Refresh model files for 1.11.0-rc3 #253
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,284 @@ | ||
| # Auto generated from array.yaml by pythongen.py version: 0.0.1 | ||
| # Generation date: 2026-05-05T18:49:10 | ||
| # Schema: arrays | ||
| # | ||
| # id: https://w3id.org/linkml/lib/arrays | ||
| # description: LinkML templates for storing one-dimensional series, two-dimensional arrays, and arrays of higher dimensionality. | ||
| # Status: Experimental | ||
| # Note that this model is not intended to be imported directly. Instead, use `implements` to denote conformance. | ||
| # license: https://creativecommons.org/publicdomain/zero/1.0/ | ||
|
|
||
| import dataclasses | ||
| import re | ||
| from dataclasses import dataclass | ||
| from datetime import ( | ||
| date, | ||
| datetime, | ||
| time | ||
| ) | ||
| from typing import ( | ||
| Any, | ||
| ClassVar, | ||
| Dict, | ||
| List, | ||
| Optional, | ||
| Union | ||
| ) | ||
|
|
||
| from jsonasobj2 import ( | ||
| JsonObj, | ||
| as_dict | ||
| ) | ||
| from linkml_runtime.utils.curienamespace import CurieNamespace | ||
| from linkml_runtime.utils.enumerations import EnumDefinitionImpl | ||
| from linkml_runtime.utils.formatutils import ( | ||
| camelcase, | ||
| sfx, | ||
| underscore | ||
| ) | ||
| from linkml_runtime.utils.metamodelcore import ( | ||
| bnode, | ||
| empty_dict, | ||
| empty_list | ||
| ) | ||
| from linkml_runtime.utils.slot import Slot | ||
| from linkml_runtime.utils.yamlutils import ( | ||
| YAMLRoot, | ||
| extended_float, | ||
| extended_int, | ||
| extended_str | ||
| ) | ||
| from rdflib import ( | ||
| Namespace, | ||
| URIRef | ||
| ) | ||
|
|
||
| from .types import Integer, String | ||
|
|
||
| metamodel_version = "1.7.0" | ||
| version = None | ||
|
|
||
| # Namespaces | ||
| GITHUB = CurieNamespace('github', 'https://github.com/') | ||
| GOM = CurieNamespace('gom', 'https://w3id.org/gom#') | ||
| LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/') | ||
| DEFAULT_ = LINKML | ||
|
|
||
|
|
||
| # Types | ||
|
|
||
| # Class references | ||
|
|
||
|
|
||
|
|
||
| Any = Any | ||
|
|
||
| class DataStructure(YAMLRoot): | ||
| _inherited_slots: ClassVar[list[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = LINKML["DataStructure"] | ||
| class_class_curie: ClassVar[str] = "linkml:DataStructure" | ||
| class_name: ClassVar[str] = "DataStructure" | ||
| class_model_uri: ClassVar[URIRef] = LINKML.DataStructure | ||
|
|
||
|
|
||
| @dataclass(repr=False) | ||
| class NDArray(DataStructure): | ||
| """ | ||
| a data structure consisting of a collection of *elements*, each identified by at least one array index tuple. | ||
| """ | ||
| _inherited_slots: ClassVar[list[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = LINKML["NDArray"] | ||
| class_class_curie: ClassVar[str] = "linkml:NDArray" | ||
| class_name: ClassVar[str] = "NDArray" | ||
| class_model_uri: ClassVar[URIRef] = LINKML.NDArray | ||
|
|
||
| elements: Union[Union[dict, Any], list[Union[dict, Any]]] = None | ||
|
Contributor
There was a problem hiding this comment. The type hint says that if self._is_empty(self.elements):
self.MissingRequiredField("elements")like in |
||
| dimensions: Optional[int] = None | ||
| array_linearization_order: Optional[Union[str, "ArrayLinearizationOrderOptions"]] = 'ROW_MAJOR_ARRAY_ORDER' | ||
|
|
||
| def __post_init__(self, *_: str, **kwargs: Any): | ||
| if self.dimensions is not None and not isinstance(self.dimensions, int): | ||
| self.dimensions = int(self.dimensions) | ||
|
|
||
| if self.array_linearization_order is not None and not isinstance(self.array_linearization_order, ArrayLinearizationOrderOptions): | ||
| self.array_linearization_order = ArrayLinearizationOrderOptions(self.array_linearization_order) | ||
|
|
||
| super().__post_init__(**kwargs) | ||
|
|
||
|
|
||
| @dataclass(repr=False) | ||
| class OneDimensionalSeries(NDArray): | ||
| """ | ||
| an NDArray whose dimensionality is constrained to 1 | ||
| """ | ||
| _inherited_slots: ClassVar[list[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = LINKML["OneDimensionalSeries"] | ||
| class_class_curie: ClassVar[str] = "linkml:OneDimensionalSeries" | ||
| class_name: ClassVar[str] = "OneDimensionalSeries" | ||
| class_model_uri: ClassVar[URIRef] = LINKML.OneDimensionalSeries | ||
|
|
||
| elements: Union[Union[dict, Any], list[Union[dict, Any]]] = None | ||
| dimensions: Optional[int] = None | ||
|
|
||
| def __post_init__(self, *_: str, **kwargs: Any): | ||
| if self.dimensions is not None and not isinstance(self.dimensions, int): | ||
| self.dimensions = int(self.dimensions) | ||
|
|
||
| super().__post_init__(**kwargs) | ||
|
|
||
|
|
||
| @dataclass(repr=False) | ||
| class DataArray(DataStructure): | ||
| """ | ||
| a data structure containing an NDArray and a set of one-dimensional series that are used to label the elements of | ||
| the array | ||
| """ | ||
| _inherited_slots: ClassVar[list[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = LINKML["DataArray"] | ||
| class_class_curie: ClassVar[str] = "linkml:DataArray" | ||
| class_name: ClassVar[str] = "DataArray" | ||
| class_model_uri: ClassVar[URIRef] = LINKML.DataArray | ||
|
|
||
| axis: Union[dict, OneDimensionalSeries] = None | ||
| array: Union[dict, NDArray] = None | ||
|
|
||
| def __post_init__(self, *_: str, **kwargs: Any): | ||
| if self._is_empty(self.axis): | ||
| self.MissingRequiredField("axis") | ||
| if not isinstance(self.axis, OneDimensionalSeries): | ||
| self.axis = OneDimensionalSeries(**as_dict(self.axis)) | ||
|
|
||
| if self._is_empty(self.array): | ||
| self.MissingRequiredField("array") | ||
| if not isinstance(self.array, NDArray): | ||
| self.array = NDArray(**as_dict(self.array)) | ||
|
|
||
| super().__post_init__(**kwargs) | ||
|
|
||
|
|
||
| class GroupingByArrayOrder(YAMLRoot): | ||
| """ | ||
| A mixin that describes an array whose elements are mapped from a linear sequence to an array index via a specified | ||
| mapping | ||
| """ | ||
| _inherited_slots: ClassVar[list[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = LINKML["GroupingByArrayOrder"] | ||
| class_class_curie: ClassVar[str] = "linkml:GroupingByArrayOrder" | ||
| class_name: ClassVar[str] = "GroupingByArrayOrder" | ||
| class_model_uri: ClassVar[URIRef] = LINKML.GroupingByArrayOrder | ||
|
|
||
|
|
||
| @dataclass(repr=False) | ||
| class ColumnOrderedArray(GroupingByArrayOrder): | ||
| """ | ||
| An array ordering that is column-order | ||
| """ | ||
| _inherited_slots: ClassVar[list[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = LINKML["ColumnOrderedArray"] | ||
| class_class_curie: ClassVar[str] = "linkml:ColumnOrderedArray" | ||
