc'), '%Y%m%d%H') - half_assim_freq
 window_begin_iso = window_begin.strftime('%Y-%m-%dT%H:%M:%SZ')
 fcst_begin = datetime.strptime(os.getenv('PDY')+os.getenv('cyc'), '%Y%m%d%H')
+RUN = os.getenv('RUN')
+cyc = os.getenv('cyc')
+PDY = os.getenv('PDY')
 
 ################################################################################
 # fetch observations
@@ -235,17 +235,34 @@ def find_bkgerr(input_date, domain):
 ufsda.r2d2.setup(r2d2_config_yaml=os.path.join(anl_dir, 'r2d2_config.yaml'), shared_root=comin_obs)
 
 # create config dict from runtime env
-envconfig = ufsda.misc_utils.get_env_config(component='soca')
-stage_cfg = YAMLFile(path=os.path.join(gdas_home,
-                                       'parm',
-                                       'templates',
-                                       'stage.yaml'))
+envconfig = {'window_begin': f"{window_begin.strftime('%Y-%m-%dT%H:%M:%SZ')}",
+             'r2d2_obs_src': os.getenv('R2D2_OBS_SRC'),
+             'r2d2_obs_dump': os.getenv('R2D2_OBS_DUMP'),
+             'r2d2_obs_db': os.getenv('R2D2_OBS_DB'),
+             'ATM_WINDOW_BEGIN': window_begin_iso,
+             'ATM_WINDOW_LENGTH': f"PT{os.getenv('assim_freq')}H"}
+stage_cfg = YAMLFile(path=os.path.join(gdas_home, 'parm', 'templates', 'stage.yaml'))
 stage_cfg = Template.substitute_structure(stage_cfg, TemplateConstants.DOUBLE_CURLY_BRACES, envconfig.get)
 stage_cfg = Template.substitute_structure(stage_cfg, TemplateConstants.DOLLAR_PARENTHESES, envconfig.get)
+stage_cfg['r2d2_obs_out'] = os.getenv('COM_OBS')
 
-# stage observations from R2D2 to COMIN_OBS and then link to analysis subdir
+# stage observations from R2D2 COMIN_OBS to COM_OBS
 ufsda.stage.obs(stage_cfg)
 
+# get the list of observations
+obs_files = []
+for ob in stage_cfg['observations']['observers']:
+    obs_files.append(f"{RUN}.t{cyc}z.{ob['obs space']['name'].lower()}.{PDY}{cyc}.nc4")
+obs_list = []
+
+# copy obs from COM_OBS to DATA/obs
+for obs_file in obs_files:
+    logging.info(f"******* {obs_file}")
+    obs_src = os.path.join(os.getenv('COM_OBS'), obs_file)
+    obs_dst = os.path.join(os.path.abspath(obs_in), obs_file)
+    obs_list.append([obs_src, obs_dst])
+FileHandler({'copy': obs_list}).sync()
+
 ################################################################################
 # stage static files
 
@@ -256,10 +273,12 @@ def find_bkgerr(input_date, domain):
 # stage background error files
 
 logging.info(f"---------------- Stage static files")
+bkgerr_list = []
 for domain in ['ocn', 'ice']:
     fname_stddev = find_bkgerr(pytz.utc.localize(window_begin, is_dst=None), domain=domain)
     fname_out = domain+'.bkgerr_stddev.incr.'+window_begin_iso+'.nc'
-    ufsda.disk_utils.copyfile(fname_stddev, os.path.join(stage_cfg['stage_dir'], fname_out))
+    bkgerr_list.append([fname_stddev, fname_out])
+FileHandler({'copy': bkgerr_list}).sync()
 
 ################################################################################
 # prepare JEDI yamls
@@ -267,15 +286,12 @@ def find_bkgerr(input_date, domain):
 logging.info(f"---------------- Generate JEDI yaml files")
 
 ################################################################################
-# link yaml for grid generation
+# copy yaml for grid generation
+
+gridgen_yaml_src = os.path.abspath(os.path.join(gdas_home, 'parm', 'soca', 'gridgen', 'gridgen.yaml'))
+gridgen_yaml_dst = os.path.abspath(os.path.join(stage_cfg['stage_dir'], 'gridgen.yaml'))
+FileHandler({'copy': [[gridgen_yaml_src, gridgen_yaml_dst]]}).sync()
 
-gridgen_yaml = os.path.join(gdas_home,
-                            'parm',
-                            'soca',
-                            'gridgen',
-                            'gridgen.yaml')
-ufsda.disk_utils.symlink(gridgen_yaml,
-                         os.path.join(stage_cfg['stage_dir'], 'gridgen.yaml'))
 
 ################################################################################
 # generate YAML file for parametric diag of B
@@ -292,15 +308,11 @@ def find_bkgerr(input_date, domain):
 config.save(berr_yaml)
 
 ################################################################################
-# link yaml for decorrelation length scales
+# copy yaml for decorrelation length scales
 
-corscales_yaml = os.path.join(gdas_home,
-                              'parm',
-                              'soca',
-                              'berror',
-                              'soca_setcorscales.yaml')
-ufsda.disk_utils.symlink(corscales_yaml,
-                         os.path.join(stage_cfg['stage_dir'], 'soca_setcorscales.yaml'))
+corscales_yaml_src = os.path.join(gdas_home, 'parm', 'soca', 'berror', 'soca_setcorscales.yaml')
+corscales_yaml_dst = os.path.join(stage_cfg['stage_dir'], 'soca_setcorscales.yaml')
+FileHandler({'copy': [[corscales_yaml_src, corscales_yaml_dst]]}).sync()
 
