fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/chemicals/chemical_substance.py

@@ -0,0 +1,67 @@
+"""
+Structured information about a chemical substance.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.chemicals import ChemicalSubstance as OMChemicalSubstance
+from fairgraph import KGObject
+
+
+class ChemicalSubstance(KGObject, OMChemicalSubstance):
+    """
+    Structured information about a chemical substance.
+    """
+
+    type_ = "https://openminds.om-i.org/types/ChemicalSubstance"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "composes",
+            ["openminds.v4.ephys.Electrode", "openminds.v4.ephys.ElectrodeArray", "openminds.v4.ephys.Pipette"],
+            ["insulatorMaterial", "material"],
+            reverse=["insulator_material", "material"],
+            multiple=True,
+            description="reverse of insulator_material, material",
+        ),
+        Property(
+            "labels",
+            "openminds.v4.ephys.PipetteUsage",
+            "labelingCompound",
+            reverse="labeling_compound",
+            multiple=True,
+            description="reverse of 'labeling_compound'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        additional_remarks=None,
+        composes=None,
+        labels=None,
+        molecular_entity=None,
+        product_source=None,
+        purity=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,
+            composes=composes,
+            labels=labels,
+            molecular_entity=molecular_entity,
+            product_source=product_source,
+            purity=purity,
+        )

fairgraph/openminds/chemicals/product_source.py

@@ -0,0 +1,57 @@
+"""
+Structured information about the source of a chemical substance or mixture.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.chemicals import ProductSource as OMProductSource
+from fairgraph import KGObject
+
+
+class ProductSource(KGObject, OMProductSource):
+    """
+    Structured information about the source of a chemical substance or mixture.
+    """
+
+    type_ = "https://openminds.om-i.org/types/ProductSource"
+    default_space = "in-depth"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_source_of",
+            ["openminds.v4.chemicals.ChemicalMixture", "openminds.v4.chemicals.ChemicalSubstance"],
+            "productSource",
+            reverse="product_source",
+            multiple=True,
+            description="reverse of 'product_source'",
+        ),
+    ]
+    existence_query_properties = ("product_name", "provider")
+
+    def __init__(
+        self,
+        digital_identifier=None,
+        identifier=None,
+        is_source_of=None,
+        product_name=None,
+        provider=None,
+        purity=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            digital_identifier=digital_identifier,
+            identifier=identifier,
+            is_source_of=is_source_of,
+            product_name=product_name,
+            provider=provider,
+            purity=purity,
+        )

fairgraph/openminds/computation/__init__.py

@@ -0,0 +1,53 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import EmbeddedMetadata
+
+from .data_analysis import DataAnalysis
+from .data_copy import DataCopy
+from .environment import Environment
+from .generic_computation import GenericComputation
+from .hardware_system import HardwareSystem
+from .launch_configuration import LaunchConfiguration
+from .local_file import LocalFile
+from .model_validation import ModelValidation
+from .optimization import Optimization
+from .simulation import Simulation
+from .software_agent import SoftwareAgent
+from .validation_test import ValidationTest
+from .validation_test_version import ValidationTestVersion
+from .visualization import Visualization
+from .workflow_execution import WorkflowExecution
+from .workflow_recipe import WorkflowRecipe
+from .workflow_recipe_version import WorkflowRecipeVersion
+
+
+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/computation/data_analysis.py

