Output Metadata Validation Testing

rose-stem/app/validate_output_file_metadata/bin/conftest.py

@@ -0,0 +1,16 @@
+##############################################################################
+# (c) Crown copyright Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+import pytest
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--lfric_diag_file", action="store", required=True,
+        help="Input lfric_diagnostics.nc netCDF file"
+    )
+
+@pytest.fixture
+def diag_infile(request):
+    return request.config.getoption("--lfric_diag_file")

rose-stem/app/validate_output_file_metadata/bin/test_validate_metadata.py

@@ -0,0 +1,73 @@
+##############################################################################
+# (c) Crown copyright Met Office. All rights reserved.
+# The file LICENCE, distributed with this code, contains details of the terms
+# under which the code may be used.
+##############################################################################
+"""
+Module to analyse metadata structures in lfric_diagnostics output files
+from LFRic.
+Rules for metadata output are encoded.
+
+"""
+
+import netCDF4
+import os
+import pytest
+
+@pytest.fixture
+def load_rootgrp(diag_infile):
+    rootgrp = None
+    if os.path.exists(diag_infile):
+        rootgrp = netCDF4.Dataset(diag_infile, format="NETCDF4")
+
+    return rootgrp
+
+class TestTemporalMetadata:
+    def test_time_centered_exists(self, load_rootgrp):
+        """
+        Validate that the output file has a variable named 'time_instant'
+        """
+        assert "time_centered" in load_rootgrp.variables
+
+    def test_time_counter_not_exists(self, load_rootgrp):
+        """
+        Validate that the output file does not have a variable named 'time_counter'
+        """
+        assert "time_counter" not in load_rootgrp.variables
+
+class TestSpatialMetadata:
+    def test_Mesh2d_node_x_exists(self, load_rootgrp):
+        """
+        Validate that the output file has a variable named 'Mesh2d_node_x'
+        """
+        assert "Mesh2d_node_x" in load_rootgrp.variables
+
+    def test_Mesh2d_node_x_stdname(self, load_rootgrp):
+        """
+        Validate that the output file x variable has longitude standard_name
+        """
+        assert load_rootgrp.variables.get("Mesh2d_node_x").standard_name == 'longitude'
+
+    def test_Mesh2d_node_x_units(self, load_rootgrp):
+        """
+        Validate that the output file x variable has degrees_east units
+        """
+        assert load_rootgrp.variables.get("Mesh2d_node_x").units == 'degrees_east'
+
+    def test_Mesh2d_node_y_exists(self, load_rootgrp):
+        """
+        Validate that the output file has a variable named 'Mesh2d_node_y'
+        """
+        assert "Mesh2d_node_y" in load_rootgrp.variables
+
+    def test_Mesh2d_node_y_stdname(self, load_rootgrp):
+        """
+        Validate that the output file y variable has latitude standard_name
+        """
+        assert load_rootgrp.variables.get("Mesh2d_node_y").standard_name == 'latitude'
+
+    def test_Mesh2d_node_y_units(self, load_rootgrp):
+        """
+        Validate that the output file y variable has degrees_north units
+        """
+        assert load_rootgrp.variables.get("Mesh2d_node_y").units == 'degrees_north'

rose-stem/app/validate_output_file_metadata/rose-app.conf

@@ -0,0 +1,2 @@
+[command]
+default=pytest $CYLC_WORKFLOW_RUN_DIR/app/validate_output_file_metadata/bin --lfric_diag_file=$INPUT_RESULTS_DIR/lfric_diagnostics.nc

rose-stem/site/common/lfric_atm/tasks_lfric_atm.cylc

@@ -18,6 +18,7 @@
         "tsteps": 144,
         "crun": 2,
         "crun_compare": false,
+        "metadata_test": true,
         "mpi_parts": 6,
         "kgo_checks": ["checksum"],
         "plot_str": "plot_map.py $NODAL_DATA_DIR/lfric_diagnostics.nc  $PLOT_DIR",
@@ -291,6 +292,7 @@
         "tsteps": 144,
         "crun": 2,
         "crun_compare": false,
+        "metadata_test": true,
         "mpi_parts": 6,
         "kgo_checks": ["checksum"],
         "plot_str": "plot_map.py $NODAL_DATA_DIR/lfric_diagnostics.nc  $PLOT_DIR",