 ################################################################################
 # generate yaml for bump/nicas (used for correlation and/or localization)
@@ -357,7 +369,7 @@ def find_bkgerr(input_date, domain):
                                  'soca',
                                  'variational',
                                  '3dvarfgat.yaml')
-gen_bkg_list(bkg_path=os.getenv('COMIN_GES'),
+gen_bkg_list(bkg_path=os.getenv('COM_OCEAN_HISTORY_PREV'),
              out_path=bkg_dir,
              window_begin=window_begin,
              yaml_name='bkg_list.yaml')
@@ -387,10 +399,9 @@ def find_bkgerr(input_date, domain):
 
 # make a copy of the CICE6 restart
 rst_date = fcst_begin.strftime('%Y%m%d.%H%M%S')
-ice_rst = os.path.join(os.getenv('COMIN_GES'), '..', 'ice', 'RESTART',
-                       rst_date+'.cice_model.res.nc')
+ice_rst = os.path.join(os.getenv('COM_ICE_RESTART_PREV'), f'{rst_date}.cice_model.res.nc')
 ice_rst_ana = os.path.join(anl_out, rst_date+'.cice_model.res.nc')
-ufsda.disk_utils.copyfile(ice_rst, ice_rst_ana)
+FileHandler({'copy': [[ice_rst, ice_rst_ana]]}).sync()
 
 # write the two seaice analysis to model change of variable yamls
 varchgyamls = ['soca_2cice_arctic.yaml', 'soca_2cice_antarctic.yaml']
@@ -408,26 +419,33 @@ def find_bkgerr(input_date, domain):
 for varchgyaml in varchgyamls:
     soca2cice_cfg['template'] = os.path.join(gdas_home, 'parm', 'soca', 'varchange', varchgyaml)
     f = open('tmp.yaml', 'w')
+    # TODO: use YAMLFile instead
     yaml.dump(soca2cice_cfg, f, sort_keys=False, default_flow_style=False)
     ufsda.genYAML.genYAML('tmp.yaml', output=varchgyaml)
 
 ################################################################################
-# links of convenience
-RUN = os.getenv('RUN')
-mom_ic = glob.glob(os.path.join(bkg_dir, f'{RUN}.*.ocnf003.nc'))[0]
-ufsda.disk_utils.symlink(mom_ic, os.path.join(anl_dir, 'INPUT', 'MOM.res.nc'))
-
-cice_ic = glob.glob(os.path.join(bkg_dir, f'{RUN}.*.agg_icef003.nc'))[0]
-ufsda.disk_utils.symlink(cice_ic, os.path.join(anl_dir, 'INPUT', 'cice.res.nc'))
+# Copy initial condition
+ics_list = []
+# ocean IC's
+mom_ic_src = glob.glob(os.path.join(bkg_dir, f'{RUN}.*.ocnf003.nc'))[0]
+mom_ic_dst = os.path.join(anl_dir, 'INPUT', 'MOM.res.nc')
+ics_list.append([mom_ic_src, mom_ic_dst])
+
+# seaice IC's
+cice_ic_src = glob.glob(os.path.join(bkg_dir, f'{RUN}.*.agg_icef003.nc'))[0]
+cice_ic_dst = os.path.join(anl_dir, 'INPUT', 'cice.res.nc')
+ics_list.append([cice_ic_src, cice_ic_dst])
+FileHandler({'copy': ics_list}).sync()
 
 ################################################################################
 # prepare input.nml
 mom_input_nml_src = os.path.join(gdas_home, 'parm', 'soca', 'fms', 'input.nml')
 mom_input_nml_tmpl = os.path.join(stage_cfg['stage_dir'], 'mom_input.nml.tmpl')
 mom_input_nml = os.path.join(stage_cfg['stage_dir'], 'mom_input.nml')
-ufsda.disk_utils.copyfile(mom_input_nml_src, mom_input_nml_tmpl)
-domain_stack_size = os.getenv('DOMAIN_STACK_SIZE')
+FileHandler({'copy': [[mom_input_nml_src, mom_input_nml_tmpl]]}).sync()
 
+# swap date and stack size
+domain_stack_size = os.getenv('DOMAIN_STACK_SIZE')
 ymdhms = [int(s) for s in window_begin.strftime('%Y,%m,%d,%H,%M,%S').split(',')]
 with open(mom_input_nml_tmpl, 'r') as nml_file:
     nml = f90nml.read(nml_file)
diff --git a/scripts/exgdas_global_marine_analysis_vrfy.py b/scripts/exgdas_global_marine_analysis_vrfy.py
index c49025af3..f26cdd631 100755
--- a/scripts/exgdas_global_marine_analysis_vrfy.py
+++ b/scripts/exgdas_global_marine_analysis_vrfy.py
@@ -120,7 +120,9 @@ def plot_zonal_slice(config):
     plt.savefig(figname, bbox_inches='tight', dpi=600)
 
 
-comout = os.getenv('COMOUT')
+comout = os.getenv('COM_OCEAN_ANALYSIS')
+com_ice_history = os.getenv('COM_ICE_HISTORY_PREV')
+com_ocean_history = os.getenv('COM_OCEAN_HISTORY_PREV')
 data = os.getenv('DATA')
 pdy = os.getenv('PDY')
 cyc = os.getenv('cyc')
@@ -205,8 +207,8 @@ def plot_zonal_slice(config):
 
