Add rocoto sh tag, script to check netcdf file and apply this to check ocean output

ush/check_netcdf.sh

@@ -0,0 +1,15 @@
+#! /usr/bin/env bash
+
+# shellcheck disable=SC2155,SC2312
+HOMEgfs=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )/.." && pwd -P)
+declare -rx HOMEgfs
+
+source "${HOMEgfs}/ush/load_fv3gfs_modules.sh" 1>/dev/null 2>&1
+
+ncfile=${1?}
+
+ncdump -h "${ncfile}"
+rc=$?
+# If there is no error, rc=0, else rc!=0
+
+exit "${rc}"

workflow/rocoto/gefs_tasks.py

@@ -191,7 +191,13 @@ def _atmosoceaniceprod(self, component: str):
         data = f'{history_path}/{history_file_tmpl}'
         dep_dict = {'type': 'data', 'data': data, 'age': 120}
         deps.append(rocoto.add_dependency(dep_dict))
-        dependencies = rocoto.create_dependency(dep=deps)
+        if component in ['ocean']:
+            command = f"{self.HOMEgfs}/ush/check_netcdf.sh {history_path}/{history_file_tmpl}"
+            dep_dict = {'type': 'sh', 'command': command}
+            deps.append(rocoto.add_dependency(dep_dict))
+            dependencies = rocoto.create_dependency(dep=deps, dep_condition='and')
+        else:
+            dependencies = rocoto.create_dependency(dep=deps)
 
         postenvars = self.envars.copy()
         postenvar_dict = {'ENSMEM': '#member#',

workflow/rocoto/gfs_tasks.py

@@ -1069,7 +1069,14 @@ def _atmosoceaniceprod(self, component: str):
         data = f'{history_path}/{history_file_tmpl}'
         dep_dict = {'type': 'data', 'data': data, 'age': 120}
         deps.append(rocoto.add_dependency(dep_dict))
-        dependencies = rocoto.create_dependency(dep=deps)
+        if component in ['ocean']:
+            command = f"{self.HOMEgfs}/ush/check_netcdf.sh {history_path}/{history_file_tmpl}"
+            dep_dict = {'type': 'sh', 'command': command}
+            deps.append(rocoto.add_dependency(dep_dict))
+            dependencies = rocoto.create_dependency(dep=deps, dep_condition='and')
+        else:
+            dependencies = rocoto.create_dependency(dep=deps)
+
         cycledef = 'gdas_half,gdas' if self.cdump in ['gdas'] else self.cdump
         resources = self.get_resource(component_dict['config'])
 

workflow/rocoto/rocoto.py

@@ -8,6 +8,7 @@
 
     ABOUT:
         Helper module to create tasks, metatasks, and dependencies for Rocoto
+        Rocoto documentation is available at https://christopherwharrop.github.io/rocoto
 '''
 
 __all__ = ['create_task',
@@ -182,7 +183,8 @@ def add_dependency(dep_dict: Dict[str, Any]) -> str:
                'data': _add_data_tag,
                'cycleexist': _add_cycle_tag,
                'streq': _add_streq_tag,
-               'strneq': _add_streq_tag}
+               'strneq': _add_streq_tag,
+               'sh': _add_sh_tag}
 
     dep_condition = dep_dict.get('condition', None)
     dep_type = dep_dict.get('type', None)
@@ -333,6 +335,31 @@ def _add_streq_tag(dep_dict: Dict[str, Any]) -> str:
     return string
 
 
+def _add_sh_tag(dep_dict: Dict[str, Any]) -> str:
+    """
+    create a simple shell execution tag
+    :param: dep_dict: shell command to execute
+    :type dep_dict: dict
+    :return: Rocoto simple shell execution dependency
+    :rtype: str
+    """
+
+    shell = dep_dict.get('shell', '/bin/sh')
+    command = dep_dict.get('command', 'echo "Hello World"')
+
+    if '@' in command:
+        offset_string_b = f'<cyclestr>'
+        offset_string_e = '</cyclestr>'
+    else:
+        offset_string_b = ''
+        offset_string_e = ''
+    cmd = f'{offset_string_b}{command}{offset_string_e}'
+
+    string = f'<sh shell="{shell}">{cmd}</sh>'
+
+    return string
+
+
 def _traverse(o, tree_types=(list, tuple)):
     """
     Traverse through a list of lists or tuples and yield the value