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[tests] nocover stuff that's just from the source module

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sneakers-the-rat 2023-10-05 21:35:25 -07:00
parent a0d96014e1
commit c215e69fd8
2 changed files with 36 additions and 29 deletions
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49
nwb_linkml/src/nwb_linkml/generators/pydantic.py
View file

@ -254,7 +254,7 @@ class NWBPydanticGenerator(PydanticGenerator):
skips = ('AnyType',) skips = ('AnyType',)
for cls in needed_classes: for cls in needed_classes:
if cls in skips: if cls in skips: # pragma: no cover
continue continue
# Find module that contains class # Find module that contains class
module_name = sv.element_by_schema_map()[ElementName(cls)] module_name = sv.element_by_schema_map()[ElementName(cls)]
@ -306,7 +306,7 @@ class NWBPydanticGenerator(PydanticGenerator):
needed_classes.append(cls.is_a) needed_classes.append(cls.is_a)
# get needed classes used as ranges in class attributes # get needed classes used as ranges in class attributes
for slot in class_slots[cls.name]: for slot in class_slots[cls.name]:
if slot.name in self.SKIP_SLOTS: if slot.name in self.SKIP_SLOTS: # pragma: no cover
continue continue
if slot.range in all_classes: if slot.range in all_classes:
needed_classes.append(slot.range) needed_classes.append(slot.range)
@ -417,7 +417,7 @@ class NWBPydanticGenerator(PydanticGenerator):
# all dimensions should be the same dtype # all dimensions should be the same dtype
try: try:
dtype = flat_to_npytyping[list(attrs.values())[0].range] dtype = flat_to_npytyping[list(attrs.values())[0].range]
except KeyError as e: except KeyError as e: # pragma: no cover
warnings.warn(str(e)) warnings.warn(str(e))
range = list(attrs.values())[0].range range = list(attrs.values())[0].range
return f'List[{range}] | {range}' return f'List[{range}] | {range}'
@ -428,7 +428,7 @@ class NWBPydanticGenerator(PydanticGenerator):
def _get_numpy_slot_range(self, cls:ClassDefinition) -> str: def _get_numpy_slot_range(self, cls:ClassDefinition) -> str:
# if none of the dimensions are optional, we just have one possible array shape # if none of the dimensions are optional, we just have one possible array shape
if all([s.required for s in cls.attributes.values()]): if all([s.required for s in cls.attributes.values()]): # pragma: no cover
return self._make_npytyping_range(cls.attributes) return self._make_npytyping_range(cls.attributes)
# otherwise we need to make permutations # otherwise we need to make permutations
# but not all permutations, because we typically just want to be able to exlude the last possible dimensions # but not all permutations, because we typically just want to be able to exlude the last possible dimensions
@ -500,7 +500,7 @@ class NWBPydanticGenerator(PydanticGenerator):
slist = slist + [candidate] slist = slist + [candidate]
del clist[i] del clist[i]
break break
if not can_add: if not can_add: # pragma: no cover
raise ValueError( raise ValueError(
f"could not find suitable element in {clist} that does not ref {slist}" f"could not find suitable element in {clist} that does not ref {slist}"
) )
@ -525,12 +525,14 @@ class NWBPydanticGenerator(PydanticGenerator):
Parent class get class range Parent class get class range
Overriding to not use strings in the type hint when a class has an identifier value Overriding to not use strings in the type hint when a class has an identifier value
Not testing this method except for what we changes
""" """
sv = self.schemaview sv = self.schemaview
range_cls = sv.get_class(slot_range) range_cls = sv.get_class(slot_range)
# Hardcoded handling for Any # Hardcoded handling for Any
if range_cls.class_uri == "linkml:Any": if range_cls.class_uri == "linkml:Any": # pragma: no cover
