fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/sands/non_atlas/custom_anatomical_entity.py

@@ -0,0 +1,110 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import CustomAnatomicalEntity as OMCustomAnatomicalEntity
+from fairgraph import KGObject
+
+
+class CustomAnatomicalEntity(KGObject, OMCustomAnatomicalEntity):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/CustomAnatomicalEntity"
+    default_space = "spatial"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_location_of",
+            [
+                "openminds.v4.core.TissueSample",
+                "openminds.v4.core.TissueSampleCollection",
+                "openminds.v4.ephys.ElectrodeArrayUsage",
+                "openminds.v4.ephys.ElectrodeUsage",
+                "openminds.v4.ephys.PipetteUsage",
+            ],
+            ["anatomicalLocation", "anatomicalLocationOfElectrodes"],
+            reverse=["anatomical_location", "anatomical_locations", "anatomical_locations_of_electrodes"],
+            multiple=True,
+            description="reverse of anatomical_location, anatomical_locations, anatomical_locations_of_electrodes",
+        ),
+        Property(
+            "is_target_of",
+            "openminds.v4.sands.AnatomicalTargetPosition",
+            "anatomicalTarget",
+            reverse="anatomical_targets",
+            multiple=True,
+            description="reverse of 'anatomical_targets'",
+        ),
+        Property(
+            "is_used_to_group",
+            "openminds.v4.core.FileBundle",
+            "groupedBy",
+            reverse="grouped_by",
+            multiple=True,
+            description="reverse of 'grouped_by'",
+        ),
+        Property(
+            "studied_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.ValidationTest",
+                "openminds.v4.computation.Visualization",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.Model",
+                "openminds.v4.core.ProtocolExecution",
+                "openminds.v4.ephys.CellPatching",
+                "openminds.v4.ephys.ElectrodePlacement",
+                "openminds.v4.ephys.RecordingActivity",
+                "openminds.v4.specimen_prep.CranialWindowPreparation",
+                "openminds.v4.specimen_prep.TissueCulturePreparation",
+                "openminds.v4.specimen_prep.TissueSampleSlicing",
+                "openminds.v4.stimulation.StimulationActivity",
+            ],
+            "studyTarget",
+            reverse="study_targets",
+            multiple=True,
+            description="reverse of 'study_targets'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        has_annotations=None,
+        is_location_of=None,
+        is_target_of=None,
+        is_used_to_group=None,
+        related_uberon_term=None,
+        relation_assessments=None,
+        studied_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,
+            has_annotations=has_annotations,
+            is_location_of=is_location_of,
+            is_target_of=is_target_of,
+            is_used_to_group=is_used_to_group,
+            related_uberon_term=related_uberon_term,
+            relation_assessments=relation_assessments,
+            studied_in=studied_in,
+        )

fairgraph/openminds/sands/non_atlas/custom_annotation.py

@@ -0,0 +1,54 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import CustomAnnotation as OMCustomAnnotation
+from fairgraph import EmbeddedMetadata
+
+
+class CustomAnnotation(EmbeddedMetadata, OMCustomAnnotation):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/CustomAnnotation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("coordinate_space", "criteria_quality_type", "criteria_type", "type")
+
+    def __init__(
+        self,
+        anchor_points=None,
+        coordinate_space=None,
+        criteria=None,
+        criteria_quality_type=None,
+        criteria_type=None,
+        inspired_by=None,
+        internal_identifier=None,
+        lateralities=None,
+        preferred_visualization=None,
+        specification=None,
+        type=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return EmbeddedMetadata.__init__(
+            self,
+            data=data,
+            anchor_points=anchor_points,
+            coordinate_space=coordinate_space,
+            criteria=criteria,
+            criteria_quality_type=criteria_quality_type,
+            criteria_type=criteria_type,
+            inspired_by=inspired_by,
+            internal_identifier=internal_identifier,
+            lateralities=lateralities,
+            preferred_visualization=preferred_visualization,
+            specification=specification,
+            type=type,
+        )

