fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/ephys/device/electrode_array.py

@@ -0,0 +1,85 @@
+"""
+Structured information on an electrode array.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import ElectrodeArray as OMElectrodeArray
+from fairgraph import KGObject
+
+
+class ElectrodeArray(KGObject, OMElectrodeArray):
+    """
+    Structured information on an electrode array.
+    """
+
+    type_ = "https://openminds.om-i.org/types/ElectrodeArray"
+    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.ephys.ElectrodeArrayUsage",
+            "device",
+            reverse="device",
+            multiple=True,
+            description="reverse of 'device'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        name=None,
+        lookup_label=None,
+        conductor_material=None,
+        description=None,
+        device_type=None,
+        digital_identifier=None,
+        electrode_identifiers=None,
+        insulator_material=None,
+        internal_identifier=None,
+        intrinsic_resistance=None,
+        is_part_of=None,
+        manufacturers=None,
+        number_of_electrodes=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,
+            conductor_material=conductor_material,
+            description=description,
+            device_type=device_type,
+            digital_identifier=digital_identifier,
+            electrode_identifiers=electrode_identifiers,
+            insulator_material=insulator_material,
+            internal_identifier=internal_identifier,
+            intrinsic_resistance=intrinsic_resistance,
+            is_part_of=is_part_of,
+            manufacturers=manufacturers,
+            number_of_electrodes=number_of_electrodes,
+            owners=owners,
+            serial_number=serial_number,
+            usage=usage,
+        )

fairgraph/openminds/ephys/device/electrode_array_usage.py

@@ -0,0 +1,105 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import ElectrodeArrayUsage as OMElectrodeArrayUsage
+from fairgraph import KGObject
+
+
+class ElectrodeArrayUsage(KGObject, OMElectrodeArrayUsage):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/ElectrodeArrayUsage"
+    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_in",
+            ["openminds.v4.ephys.CellPatching", "openminds.v4.ephys.RecordingActivity"],
+            "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,
+        anatomical_locations_of_arrays=None,
+        anatomical_locations_of_electrodes=None,
+        contact_resistances=None,
+        device=None,
+        generation_device=None,
+        metadata_locations=None,
+        placed_by=None,
+        spatial_locations_of_electrodes=None,
+        used_electrodes=None,
+        used_in=None,
+        used_specimen=None,
+        used_to_measure=None,
+        used_to_record=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,
+            anatomical_locations_of_arrays=anatomical_locations_of_arrays,
+            anatomical_locations_of_electrodes=anatomical_locations_of_electrodes,
+            contact_resistances=contact_resistances,
+            device=device,
+            generation_device=generation_device,
+            metadata_locations=metadata_locations,
+            placed_by=placed_by,
+            spatial_locations_of_electrodes=spatial_locations_of_electrodes,
+            used_electrodes=used_electrodes,
+            used_in=used_in,
+            used_specimen=used_specimen,
+            used_to_measure=used_to_measure,
+            used_to_record=used_to_record,
+        )

fairgraph/openminds/ephys/device/electrode_usage.py

@@ -0,0 +1,101 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import ElectrodeUsage as OMElectrodeUsage
+from fairgraph import KGObject
+
+
+class ElectrodeUsage(KGObject, OMElectrodeUsage):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/ElectrodeUsage"
+    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_in",
+            ["openminds.v4.ephys.CellPatching", "openminds.v4.ephys.RecordingActivity"],
+            "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,
+        anatomical_location=None,
+        contact_resistance=None,
+        device=None,
+        generation_device=None,
+        metadata_locations=None,
+        placed_by=None,
+        spatial_location=None,
+        used_in=None,
+        used_specimen=None,
+        used_to_measure=None,
+        used_to_record=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,
+            anatomical_location=anatomical_location,
+            contact_resistance=contact_resistance,
+            device=device,
+            generation_device=generation_device,
+            metadata_locations=metadata_locations,
+            placed_by=placed_by,
+            spatial_location=spatial_location,
+            used_in=used_in,
+            used_specimen=used_specimen,
+            used_to_measure=used_to_measure,
+            used_to_record=used_to_record,
+        )

fairgraph/openminds/ephys/device/pipette.py

@@ -0,0 +1,81 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import Pipette as OMPipette
+from fairgraph import KGObject
+
+
+class Pipette(KGObject, OMPipette):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/Pipette"
+    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.ephys.PipetteUsage",
+            "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,
+        external_diameter=None,
+        internal_diameter=None,
+        internal_identifier=None,
+        is_part_of=None,
+        manufacturers=None,
+        material=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,
+            external_diameter=external_diameter,
+            internal_diameter=internal_diameter,
+            internal_identifier=internal_identifier,
+            is_part_of=is_part_of,
+            manufacturers=manufacturers,
+            material=material,
+            owners=owners,
+            serial_number=serial_number,
+            usage=usage,
+        )