 #######################################
 # Sea ice
-data_files = [os.path.join(comout, f'{RUN}.t'+cyc+'z.iceana.nc'),
-              os.path.join(comout, '..', '..', '..', gcdate.strftime(f'{RUN}.%Y%m%d/%H'), 'ice', f'{RUN}.t'+gcyc+'z.icef006.nc')]
+data_files = [os.path.join(comout, f'{RUN}.t{cyc}z.iceana.nc'),
+              os.path.join(com_ice_history, f'{RUN}.t{gcyc}z.icef006.nc')]
 dirs_out = ['ana', 'bkg']
 ice_vars = {'bkg': ['aice_h', 'hs_h', 'hi_h'], 'ana': ['aicen', 'hicen', 'hsnon']}
 for data_file, dir_out in zip(data_files, dirs_out):
@@ -232,7 +234,7 @@ def plot_zonal_slice(config):
 #######################################
 # Ocean surface
 data_files = [os.path.join(comout, f'{RUN}.t'+cyc+'z.ocnana.nc'),
-              os.path.join(comout, '..', '..', '..', gcdate.strftime(f'{RUN}.%Y%m%d/%H'), 'ocean', f'{RUN}.t'+gcyc+'z.ocnf006.nc')]
+              os.path.join(com_ocean_history, f'{RUN}.t{gcyc}z.ocnf006.nc')]
 dirs_out = ['ana', 'bkg']
 ocn_vars = ['ave_ssh', 'Temp', 'Salt']
 for data_file, dir_out in zip(data_files, dirs_out):
diff --git a/test/atm/global-workflow/run_jedi_exe_3denvar.sh b/test/atm/global-workflow/run_jedi_exe_3denvar.sh
index faa6d09dc..4e7b9b24c 100755
--- a/test/atm/global-workflow/run_jedi_exe_3denvar.sh
+++ b/test/atm/global-workflow/run_jedi_exe_3denvar.sh
@@ -15,10 +15,10 @@ else
 fi
 
 # Load modules
-set +x
-module use ${srcdir}/modulefiles
-module load GDAS/${machine}
-set -x
+#set +x
+#module use ${srcdir}/modulefiles
+#module load GDAS/${machine}
+#set -x
 module list
 
 # Set machine dependent variables
diff --git a/test/atm/global-workflow/run_jedi_exe_3dhofx.sh b/test/atm/global-workflow/run_jedi_exe_3dhofx.sh
index f55fb6415..d7c3b3d86 100755
--- a/test/atm/global-workflow/run_jedi_exe_3dhofx.sh
+++ b/test/atm/global-workflow/run_jedi_exe_3dhofx.sh
@@ -15,10 +15,10 @@ else
 fi
 
 # Load modules
-set +x
-module use ${srcdir}/modulefiles
-module load GDAS/${machine}
-set -x
+#set +x
+#module use ${srcdir}/modulefiles
+#module load GDAS/${machine}
+#set -x
 module list
 
 # Set machine dependent variables
diff --git a/test/atm/global-workflow/run_jedi_exe_3dvar.sh b/test/atm/global-workflow/run_jedi_exe_3dvar.sh
index d333db3cc..ca530f280 100755
--- a/test/atm/global-workflow/run_jedi_exe_3dvar.sh
+++ b/test/atm/global-workflow/run_jedi_exe_3dvar.sh
@@ -15,10 +15,10 @@ else
 fi
 
 # Load modules
-set +x
-module use ${srcdir}/modulefiles
-module load GDAS/${machine}
-set -x
+#set +x
+#module use ${srcdir}/modulefiles
+#module load GDAS/${machine}
+#set -x
 module list
 
 # Set machine dependent variables
diff --git a/test/atm/global-workflow/run_jedi_exe_letkf.sh b/test/atm/global-workflow/run_jedi_exe_letkf.sh
index 287b67641..0574184b1 100755
--- a/test/atm/global-workflow/run_jedi_exe_letkf.sh
+++ b/test/atm/global-workflow/run_jedi_exe_letkf.sh
@@ -15,10 +15,10 @@ else
 fi
 
 # Load modules
-set +x
-module use ${srcdir}/modulefiles
-module load GDAS/${machine}
-set -x
+#set +x
+#module use ${srcdir}/modulefiles
+#module load GDAS/${machine}
+#set -x
 module list
 
 # Set machine dependent variables
diff --git a/test/soca/CMakeLists.txt b/test/soca/CMakeLists.txt
index fbeab7700..a0383f260 100644
--- a/test/soca/CMakeLists.txt
+++ b/test/soca/CMakeLists.txt
@@ -1,14 +1,6 @@
 # Copy the bkg files
 # ------------------
 set( TESTDATA ${PROJECT_BINARY_DIR}/test/testdata )
-file(GLOB bkg_diag "${TESTDATA}/ocn_da_2018_04_15_*.nc")
-file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/bkg/RESTART)
-file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/bkg/RESTART_GES)
-file(COPY ${bkg_diag} DESTINATION ${PROJECT_BINARY_DIR}/test/soca/bkg/RESTART)
-configure_file(${TESTDATA}/iced.2019-04-15-43200.nc
-  ${PROJECT_BINARY_DIR}/test/soca/ice/RESTART/20180415.120000.cice_model.res.nc
-  COPYONLY)
-file(COPY ${TESTDATA}/cice_hist.nc DESTINATION ${PROJECT_BINARY_DIR}/test/soca/bkg/RESTART)
 
 # link input file from iodaconv to test directory
 # test convert BUFR to IODA
@@ -79,18 +71,6 @@ set_tests_properties(test_gdasapp_soca_obsdb
     PROPERTIES
     ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_SOURCE_DIR}/../../ush/python/pygw/src:$ENV{PYTHONPATH};SOCA_TEST_OBS=${PROJECT_SOURCE_DIR}/test/soca/testdata")
 
