fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/core/research/tissue_sample_collection.py

@@ -0,0 +1,99 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import TissueSampleCollection as OMTissueSampleCollection
+from fairgraph import KGObject
+
+
+class TissueSampleCollection(KGObject, OMTissueSampleCollection):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/TissueSampleCollection"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_parts",
+            "openminds.v4.core.TissueSample",
+            "isPartOf",
+            reverse="is_part_of",
+            multiple=True,
+            description="reverse of 'is_part_of'",
+        ),
+        Property(
+            "has_study_results_in",
+            "openminds.v4.core.DatasetVersion",
+            "studiedSpecimen",
+            reverse="studied_specimens",
+            multiple=True,
+            description="reverse of 'studied_specimens'",
+        ),
+        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.sands.BrainAtlasVersion", "openminds.v4.sands.CommonCoordinateSpaceVersion"],
+            "usedSpecimen",
+            reverse="used_specimens",
+            multiple=True,
+            description="reverse of 'used_specimens'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        additional_remarks=None,
+        anatomical_locations=None,
+        biological_sexes=None,
+        has_parts=None,
+        has_study_results_in=None,
+        internal_identifier=None,
+        is_used_to_group=None,
+        lateralities=None,
+        number_of_tissue_samples=None,
+        origins=None,
+        species=None,
+        studied_states=None,
+        types=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,
+            lookup_label=lookup_label,
+            additional_remarks=additional_remarks,
+            anatomical_locations=anatomical_locations,
+            biological_sexes=biological_sexes,
+            has_parts=has_parts,
+            has_study_results_in=has_study_results_in,
+            internal_identifier=internal_identifier,
+            is_used_to_group=is_used_to_group,
+            lateralities=lateralities,
+            number_of_tissue_samples=number_of_tissue_samples,
+            origins=origins,
+            species=species,
+            studied_states=studied_states,
+            types=types,
+            used_in=used_in,
+        )

fairgraph/openminds/core/research/tissue_sample_collection_state.py

@@ -0,0 +1,109 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import TissueSampleCollectionState as OMTissueSampleCollectionState
+from fairgraph import KGObject
+
+
+class TissueSampleCollectionState(KGObject, OMTissueSampleCollectionState):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/TissueSampleCollectionState"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_children",
+            ["openminds.v4.core.TissueSampleCollectionState", "openminds.v4.core.TissueSampleState"],
+            "descendedFrom",
+            reverse="descended_from",
+            multiple=True,
+            description="reverse of 'descended_from'",
+        ),
+        Property(
+            "is_input_to",
+            ["openminds.v4.ephys.RecordingActivity", "openminds.v4.specimen_prep.TissueCulturePreparation"],
+            "input",
+            reverse="inputs",
+            multiple=True,
+            description="reverse of 'inputs'",
+        ),
+        Property(
+            "is_output_of",
+            [
+                "openminds.v4.core.ProtocolExecution",
+                "openminds.v4.specimen_prep.TissueSampleSlicing",
+                "openminds.v4.stimulation.StimulationActivity",
+            ],
+            "output",
+            reverse="outputs",
+            multiple=True,
+            description="reverse of 'outputs'",
+        ),
+        Property(
+            "is_state_of",
+            "openminds.v4.core.TissueSampleCollection",
+            "studiedState",
+            reverse="studied_states",
+            multiple=True,
+            description="reverse of 'studied_states'",
+        ),
+        Property(
+            "is_used_to_group",
+            "openminds.v4.core.FileBundle",
+            "groupedBy",
+            reverse="grouped_by",
+            multiple=True,
+            description="reverse of 'grouped_by'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        additional_remarks=None,
+        age=None,
+        attributes=None,
+        descended_from=None,
+        has_children=None,
+        internal_identifier=None,
+        is_input_to=None,
+        is_output_of=None,
+        is_state_of=None,
+        is_used_to_group=None,
+        pathologies=None,
+        relative_time_indication=None,
+        weight=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,
+            additional_remarks=additional_remarks,
+            age=age,
+            attributes=attributes,
+            descended_from=descended_from,
+            has_children=has_children,
+            internal_identifier=internal_identifier,
+            is_input_to=is_input_to,
+            is_output_of=is_output_of,
+            is_state_of=is_state_of,
+            is_used_to_group=is_used_to_group,
+            pathologies=pathologies,
+            relative_time_indication=relative_time_indication,
+            weight=weight,
+        )