fairgraph/openminds/sands/non_atlas/custom_coordinate_space.py

@@ -0,0 +1,67 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import CustomCoordinateSpace as OMCustomCoordinateSpace
+from fairgraph import KGObject
+
+
+class CustomCoordinateSpace(KGObject, OMCustomCoordinateSpace):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/CustomCoordinateSpace"
+    default_space = "spatial"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_coordinate_space_of",
+            "openminds.v4.sands.CustomAnnotation",
+            "coordinateSpace",
+            reverse="coordinate_space",
+            multiple=True,
+            description="reverse of 'coordinate_space'",
+        ),
+        Property(
+            "is_used_to_group",
+            "openminds.v4.core.FileBundle",
+            "groupedBy",
+            reverse="grouped_by",
+            multiple=True,
+            description="reverse of 'grouped_by'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        anatomical_axes_orientation=None,
+        axes_origins=None,
+        default_images=None,
+        is_coordinate_space_of=None,
+        is_used_to_group=None,
+        native_unit=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,
+            anatomical_axes_orientation=anatomical_axes_orientation,
+            axes_origins=axes_origins,
+            default_images=default_images,
+            is_coordinate_space_of=is_coordinate_space_of,
+            is_used_to_group=is_used_to_group,
+            native_unit=native_unit,
+        )

fairgraph/openminds/specimen_prep/__init__.py

@@ -0,0 +1,38 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import EmbeddedMetadata
+
+from .activity import CranialWindowPreparation, TissueCulturePreparation, TissueSampleSlicing
+from .device import SlicingDevice, SlicingDeviceUsage
+
+
+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/specimen_prep/activity/__init__.py

@@ -0,0 +1,3 @@
+from .cranial_window_preparation import CranialWindowPreparation
+from .tissue_culture_preparation import TissueCulturePreparation
+from .tissue_sample_slicing import TissueSampleSlicing

fairgraph/openminds/specimen_prep/activity/cranial_window_preparation.py

@@ -0,0 +1,69 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.specimen_prep import CranialWindowPreparation as OMCranialWindowPreparation
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class CranialWindowPreparation(KGObject, OMCranialWindowPreparation):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/CranialWindowPreparation"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        construction_type=None,
+        custom_property_sets=None,
+        description=None,
+        dimension=None,
+        end_time=None,
+        inputs=None,
+        is_part_of=None,
+        outputs=None,
+        performed_by=None,
+        preparation_design=None,
+        protocols=None,
+        reinforcement_type=None,
+        start_time=None,
+        study_targets=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            lookup_label=lookup_label,
+            construction_type=construction_type,
+            custom_property_sets=custom_property_sets,
+            description=description,
+            dimension=dimension,
+            end_time=end_time,
+            inputs=inputs,
+            is_part_of=is_part_of,
+            outputs=outputs,
+            performed_by=performed_by,
+            preparation_design=preparation_design,
+            protocols=protocols,
+            reinforcement_type=reinforcement_type,
+            start_time=start_time,
+            study_targets=study_targets,
+        )

fairgraph/openminds/specimen_prep/activity/tissue_culture_preparation.py

@@ -0,0 +1,67 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.specimen_prep import TissueCulturePreparation as OMTissueCulturePreparation
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class TissueCulturePreparation(KGObject, OMTissueCulturePreparation):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/TissueCulturePreparation"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        culture_medium=None,
+        culture_type=None,
+        custom_property_sets=None,
+        description=None,
+        end_time=None,
+        inputs=None,
+        is_part_of=None,
+        outputs=None,
+        performed_by=None,
+        preparation_design=None,
+        protocols=None,
+        start_time=None,
+        study_targets=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            lookup_label=lookup_label,
+            culture_medium=culture_medium,
+            culture_type=culture_type,
+            custom_property_sets=custom_property_sets,
+            description=description,
+            end_time=end_time,
+            inputs=inputs,
+            is_part_of=is_part_of,
+            outputs=outputs,
+            performed_by=performed_by,
+            preparation_design=preparation_design,
+            protocols=protocols,
+            start_time=start_time,
+            study_targets=study_targets,
+        )

fairgraph/openminds/specimen_prep/activity/tissue_sample_slicing.py

@@ -0,0 +1,69 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.specimen_prep import TissueSampleSlicing as OMTissueSampleSlicing
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class TissueSampleSlicing(KGObject, OMTissueSampleSlicing):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/TissueSampleSlicing"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        custom_property_sets=None,
+        description=None,
+        device=None,
+        end_time=None,
+        inputs=None,
+        is_part_of=None,
+        outputs=None,
+        performed_by=None,
+        preparation_design=None,
+        protocols=None,
+        start_time=None,
+        study_targets=None,
+        temperature=None,
+        tissue_bath_solution=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            lookup_label=lookup_label,
+            custom_property_sets=custom_property_sets,
+            description=description,
+            device=device,
+            end_time=end_time,
+            inputs=inputs,
+            is_part_of=is_part_of,
+            outputs=outputs,
+            performed_by=performed_by,
+            preparation_design=preparation_design,
+            protocols=protocols,
+            start_time=start_time,
+            study_targets=study_targets,
+            temperature=temperature,
+            tissue_bath_solution=tissue_bath_solution,
+        )