-# Test exgdas_global_marine_analysis_prep.py
-# ------------------------------------------
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/3dvar)
-
-# Prep
-add_test(NAME test_gdasapp_soca_ana_prep
-         COMMAND ${PROJECT_SOURCE_DIR}/test/soca/test_prep.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
-         WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/3dvar)
-       set_tests_properties(test_gdasapp_soca_ana_prep
-      PROPERTIES
-      ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_SOURCE_DIR}/../../ush/python/pygw/src:$ENV{PYTHONPATH}")
-
 # Test exgdas scripts from the global-worflow
 if (WORKFLOW_TESTS)
   add_subdirectory(gw)
diff --git a/test/soca/gw/CMakeLists.txt b/test/soca/gw/CMakeLists.txt
index 3846dd923..d193095e3 100644
--- a/test/soca/gw/CMakeLists.txt
+++ b/test/soca/gw/CMakeLists.txt
@@ -2,6 +2,13 @@
 file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/gw/testrun)
 file(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/gw/concatioda)
 
+# Prepare COMROT and static dir
+add_test(NAME test_gdasapp_soca_prep
+         COMMAND ${PROJECT_SOURCE_DIR}/test/soca/gw/prep.sh ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
+         WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/soca/gw)
+       set_tests_properties(test_gdasapp_soca_prep
+      PROPERTIES
+      ENVIRONMENT "PYTHONPATH=${PROJECT_BINARY_DIR}/ush:${PROJECT_SOURCE_DIR}/../../ush/python/pygw/src:$ENV{PYTHONPATH}")
 
 # Identify machine
 set(MACHINE "container")
diff --git a/test/soca/gw/prep.sh b/test/soca/gw/prep.sh
new file mode 100755
index 000000000..436db4636
--- /dev/null
+++ b/test/soca/gw/prep.sh
@@ -0,0 +1,40 @@
+#!/bin/bash
+set -e
+
+project_binary_dir=$1
+project_source_dir=$2
+
+# Get low res static files from the soca sandbox
+${project_source_dir}/test/soca/gw/static.sh $project_binary_dir $project_source_dir
+
+# Stage history and restart files following the "COM" structure
+
+COM=${project_binary_dir}/test/soca/gw/COM/gdas.20180415
+
+mkdir -p ${COM}/06/model_data/ice/history
+mkdir -p ${COM}/06/model_data/ice/restart
+mkdir -p ${COM}/06/model_data/ocean/history
+mkdir -p ${COM}/06/model_data/atmos/analysis
+
+# copy CICE6 restart
+ice_rst=${project_binary_dir}/test/testdata/iced.2019-04-15-43200.nc
+hist_icef=${project_binary_dir}/test/testdata/cice_hist.nc
+
+cp ${ice_rst} ${COM}/06/model_data/ice/restart/20180415.120000.cice_model.res.nc
+
+# invent MOM6 and CICE6 history files
+i=3
+lof=`ls ${project_binary_dir}/test/testdata/ocn_da_*`
+for ocnf in $lof; do
+  cp $ocnf ${COM}/06/model_data/ocean/history/gdas.t06z.ocnf00$i.nc
+  cp $hist_icef ${COM}/06/model_data/ice/history/gdas.t06z.icef00$i.nc
+  i=$(($i+1))
+done
+
+# invent background error
+for day in $(seq 1 2 9); do
+    cp ${COM}/06/model_data/ocean/history/gdas.t06z.ocnf003.nc \
+       ${project_binary_dir}/soca_static/bkgerr/stddev/ocn.ensstddev.fc.2019-04-0${day}T00:00:00Z.PT0S.nc
+    cp ${project_source_dir}/soca/test/Data/72x35x25/ice.bkgerror.nc \
+       ${project_binary_dir}/soca_static/bkgerr/stddev/ice.ensstddev.fc.2019-04-0${day}T00:00:00Z.PT0S.nc
+done
diff --git a/test/soca/gw/run_jjobs.yaml.test b/test/soca/gw/run_jjobs.yaml.test
index b58843a7b..47b448d04 100644
--- a/test/soca/gw/run_jjobs.yaml.test
+++ b/test/soca/gw/run_jjobs.yaml.test
@@ -9,7 +9,7 @@ gw environement:
     PSLOT: gdas_test
     HOMEgfs: @HOMEgfs@
     COMPONENT: ocean
-    CDUMP: gdas
+    RUN: gdas
 
   cycle info:
     PDY: 20180415
@@ -17,10 +17,10 @@ gw environement:
     assym_freq: 6
 
   backgrounds:
-    COMIN_GES: @HOMEgfs@/sorc/gdas.cd/build/test/soca/bkg
+    COM_SRC: @HOMEgfs@/sorc/gdas.cd/build/test/soca/gw/COM
 
   working directories:
-    ROTDIR: @HOMEgfs@/sorc/gdas.cd/build/test/soca/gw/testrun/testjjobs/ROTDIRS
+    ROTDIRS: @HOMEgfs@/sorc/gdas.cd/build/test/soca/gw/testrun/testjjobs/ROTDIRS
     EXPDIRS: @HOMEgfs@/sorc/gdas.cd/build/test/soca/gw/testrun/testjjobs/experiments
     STMP: @HOMEgfs@/sorc/gdas.cd/build/test/soca/gw/testrun/testjjobs
 