rose-stem/templates/common_macros.cylc

@@ -154,6 +154,7 @@
         "plot",
         "memory_plot_ex",
         "check",
+        "metadata_test",
         "publish",
         "phystest",
         "fcm_make",

rose-stem/templates/graph/populate_crun_graph.cylc

@@ -128,6 +128,19 @@
                     crun_task,
                     plot_task]) %}
             {% endif %}
+
+            {% if metadatatest %}
+                {% set metadatatest_task = "metadata_test_"~
+                                           task_values["task_family"]~
+                                           "-crun"~restart_no %}
+                {% if metadatatest_task not in tasks_to_run %}
+                    {% do tasks_to_run.update({metadatatest_task: crun_values }) %}
+                {% endif %}
+                {% do graph_sections.append([
+                    crun_task,
+                    metadatatest_task]) %}
+            {% endif %}
+
         {% endif %}
     {% endif %}
 {% endfor %}

rose-stem/templates/graph/populate_graph_sections.cylc

@@ -53,6 +53,13 @@
     {% set phystest = false %}
 {% endif %}
 
+{# metadatatest settings #}
+{% if "metadata_test" in task_values %}
+    {% set metadatatest = true %}
+{% else %}
+    {% set metadatatest = false %}
+{% endif %}
+
 {# If the task has a restart and has set crun_compare=false, there is no #}
 {# nrun-crun comparison to be made, so don't run the nrun test #}
 {% set running_nrun = true %}
@@ -292,6 +299,21 @@
             application_run_task,
             app_perftools_export_task]) %}
     {% endif %}
+
+    {% if metadatatest %}
+        {% set metadatatest_task = "metadata_test_"~
+                               task_ns.application~"_"~
+                               task_ns.conf_name~"_"~
+                               task_ns.platform~"_"~
+                               task_ns.compiler~"_"~
+                               task_ns.extras %}
+        {% if metadatatest_task not in tasks_to_run %}
+            {% do tasks_to_run.update({metadatatest_task: task_values }) %}
+        {% endif %}
+        {% do graph_sections.append([
+            application_run_task,
+            metadatatest_task]) %}
+    {% endif %}
 {% endif %}
 
 {# lfric_coupled graphs require fcm_make tasks before the application run #}

rose-stem/templates/runtime/generate_runtime.cylc

@@ -104,7 +104,8 @@
     {% elif task.startswith("check") or
             task.startswith("rose_ana") or
             task.startswith("pert_compare") or
-            task.startswith("phystest") %}
+            task.startswith("phystest") or
+            task.startswith("metadata_test") %}
 
         {% include "templates/runtime/generate_runtime_check.cylc" %}
 

rose-stem/templates/runtime/generate_runtime_check.cylc

@@ -112,6 +112,19 @@
         [[[directives]]]
     {{ set_task_resources(task_values["tech-tests_cpus"], task_values["tech-tests_memory"]) }}
 
+{% elif task.startswith("metadata_test") %}
+    {% for family in task_values["plot_families"] %}
+        {% set inherit.str = inherit.str~","~family|upper %}
+    {% endfor %}
+
+    [[{{task}}]]
+        inherit = {{inherit.str|upper}}
+        script = rose task-run --app-key=validate_output_file_metadata
+        [[[environment]]]
+            INPUT_RESULTS_DIR = {{task_output_dir}}/results
+        [[[directives]]]
+    {{ set_task_resources(task_values["tech-tests_cpus"], task_values["tech-tests_memory"]) }}
+
 {% endif %}
 
 {% do LOG.debug("Finished in templates/runtime/generate_runtime_check.cylc") %}