fairgraph/openminds/specimen_prep/device/__init__.py

@@ -0,0 +1,2 @@
+from .slicing_device import SlicingDevice
+from .slicing_device_usage import SlicingDeviceUsage

fairgraph/openminds/specimen_prep/device/slicing_device.py

@@ -0,0 +1,73 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.specimen_prep import SlicingDevice as OMSlicingDevice
+from fairgraph import KGObject
+
+
+class SlicingDevice(KGObject, OMSlicingDevice):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/SlicingDevice"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_part_of",
+            "openminds.v4.core.Setup",
+            "hasPart",
+            reverse="has_parts",
+            multiple=True,
+            description="reverse of 'has_parts'",
+        ),
+        Property(
+            "usage",
+            "openminds.v4.specimen_prep.SlicingDeviceUsage",
+            "device",
+            reverse="device",
+            multiple=True,
+            description="reverse of 'device'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        name=None,
+        lookup_label=None,
+        description=None,
+        device_type=None,
+        digital_identifier=None,
+        is_part_of=None,
+        manufacturers=None,
+        owners=None,
+        serial_number=None,
+        usage=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,
+            lookup_label=lookup_label,
+            description=description,
+            device_type=device_type,
+            digital_identifier=digital_identifier,
+            is_part_of=is_part_of,
+            manufacturers=manufacturers,
+            owners=owners,
+            serial_number=serial_number,
+            usage=usage,
+        )

fairgraph/openminds/specimen_prep/device/slicing_device_usage.py

@@ -0,0 +1,117 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.specimen_prep import SlicingDeviceUsage as OMSlicingDeviceUsage
+from fairgraph import KGObject
+
+
+class SlicingDeviceUsage(KGObject, OMSlicingDeviceUsage):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/SlicingDeviceUsage"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "generation_device",
+            "openminds.v4.stimulation.EphysStimulus",
+            "generatedBy",
+            reverse="generated_by",
+            multiple=True,
+            description="reverse of 'generated_by'",
+        ),
+        Property(
+            "placed_by",
+            "openminds.v4.ephys.ElectrodePlacement",
+            "device",
+            reverse="devices",
+            multiple=True,
+            description="reverse of 'devices'",
+        ),
+        Property(
+            "used_for",
+            "openminds.v4.specimen_prep.TissueSampleSlicing",
+            "device",
+            reverse="device",
+            multiple=True,
+            description="reverse of 'device'",
+        ),
+        Property(
+            "used_in",
+            "openminds.v4.ephys.CellPatching",
+            "device",
+            reverse="devices",
+            multiple=True,
+            description="reverse of 'devices'",
+        ),
+        Property(
+            "used_to_measure",
+            "openminds.v4.core.Measurement",
+            "measuredWith",
+            reverse="measured_with",
+            multiple=True,
+            description="reverse of 'measured_with'",
+        ),
+        Property(
+            "used_to_record",
+            "openminds.v4.ephys.Recording",
+            "recordedWith",
+            reverse="recorded_with",
+            multiple=True,
+            description="reverse of 'recorded_with'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        device=None,
+        generation_device=None,
+        metadata_locations=None,
+        oscillation_amplitude=None,
+        placed_by=None,
+        slice_thickness=None,
+        slicing_angles=None,
+        slicing_plane=None,
+        slicing_speed=None,
+        used_for=None,
+        used_in=None,
+        used_specimen=None,
+        used_to_measure=None,
+        used_to_record=None,
+        vibration_frequency=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            lookup_label=lookup_label,
+            device=device,
+            generation_device=generation_device,
+            metadata_locations=metadata_locations,
+            oscillation_amplitude=oscillation_amplitude,
+            placed_by=placed_by,
+            slice_thickness=slice_thickness,
+            slicing_angles=slicing_angles,
+            slicing_plane=slicing_plane,
+            slicing_speed=slicing_speed,
+            used_for=used_for,
+            used_in=used_in,
+            used_specimen=used_specimen,
+            used_to_measure=used_to_measure,
+            used_to_record=used_to_record,
+            vibration_frequency=vibration_frequency,
+        )

fairgraph/openminds/specimenprep.py

@@ -0,0 +1,4 @@
+from warnings import warn
+from .specimen_prep import *
+
+warn("The `specimenprep` module has been renamed to `specimen_prep`, please update your code", DeprecationWarning)