diff --git a/test/soca/static.sh b/test/soca/gw/static.sh
old mode 100644
new mode 100755
similarity index 100%
rename from test/soca/static.sh
rename to test/soca/gw/static.sh
diff --git a/test/soca/runtime_vars.sh b/test/soca/runtime_vars.sh
deleted file mode 100644
index 90aa63c46..000000000
--- a/test/soca/runtime_vars.sh
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/bin/bash
-set -e
-
-project_binary_dir=$1
-project_source_dir=$2
-
-# Prepare runtime environement
-export PDY=20180415        # Center of current cycle date
-export cyc=12        # Center of current cycle date
-export GDATE=2018041506        # Center of previous cycle date
-export gcyc=$(echo $GDATE | cut -c9-10)
-export CDUMP=gdas # still uised in ufsda.misc_utils.get_env_config
-export RUN=gdas
-export GDUMP=gdas
-export OPREFIX=${RUN}.t${cyc}z.
-export assim_freq=6            # DA window
-export COMOUT=${project_binary_dir}/test/soca/3dvar
-export DATA=${project_binary_dir}/test/soca/3dvar/ocnanal_${cyc}
-export COMIN_OBS=${project_binary_dir}/test/soca/obs/r2d2-shared
-export COMIN_GES=${project_binary_dir}/test/soca/bkg  # Backgrounds from previous forecast
-export CASE_ANL="C48"           # TODO: Replace with or add OCNRES
-export CASE="C48"               # TODO: Replace with or add OCNRES
-export DOHYBVAR=False
-export CASE_ENKF="C192"         # TODO: Needed but doesn't mean anything in this ctest context
-export LEVS="75"                # TODO: Same as above
-export OBS_LIST=${project_binary_dir}/test/soca/testinput/obs_list.yaml # list of obs for the experiment
-export OBS_YAML=${project_binary_dir}/test/soca/testinput/obs_list.yaml # list of obs for the experiment
-export OBS_YAML_DIR=${project_source_dir}/parm/soca/obs/config      # path to UFO yaml files
-
-mkdir -p ${project_binary_dir}/test/soca/HOMEgfs/sorc/
-export HOMEgfs=${project_binary_dir}/test/soca/HOMEgfs
-
-ufsda_link=${project_binary_dir}/test/soca/HOMEgfs/sorc/gdas.cd
-[ ! -L "${ufsda_link}" ] && ln -s ${project_source_dir} ${ufsda_link}
-
-ush_link=${project_binary_dir}/test/soca/HOMEgfs/ush
-[ ! -L "${ush_link}" ] && ln -s ${project_source_dir}/ush ${ush_link}
-
-export JEDI_BIN=${project_binary_dir}/bin
-export SOCA_INPUT_FIX_DIR=${project_binary_dir}/soca_static      # static soca files
-export SOCA_VARS=tocn,socn,ssh,cicen,hicen                       # Should be renamed, these are the control variables
-export DOMAIN_STACK_SIZE=2000000
-export STATICB_DIR=${project_binary_dir}/test/soca/staticb       # Static B-matrix
-export FV3JEDI_STAGE_YAML=${project_binary_dir}/test/soca/testinput/dumy.yaml # Useless atmospheric stuff
-export R2D2_OBS_DB=shared
-export R2D2_OBS_DUMP=soca
-export R2D2_OBS_SRC=gdasapp
-export R2D2_OBS_WINDOW=24     # R2D2 sampling DB window
-export SOCA_NINNER=2
-export NICAS_RESOL=1
-export NICAS_GRID_SIZE=15000
-export APRUN_OCNANAL="$MPIEXEC_EXEC $MPIEXEC_NPROC 2"
diff --git a/test/soca/test_bmat.sh b/test/soca/test_bmat.sh
deleted file mode 100755
index 5560fef99..000000000
--- a/test/soca/test_bmat.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-set -e
-
-project_binary_dir=$1
-project_source_dir=$2
-
-source ${project_source_dir}/test/soca/test_utils.sh
-
-# Clean test files created during a previous test
-echo "============================= Test that the grid has been generated"
-rm -f  ${DATA}/soca_gridspec.nc
-rm -f  ${DATA}/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
-rm -f  ${DATA}/bump/bump[23]d_nicas_local_000002-00000[12].nc
-
-# Export runtime env. variables
-source ${project_source_dir}/test/soca/runtime_vars.sh $project_binary_dir $project_source_dir
-
-# Run step
-echo "============================= Testing exgdas_global_marine_analysis_bmat.sh for clean exit"
-${project_source_dir}/scripts/exgdas_global_marine_analysis_bmat.sh > exgdas_global_marine_analysis_bmat.log
-
-echo "============================= Test that the grid has been generated"
-test_file  ${DATA}/soca_gridspec.nc
-
-echo "============================= Test that the parametric diag of B was generated"
-test_file  ${DATA}/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
-test_file  ${DATA}/bump/bump2d_nicas_local_000002-000001.nc
-test_file  ${DATA}/bump/bump3d_nicas_local_000002-000001.nc
diff --git a/test/soca/test_bmat_vrfy.sh b/test/soca/test_bmat_vrfy.sh
deleted file mode 100755
index 3f8838b5d..000000000
--- a/test/soca/test_bmat_vrfy.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/bin/bash
-set -e
-
-project_binary_dir=$1
-project_source_dir=$2
-
-source ${project_source_dir}/test/soca/test_utils.sh
-
-# Clean test files created during a previous test
-echo "============================= Test that the grid has been generated"
-rm -f  ${DATA}/Data/*dirac*
-
-# Export runtime env. variables
-source ${project_source_dir}/test/soca/runtime_vars.sh $project_binary_dir $project_source_dir
-
-# B-matrix diagnostic step
-echo "============================= Testing exgdas_global_marine_analysis_bamt_vrfy.sh for clean exit"
-${project_source_dir}/scripts/exgdas_global_marine_analysis_bmat_vrfy.sh > exgdas_global_marine_analysis_bmat_vrfy.log
-
-echo "============================= Test that the dirac file has been generated"
-arr=("tocn" "socn" "ssh" "cicen" "hicen")
-for i in "${!arr[@]}"
-do
-    test_file  ${DATA}/Data/ice.dirac_${arr[i]}_1.an.2018-04-15T09:00:00Z.nc
-    test_file  ${DATA}/Data/ocn.dirac_${arr[i]}_1.an.2018-04-15T09:00:00Z.nc
-done
diff --git a/test/soca/test_prep.sh b/test/soca/test_prep.sh
deleted file mode 100755
index 961b16405..000000000
