Pick the relevant changes for the deterministic from PR NOAA-EMC#2033 …

…for PR NOAA-EMC#2199

jobs/rocoto/landanl.sh

@@ -14,7 +14,8 @@ export jobid="${job}.$$"
 ###############################################################
 # setup python path for workflow utilities and tasks
 wxflowPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/wxflow/src"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}"
+gdasappPATH="${HOMEgfs}/sorc/gdas.cd/iodaconv/src:${HOMEgfs}/sorc/gdas.cd/build/lib/python3.7"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${wxflowPATH}:${gdasappPATH}"
 export PYTHONPATH
 
 ###############################################################

parm/config/gfs/config.landanl

@@ -16,6 +16,12 @@ fi
 export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/land/obs/config/
 export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/land/obs/lists/${obs_list_name}
 
+# Prepare IMS snow observations
+export FIMS_NML_TMPL="${HOMEgfs}/sorc/gdas.cd/parm/land/prep/fims.nml.j2"
+export IMS_OBS_LIST="${HOMEgfs}/sorc/gdas.cd/parm/land/prep/prep_ims.yaml"
+export CALCFIMSEXE="${HOMEgfs}/exec/calcfIMS.exe"
+export IMS2IODACONV="${HOMEgfs}/ush/imsfv3_scf2ioda.py"
+
 # Name of the JEDI executable and its yaml template
 export JEDIEXE="${HOMEgfs}/exec/fv3jedi_letkf.x"
 export JEDIYAML="${HOMEgfs}/sorc/gdas.cd/parm/land/letkfoi/letkfoi.yaml"

parm/config/gfs/config.preplandobs

@@ -10,9 +10,5 @@ echo "BEGIN: config.preplandobs"
 
 export GTS_OBS_LIST="${HOMEgfs}/sorc/gdas.cd/parm/land/prep/prep_gts.yaml"
 export BUFR2IODAX="${HOMEgfs}/exec/bufr2ioda.x"
-export FIMS_NML_TMPL="${HOMEgfs}/sorc/gdas.cd/parm/land/prep/fims.nml.j2"
-export IMS_OBS_LIST="${HOMEgfs}/sorc/gdas.cd/parm/land/prep/prep_ims.yaml"
-export CALCFIMSEXE="${HOMEgfs}/exec/calcfIMS.exe"
-export IMS2IODACONV="${HOMEgfs}/ush/imsfv3_scf2ioda.py"
 
 echo "END: config.preplandobs"

scripts/exglobal_prep_land_obs.py

@@ -21,5 +21,3 @@
     # Instantiate the land prepare task
     LandAnl = LandAnalysis(config)
     LandAnl.prepare_GTS()
-    if f"{ LandAnl.runtime_config.cyc }" == '18':
-        LandAnl.prepare_IMS()

ush/python/pygfs/task/land_analysis.py

@@ -45,7 +45,7 @@ def __init__(self, config):
                 'npz': self.config.LEVS - 1,
                 'LAND_WINDOW_BEGIN': _window_begin,
                 'LAND_WINDOW_LENGTH': f"PT{self.config['assim_freq']}H",
-                'OPREFIX': f"{self.runtime_config.RUN}.t{self.runtime_config.cyc:02d}z.",
+                'OPREFIX': f"{self.runtime_config.CDUMP}.t{self.runtime_config.cyc:02d}z.",
                 'APREFIX': f"{self.runtime_config.RUN}.t{self.runtime_config.cyc:02d}z.",
                 'jedi_yaml': _letkfoi_yaml
             }
@@ -187,6 +187,7 @@ def prepare_IMS(self) -> None:
         os.symlink(exe_src, exe_dest)
 
         # execute CALCFIMSEXE to calculate IMS snowdepth
+        os.chdir(localconf.DATA)
         exe = Executable(self.task_config.APRUN_CALCFIMS)
         exe.add_default_arg(os.path.join(localconf.DATA, os.path.basename(exe_src)))
         logger.info(f"Executing {exe}")
@@ -244,7 +245,12 @@ def initialize(self) -> None:
             Instance of the LandAnalysis object
         """
 
-        super().initialize()
+        # Stage observations
+        obs_dict = self.get_obs_dict()
+        FileHandler(obs_dict).sync()
+
+        # link jedi executable to run directory
+        self.link_jediexe()
 
         # create a temporary dict of all keys needed in this method
         localconf = AttrDict()
@@ -307,6 +313,10 @@ def execute(self) -> None:
         for key in keys:
             localconf[key] = self.task_config[key]
 
+        logger.info("Generating IMS snow OBS")
+        if f"{ self.runtime_config.cyc }" == '18':
+            self.prepare_IMS()
+
         logger.info("Creating ensemble")
         self.create_ensemble(localconf.SNOWDEPTHVAR,
                              localconf.BESTDDEV,
@@ -369,6 +379,39 @@ def finalize(self) -> None:
             inclist.append([src, dest])
         FileHandler({'copy': inclist}).sync()
 
+    @logit(logger)
+    def get_obs_dict(self) -> None:
+        """Compile a dictionary of observation files to copy
+
+        This method uses the OBS_LIST configuration variable to generate a dictionary
+        from a list of YAML files that specify what observation files are to be
+        copied to the run directory from the observation input directory
+
+        Parameters
+        ----------
+
+        Returns
+        ----------
+        obs_dict: Dict
+            a dictionary containing the list of observation files to copy for FileHandler
+        """
+        logger.debug(f"OBS_LIST: {self.task_config['OBS_LIST']}")
+        obs_list_config = parse_j2yaml(self.task_config["OBS_LIST"], self.task_config)
+        logger.debug(f"obs_list_config: {obs_list_config}")
+        # get observers from master dictionary
+        observers = obs_list_config['observers']
+        copylist = []
+        for ob in observers:
+            obfile = ob['obs space']['obsdatain']['engine']['obsfile']
+            basename = os.path.basename(obfile)
+            if 'ims_snow' not in obfile:
+                copylist.append([os.path.join(self.task_config['COM_OBS'], basename), obfile])
+        obs_dict = {
+            'mkdir': [os.path.join(self.runtime_config['DATA'], 'obs')],
+            'copy': copylist
+        }
+        return obs_dict
+
     @staticmethod
     @logit(logger)
     def get_bkg_dict(config: Dict) -> Dict[str, List[str]]: