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https://github.com/p2p-ld/nwb-linkml.git
synced 2024-09-19 15:34:28 +00:00
[tests] nocover stuff that's just from the source module
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parent
a0d96014e1
commit
c215e69fd8
2 changed files with 36 additions and 29 deletions
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@ -254,7 +254,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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skips = ('AnyType',)
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for cls in needed_classes:
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if cls in skips:
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if cls in skips: # pragma: no cover
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continue
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# Find module that contains class
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module_name = sv.element_by_schema_map()[ElementName(cls)]
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@ -306,7 +306,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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needed_classes.append(cls.is_a)
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# get needed classes used as ranges in class attributes
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for slot in class_slots[cls.name]:
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if slot.name in self.SKIP_SLOTS:
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if slot.name in self.SKIP_SLOTS: # pragma: no cover
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continue
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if slot.range in all_classes:
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needed_classes.append(slot.range)
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@ -417,7 +417,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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# all dimensions should be the same dtype
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try:
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dtype = flat_to_npytyping[list(attrs.values())[0].range]
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except KeyError as e:
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except KeyError as e: # pragma: no cover
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warnings.warn(str(e))
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range = list(attrs.values())[0].range
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return f'List[{range}] | {range}'
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@ -428,7 +428,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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def _get_numpy_slot_range(self, cls:ClassDefinition) -> str:
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# if none of the dimensions are optional, we just have one possible array shape
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if all([s.required for s in cls.attributes.values()]):
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if all([s.required for s in cls.attributes.values()]): # pragma: no cover
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return self._make_npytyping_range(cls.attributes)
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# otherwise we need to make permutations
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# but not all permutations, because we typically just want to be able to exlude the last possible dimensions
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@ -500,7 +500,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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slist = slist + [candidate]
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del clist[i]
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break
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if not can_add:
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if not can_add: # pragma: no cover
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raise ValueError(
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f"could not find suitable element in {clist} that does not ref {slist}"
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)
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@ -525,12 +525,14 @@ class NWBPydanticGenerator(PydanticGenerator):
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Parent class get class range
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Overriding to not use strings in the type hint when a class has an identifier value
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Not testing this method except for what we changes
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"""
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sv = self.schemaview
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range_cls = sv.get_class(slot_range)
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# Hardcoded handling for Any
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if range_cls.class_uri == "linkml:Any":
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if range_cls.class_uri == "linkml:Any": # pragma: no cover
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return "Any"
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# Inline the class itself only if the class is defined as inline, or if the class has no
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@ -546,7 +548,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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if (
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len([x for x in sv.class_induced_slots(slot_range) if x.designates_type]) > 0
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and len(sv.class_descendants(slot_range)) > 1
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):
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): # pragma: no cover
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return (
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"Union["
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+ ",".join([camelcase(c) for c in sv.class_descendants(slot_range)])
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@ -556,26 +558,17 @@ class NWBPydanticGenerator(PydanticGenerator):
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return f"{camelcase(slot_range)}"
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# For the more difficult cases, set string as the default and attempt to improve it
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range_cls_identifier_slot_range = "str"
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range_cls_identifier_slot_range = "str" # pragma: no cover
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# For mixins, try to use the identifier slot of descendant classes
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if (
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self.gen_mixin_inheritance
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and sv.is_mixin(range_cls.name)
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and sv.get_identifier_slot(range_cls.name)
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):
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): # pragma: no cover
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range_cls_identifier_slot_range = self.get_mixin_identifier_range(range_cls)
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# If the class itself has an identifier slot, it can be allowed to overwrite a value from mixin above
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# if (
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# sv.get_identifier_slot(range_cls.name) is not None
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# and sv.get_identifier_slot(range_cls.name).range is not None
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# ):
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# range_cls_identifier_slot_range = _get_pyrange(
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# sv.get_type(sv.get_identifier_slot(range_cls.name).range), sv
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# )
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return range_cls_identifier_slot_range
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return range_cls_identifier_slot_range # pragma: no cover
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def get_class_isa_plus_mixins(self, classes:Optional[List[ClassDefinition]] = None) -> Dict[str, List[str]]:
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@ -587,7 +580,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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:return:
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"""
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sv = self.schemaview
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if classes is None:
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if classes is None: # pragma: no cover
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classes = sv.all_classes(imports=False).values()
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parents = {}
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@ -595,7 +588,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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class_parents = []
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if class_def.is_a:
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class_parents.append(camelcase(class_def.is_a))
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if self.gen_mixin_inheritance and class_def.mixins:
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if self.gen_mixin_inheritance and class_def.mixins: # pragma: no cover
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class_parents.extend([camelcase(mixin) for mixin in class_def.mixins])
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if len(class_parents) > 0:
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# Use the sorted list of classes to order the parent classes, but reversed to match MRO needs
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@ -636,7 +629,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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if slot.inlined and not slot.inlined_as_list: # and has_identifier_slot:
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slot_value = "default_factory=dict"
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else:
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else: # pragma: no cover
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slot_value = "default_factory=list"
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return slot_value
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@ -686,7 +679,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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# skip actually generating arraylike classes, just use them to generate
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# the npytyping annotations
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pyschema.classes[class_def.name] = class_def
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else:
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else: # pragma: no cover
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continue
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# Not sure why this happens
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@ -729,7 +722,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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# model classes, we allow container classes to also
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# be generic descendants of BaseModel
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# --------------------------------------------------
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if 'DynamicTable' in pyranges:
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if 'DynamicTable' in pyranges: # pragma: no cover
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pyranges.append('BaseModel')
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pyranges = list(set(pyranges)) # remove duplicates
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@ -739,15 +732,15 @@ class NWBPydanticGenerator(PydanticGenerator):
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pyrange = pyranges[0]
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elif len(pyranges) > 1:
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pyrange = f"Union[{', '.join(pyranges)}]"
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else:
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else: # pragma: no cover
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raise Exception(f"Could not generate python range for {class_name}.{s.name}")
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if s.multivalued:
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if s.inlined or s.inlined_as_list:
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collection_key = self.generate_collection_key(slot_ranges, s, class_def)
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else:
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else: # pragma: no cover
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collection_key = None
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if s.inlined is False or collection_key is None or s.inlined_as_list is True:
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if s.inlined is False or collection_key is None or s.inlined_as_list is True: # pragma: no cover
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pyrange = f"List[{pyrange}]"
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else:
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pyrange = f"Dict[{collection_key}, {pyrange}]"
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@ -770,7 +763,7 @@ class NWBPydanticGenerator(PydanticGenerator):
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)
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return code
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def compile_module(self, module_path:Path=None, module_name:str='test') -> ModuleType: # pragma: no cover - replaced with provider
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def compile_module(self, module_path:Path=None, module_name:str='test') -> ModuleType:
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"""
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Compiles generated python code to a module
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:return:
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@ -164,7 +164,8 @@ def test_versions(linkml_schema):
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core_str = NWBPydanticGenerator(
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str(linkml_schema.core_path),
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versions={'imported': 'v4.2.0'}
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versions={'imported': 'v4.2.0'},
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split=False
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).serialize()
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# the import should be like
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@ -174,6 +175,19 @@ def test_versions(linkml_schema):
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match = re.findall(r'from \.\.\.imported\.v4_2_0.*?MainThing.*?\)', core_str, flags=re.DOTALL)
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assert len(match) == 1
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core_str = NWBPydanticGenerator(
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str(linkml_schema.core_path),
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versions={'imported': 'v4.2.0'},
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split=True
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).serialize()
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# the import should be like
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# from ...imported.v4_2_0.namespace import (
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# MainThing
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# )
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match = re.findall(r'from \.\.\.imported\.v4_2_0\.namespace.*?MainThing.*?\)', core_str, flags=re.DOTALL)
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assert len(match) == 1
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def test_arraylike(imported_schema):
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"""
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