Allow use of ocean obs prep in WCDA cycling and remove R2D2 (NOAA-EMC#2215)

Enables use of ocean obs prep task in WCDA cycling and removes R2D2 from same. 
Runs task gdasprepoceanobs before gdasocnanalprep -- obtains ocean data nc4 files from DMPDIR, processes them into IODA format and copies them to COM_OBS. 
Replaces the current R2D2 processing.

Author: AndrewEichmann-NOAA

parm/config/gfs/config.ocnanal

@@ -17,11 +17,6 @@ export CASE_ANL=@CASE_ANL@
 export DOMAIN_STACK_SIZE=116640000  #TODO: Make the stack size resolution dependent
 export JEDI_BIN=${HOMEgfs}/sorc/gdas.cd/build/bin
 
-# R2D2
-export R2D2_OBS_DB=shared
-export R2D2_OBS_DUMP=@R2D2_OBS_DUMP@
-export R2D2_OBS_SRC=@R2D2_OBS_SRC@
-export R2D2_OBS_WINDOW=24     # TODO: Check if the R2D2 sampling DB window is still needed
 export COMIN_OBS=@COMIN_OBS@
 
 # NICAS

parm/config/gfs/config.prepoceanobs

@@ -7,11 +7,14 @@ echo "BEGIN: config.prepoceanobs"
 export OCNOBS2IODAEXEC=${HOMEgfs}/sorc/gdas.cd/build/bin/gdas_obsprovider2ioda.x
 
 export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/config
-export OBSPROC_YAML=@OBSPROC_CONFIG@
+export OBSPROC_YAML=@OBSPROC_YAML@
 export OBS_LIST=@SOCA_OBS_LIST@
 [[ -n "${OBS_LIST}" ]] || export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/soca/obs/obs_list.yaml
 export OBS_YAML=${OBS_LIST}
 
+# ocean analysis needs own dmpdir until standard dmpdir has full ocean obs
+export DMPDIR=@DMPDIR@
+
 # Get task specific resources
 . "${EXPDIR}/config.resources" prepoceanobs
 echo "END: config.prepoceanobs"

workflow/applications/gfs_cycled.py

@@ -42,7 +42,9 @@ def _get_app_configs(self):
             configs += ['anal', 'analdiag']
 
         if self.do_jediocnvar:
-            configs += ['ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy']
+            configs += ['prepoceanobs', 'ocnanalprep', 'ocnanalbmat',
+                        'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost',
+                        'ocnanalvrfy']
 
         if self.do_ocean:
             configs += ['ocnpost']
@@ -133,8 +135,10 @@ def get_task_names(self):
             gdas_gfs_common_tasks_before_fcst += ['anal']
 
         if self.do_jediocnvar:
-            gdas_gfs_common_tasks_before_fcst += ['ocnanalprep', 'ocnanalbmat', 'ocnanalrun',
-                                                  'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy']
+            gdas_gfs_common_tasks_before_fcst += ['prepoceanobs', 'ocnanalprep',
+                                                  'ocnanalbmat', 'ocnanalrun',
+                                                  'ocnanalchkpt', 'ocnanalpost',
+                                                  'ocnanalvrfy']
 
         gdas_gfs_common_tasks_before_fcst += ['sfcanl', 'analcalc']
 

workflow/rocoto/gfs_tasks.py

@@ -578,7 +578,7 @@ def landanl(self):
         task = rocoto.create_task(task_dict)
         return task
 
-    def ocnanalprep(self):
+    def prepoceanobs(self):
 
         ocean_hist_path = self._template_to_rocoto_cycstring(self._base["COM_OCEAN_HISTORY_TMPL"], {'RUN': 'gdas'})
 
@@ -588,6 +588,30 @@ def ocnanalprep(self):
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)
 
+        resources = self.get_resource('prepoceanobs')
+        task_name = f'{self.cdump}prepoceanobs'
+        task_dict = {'task_name': task_name,
+                     'resources': resources,
+                     'dependency': dependencies,
+                     'envars': self.envars,
+                     'cycledef': self.cdump.replace('enkf', ''),
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/prepoceanobs.sh',
+                     'job_name': f'{self.pslot}_{task_name}_@H',
+                     'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
+                     'maxtries': '&MAXTRIES;'
+                     }
+
+        task = rocoto.create_task(task_dict)
+
+        return task
+
+    def ocnanalprep(self):
+
+        deps = []
+        dep_dict = {'type': 'task', 'name': f'{self.cdump}prepoceanobs'}
+        deps.append(rocoto.add_dependency(dep_dict))
+        dependencies = rocoto.create_dependency(dep=deps)
+
         resources = self.get_resource('ocnanalprep')
         task_name = f'{self.cdump}ocnanalprep'
         task_dict = {'task_name': task_name,
@@ -637,13 +661,13 @@ def ocnanalrun(self):
         dependencies = rocoto.create_dependency(dep=deps)
 
         resources = self.get_resource('ocnanalrun')
-        task_name = f'{self.cdump}ocnanlrun'
+        task_name = f'{self.cdump}ocnanalrun'
         task_dict = {'task_name': task_name,
                      'resources': resources,
                      'dependency': dependencies,
                      'envars': self.envars,
                      'cycledef': self.cdump.replace('enkf', ''),
-                     'command': f'{self.HOMEgfs}/jobs/rocoto/ocnanlrun.sh',
+                     'command': f'{self.HOMEgfs}/jobs/rocoto/ocnanalrun.sh',
                      'job_name': f'{self.pslot}_{task_name}_@H',
                      'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
                      'maxtries': '&MAXTRIES;'

workflow/rocoto/tasks.py

@@ -13,6 +13,7 @@ class Tasks:
     VALID_TASKS = ['aerosol_init', 'stage_ic',
                    'prep', 'anal', 'sfcanl', 'analcalc', 'analdiag', 'arch', "cleanup",
                    'prepatmiodaobs', 'atmanlinit', 'atmanlrun', 'atmanlfinal',
+                   'prepoceanobs',
                    'ocnanalprep', 'ocnanalbmat', 'ocnanalrun', 'ocnanalchkpt', 'ocnanalpost', 'ocnanalvrfy',
                    'earc', 'ecen', 'echgres', 'ediag', 'efcs',
                    'eobs', 'eomg', 'epos', 'esfc', 'eupd',