fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/controlled_terms/__init__.py

@@ -0,0 +1,116 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import EmbeddedMetadata
+
+from .action_status_type import ActionStatusType
+from .age_category import AgeCategory
+from .analysis_technique import AnalysisTechnique
+from .anatomical_axes_orientation import AnatomicalAxesOrientation
+from .anatomical_identification_type import AnatomicalIdentificationType
+from .anatomical_plane import AnatomicalPlane
+from .annotation_criteria_type import AnnotationCriteriaType
+from .annotation_type import AnnotationType
+from .atlas_type import AtlasType
+from .auditory_stimulus_type import AuditoryStimulusType
+from .biological_order import BiologicalOrder
+from .biological_process import BiologicalProcess
+from .biological_sex import BiologicalSex
+from .breeding_type import BreedingType
+from .cell_culture_type import CellCultureType
+from .cell_type import CellType
+from .chemical_mixture_type import ChemicalMixtureType
+from .colormap import Colormap
+from .contribution_type import ContributionType
+from .cranial_window_construction_type import CranialWindowConstructionType
+from .cranial_window_reinforcement_type import CranialWindowReinforcementType
+from .criteria_quality_type import CriteriaQualityType
+from .data_type import DataType
+from .device_type import DeviceType
+from .difference_measure import DifferenceMeasure
+from .disease import Disease
+from .disease_model import DiseaseModel
+from .educational_level import EducationalLevel
+from .electrical_stimulus_type import ElectricalStimulusType
+from .ethics_assessment import EthicsAssessment
+from .experimental_approach import ExperimentalApproach
+from .file_bundle_grouping import FileBundleGrouping
+from .file_repository_type import FileRepositoryType
+from .file_usage_role import FileUsageRole
+from .genetic_strain_type import GeneticStrainType
+from .gustatory_stimulus_type import GustatoryStimulusType
+from .handedness import Handedness
+from .language import Language
+from .laterality import Laterality
+from .learning_resource_type import LearningResourceType
+from .measured_quantity import MeasuredQuantity
+from .measured_signal_type import MeasuredSignalType
+from .meta_data_model_type import MetaDataModelType
+from .model_abstraction_level import ModelAbstractionLevel
+from .model_scope import ModelScope
+from .molecular_entity import MolecularEntity
+from .mri_pulse_sequence import MRIPulseSequence
+from .mri_weighting import MRIWeighting
+from .olfactory_stimulus_type import OlfactoryStimulusType
+from .operating_device import OperatingDevice
+from .operating_system import OperatingSystem
+from .optical_stimulus_type import OpticalStimulusType
+from .organ import Organ
+from .organism_substance import OrganismSubstance
+from .organism_system import OrganismSystem
+from .patch_clamp_variation import PatchClampVariation
+from .preparation_type import PreparationType
+from .product_accessibility import ProductAccessibility
+from .programming_language import ProgrammingLanguage
+from .qualitative_overlap import QualitativeOverlap
+from .semantic_data_type import SemanticDataType
+from .service import Service
+from .setup_type import SetupType
+from .software_application_category import SoftwareApplicationCategory
+from .software_feature import SoftwareFeature
+from .species import Species
+from .stimulation_approach import StimulationApproach
+from .stimulation_technique import StimulationTechnique
+from .subcellular_entity import SubcellularEntity
+from .subject_attribute import SubjectAttribute
+from .tactile_stimulus_type import TactileStimulusType
+from .technique import Technique
+from .term_suggestion import TermSuggestion
+from .terminology import Terminology
+from .tissue_sample_attribute import TissueSampleAttribute
+from .tissue_sample_type import TissueSampleType
+from .type_of_uncertainty import TypeOfUncertainty
+from .uberon_parcellation import UBERONParcellation
+from .unit_of_measurement import UnitOfMeasurement
+from .visual_stimulus_type import VisualStimulusType
+
+
+def list_kg_classes():
+    """List all KG classes defined in this module"""
+    return [
+        obj
+        for name, obj in inspect.getmembers(sys.modules[__name__])
+        if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)
+    ]
+
+
+def list_embedded_metadata_classes():
+    """List all embedded metadata classes defined in this module"""
+    return [
+        obj
+        for name, obj in inspect.getmembers(sys.modules[__name__])
+        if inspect.isclass(obj) and issubclass(obj, EmbeddedMetadata) and obj.__module__.startswith(__name__)
+    ]
+
+
+def set_error_handling(value):
+    """
+    Control validation for all classes in this module.
+
+    Args:
+        value (str): action to follow when there is a validation failure.
+            (e.g. if a required property is not provided).
+            Possible values: "error", "warning", "log", None
+    """
+    for cls in list_kg_classes() + list_embedded_metadata_classes():
+        cls.set_error_handling(value)

