fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/core/research/protocol_execution.py

@@ -0,0 +1,76 @@
+"""
+Structured information on a protocol execution.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import ProtocolExecution as OMProtocolExecution
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class ProtocolExecution(KGObject, OMProtocolExecution):
+    """
+    Structured information on a protocol execution.
+    """
+
+    type_ = "https://openminds.om-i.org/types/ProtocolExecution"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "based_on_protocol_execution",
+            ["openminds.v4.sands.AtlasAnnotation", "openminds.v4.sands.CustomAnnotation"],
+            "criteria",
+            reverse="criteria",
+            multiple=True,
+            description="reverse of 'criteria'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        based_on_protocol_execution=None,
+        behavioral_protocols=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,
+            based_on_protocol_execution=based_on_protocol_execution,
+            behavioral_protocols=behavioral_protocols,
+            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/core/research/strain.py

@@ -0,0 +1,90 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import Strain as OMStrain
+from fairgraph import KGObject
+
+
+class Strain(KGObject, OMStrain):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/Strain"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_background_strain_of",
+            "openminds.v4.core.Strain",
+            "backgroundStrain",
+            reverse="background_strains",
+            multiple=True,
+            description="reverse of 'background_strains'",
+        ),
+        Property(
+            "is_species_of",
+            [
+                "openminds.v4.core.Subject",
+                "openminds.v4.core.SubjectGroup",
+                "openminds.v4.core.TissueSample",
+                "openminds.v4.core.TissueSampleCollection",
+            ],
+            "species",
+            reverse="species",
+            multiple=True,
+            description="reverse of 'species'",
+        ),
+    ]
+    existence_query_properties = ("genetic_strain_type", "name", "species")
+
+    def __init__(
+        self,
+        name=None,
+        alternate_identifiers=None,
+        background_strains=None,
+        breeding_type=None,
+        description=None,
+        digital_identifier=None,
+        disease_models=None,
+        genetic_strain_type=None,
+        is_background_strain_of=None,
+        is_species_of=None,
+        laboratory_code=None,
+        ontology_identifiers=None,
+        phenotype=None,
+        species=None,
+        stock_number=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,
+            alternate_identifiers=alternate_identifiers,
+            background_strains=background_strains,
+            breeding_type=breeding_type,
+            description=description,
+            digital_identifier=digital_identifier,
+            disease_models=disease_models,
+            genetic_strain_type=genetic_strain_type,
+            is_background_strain_of=is_background_strain_of,
+            is_species_of=is_species_of,
+            laboratory_code=laboratory_code,
+            ontology_identifiers=ontology_identifiers,
+            phenotype=phenotype,
+            species=species,
+            stock_number=stock_number,
+            synonyms=synonyms,
+        )

fairgraph/openminds/core/research/string_property.py

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

fairgraph/openminds/core/research/subject.py

@@ -0,0 +1,79 @@
+"""
+Structured information on a subject.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import Subject as OMSubject
+from fairgraph import KGObject
+
+
+class Subject(KGObject, OMSubject):
+    """
+    Structured information on a subject.
+    """
+
+    type_ = "https://openminds.om-i.org/types/Subject"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        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,
+        biological_sex=None,
+        has_study_results_in=None,
+        internal_identifier=None,
+        is_part_of=None,
+        is_used_to_group=None,
+        species=None,
+        studied_states=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,
+            biological_sex=biological_sex,
+            has_study_results_in=has_study_results_in,
+            internal_identifier=internal_identifier,
+            is_part_of=is_part_of,
+            is_used_to_group=is_used_to_group,
+            species=species,
+            studied_states=studied_states,
+            used_in=used_in,
+        )

fairgraph/openminds/core/research/subject_group.py

@@ -0,0 +1,91 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import SubjectGroup as OMSubjectGroup
+from fairgraph import KGObject
+
+
+class SubjectGroup(KGObject, OMSubjectGroup):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/SubjectGroup"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_parts",
+            "openminds.v4.core.Subject",
+            "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,
+        biological_sexes=None,
+        has_parts=None,
+        has_study_results_in=None,
+        internal_identifier=None,
+        is_used_to_group=None,
+        number_of_subjects=None,
+        species=None,
+        studied_states=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,
+            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,
+            number_of_subjects=number_of_subjects,
+            species=species,
+            studied_states=studied_states,
+            used_in=used_in,
+        )

fairgraph/openminds/core/research/subject_group_state.py

@@ -0,0 +1,113 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import SubjectGroupState as OMSubjectGroupState
+from fairgraph import KGObject
+
+
+class SubjectGroupState(KGObject, OMSubjectGroupState):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/SubjectGroupState"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_children",
+            [
+                "openminds.v4.core.SubjectGroupState",
+                "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.stimulation.StimulationActivity"],
+            "output",
+            reverse="outputs",
+            multiple=True,
+            description="reverse of 'outputs'",
+        ),
+        Property(
+            "is_state_of",
+            "openminds.v4.core.SubjectGroup",
+            "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,
+        age_categories=None,
+        attributes=None,
+        descended_from=None,
+        handedness=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,
+            age_categories=age_categories,
+            attributes=attributes,
+            descended_from=descended_from,
+            handedness=handedness,
+            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/subject_state.py

@@ -0,0 +1,138 @@
+"""
+Structured information on a temporary state of a subject.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import SubjectState as OMSubjectState
+from fairgraph import KGObject
+
+
+class SubjectState(KGObject, OMSubjectState):
+    """
+    Structured information on a temporary state of a subject.
+    """
+
+    type_ = "https://openminds.om-i.org/types/SubjectState"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_children",
+            [
+                "openminds.v4.core.SubjectState",
+                "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",
+                "openminds.v4.specimen_prep.TissueSampleSlicing",
+            ],
+            "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.CranialWindowPreparation",
+                "openminds.v4.stimulation.StimulationActivity",
+            ],
+            "output",
+            reverse="outputs",
+            multiple=True,
+            description="reverse of 'outputs'",
+        ),
+        Property(
+            "is_state_of",
+            "openminds.v4.core.Subject",
+            "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,
+        age_category=None,
+        attributes=None,
+        descended_from=None,
+        handedness=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,
+            age_category=age_category,
+            attributes=attributes,
+            descended_from=descended_from,
+            handedness=handedness,
+            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/core/research/tissue_sample.py

@@ -0,0 +1,87 @@
+"""
+Structured information on a tissue sample.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import TissueSample as OMTissueSample
+from fairgraph import KGObject
+
+
+class TissueSample(KGObject, OMTissueSample):
+    """
+    Structured information on a tissue sample.
+    """
+
+    type_ = "https://openminds.om-i.org/types/TissueSample"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        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,
+        anatomical_locations=None,
+        biological_sex=None,
+        has_study_results_in=None,
+        internal_identifier=None,
+        is_part_of=None,
+        is_used_to_group=None,
+        lateralities=None,
+        origin=None,
+        species=None,
+        studied_states=None,
+        type=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,
+            anatomical_locations=anatomical_locations,
+            biological_sex=biological_sex,
+            has_study_results_in=has_study_results_in,
+            internal_identifier=internal_identifier,
+            is_part_of=is_part_of,
+            is_used_to_group=is_used_to_group,
+            lateralities=lateralities,
+            origin=origin,
+            species=species,
+            studied_states=studied_states,
+            type=type,
+            used_in=used_in,
+        )