return "Any" return "Any"
# Inline the class itself only if the class is defined as inline, or if the class has no # Inline the class itself only if the class is defined as inline, or if the class has no
@ -546,7 +548,7 @@ class NWBPydanticGenerator(PydanticGenerator):
if ( if (
len([x for x in sv.class_induced_slots(slot_range) if x.designates_type]) > 0 len([x for x in sv.class_induced_slots(slot_range) if x.designates_type]) > 0
and len(sv.class_descendants(slot_range)) > 1 and len(sv.class_descendants(slot_range)) > 1
): ): # pragma: no cover
return ( return (
"Union[" "Union["
+ ",".join([camelcase(c) for c in sv.class_descendants(slot_range)]) + ",".join([camelcase(c) for c in sv.class_descendants(slot_range)])
@ -556,26 +558,17 @@ class NWBPydanticGenerator(PydanticGenerator):
return f"{camelcase(slot_range)}" return f"{camelcase(slot_range)}"
# For the more difficult cases, set string as the default and attempt to improve it # For the more difficult cases, set string as the default and attempt to improve it
range_cls_identifier_slot_range = "str" range_cls_identifier_slot_range = "str" # pragma: no cover
# For mixins, try to use the identifier slot of descendant classes # For mixins, try to use the identifier slot of descendant classes
if ( if (
self.gen_mixin_inheritance self.gen_mixin_inheritance
and sv.is_mixin(range_cls.name) and sv.is_mixin(range_cls.name)
and sv.get_identifier_slot(range_cls.name) and sv.get_identifier_slot(range_cls.name)
): ): # pragma: no cover
range_cls_identifier_slot_range = self.get_mixin_identifier_range(range_cls) range_cls_identifier_slot_range = self.get_mixin_identifier_range(range_cls)
# If the class itself has an identifier slot, it can be allowed to overwrite a value from mixin above return range_cls_identifier_slot_range # pragma: no cover
# if (
# sv.get_identifier_slot(range_cls.name) is not None
# and sv.get_identifier_slot(range_cls.name).range is not None
# ):
# range_cls_identifier_slot_range = _get_pyrange(
# sv.get_type(sv.get_identifier_slot(range_cls.name).range), sv
# )
return range_cls_identifier_slot_range
def get_class_isa_plus_mixins(self, classes:Optional[List[ClassDefinition]] = None) -> Dict[str, List[str]]: def get_class_isa_plus_mixins(self, classes:Optional[List[ClassDefinition]] = None) -> Dict[str, List[str]]:
@ -587,7 +580,7 @@ class NWBPydanticGenerator(PydanticGenerator):
:return: :return:
""" """
sv = self.schemaview sv = self.schemaview
if classes is None: if classes is None: # pragma: no cover
classes = sv.all_classes(imports=False).values() classes = sv.all_classes(imports=False).values()
parents = {} parents = {}
@ -595,7 +588,7 @@ class NWBPydanticGenerator(PydanticGenerator):
class_parents = [] class_parents = []
if class_def.is_a: if class_def.is_a:
class_parents.append(camelcase(class_def.is_a)) class_parents.append(camelcase(class_def.is_a))
if self.gen_mixin_inheritance and class_def.mixins: if self.gen_mixin_inheritance and class_def.mixins: # pragma: no cover
class_parents.extend([camelcase(mixin) for mixin in class_def.mixins]) class_parents.extend([camelcase(mixin) for mixin in class_def.mixins])
if len(class_parents) > 0: if len(class_parents) > 0:
# Use the sorted list of classes to order the parent classes, but reversed to match MRO needs # Use the sorted list of classes to order the parent classes, but reversed to match MRO needs
@ -636,7 +629,7 @@ class NWBPydanticGenerator(PydanticGenerator):
if slot.inlined and not slot.inlined_as_list: # and has_identifier_slot: if slot.inlined and not slot.inlined_as_list: # and has_identifier_slot:
slot_value = "default_factory=dict" slot_value = "default_factory=dict"
else: else: # pragma: no cover
slot_value = "default_factory=list" slot_value = "default_factory=list"
