fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/core/__init__.py

@@ -0,0 +1,107 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import EmbeddedMetadata
+
+from .research import (
+    ProtocolExecution,
+    SubjectGroup,
+    Subject,
+    Strain,
+    TissueSampleCollection,
+    BehavioralProtocol,
+    StringProperty,
+    CustomPropertySet,
+    TissueSampleState,
+    SubjectState,
+    TissueSample,
+    Protocol,
+    TissueSampleCollectionState,
+    Configuration,
+    NumericalProperty,
+    SubjectGroupState,
+    PropertyValueList,
+)
+from .products import (
+    Dataset,
+    Project,
+    DatasetVersion,
+    SoftwareVersion,
+    MetaDataModelVersion,
+    Model,
+    Software,
+    Setup,
+    WebServiceVersion,
+    MetaDataModel,
+    WebService,
+    ModelVersion,
+)
+from .digital_identifier import (
+    ISSN,
+    IdentifiersDotOrgID,
+    DOI,
+    RORID,
+    RRID,
+    ORCID,
+    GRIDID,
+    ISBN,
+    StockNumber,
+    HANDLE,
+    SWHID,
+)
+from .miscellaneous import (
+    QuantitativeValue,
+    Funding,
+    ResearchProductGroup,
+    WebResource,
+    QuantitativeValueRange,
+    QuantitativeValueArray,
+    Comment,
+)
+from .actors import Contribution, AccountInformation, Consortium, Affiliation, Organization, ContactInformation, Person
+from .data import (
+    ServiceLink,
+    ContentTypePattern,
+    Copyright,
+    FileArchive,
+    Hash,
+    ContentType,
+    FilePathPattern,
+    FileRepository,
+    License,
+    File,
+    FileBundle,
+    FileRepositoryStructure,
+    Measurement,
+)
+
+
+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/core/actors/__init__.py

@@ -0,0 +1,7 @@
+from .account_information import AccountInformation
+from .affiliation import Affiliation
+from .consortium import Consortium
+from .contact_information import ContactInformation
+from .contribution import Contribution
+from .organization import Organization
+from .person import Person

fairgraph/openminds/core/actors/account_information.py

@@ -0,0 +1,44 @@
+"""
+Structured information about a user account for a web service.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import AccountInformation as OMAccountInformation
+from fairgraph import KGObject
+
+
+class AccountInformation(KGObject, OMAccountInformation):
+    """
+    Structured information about a user account for a web service.
+    """
+
+    type_ = "https://openminds.om-i.org/types/AccountInformation"
+    default_space = "common"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "belongs_to",
+            "openminds.v4.core.Person",
+            "associatedAccount",
+            reverse="associated_accounts",
+            multiple=True,
+            description="reverse of 'associated_accounts'",
+        ),
+    ]
+    existence_query_properties = ("service", "user_name")
+
+    def __init__(
+        self, belongs_to=None, service=None, user_name=None, id=None, data=None, space=None, release_status=None
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            belongs_to=belongs_to,
+            service=service,
+            user_name=user_name,
+        )

fairgraph/openminds/core/actors/affiliation.py

@@ -0,0 +1,30 @@
+"""
+Structured information about a relationship between two entities, such as a person and their employer.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import Affiliation as OMAffiliation
+from fairgraph import EmbeddedMetadata
+
+
+from datetime import date
+
+
+class Affiliation(EmbeddedMetadata, OMAffiliation):
+    """
+    Structured information about a relationship between two entities, such as a person and their employer.
+    """
+
+    type_ = "https://openminds.om-i.org/types/Affiliation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("member_of",)
+
+    def __init__(
+        self, end_date=None, member_of=None, start_date=None, id=None, data=None, space=None, release_status=None
+    ):
+        return EmbeddedMetadata.__init__(
+            self, data=data, end_date=end_date, member_of=member_of, start_date=start_date
+        )