--- a/test/soca/test_prep.sh
+++ /dev/null
@@ -1,75 +0,0 @@
-#!/bin/bash
-set -e
-
-project_binary_dir=$1
-project_source_dir=$2
-
-source ${project_source_dir}/test/soca/test_utils.sh
-
-# Remove previously fetched obs
-rm -f ${project_binary_dir}/test/soca/3dvar/ocnanal_12/obs/gdas.t12z.{sst,adt,sss,salt,icec}*.nc4
-
-# Export runtime env. variables
-source ${project_source_dir}/test/soca/runtime_vars.sh $project_binary_dir $project_source_dir
-
-# Get low res static files from the soca sandbox
-source ${project_source_dir}/test/soca/static.sh $project_binary_dir $project_source_dir
-
-# MOM6's diag output needs to be renamed, CICE restarts are made up
-i=3
-lof=`ls ${project_binary_dir}/test/soca/bkg/RESTART/ocn_da_*`
-icef=${project_binary_dir}/test/soca/bkg/RESTART/iced.2019-04-15-43200.nc # TODO: cice restart is made up
-hist_icef=${project_binary_dir}/test/soca/bkg/RESTART/cice_hist.nc        # TODO: cice hist date is no ggod
-mkdir -p ${project_binary_dir}/test/soca/ice
-for ocnf in $lof; do
-  cp $ocnf ${project_binary_dir}/test/soca/bkg/gdas.t06z.ocnf00$i.nc
-  cp $hist_icef ${project_binary_dir}/test/soca/ice/gdas.t06z.icef00$i.nc
-  i=$(($i+1))
-done
-
-# Invent background error
-for day in $(seq 1 2 9); do
-    cp ${project_binary_dir}/test/soca/bkg/gdas.t06z.ocnf003.nc \
-       ${project_binary_dir}/soca_static/bkgerr/stddev/ocn.ensstddev.fc.2019-04-0${day}T00:00:00Z.PT0S.nc
-    cp ${project_source_dir}/soca/test/Data/72x35x25/ice.bkgerror.nc \
-       ${project_binary_dir}/soca_static/bkgerr/stddev/ice.ensstddev.fc.2019-04-0${day}T00:00:00Z.PT0S.nc
-done
-
-# Run prep step
-echo "============================= Testing exgdas_global_marine_analysis_prep.py for clean exit"
-${project_source_dir}/scripts/exgdas_global_marine_analysis_prep.py
-
-# Test that the obs path in var.yaml exist
-echo "============================= Testing the existence of obs and bkg in var.vaml"
-obslist=`grep 'gdas.t12z' ${DATA}/var.yaml`
-for o in $obslist; do
-    echo "----------------------- "$o
-    case $o in
-        "obsfile:")
-            base=''
-            continue
-            ;;
-        "ocn_filename:")
-            base=${project_binary_dir}/test/soca/3dvar/ocnanal_12/bkg/
-            continue
-            ;;
-        "ice_filename:")
-            base=${project_binary_dir}/test/soca/3dvar/ocnanal_12/bkg/
-            continue
-            ;;
-        "remap_filename:")
-            base=${project_binary_dir}/test/soca/3dvar/ocnanal_12/
-            continue
-            ;;
-    esac
-    test_file ${base}$o
-done
-
-# Test that the static files have been linked properly
-echo "============================= Test that the static files have been linked properly"
-test_file $(readlink ${DATA}/diag_table)
-test_file $(readlink ${DATA}/field_table)
-test_file $(readlink ${DATA}/fields_metadata.yaml)
-test_file $(readlink ${DATA}/godas_sst_bgerr.nc)
-test_file $(readlink ${DATA}/rossrad.dat)
-test_file $(readlink ${DATA}/MOM_input)
diff --git a/test/soca/test_run.sh b/test/soca/test_run.sh
deleted file mode 100755
index ba653433b..000000000
--- a/test/soca/test_run.sh
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/bin/bash
-set -e
-
-project_binary_dir=$1
-project_source_dir=$2
-
-source ${project_source_dir}/test/soca/test_utils.sh
-
-# Clean test files created during a previous test
-echo "============================= Test that the grid has been generated"
-rm -f  ${DATA}/soca_gridspec.nc
-rm -f  ${DATA}/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
-rm -f  ${DATA}/Data/ocn.iter1.incr.2018-04-15T09:00:00Z.nc
-rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.incr.2018-04-15T09:00:00Z.nc
-rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T09:00:00Z.nc
-rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T12:00:00Z.nc
-rm -f  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T15:00:00Z.nc
-rm -f  ${DATA}/Data/inc.nc
-
-# Export runtime env. variables
-source ${project_source_dir}/test/soca/runtime_vars.sh $project_binary_dir $project_source_dir
-
-# Run step
-echo "============================= Testing exgdas_global_marine_analysis_run.sh for clean exit"
-${project_source_dir}/scripts/exgdas_global_marine_analysis_run.sh > exgdas_global_marine_analysis_run.log
-
-echo "============================= Test that the grid has been generated"
-test_file  ${DATA}/soca_gridspec.nc
-
-echo "============================= Test that the parametric diag of B was generated"
-test_file  ${DATA}/ocn.bkgerr_stddev.incr.2018-04-15T09:00:00Z.nc
-
-echo "============================= Test that an increment and an analysis were created"
-test_file  ${DATA}/Data/ocn.iter1.incr.2018-04-15T09:00:00Z.nc
-test_file  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T09:00:00Z.nc
-test_file  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T12:00:00Z.nc
-test_file  ${DATA}/Data/ocn.3dvarfgat_pseudo.an.2018-04-15T15:00:00Z.nc
-test_file  ${COMOUT}/ocnanal_12/inc.nc
diff --git a/test/soca/test_utils.sh b/test/soca/test_utils.sh
deleted file mode 100644
index 04aced55c..000000000
--- a/test/soca/test_utils.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-test_file () {
-    if test -f "$1"; then
-        echo " - $1 exists"
-    else
-        echo " - $1 does not exist"
-        exit 1
-    fi
-}
diff --git a/ush/soca/run_jjobs.py b/ush/soca/run_jjobs.py
index 8bb834336..cbb4a3567 100755
--- a/ush/soca/run_jjobs.py
+++ b/ush/soca/run_jjobs.py
@@ -4,16 +4,12 @@
 import sys
 import subprocess
 import argparse
-
+from datetime import datetime, timedelta
 