return slot_value return slot_value
@ -686,7 +679,7 @@ class NWBPydanticGenerator(PydanticGenerator):
# skip actually generating arraylike classes, just use them to generate # skip actually generating arraylike classes, just use them to generate
# the npytyping annotations # the npytyping annotations
pyschema.classes[class_def.name] = class_def pyschema.classes[class_def.name] = class_def
else: else: # pragma: no cover
continue continue
# Not sure why this happens # Not sure why this happens
@ -729,7 +722,7 @@ class NWBPydanticGenerator(PydanticGenerator):
# model classes, we allow container classes to also # model classes, we allow container classes to also
# be generic descendants of BaseModel # be generic descendants of BaseModel
# -------------------------------------------------- # --------------------------------------------------
if 'DynamicTable' in pyranges: if 'DynamicTable' in pyranges: # pragma: no cover
pyranges.append('BaseModel') pyranges.append('BaseModel')
pyranges = list(set(pyranges)) # remove duplicates pyranges = list(set(pyranges)) # remove duplicates
@ -739,15 +732,15 @@ class NWBPydanticGenerator(PydanticGenerator):
pyrange = pyranges[0] pyrange = pyranges[0]
elif len(pyranges) > 1: elif len(pyranges) > 1:
pyrange = f"Union[{', '.join(pyranges)}]" pyrange = f"Union[{', '.join(pyranges)}]"
else: else: # pragma: no cover
raise Exception(f"Could not generate python range for {class_name}.{s.name}") raise Exception(f"Could not generate python range for {class_name}.{s.name}")
if s.multivalued: if s.multivalued:
if s.inlined or s.inlined_as_list: if s.inlined or s.inlined_as_list:
collection_key = self.generate_collection_key(slot_ranges, s, class_def) collection_key = self.generate_collection_key(slot_ranges, s, class_def)
else: else: # pragma: no cover
collection_key = None collection_key = None
if s.inlined is False or collection_key is None or s.inlined_as_list is True: if s.inlined is False or collection_key is None or s.inlined_as_list is True: # pragma: no cover
pyrange = f"List[{pyrange}]" pyrange = f"List[{pyrange}]"
else: else:
pyrange = f"Dict[{collection_key}, {pyrange}]" pyrange = f"Dict[{collection_key}, {pyrange}]"
@ -770,7 +763,7 @@ class NWBPydanticGenerator(PydanticGenerator):
) )
return code return code
def compile_module(self, module_path:Path=None, module_name:str='test') -> ModuleType: # pragma: no cover - replaced with provider def compile_module(self, module_path:Path=None, module_name:str='test') -> ModuleType:
""" """
Compiles generated python code to a module Compiles generated python code to a module
:return: :return:

16
nwb_linkml/tests/test_generators/test_generator_pydantic.py
View file

@ -164,7 +164,8 @@ def test_versions(linkml_schema):
core_str = NWBPydanticGenerator( core_str = NWBPydanticGenerator(
str(linkml_schema.core_path), str(linkml_schema.core_path),
versions={'imported': 'v4.2.0'} versions={'imported': 'v4.2.0'},
split=False
).serialize() ).serialize()
# the import should be like # the import should be like
@ -174,6 +175,19 @@ def test_versions(linkml_schema):
match = re.findall(r'from \.\.\.imported\.v4_2_0.*?MainThing.*?\)', core_str, flags=re.DOTALL) match = re.findall(r'from \.\.\.imported\.v4_2_0.*?MainThing.*?\)', core_str, flags=re.DOTALL)
assert len(match) == 1 assert len(match) == 1
core_str = NWBPydanticGenerator(
str(linkml_schema.core_path),
versions={'imported': 'v4.2.0'},
split=True
).serialize()
# the import should be like
# from ...imported.v4_2_0.namespace import (
# MainThing
# )
match = re.findall(r'from \.\.\.imported\.v4_2_0\.namespace.*?MainThing.*?\)', core_str, flags=re.DOTALL)
assert len(match) == 1
def test_arraylike(imported_schema): def test_arraylike(imported_schema):
""" """