fairgraph/openminds/ephys/device/pipette_usage.py

@@ -0,0 +1,123 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import PipetteUsage as OMPipetteUsage
+from fairgraph import KGObject
+
+
+class PipetteUsage(KGObject, OMPipetteUsage):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/PipetteUsage"
+    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_in",
+            ["openminds.v4.ephys.CellPatching", "openminds.v4.ephys.RecordingActivity"],
+            "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,
+        anatomical_location=None,
+        chloride_reversal_potentials=None,
+        compensation_current=None,
+        device=None,
+        end_membrane_potential=None,
+        generation_device=None,
+        holding_potential=None,
+        input_resistance=None,
+        labeling_compound=None,
+        liquid_junction_potential=None,
+        metadata_locations=None,
+        pipette_resistance=None,
+        pipette_solution=None,
+        placed_by=None,
+        seal_resistance=None,
+        series_resistance=None,
+        spatial_location=None,
+        start_membrane_potential=None,
+        used_in=None,
+        used_specimen=None,
+        used_to_measure=None,
+        used_to_record=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,
+            anatomical_location=anatomical_location,
+            chloride_reversal_potentials=chloride_reversal_potentials,
+            compensation_current=compensation_current,
+            device=device,
+            end_membrane_potential=end_membrane_potential,
+            generation_device=generation_device,
+            holding_potential=holding_potential,
+            input_resistance=input_resistance,
+            labeling_compound=labeling_compound,
+            liquid_junction_potential=liquid_junction_potential,
+            metadata_locations=metadata_locations,
+            pipette_resistance=pipette_resistance,
+            pipette_solution=pipette_solution,
+            placed_by=placed_by,
+            seal_resistance=seal_resistance,
+            series_resistance=series_resistance,
+            spatial_location=spatial_location,
+            start_membrane_potential=start_membrane_potential,
+            used_in=used_in,
+            used_specimen=used_specimen,
+            used_to_measure=used_to_measure,
+            used_to_record=used_to_record,
+        )

fairgraph/openminds/ephys/entity/__init__.py

@@ -0,0 +1,2 @@
+from .channel import Channel
+from .recording import Recording

fairgraph/openminds/ephys/entity/channel.py

@@ -0,0 +1,23 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import Channel as OMChannel
+from fairgraph import EmbeddedMetadata
+
+
+class Channel(EmbeddedMetadata, OMChannel):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/Channel"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("internal_identifier", "unit")
+
+    def __init__(self, internal_identifier=None, unit=None, id=None, data=None, space=None, release_status=None):
+        return EmbeddedMetadata.__init__(self, data=data, internal_identifier=internal_identifier, unit=unit)

fairgraph/openminds/ephys/entity/recording.py

@@ -0,0 +1,63 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import Recording as OMRecording
+from fairgraph import KGObject
+
+
+class Recording(KGObject, OMRecording):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/Recording"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "next_recording",
+            "openminds.v4.ephys.Recording",
+            "previousRecording",
+            reverse="previous_recording",
+            multiple=True,
+            description="reverse of 'previous_recording'",
+        ),
+    ]
+    existence_query_properties = ("channels", "data_location", "recorded_with", "sampling_frequency")
+
+    def __init__(
+        self,
+        name=None,
+        additional_remarks=None,
+        channels=None,
+        data_location=None,
+        internal_identifier=None,
+        next_recording=None,
+        previous_recording=None,
+        recorded_with=None,
+        sampling_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,
+            name=name,
+            additional_remarks=additional_remarks,
+            channels=channels,
+            data_location=data_location,
+            internal_identifier=internal_identifier,
+            next_recording=next_recording,
+            previous_recording=previous_recording,
+            recorded_with=recorded_with,
+            sampling_frequency=sampling_frequency,
+        )

fairgraph/openminds/publications/__init__.py

@@ -0,0 +1,47 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import EmbeddedMetadata
+
+from .book import Book
+from .chapter import Chapter
+from .learning_resource import LearningResource
+from .live_paper import LivePaper
+from .live_paper_resource_item import LivePaperResourceItem
+from .live_paper_section import LivePaperSection
+from .live_paper_version import LivePaperVersion
+from .periodical import Periodical
+from .publication_issue import PublicationIssue
+from .publication_volume import PublicationVolume
+from .scholarly_article import ScholarlyArticle
+
+
+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)