fairgraph/openminds/core/research/tissue_sample_state.py

@@ -0,0 +1,127 @@
+"""
+Structured information on a temporary state of a tissue sample.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import TissueSampleState as OMTissueSampleState
+from fairgraph import KGObject
+
+
+class TissueSampleState(KGObject, OMTissueSampleState):
+    """
+    Structured information on a temporary state of a tissue sample.
+    """
+
+    type_ = "https://openminds.om-i.org/types/TissueSampleState"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_children",
+            ["openminds.v4.core.TissueSampleCollectionState", "openminds.v4.core.TissueSampleState"],
+            "descendedFrom",
+            reverse="descended_from",
+            multiple=True,
+            description="reverse of 'descended_from'",
+        ),
+        Property(
+            "is_input_to",
+            "openminds.v4.ephys.RecordingActivity",
+            "input",
+            reverse="inputs",
+            multiple=True,
+            description="reverse of 'inputs'",
+        ),
+        Property(
+            "is_output_of",
+            [
+                "openminds.v4.core.ProtocolExecution",
+                "openminds.v4.ephys.CellPatching",
+                "openminds.v4.ephys.ElectrodePlacement",
+                "openminds.v4.specimen_prep.TissueCulturePreparation",
+                "openminds.v4.specimen_prep.TissueSampleSlicing",
+                "openminds.v4.stimulation.StimulationActivity",
+            ],
+            "output",
+            reverse="outputs",
+            multiple=True,
+            description="reverse of 'outputs'",
+        ),
+        Property(
+            "is_state_of",
+            "openminds.v4.core.TissueSample",
+            "studiedState",
+            reverse="studied_states",
+            multiple=True,
+            description="reverse of 'studied_states'",
+        ),
+        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.ephys.ElectrodeArrayUsage",
+                "openminds.v4.ephys.ElectrodeUsage",
+                "openminds.v4.ephys.PipetteUsage",
+                "openminds.v4.specimen_prep.SlicingDeviceUsage",
+            ],
+            "usedSpecimen",
+            reverse="used_specimen",
+            multiple=True,
+            description="reverse of 'used_specimen'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        additional_remarks=None,
+        age=None,
+        attributes=None,
+        descended_from=None,
+        has_children=None,
+        internal_identifier=None,
+        is_input_to=None,
+        is_output_of=None,
+        is_state_of=None,
+        is_used_to_group=None,
+        pathologies=None,
+        relative_time_indication=None,
+        used_in=None,
+        weight=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,
+            additional_remarks=additional_remarks,
+            age=age,
+            attributes=attributes,
+            descended_from=descended_from,
+            has_children=has_children,
+            internal_identifier=internal_identifier,
+            is_input_to=is_input_to,
+            is_output_of=is_output_of,
+            is_state_of=is_state_of,
+            is_used_to_group=is_used_to_group,
+            pathologies=pathologies,
+            relative_time_indication=relative_time_indication,
+            used_in=used_in,
+            weight=weight,
+        )

fairgraph/openminds/ephys/__init__.py

@@ -0,0 +1,39 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import EmbeddedMetadata
+
+from .activity import RecordingActivity, ElectrodePlacement, CellPatching
+from .entity import Channel, Recording
+from .device import ElectrodeArray, PipetteUsage, Pipette, Electrode, ElectrodeArrayUsage, ElectrodeUsage
+
+
+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/ephys/activity/__init__.py

@@ -0,0 +1,3 @@
+from .cell_patching import CellPatching
+from .electrode_placement import ElectrodePlacement
+from .recording_activity import RecordingActivity

fairgraph/openminds/ephys/activity/cell_patching.py

@@ -0,0 +1,73 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import CellPatching as OMCellPatching
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class CellPatching(KGObject, OMCellPatching):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/CellPatching"
+    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,
+        bath_temperature=None,
+        custom_property_sets=None,
+        description=None,
+        devices=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,
+        target_position=None,
+        tissue_bath_solution=None,
+        variation=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,
+            bath_temperature=bath_temperature,
+            custom_property_sets=custom_property_sets,
+            description=description,
+            devices=devices,
+            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,
+            target_position=target_position,
+            tissue_bath_solution=tissue_bath_solution,
+            variation=variation,
+        )

fairgraph/openminds/ephys/activity/electrode_placement.py

@@ -0,0 +1,67 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import ElectrodePlacement as OMElectrodePlacement
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class ElectrodePlacement(KGObject, OMElectrodePlacement):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/ElectrodePlacement"
+    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,
+        devices=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,
+        target_position=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,
+            devices=devices,
+            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,
+            target_position=target_position,
+        )

fairgraph/openminds/ephys/activity/recording_activity.py

@@ -0,0 +1,67 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import RecordingActivity as OMRecordingActivity
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class RecordingActivity(KGObject, OMRecordingActivity):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/RecordingActivity"
+    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,
+        devices=None,
+        end_time=None,
+        inputs=None,
+        internal_identifier=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,
+            custom_property_sets=custom_property_sets,
+            description=description,
+            devices=devices,
+            end_time=end_time,
+            inputs=inputs,
+            internal_identifier=internal_identifier,
+            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/ephys/device/__init__.py

@@ -0,0 +1,6 @@
+from .electrode import Electrode
+from .electrode_array import ElectrodeArray
+from .electrode_array_usage import ElectrodeArrayUsage
+from .electrode_usage import ElectrodeUsage
+from .pipette import Pipette
+from .pipette_usage import PipetteUsage

fairgraph/openminds/ephys/device/electrode.py

@@ -0,0 +1,81 @@
+"""
+Structured information on an electrode.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.ephys import Electrode as OMElectrode
+from fairgraph import KGObject
+
+
+class Electrode(KGObject, OMElectrode):
+    """
+    Structured information on an electrode.
+    """
+
+    type_ = "https://openminds.om-i.org/types/Electrode"
+    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.ElectrodeUsage",
+            "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,
+        insulator_material=None,
+        internal_identifier=None,
+        intrinsic_resistance=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,
+            conductor_material=conductor_material,
+            description=description,
+            device_type=device_type,
+            digital_identifier=digital_identifier,
+            insulator_material=insulator_material,
+            internal_identifier=internal_identifier,
+            intrinsic_resistance=intrinsic_resistance,
+            is_part_of=is_part_of,
+            manufacturers=manufacturers,
+            owners=owners,
+            serial_number=serial_number,
+            usage=usage,
+        )