| class_name: ClassVar[str] = "ColumnOrderedArray" | ||
| class_model_uri: ClassVar[URIRef] = LINKML.ColumnOrderedArray | ||
|
|
||
| array_linearization_order: Optional[Union[str, "ArrayLinearizationOrderOptions"]] = 'COLUMN_MAJOR_ARRAY_ORDER' | ||
|
|
||
| def __post_init__(self, *_: str, **kwargs: Any): | ||
| if self.array_linearization_order is not None and not isinstance(self.array_linearization_order, ArrayLinearizationOrderOptions): | ||
| self.array_linearization_order = ArrayLinearizationOrderOptions(self.array_linearization_order) | ||
|
|
||
| super().__post_init__(**kwargs) | ||
|
|
||
|
|
||
| @dataclass(repr=False) | ||
| class RowOrderedArray(GroupingByArrayOrder): | ||
| """ | ||
| An array ordering that is row-order or generalizations thereof | ||
| """ | ||
| _inherited_slots: ClassVar[list[str]] = [] | ||
|
|
||
| class_class_uri: ClassVar[URIRef] = LINKML["RowOrderedArray"] | ||
| class_class_curie: ClassVar[str] = "linkml:RowOrderedArray" | ||
| class_name: ClassVar[str] = "RowOrderedArray" | ||
| class_model_uri: ClassVar[URIRef] = LINKML.RowOrderedArray | ||
|
|
||
| array_linearization_order: Optional[Union[str, "ArrayLinearizationOrderOptions"]] = 'ROW_MAJOR_ARRAY_ORDER' | ||
|
|
||
| def __post_init__(self, *_: str, **kwargs: Any): | ||
| if self.array_linearization_order is not None and not isinstance(self.array_linearization_order, ArrayLinearizationOrderOptions): | ||
| self.array_linearization_order = ArrayLinearizationOrderOptions(self.array_linearization_order) | ||
|
|
||
| super().__post_init__(**kwargs) | ||
|
|
||
|
|
||
| # Enumerations | ||
| class ArrayLinearizationOrderOptions(EnumDefinitionImpl): | ||
| """ | ||
| Determines how a linear contiguous representation of the elements of an array map to array indices | ||
| """ | ||
| COLUMN_MAJOR_ARRAY_ORDER = PermissibleValue( | ||
|
Contributor
There was a problem hiding this comment. Sorry, I'm looking at this in more detail now. Claude flagged this -- |
||
| text="COLUMN_MAJOR_ARRAY_ORDER", | ||
| description="""An array layout option in which the elements in each column is stored in consecutive positions, or any generalization thereof to dimensionality greater than 2""", | ||
| meaning=GOM["columnMajorArray"]) | ||
| ROW_MAJOR_ARRAY_ORDER = PermissibleValue( | ||
| text="ROW_MAJOR_ARRAY_ORDER", | ||
| description="""An array layout option in which the elements in each row is stored in consecutive positions, or any generalization thereof to dimensionality greater than 2""", | ||
| meaning=GOM["rowMajorArray"]) | ||
|
|
||
| _defn = EnumDefinition( | ||
|
|
||
| name="ArrayLinearizationOrderOptions", | ||
| description="Determines how a linear contiguous representation of the elements of an array map to array indices", | ||
| ) | ||
|
|
||
| # Slots | ||
| class slots: | ||
| pass | ||
|
|
||
| slots.dimensions = Slot(uri=LINKML.dimensions, name="dimensions", curie=LINKML.curie('dimensions'), | ||
| model_uri=LINKML.dimensions, domain=None, range=Optional[int]) | ||
|
|
||
| slots.axis = Slot(uri=LINKML.axis, name="axis", curie=LINKML.curie('axis'), | ||
| model_uri=LINKML.axis, domain=None, range=Union[dict, OneDimensionalSeries]) | ||
|
|
||
| slots.axis_index = Slot(uri=LINKML.axis_index, name="axis_index", curie=LINKML.curie('axis_index'), | ||
| model_uri=LINKML.axis_index, domain=None, range=Optional[int]) | ||
|
|
||