@@ -0,0 +1,104 @@
+"""
+Structured information on inspecting, cleansing, transforming, and modelling data.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.computation import DataAnalysis as OMDataAnalysis
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class DataAnalysis(KGObject, OMDataAnalysis):
+    """
+    Structured information on inspecting, cleansing, transforming, and modelling data.
+    """
+
+    type_ = "https://openminds.om-i.org/types/DataAnalysis"
+    default_space = "computation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "informed",
+            [
+                "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",
+            ],
+            "wasInformedBy",
+            reverse="was_informed_by",
+            multiple=True,
+            description="reverse of 'was_informed_by'",
+        ),
+        Property(
+            "is_part_of",
+            "openminds.v4.computation.WorkflowExecution",
+            "stage",
+            reverse="stages",
+            multiple=True,
+            description="reverse of 'stages'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        custom_property_sets=None,
+        description=None,
+        end_time=None,
+        environment=None,
+        informed=None,
+        inputs=None,
+        is_part_of=None,
+        launch_configuration=None,
+        outputs=None,
+        performed_by=None,
+        recipe=None,
+        resource_usages=None,
+        start_time=None,
+        started_by=None,
+        status=None,
+        study_targets=None,
+        tags=None,
+        techniques=None,
+        was_informed_by=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,
+            end_time=end_time,
+            environment=environment,
+            informed=informed,
+            inputs=inputs,
+            is_part_of=is_part_of,
+            launch_configuration=launch_configuration,
+            outputs=outputs,
+            performed_by=performed_by,
+            recipe=recipe,
+            resource_usages=resource_usages,
+            start_time=start_time,
+            started_by=started_by,
+            status=status,
+            study_targets=study_targets,
+            tags=tags,
+            techniques=techniques,
+            was_informed_by=was_informed_by,
+        )

fairgraph/openminds/computation/data_copy.py

@@ -0,0 +1,104 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.computation import DataCopy as OMDataCopy
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class DataCopy(KGObject, OMDataCopy):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/DataCopy"
+    default_space = "computation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "informed",
+            [
+                "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",
+            ],
+            "wasInformedBy",
+            reverse="was_informed_by",
+            multiple=True,
+            description="reverse of 'was_informed_by'",
+        ),
+        Property(
+            "is_part_of",
+            "openminds.v4.computation.WorkflowExecution",
+            "stage",
+            reverse="stages",
+            multiple=True,
+            description="reverse of 'stages'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        custom_property_sets=None,
+        description=None,
+        end_time=None,
+        environment=None,
+        informed=None,
+        inputs=None,
+        is_part_of=None,
+        launch_configuration=None,
+        outputs=None,
+        performed_by=None,
+        recipe=None,
+        resource_usages=None,
+        start_time=None,
+        started_by=None,
+        status=None,
+        study_targets=None,
+        tags=None,
+        techniques=None,
+        was_informed_by=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,
+            end_time=end_time,
+            environment=environment,
+            informed=informed,
+            inputs=inputs,
+            is_part_of=is_part_of,
+            launch_configuration=launch_configuration,
+            outputs=outputs,
+            performed_by=performed_by,
+            recipe=recipe,
+            resource_usages=resource_usages,
+            start_time=start_time,
+            started_by=started_by,
+            status=status,
+            study_targets=study_targets,
+            tags=tags,
+            techniques=techniques,
+            was_informed_by=was_informed_by,
+        )

fairgraph/openminds/computation/environment.py

@@ -0,0 +1,66 @@
+"""
+Structured information on the computer system or set of systems in which a computation is deployed and executed.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.computation import Environment as OMEnvironment
+from fairgraph import KGObject
+
+
+class Environment(KGObject, OMEnvironment):
+    """
+    Structured information on the computer system or set of systems in which a computation is deployed and executed.
+    """
+
+    type_ = "https://openminds.om-i.org/types/Environment"
+    default_space = "computation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "used_for",
+            [
+                "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.SoftwareAgent",
+                "openminds.v4.computation.Visualization",
+            ],
+            "environment",
+            reverse="environment",
+            multiple=True,
+            description="reverse of 'environment'",
+        ),
+    ]
+    existence_query_properties = ("hardware", "name")
+
+    def __init__(
+        self,
+        name=None,
+        configuration=None,
+        description=None,
+        hardware=None,
+        software=None,
+        used_for=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,
+            configuration=configuration,
+            description=description,
+            hardware=hardware,
+            software=software,
+            used_for=used_for,
+        )

