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Add 'bounds inherit' checks from Appendix A (ioos#1217)
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‎compliance_checker/cf/appendix_a.py‎

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appendix_a = {
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"actual_range": {"Type": "N", "Use": ["C", "D", "BO"]},
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"add_offset": {"Type": "N", "Use": ["C", "D", "BO"]},
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"ancillary_variables": {"Type": "S", "Use": ["D"]},
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"axis": {"Type": "S", "Use": ["C", "BI"]},
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"bounds": {"Type": "S", "Use": ["C"]},
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"calendar": {"Type": "S", "Use": ["C", "BI"]},
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"cell_measures": {"Type": "S", "Use": ["D", "Do"]},
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"cell_methods": {"Type": "S", "Use": ["D"]},
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"cf_role": {"Type": "S", "Use": ["C", "BI"]},
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"climatology": {"Type": "S", "Use": ["C"]},
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"comment": {"Type": "S", "Use": ["G", "C", "D"]},
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"compress": {"Type": "S", "Use": ["C"]},
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"computed_standard_name": {"Type": "S", "Use": ["C", "BI"]},
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"Conventions": {"Type": "S", "Use": ["G"]},
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"coordinate_interpolation": {"Type": "S", "Use": ["D", "Do"]},
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"coordinates": {"Type": "S", "Use": ["D", "M", "Do"]},
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"dimensions": {"Type": "S", "Use": ["Do"]},
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"external_variables": {"Type": "S", "Use": ["G"]},
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"_FillValue": {"Type": "D", "Use": ["C", "D", "BO"]},
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"featureType": {"Type": "S", "Use": ["G"]},
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"flag_masks": {"Type": "D", "Use": ["D"]},
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"flag_meanings": {"Type": "S", "Use": ["D"]},
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"flag_values": {"Type": "D", "Use": ["D"]},
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"formula_terms": {"Type": "S", "Use": ["C", "BO"]},
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"geometry": {"Type": "S", "Use": ["C", "D", "Do"]},
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"geometry_type": {"Type": "S", "Use": ["M"]},
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"grid_mapping": {"Type": "S", "Use": ["D", "M", "Do"]},
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"history": {"Type": "S", "Use": ["G", "Gr"]},
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"instance_dimension": {"Type": "S", "Use": []},
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"institution": {"Type": "S", "Use": ["G", "D"]},
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"interior_ring": {"Type": "S", "Use": ["M"]},
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"leap_month": {"Type": "N", "Use": ["C", "BI"]},
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"leap_year": {"Type": "N", "Use": ["C", "BI"]},
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"location": {"Type": "S", "Use": ["D", "Do"]},
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"location_index_set": {"Type": "S", "Use": ["D", "Do"]},
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"long_name": {"Type": "S", "Use": ["C", "D", "Do", "BI"]},
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"mesh": {"Type": "S", "Use": ["D", "Do"]},
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"missing_value": {"Type": "D", "Use": ["C", "D", "BO"]},
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"month_lengths": {"Type": "N", "Use": ["C", "BI"]},
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"node_coordinates": {"Type": "S", "Use": ["M"]},
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"node_count": {"Type": "S", "Use": ["M"]},
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"nodes": {"Type": "S", "Use": ["C"]},
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"part_node_count": {"Type": "S", "Use": ["M"]},
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"positive": {"Type": "S", "Use": ["C", "BI"]},
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"references": {"Type": "S", "Use": ["G", "D"]},
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"sample_dimension": {"Type": "S", "Use": []},
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"scale_factor": {"Type": "N", "Use": ["C", "D", "BO"]},
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"source": {"Type": "S", "Use": ["G", "D"]},
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"standard_error_multiplier": {"Type": "N", "Use": ["D"]},
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"standard_name": {"Type": "S", "Use": ["C", "D", "BI"]},
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"title": {"Type": "S", "Use": ["G", "Gr"]},
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"units": {"Type": "S", "Use": ["C", "D", "BI"]},
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"units_metadata": {"Type": "S", "Use": ["C", "D", "BI"]},
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"valid_max": {"Type": "N", "Use": ["C", "D", "BO"]},
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"valid_min": {"Type": "N", "Use": ["C", "D", "BO"]},
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"valid_range": {"Type": "N", "Use": ["C", "D", "BO"]},
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}