| slots.array = Slot(uri=LINKML.array, name="array", curie=LINKML.curie('array'), | ||
| model_uri=LINKML.array, domain=None, range=Union[dict, NDArray]) | ||
|
|
||
| slots.elements = Slot(uri=LINKML.elements, name="elements", curie=LINKML.curie('elements'), | ||
| model_uri=LINKML.elements, domain=None, range=Union[Union[dict, Any], list[Union[dict, Any]]]) | ||
|
|
||
| slots.series_label = Slot(uri=LINKML.series_label, name="series_label", curie=LINKML.curie('series_label'), | ||
| model_uri=LINKML.series_label, domain=None, range=URIRef) | ||
|
|
||
| slots.length = Slot(uri=LINKML.length, name="length", curie=LINKML.curie('length'), | ||
| model_uri=LINKML.length, domain=None, range=Optional[int]) | ||
|
|
||
| slots.array_linearization_order = Slot(uri=LINKML.array_linearization_order, name="array_linearization_order", curie=LINKML.curie('array_linearization_order'), | ||
| model_uri=LINKML.array_linearization_order, domain=None, range=Optional[Union[str, "ArrayLinearizationOrderOptions"]]) | ||
|
|
||
| slots.specified_input = Slot(uri=LINKML.specified_input, name="specified_input", curie=LINKML.curie('specified_input'), | ||
| model_uri=LINKML.specified_input, domain=None, range=Optional[Union[Union[dict, DataStructure], list[Union[dict, DataStructure]]]]) | ||
|
|
||
| slots.specified_output = Slot(uri=LINKML.specified_output, name="specified_output", curie=LINKML.curie('specified_output'), | ||
| model_uri=LINKML.specified_output, domain=None, range=Optional[Union[Union[dict, DataStructure], list[Union[dict, DataStructure]]]]) | ||
|
|
||
| slots.operation_parameters = Slot(uri=LINKML.operation_parameters, name="operation_parameters", curie=LINKML.curie('operation_parameters'), | ||
| model_uri=LINKML.operation_parameters, domain=None, range=Optional[Union[Union[dict, Any], list[Union[dict, Any]]]]) | ||
|
|
||
| slots.NDArray_elements = Slot(uri=LINKML.elements, name="NDArray_elements", curie=LINKML.curie('elements'), | ||
| model_uri=LINKML.NDArray_elements, domain=NDArray, range=Union[Union[dict, Any], list[Union[dict, Any]]]) | ||
|
|
||
| slots.OneDimensionalSeries_dimensions = Slot(uri=LINKML.dimensions, name="OneDimensionalSeries_dimensions", curie=LINKML.curie('dimensions'), | ||
| model_uri=LINKML.OneDimensionalSeries_dimensions, domain=OneDimensionalSeries, range=Optional[int]) | ||
|
|
||
| slots.ColumnOrderedArray_array_linearization_order = Slot(uri=LINKML.array_linearization_order, name="ColumnOrderedArray_array_linearization_order", curie=LINKML.curie('array_linearization_order'), | ||
| model_uri=LINKML.ColumnOrderedArray_array_linearization_order, domain=None, range=Optional[Union[str, "ArrayLinearizationOrderOptions"]]) | ||
|
|
||
| slots.RowOrderedArray_array_linearization_order = Slot(uri=LINKML.array_linearization_order, name="RowOrderedArray_array_linearization_order", curie=LINKML.curie('array_linearization_order'), | ||
| model_uri=LINKML.RowOrderedArray_array_linearization_order, domain=None, range=Optional[Union[str, "ArrayLinearizationOrderOptions"]]) | ||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file not shown.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| # metamodel_version: 1.11.0 | ||
| enum AliasPredicateEnum | ||
| { | ||
| EXACT_SYNONYM | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Uh oh!
There was an error while loading. Please reload this page.