fairgraph/openminds/computation/generic_computation.py

@@ -0,0 +1,104 @@
+"""
+Structured information about a computation whose type is unknown or unspecified.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.computation import GenericComputation as OMGenericComputation
+from fairgraph import KGObject
+
+
+from datetime import datetime, time
+
+
+class GenericComputation(KGObject, OMGenericComputation):
+    """
+    Structured information about a computation whose type is unknown or unspecified.
+    """
+
+    type_ = "https://openminds.om-i.org/types/GenericComputation"
+    default_space = "computation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "informed",
+            [
+                "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",
+            ],
+            "wasInformedBy",
+            reverse="was_informed_by",
+            multiple=True,
+            description="reverse of 'was_informed_by'",
+        ),
+        Property(
+            "is_part_of",
+            "openminds.v4.computation.WorkflowExecution",
+            "stage",
+            reverse="stages",
+            multiple=True,
+            description="reverse of 'stages'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        custom_property_sets=None,
+        description=None,
+        end_time=None,
+        environment=None,
+        informed=None,
+        inputs=None,
+        is_part_of=None,
+        launch_configuration=None,
+        outputs=None,
+        performed_by=None,
+        recipe=None,
+        resource_usages=None,
+        start_time=None,
+        started_by=None,
+        status=None,
+        study_targets=None,
+        tags=None,
+        techniques=None,
+        was_informed_by=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,
+            end_time=end_time,
+            environment=environment,
+            informed=informed,
+            inputs=inputs,
+            is_part_of=is_part_of,
+            launch_configuration=launch_configuration,
+            outputs=outputs,
+            performed_by=performed_by,
+            recipe=recipe,
+            resource_usages=resource_usages,
+            start_time=start_time,
+            started_by=started_by,
+            status=status,
+            study_targets=study_targets,
+            tags=tags,
+            techniques=techniques,
+            was_informed_by=was_informed_by,
+        )

fairgraph/openminds/computation/hardware_system.py

@@ -0,0 +1,53 @@
+"""
+Structured information about computing hardware.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.computation import HardwareSystem as OMHardwareSystem
+from fairgraph import KGObject
+
+
+class HardwareSystem(KGObject, OMHardwareSystem):
+    """
+    Structured information about computing hardware.
+    """
+
+    type_ = "https://openminds.om-i.org/types/HardwareSystem"
+    default_space = "computation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "used_by",
+            "openminds.v4.computation.Environment",
+            "hardware",
+            reverse="hardware",
+            multiple=True,
+            description="reverse of 'hardware'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        description=None,
+        used_by=None,
+        version_identifier=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,
+            description=description,
+            used_by=used_by,
+            version_identifier=version_identifier,
+        )

fairgraph/openminds/computation/launch_configuration.py

@@ -0,0 +1,68 @@
+"""
+Structured information about the launch of a computational process.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.computation import LaunchConfiguration as OMLaunchConfiguration
+from fairgraph import KGObject
+
+
+class LaunchConfiguration(KGObject, OMLaunchConfiguration):
+    """
+    Structured information about the launch of a computational process.
+    """
+
+    type_ = "https://openminds.om-i.org/types/LaunchConfiguration"
+    default_space = "computation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_launch_configuration_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",
+            ],
+            "launchConfiguration",
+            reverse="launch_configuration",
+            multiple=True,
+            description="reverse of 'launch_configuration'",
+        ),
+    ]
+    aliases = {"environment_variables": "environment_variable"}
+    existence_query_properties = ("executable", "name")
+
+    def __init__(
+        self,
+        name=None,
+        arguments=None,
+        description=None,
+        environment_variable=None,
+        environment_variables=None,
+        executable=None,
+        is_launch_configuration_of=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,
+            arguments=arguments,
+            description=description,
+            environment_variable=environment_variable,
+            environment_variables=environment_variables,
+            executable=executable,
+            is_launch_configuration_of=is_launch_configuration_of,
+        )