fairgraph/openminds/controlled_terms/action_status_type.py

@@ -0,0 +1,97 @@
+"""
+Structured information about the status of an action.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.controlled_terms import ActionStatusType as OMActionStatusType
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class ActionStatusType(KGObject, OMActionStatusType):
+    """
+    Structured information about the status of an action.
+    """
+
+    type_ = "https://openminds.om-i.org/types/ActionStatusType"
+    default_space = "controlled"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.publications.ScholarlyArticle",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "keyword",
+            reverse="keywords",
+            multiple=True,
+            description="reverse of 'keywords'",
+        ),
+        Property(
+            "is_status_of",
+            [
+                "openminds.v4.computation.DataAnalysis",
+                "openminds.v4.computation.DataCopy",
+                "openminds.v4.computation.GenericComputation",
+                "openminds.v4.computation.ModelValidation",
+                "openminds.v4.computation.Optimization",
+                "openminds.v4.computation.Simulation",
+                "openminds.v4.computation.Visualization",
+            ],
+            "status",
+            reverse="status",
+            multiple=True,
+            description="reverse of 'status'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        definition=None,
+        describes=None,
+        description=None,
+        interlex_identifier=None,
+        is_status_of=None,
+        knowledge_space_link=None,
+        preferred_ontology_identifier=None,
+        synonyms=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            name=name,
+            definition=definition,
+            describes=describes,
+            description=description,
+            interlex_identifier=interlex_identifier,
+            is_status_of=is_status_of,
+            knowledge_space_link=knowledge_space_link,
+            preferred_ontology_identifier=preferred_ontology_identifier,
+            synonyms=synonyms,
+        )

fairgraph/openminds/controlled_terms/age_category.py

@@ -0,0 +1,89 @@
+"""
+Structured information on the life cycle (semantic term) of a specific age group.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.controlled_terms import AgeCategory as OMAgeCategory
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class AgeCategory(KGObject, OMAgeCategory):
+    """
+    Structured information on the life cycle (semantic term) of a specific age group.
+    """
+
+    type_ = "https://openminds.om-i.org/types/AgeCategory"
+    default_space = "controlled"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.publications.ScholarlyArticle",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "keyword",
+            reverse="keywords",
+            multiple=True,
+            description="reverse of 'keywords'",
+        ),
+        Property(
+            "is_age_category_of",
+            ["openminds.v4.core.SubjectGroupState", "openminds.v4.core.SubjectState"],
+            "ageCategory",
+            reverse="age_categories",
+            multiple=True,
+            description="reverse of 'age_categories'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        definition=None,
+        describes=None,
+        description=None,
+        interlex_identifier=None,
+        is_age_category_of=None,
+        knowledge_space_link=None,
+        preferred_ontology_identifier=None,
+        synonyms=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            name=name,
+            definition=definition,
+            describes=describes,
+            description=description,
+            interlex_identifier=interlex_identifier,
+            is_age_category_of=is_age_category_of,
+            knowledge_space_link=knowledge_space_link,
+            preferred_ontology_identifier=preferred_ontology_identifier,
+            synonyms=synonyms,
+        )

fairgraph/openminds/controlled_terms/analysis_technique.py

@@ -0,0 +1,108 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.controlled_terms import AnalysisTechnique as OMAnalysisTechnique
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class AnalysisTechnique(KGObject, OMAnalysisTechnique):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/AnalysisTechnique"
+    default_space = "controlled"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.publications.ScholarlyArticle",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "keyword",
+            reverse="keywords",
+            multiple=True,
+            description="reverse of 'keywords'",
+        ),
+        Property(
+            "is_used_to_group",
+            "openminds.v4.core.FileBundle",
+            "groupedBy",
+            reverse="grouped_by",
+            multiple=True,
+            description="reverse of 'grouped_by'",
+        ),
+        Property(
+            "used_in",
+            [
+                "openminds.v4.computation.DataAnalysis",
+                "openminds.v4.computation.DataCopy",
+                "openminds.v4.computation.GenericComputation",
+                "openminds.v4.computation.ModelValidation",
+                "openminds.v4.computation.Optimization",
+                "openminds.v4.computation.Simulation",
+                "openminds.v4.computation.Visualization",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.Protocol",
+            ],
+            "technique",
+            reverse="techniques",
+            multiple=True,
+            description="reverse of 'techniques'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        definition=None,
+        describes=None,
+        description=None,
+        interlex_identifier=None,
+        is_used_to_group=None,
+        knowledge_space_link=None,
+        preferred_ontology_identifier=None,
+        synonyms=None,
+        used_in=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            name=name,
+            definition=definition,
+            describes=describes,
+            description=description,
+            interlex_identifier=interlex_identifier,
+            is_used_to_group=is_used_to_group,
+            knowledge_space_link=knowledge_space_link,
+            preferred_ontology_identifier=preferred_ontology_identifier,
+            synonyms=synonyms,
+            used_in=used_in,
+        )

