8000 Throw warning for variadic notation for non-variadic names by lukaspie · Pull Request #591 · FAIRmat-NFDI/pynxtools · GitHub
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Throw warning for variadic notation for non-variadic names #591

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Throw warning for variadic notation for non-variadic names #591

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2862f39
warning for variadic notation for non-variadic names
lukaspie Mar 20, 2025
3579f43
allow concept names for non-variadic groups if the concept name match…
lukaspie Apr 9, 2025
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1 change: 1 addition & 0 deletions src/pynxtools/data/NXtest.nxdl.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,7 @@
</group>
<group name="identified_calibration" type="NXcalibration" optional="true">
<field name="identifier_1"/>
<field name="identifier_2" optional="True"/>
</group>
<group name="named_collection" type="NXcollection" optional="true"/>
</group>
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7 changes: 7 additions & 0 deletions src/pynxtools/dataconverter/helpers.py
8000
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Expand Up @@ -67,6 +67,7 @@ class ValidationProblem(Enum):
NXdataMissingAxisData = 19
NXdataAxisMismatch = 20
KeyToBeRemoved = 21
InvalidConceptForNonVariadic = 22


class Collector:
Expand Down Expand Up @@ -151,6 +152,12 @@ def _log(self, path: str, log_type: ValidationProblem, value: Optional[Any], *ar
elif log_type == ValidationProblem.KeyToBeRemoved:
logger.warning(f"The attribute {path} will not be written.")

elif log_type == ValidationProblem.InvalidConceptForNonVariadic:
log_text = f"Given {value.type} name '{path}' conflicts with the non-variadic name '{value}'"
if value.type == "group":
log_text += f", which should be of type {value.nx_class}."
logger.warning(log_text)

def collect_and_log(
self,
path: str,
Expand Down
16 changes: 16 additions & 0 deletions src/pynxtools/dataconverter/validation.py
10000
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Expand Up @@ -155,6 +155,22 @@ def best_namefit_of(name: str, nodes: Iterable[NexusNode]) -> Optional[NexusNode
for node in nodes:
if not node.variadic:
if instance_name == node.name:
if concept_name and concept_name != node.name:
if node.type == "group":
if concept_name != node.nx_class[2:].upper():
collector.collect_and_log(
concept_name,
ValidationProblem.InvalidConceptForNonVariadic,
node,
)
return None
else:
collector.collect_and_log(
concept_name,
ValidationProblem.InvalidConceptForNonVariadic,
node,
)
return None
return node
else:
if concept_name and concept_name == node.name:
Expand Down
69 changes: 63 additions & 6 deletions tests/dataconverter/test_validation.py
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Expand Up @@ -719,6 +719,32 @@ def listify_template(data_dict: Template):
[],
id="no-child-provided-optional-parent",
),
pytest.param(
alter_dict(
remove_from_dict(
remove_from_dict(
remove_from_dict(
TEMPLATE,
"/ENTRY[my_entry]/specified_group/specified_field",
"required",
),
"/ENTRY[my_entry]/specified_group/specified_field/@specified_attr_in_field",
"required",
),
"/ENTRY[my_entry]/specified_group/@specified_attr",
"required",
),
"/ENTRY[my_entry]/SAMPLE[specified_group]/specified_field",
1.0,
),
[
"The required group, /ENTRY[my_entry]/specified_group, hasn't been supplied.",
"Given group name 'SAMPLE' conflicts with the non-variadic name 'specified_group (req)', "
"which should be of type NXdata.",
"Field /ENTRY[my_entry]/SAMPLE[specified_group]/specified_field written without documentation.",
],
id="illegal-concept-name-for-nonvariadic-group",
),
pytest.param(
alter_dict(
remove_from_dict(
Expand All @@ -729,10 +755,13 @@ def listify_template(data_dict: Template):
"/ENTRY[my_entry]/optional_parent/AXISNAME[required_child]",
1,
),
# ToDo: should not raise a warning if sibling inheritance works
# TODO: should not raise a warning if sibling inheritance works
[
"The data entry corresponding to /ENTRY[my_entry]/optional_parent/"
"required_child is required and hasn't been supplied by the reader."
"required_child is required and hasn't been supplied by the reader.",
"Given field name 'AXISNAME' conflicts with the non-variadic name "
"'required_child (req)'",
"Field /ENTRY[my_entry]/optional_parent/AXISNAME[required_child] written without documentation.",
],
id="concept-name-given-for-nonvariadic-field",
),
Expand All @@ -747,9 +776,12 @@ def listify_template(data_dict: Template):
"test value",
),
[
"The value at /ENTRY[my_entry]/optional_parent/AXISNAME[optional_child] should be "
"one of the following Python types: (<class 'int'>, <class 'numpy.integer'>), as "
"defined in the NXDL as NX_INT."
"Given field name 'AXISNAME' conflicts with the non-variadic name 'optional_child (opt)'",
"Field /ENTRY[my_entry]/optional_parent/AXISNAME[optional_child] written without documentation.",
# TODO: reactivate if sibling inheritance works
# # "The value at /ENTRY[my_entry]/optional_parent/AXISNAME[optional_child] should be "
# "one of the following Python types: (<class 'int'>, <class 'numpy.integer'>), as "
# "defined in the NXDL as NX_INT."
],
id="concept-name-given-for-nonvariadic-field-wrong-type",
),
Expand Down Expand Up @@ -1053,7 +1085,7 @@ def listify_template(data_dict: Template):
"123",
),
[],
id="specified-identifier-with-type",
id="specified-identifier-without-type",
),
# ToDo: reactivate if sibling inheritance works properly
# pytest.param(
Expand Down Expand Up @@ -1095,6 +1127,31 @@ def listify_template(data_dict: Template):
[],
id="name-fitted-identifier-with-type",
),
pytest.param(
alter_dict(
TEMPLATE,
"/ENTRY[my_entry]/CALIBRATION[identified_calibration]/identifier_1",
"123",
),
[],
id="group-with-correct-concept",
),
pytest.param(
alter_dict(
alter_dict(
TEMPLATE,
"/ENTRY[my_entry]/CALIBRATION[identified_calibration]/identifier_1",
"123",
),
"/ENTRY[my_entry]/identified_calibration/identifier_2",
"456",
),
[
"The data entry corresponding to /ENTRY[my_entry]/identified_calibration/identifier_1 is required "
"and hasn't been supplied by the reader."
],
id="group-with-correct-concept-and-non-concept-sibling",
),
# This can be re-used later when we have proper unit checking
pytest.param(
alter_dict(
Expand Down
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