‎compliance_checker/cf/cf_1_11.py‎

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from functools import lru_cache
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from compliance_checker.base import BaseCheck, TestCtx
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from compliance_checker.cf.appendix_a import appendix_a
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from compliance_checker.cf.cf_1_10 import CF1_10Check
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from compliance_checker.cf.util import VariableReferenceError, reference_attr_variables
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@lru_cache
@@ -106,6 +108,86 @@ def check_time_units_metadata(self, ds):
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return [time_units_metadata_ctx.to_result()]
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def check_bounds_inherit_attributes(self, ds):
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"""
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A boundary variable inherits the values of some attributes from its parent coordinate variable.
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If a coordinate variable has any of the attributes marked "BI" (for "inherit") in the "Use" column of <<attribute-appendix>>, they are assumed to apply to its bounds variable as well.
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It is recommended that BI attributes not be included on a boundary variable.
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If a BI attribute is included, it must also be present in the parent variable, and it must exactly match the parent attribute's data type and value.
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A boundary variable can only have inheritable attributes if they are also present on its parent coordinate variable.
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A bounds variable may have any of the attributes marked "BO" for ("own") in the "Use" column of <<attribute-appendix>>.
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These attributes take precedence over any corresponding attributes of the parent variable.
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In these cases, the parent variable's attribute does not apply to the bounds variable, regardless of whether the latter has its own attribute.
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"""
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results = []
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appendix_a_bi_attrs = {
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attribute_name
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for attribute_name, data_dict in appendix_a.items()
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if "BI" in data_dict["Use"]
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}
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for parent_variable in ds.get_variables_by_attributes(
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bounds=lambda b: b is not None,
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):
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parent_bi_attrs = set(parent_variable.ncattrs()) & appendix_a_bi_attrs
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bounds_variable = reference_attr_variables(ds, parent_variable.bounds)[0]
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# nonexistent bounds variable, skip
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if isinstance(bounds_variable, VariableReferenceError):
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continue
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bounds_bi_ctx = self.get_test_ctx(
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BaseCheck.MEDIUM,
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self.section_titles["7.1"],
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)
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bounds_ncattr_set = set(bounds_variable.ncattrs())
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# IMPLEMENTATION CONFORMANCE 7.3 REQUIRED 4
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# A boundary variable can only have inheritable attributes, i.e. any of those marked "BI" in the "Use" column of Appendix A, if they are also present on its parent coordinate variable.
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bounds_bi_attrs = bounds_ncattr_set & appendix_a_bi_attrs
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# failure case 1, BI attr is only in bounds variable
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bounds_bi_only_attrs = bounds_bi_attrs - parent_bi_attrs
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# If a boundary variable has an inheritable attribute then its data type and its value must be exactly the same as the parent variable’s attribute.
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bounds_bi_ctx.out_of += 1
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if bounds_bi_only_attrs:
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bounds_bi_ctx.messages.append(
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f"Bounds variable {bounds_variable.name} has the following attributes which must appear on the parent variable {parent_variable.name}: "
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f"{sorted(bounds_bi_only_attrs)}",
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)
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else:
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bounds_bi_ctx.score += 1
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# failure case 2, BI attrs are in both bounds and parent variable
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both_bi_attr = bounds_bi_attrs & parent_bi_attrs
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no_match_attrs, match_attrs = [], []
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for bi_attr in both_bi_attr:
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bounds_bi_ctx.out_of += 1
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parent_attr_val = getattr(parent_variable, bi_attr)
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bounds_attr_val = getattr(bounds_variable, bi_attr)
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# IMPLEMENTATION CONFORMANCE 7.3 REQUIRED 5
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# If a boundary variable has an inheritable attribute then its data type and its value must be exactly the same as the parent variable’s attribute.
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if (
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type(parent_attr_val) is not type(bounds_attr_val)
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or parent_attr_val != bounds_attr_val
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):
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no_match_attrs.append(bi_attr)
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else:
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match_attrs.append(bi_attr)
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pass_bi_both = True
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if no_match_attrs:
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pass_bi_both = False
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bounds_bi_ctx.messages.append(
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f"Bounds variable {bounds_variable.name} and parent variable {parent_variable.name} have the following non matching boundary related attributes: {sorted(no_match_attrs)}",
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)
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if match_attrs:
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pass_bi_both = False
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bounds_bi_ctx.messages.append(
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f"Bounds variable {bounds_variable.name} and parent variable {parent_variable.name} have the following matching attributes {sorted(match_attrs)}. It is recommended that only the parent variable of the bounds variable contains these attributes",
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)
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bounds_bi_ctx.score += pass_bi_both
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results.append(bounds_bi_ctx.to_result())
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return results
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def check_single_cf_role(self, ds):
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test_ctx = self.get_test_ctx(
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BaseCheck.HIGH,

‎compliance_checker/tests/test_cf.py‎

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scored, out_of, _ = get_results(results)
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assert scored == 1 and out_of == 2
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@pytest.fixture
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def bounds_ds(self):
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ds = MockTimeSeries()
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ds.createDimension("bounds", 2)
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ds.createVariable("time_bounds", "f8", ("time", "bounds"))
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ds.variables["time"].bounds = "time_bounds"
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return ds
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def test_bounds_inherit_attributes(self, bounds_ds):
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# TEST CONFORMANCE 7.3 REQUIRED 4, 5
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results = self.cf.check_bounds_inherit_attributes(bounds_ds)
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scored, out_of, _ = get_results(results)
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assert scored == out_of
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time_bounds = bounds_ds.variables["time_bounds"]
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# expected failure, not in parent variable
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time_bounds.cf_role = "timeseries_id"
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# expected failure, differing value of BI attribute (no seconds)
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time_bounds.calendar = "gregorian"
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# repeated BI attributes variable aren't recommended
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time_bounds.axis = "T"
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results = self.cf.check_bounds_inherit_attributes(bounds_ds)
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scored, out_of, messages = get_results(results)
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assert scored < out_of
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expected_msgs = {
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"Bounds variable time_bounds has the following attributes which must appear on the parent variable time: ['cf_role']",
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"Bounds variable time_bounds and parent variable time have the following non matching boundary related attributes: ['calendar']",
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"Bounds variable time_bounds and parent variable time have the following matching attributes ['axis']. It is recommended that only the parent variable of the bounds variable contains these attributes",
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}
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assert expected_msgs == set(messages)
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def test_single_cf_role(self):
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ds = MockTimeSeries()
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ds.createDimension("ts_no")

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