 machines = {"container", "hera", "orion"}
-MODS = {'JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP': 'GDAS',
-        'JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT': 'GDAS',
-        'JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT_VRFY': 'GDAS',
-        'JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN': 'GDAS',
-        'JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT': 'GDAS',
-        'JGDAS_GLOBAL_OCEAN_ANALYSIS_POST': 'GDAS',
-        'JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY': 'EVA'}
+
+# Assume the default conda environement is gdassapp
+ENVS = {'JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY': 'eva'}
 components_short = {'ocean': 'ocn', 'ice': 'ice'}  # Short names for components
 
 
@@ -28,15 +24,27 @@ def __init__(self, scriptname, config):
         self.name = scriptname
         self.f = open(self.name, "w")
         self.f.write("#!/usr/bin/env bash\n")
-        self.component = config['gw environement']['experiment identifier']['COMPONENT']
         self.pslot = config['gw environement']['experiment identifier']['PSLOT']
         self.homegfs = config['gw environement']['experiment identifier']['HOMEgfs']
         self.stmp = config['gw environement']['working directories']['STMP']
-        self.rotdirs = config['gw environement']['working directories']['ROTDIR']
+        self.rotdirs = config['gw environement']['working directories']['ROTDIRS']
+        self.rotdir = os.path.join(self.rotdirs, self.pslot)
         self.expdirs = config['gw environement']['working directories']['EXPDIRS']
         self.config = config
         self.machine = config['machine']
 
+        # get cycle info
+        self.PDY = config['gw environement']['cycle info']['PDY']
+        self.cyc = config['gw environement']['cycle info']['cyc']
+        self.assim_freq = config['gw environement']['cycle info']['assym_freq']
+        self.RUN = config['gw environement']['experiment identifier']['RUN']
+
+        # compute previous cycle info
+        gdate = datetime.strptime(f"{self.PDY}{self.cyc}", '%Y%m%d%H') - timedelta(hours=self.assim_freq)
+        self.gPDY = gdate.strftime("%Y%m%d")
+        self.gcyc = gdate.strftime("%H")
+        self.com_src = config['gw environement']['backgrounds']['COM_SRC']
+
     def header(self):
         """
         Write machine dependent scheduler header
@@ -60,12 +68,14 @@ def export_env_vars_script(self):
         # Compute remaining environment variables
         config = self.config['gw environement']
         EXPDIR = os.path.join(config['working directories']['EXPDIRS'], self.pslot)
+        ROTDIR = self.rotdir
         DATAROOT = os.path.join(config['working directories']['STMP'], 'RUNDIRS', self.pslot)
         gcyc = str((config['cycle info']['cyc'] - config['cycle info']['assym_freq']) % 24).zfill(2)
         CDATE = f"{config['cycle info']['PDY']}{config['cycle info']['cyc']}"  # TODO: Not needed after Andy's PR
 
         # Write the export commands for the remaining environment variables
         self.f.write(f"export EXPDIR='{EXPDIR}'\n")
+        self.f.write(f"export ROTDIR='{ROTDIR}'\n")
         self.f.write(f"export DATAROOT='{DATAROOT}'\n")
         self.f.write(f"export gcyc='{gcyc}'\n")
         self.f.write(f"export CDATE='{CDATE}'\n")
@@ -105,7 +115,7 @@ def setupexpt(self):
             "nens": "0",
             "pslot": "${PSLOT}",
             "configdir": "${PWD}/config",
-            "comrot": "${ROTDIR}",
+            "comrot": self.rotdir,
             "expdir": "${EXPDIRS}",
             "yaml": "overwrite_defaults.yaml"}
 
@@ -121,32 +131,47 @@ def close(self):
         self.f.close()
         subprocess.run(["chmod", "+x", self.name])
 
-    def _modules(self, jjob):
+    def _conda_envs(self, jjob):
         """
         Write a section that will load the machine dependent modules
         """
         if self.machine != "container":
-            self.f.write("module purge \n")
-            self.f.write("module use ${HOMEgfs}/sorc/gdas.cd/modulefiles \n")
-            self.f.write(f"module load {MODS[jjob]}/{self.machine} \n")
+            if jjob in ENVS:
+                # TODO: This does nothing for now. Make the conda activate work!
+                self.f.write(f"# conda activate {ENVS[jjob]} \n")
+
+    def precom(self, com, tmpl):
+        cmd = f"RUN={self.RUN} YMD={self.gPDY} HH={self.gcyc} generate_com -xr {com}:{tmpl}"
+        self.f.write(f"{cmd}\n")
 