fairgraph/openminds/controlled_terms/anatomical_axes_orientation.py

@@ -0,0 +1,89 @@
+"""
+Structured information on the anatomical directions of the X, Y, and Z axis.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.controlled_terms import AnatomicalAxesOrientation as OMAnatomicalAxesOrientation
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class AnatomicalAxesOrientation(KGObject, OMAnatomicalAxesOrientation):
+    """
+    Structured information on the anatomical directions of the X, Y, and Z axis.
+    """
+
+    type_ = "https://openminds.om-i.org/types/AnatomicalAxesOrientation"
+    default_space = "controlled"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.publications.ScholarlyArticle",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "keyword",
+            reverse="keywords",
+            multiple=True,
+            description="reverse of 'keywords'",
+        ),
+        Property(
+            "is_orientation_of",
+            "openminds.v4.sands.CustomCoordinateSpace",
+            "anatomicalAxesOrientation",
+            reverse="anatomical_axes_orientation",
+            multiple=True,
+            description="reverse of 'anatomical_axes_orientation'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        definition=None,
+        describes=None,
+        description=None,
+        interlex_identifier=None,
+        is_orientation_of=None,
+        knowledge_space_link=None,
+        preferred_ontology_identifier=None,
+        synonyms=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            name=name,
+            definition=definition,
+            describes=describes,
+            description=description,
+            interlex_identifier=interlex_identifier,
+            is_orientation_of=is_orientation_of,
+            knowledge_space_link=knowledge_space_link,
+            preferred_ontology_identifier=preferred_ontology_identifier,
+            synonyms=synonyms,
+        )

fairgraph/openminds/controlled_terms/anatomical_identification_type.py

@@ -0,0 +1,89 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.controlled_terms import AnatomicalIdentificationType as OMAnatomicalIdentificationType
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class AnatomicalIdentificationType(KGObject, OMAnatomicalIdentificationType):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/AnatomicalIdentificationType"
+    default_space = "controlled"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.publications.ScholarlyArticle",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "keyword",
+            reverse="keywords",
+            multiple=True,
+            description="reverse of 'keywords'",
+        ),
+        Property(
+            "is_type_of",
+            "openminds.v4.sands.AnatomicalTargetPosition",
+            "targetIdentificationType",
+            reverse="target_identification_type",
+            multiple=True,
+            description="reverse of 'target_identification_type'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        definition=None,
+        describes=None,
+        description=None,
+        interlex_identifier=None,
+        is_type_of=None,
+        knowledge_space_link=None,
+        preferred_ontology_identifier=None,
+        synonyms=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            name=name,
+            definition=definition,
+            describes=describes,
+            description=description,
+            interlex_identifier=interlex_identifier,
+            is_type_of=is_type_of,
+            knowledge_space_link=knowledge_space_link,
+            preferred_ontology_identifier=preferred_ontology_identifier,
+            synonyms=synonyms,
+        )

fairgraph/openminds/controlled_terms/anatomical_plane.py

@@ -0,0 +1,89 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.controlled_terms import AnatomicalPlane as OMAnatomicalPlane
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class AnatomicalPlane(KGObject, OMAnatomicalPlane):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/AnatomicalPlane"
+    default_space = "controlled"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.publications.ScholarlyArticle",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "keyword",
+            reverse="keywords",
+            multiple=True,
+            description="reverse of 'keywords'",
+        ),
+        Property(
+            "used_in",
+            "openminds.v4.specimen_prep.SlicingDeviceUsage",
+            "slicingPlane",
+            reverse="slicing_plane",
+            multiple=True,
+            description="reverse of 'slicing_plane'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        definition=None,
+        describes=None,
+        description=None,
+        interlex_identifier=None,
+        knowledge_space_link=None,
+        preferred_ontology_identifier=None,
+        synonyms=None,
+        used_in=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            name=name,
+            definition=definition,
+            describes=describes,
+            description=description,
+            interlex_identifier=interlex_identifier,
+            knowledge_space_link=knowledge_space_link,
+            preferred_ontology_identifier=preferred_ontology_identifier,
+            synonyms=synonyms,
+            used_in=used_in,
+        )