     def copy_bkgs(self):
         """
         Fill the ROTDIR with backgrounds
         TODO: replace by fill comrot?
         """
-        file_descriptor = components_short[self.component]+'f0'
-        self.f.write("mkdir -p ${ROTDIR}/${PSLOT}/gdas.${PDY}/${gcyc}/${COMPONENT}/\n")
-        command = "cp -r ${COMIN_GES}/*." + file_descriptor + "*.nc"
-        command += "  ${ROTDIR}/${PSLOT}/gdas.${PDY}/${gcyc}/${COMPONENT}/\n"
-        self.f.write(command)
-        # Special case for the ocean: DA for ice & ocean
-        if self.component == 'ocean':
-            # staging ice backgrounds
-            ice_file_descriptor = components_short['ice']
-            self.f.write("mkdir -p ${ROTDIR}/${PSLOT}/gdas.${PDY}/${gcyc}/ice/RESTART\n")
-            self.f.write("cp -r ${COMIN_GES}/../ice/*icef0*.nc ${ROTDIR}/${PSLOT}/gdas.${PDY}/${gcyc}/ice/\n")
-            self.f.write("cp -r ${COMIN_GES}/../ice/RESTART/*cice_model.res.nc ${ROTDIR}/${PSLOT}/gdas.${PDY}/${gcyc}/ice/RESTART/\n")
+        print(f"gPDY: {self.gPDY}")
+        print(f"gcyc: {self.gcyc}")
+        print(f"assim_freq: {self.assim_freq}")
+        print(f"RUN: {self.RUN}")
+
+        # setup COM variables
+        self.f.write("source ${HOMEgfs}/parm/config/config.com\n")
+        self.f.write("source ${HOMEgfs}/ush/preamble.sh\n")
+        self.precom('COM_OCEAN_HISTORY_PREV', 'COM_OCEAN_HISTORY_TMPL')
+        self.precom('COM_ICE_HISTORY_PREV', 'COM_ICE_HISTORY_TMPL')
+        self.precom('COM_ICE_RESTART_PREV', 'COM_ICE_RESTART_TMPL')
+
+        self.f.write("mkdir -p ${COM_OCEAN_HISTORY_PREV}/\n")
+        self.f.write("mkdir -p ${COM_ICE_HISTORY_PREV}/\n")
+        self.f.write("mkdir -p ${COM_ICE_RESTART_PREV}/\n")
+
+        model_data = os.path.join(self.com_src, f"{self.RUN}.{self.gPDY}", self.gcyc, "model_data")
+        com_ocean_history_src = os.path.join(model_data, 'ocean', 'history')
+        com_ice_history_src = os.path.join(model_data, 'ice', 'history')
+        com_ice_restart_src = os.path.join(model_data, 'ice', 'restart')
+        self.f.write(f"cp {com_ocean_history_src}/*ocnf*.nc $COM_OCEAN_HISTORY_PREV \n")
+        self.f.write(f"cp {com_ice_history_src}/*icef*.nc $COM_ICE_HISTORY_PREV \n")
+        self.f.write(f"cp {com_ice_restart_src}/*cice_model*.nc $COM_ICE_RESTART_PREV \n")
 
     def fixconfigs(self):
         """
@@ -165,7 +190,7 @@ def fixconfigs(self):
         # swap a few variables in config.base
         var2replace = {'HOMEgfs': self.homegfs,
                        'STMP': self.stmp,
-                       'ROTDIRS': self.rotdirs,
+                       'ROTDIR': self.rotdir,
                        'EXPDIRS': self.expdirs}
         with open(configbase, 'r') as f:
             newconfigbase = f.read()
@@ -179,7 +204,7 @@ def jjobs(self):
         Add the list of j-jobs to the job card
         """
         for job in self.config['jjobs']:
-            self._modules(job)  # Add module's jjob
+            self._conda_envs(job)  # Add module's jjob
             thejob = "${HOMEgfs}/jobs/"+job
             runjob = f"{thejob} &>{job}.out\n"
             self.f.write(runjob)
diff --git a/ush/ufsda/stage.py b/ush/ufsda/stage.py
index 3ed614dd8..32b4d5009 100644
--- a/ush/ufsda/stage.py
+++ b/ush/ufsda/stage.py
@@ -12,7 +12,7 @@
 import logging
 import glob
 import numpy as np
-from pygw.yaml_file import YAMLFile, parse_j2yaml
+from pygw.yaml_file import YAMLFile, parse_yaml, parse_j2yaml
 import ufsda.soca_utils
 
 __all__ = ['atm_background', 'atm_obs', 'bias_obs', 'background', 'background_ens', 'fv3jedi', 'obs', 'berror', 'gdas_fix', 'gdas_single_cycle']
@@ -275,7 +275,7 @@ def gdas_single_cycle(config, local_dict):
     obs_list_config = ufsda.yamltools.iter_config(config, obs_list_config)
 
     for ob in obs_list_config['observers']:
-        ob_config = parse_j2yaml(ob, local_dict)
+        ob_config = parse_yaml(ob, local_dict)
         # first get obs
         r2d2_config.pop('file_type', None)
         r2d2_config['type'] = 'ob'
@@ -340,12 +340,11 @@ def obs(config):
     Stage observations using R2D2
     based on input `config` dict
     """
-    # create directory
-    obs_dir = os.path.join(config['DATA'], 'obs')
-    mkdir(obs_dir)
     for ob in config['observations']['observers']:
         obname = ob['obs space']['name'].lower()
-        outfile = ob['obs space']['obsdatain']['engine']['obsfile']
+        outfile = os.path.join(config['r2d2_obs_out'],
+                               os.path.basename(ob['obs space']['obsdatain']['engine']['obsfile']))
+
         # grab obs using R2D2
         window_begin = config['window begin']
         window_begin = parser.parse(window_begin, fuzzy=True)