fairgraph/openminds/core/actors/consortium.py

@@ -0,0 +1,175 @@
+"""
+Structured information about an association of two or more persons or organizations, with the objective of participating in a common activity.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import Consortium as OMConsortium
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class Consortium(KGObject, OMConsortium):
+    """
+    Structured information about an association of two or more persons or organizations, with the objective of participating in a common activity.
+    """
+
+    type_ = "https://openminds.om-i.org/types/Consortium"
+    default_space = "common"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "coordinated_projects",
+            "openminds.v4.core.Project",
+            "coordinator",
+            reverse="coordinators",
+            multiple=True,
+            description="reverse of 'coordinators'",
+        ),
+        Property(
+            "developed",
+            [
+                "openminds.v4.computation.ValidationTest",
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipe",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.MetaDataModel",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.Model",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.Software",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebService",
+                "openminds.v4.core.WebServiceVersion",
+            ],
+            "developer",
+            reverse="developers",
+            multiple=True,
+            description="reverse of 'developers'",
+        ),
+        Property(
+            "funded",
+            "openminds.v4.core.Funding",
+            "funder",
+            reverse="funder",
+            multiple=True,
+            description="reverse of 'funder'",
+        ),
+        Property(
+            "has_members",
+            "openminds.v4.core.Affiliation",
+            "memberOf",
+            reverse="member_of",
+            multiple=True,
+            description="reverse of 'member_of'",
+        ),
+        Property(
+            "is_custodian_of",
+            [
+                "openminds.v4.core.Dataset",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.publications.LivePaper",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.sands.BrainAtlas",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpace",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "custodian",
+            reverse="custodians",
+            multiple=True,
+            description="reverse of 'custodians'",
+        ),
+        Property(
+            "is_owner_of",
+            [
+                "openminds.v4.ephys.Electrode",
+                "openminds.v4.ephys.ElectrodeArray",
+                "openminds.v4.ephys.Pipette",
+                "openminds.v4.specimen_prep.SlicingDevice",
+            ],
+            "owner",
+            reverse="owners",
+            multiple=True,
+            description="reverse of 'owners'",
+        ),
+        Property(
+            "is_provider_of",
+            "openminds.v4.chemicals.ProductSource",
+            "provider",
+            reverse="provider",
+            multiple=True,
+            description="reverse of 'provider'",
+        ),
+        Property(
+            "manufactured",
+            "openminds.v4.core.Setup",
+            "manufacturer",
+            reverse="manufacturers",
+            multiple=True,
+            description="reverse of 'manufacturers'",
+        ),
+        Property(
+            "published",
+            [
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.ScholarlyArticle",
+            ],
+            "publisher",
+            reverse="publisher",
+            multiple=True,
+            description="reverse of 'publisher'",
+        ),
+    ]
+    aliases = {"name": "full_name", "alias": "short_name"}
+    existence_query_properties = ("full_name",)
+
+    def __init__(
+        self,
+        name=None,
+        alias=None,
+        contact_information=None,
+        coordinated_projects=None,
+        developed=None,
+        full_name=None,
+        funded=None,
+        has_members=None,
+        homepage=None,
+        is_custodian_of=None,
+        is_owner_of=None,
+        is_provider_of=None,
+        manufactured=None,
+        published=None,
+        short_name=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,
+            alias=alias,
+            contact_information=contact_information,
+            coordinated_projects=coordinated_projects,
+            developed=developed,
+            full_name=full_name,
+            funded=funded,
+            has_members=has_members,
+            homepage=homepage,
+            is_custodian_of=is_custodian_of,
+            is_owner_of=is_owner_of,
+            is_provider_of=is_provider_of,
+            manufactured=manufactured,
+            published=published,
+            short_name=short_name,
+        )

fairgraph/openminds/core/actors/contact_information.py

@@ -0,0 +1,43 @@
+"""
+Structured information about how to contact a given person or consortium.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import ContactInformation as OMContactInformation
+from fairgraph import KGObject
+
+
+class ContactInformation(KGObject, OMContactInformation):
+    """
+    Structured information about how to contact a given person or consortium.
+    """
+
+    type_ = "https://openminds.om-i.org/types/ContactInformation"
+    default_space = "restricted"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_contact_information_of",
+            ["openminds.v4.core.Consortium", "openminds.v4.core.Person"],
+            "contactInformation",
+            reverse="contact_information",
+            multiple=True,
+            description="reverse of 'contact_information'",
+        ),
+    ]
+    existence_query_properties = ("email",)
+
+    def __init__(
+        self, email=None, is_contact_information_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,
+            email=email,
+            is_contact_information_of=is_contact_information_of,
+        )

fairgraph/openminds/core/actors/contribution.py

@@ -0,0 +1,23 @@
+"""
+Structured information on the contribution made to a research product.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import Contribution as OMContribution
+from fairgraph import EmbeddedMetadata
+
+
+class Contribution(EmbeddedMetadata, OMContribution):
+    """
+    Structured information on the contribution made to a research product.
+    """
+
+    type_ = "https://openminds.om-i.org/types/Contribution"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("contributor", "types")
+
+    def __init__(self, contributor=None, types=None, id=None, data=None, space=None, release_status=None):
+        return EmbeddedMetadata.__init__(self, data=data, contributor=contributor, types=types)

fairgraph/openminds/core/actors/organization.py

@@ -0,0 +1,199 @@
+"""
+An entity comprised of one or more natural persons with a particular purpose. [adapted from Wikipedia](https://en.wikipedia.org/wiki/Organization)
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import Organization as OMOrganization
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class Organization(KGObject, OMOrganization):
+    """
+    An entity comprised of one or more natural persons with a particular purpose. [adapted from Wikipedia](https://en.wikipedia.org/wiki/Organization)
+    """
+
+    type_ = "https://openminds.om-i.org/types/Organization"
+    default_space = "common"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "coordinated_projects",
+            "openminds.v4.core.Project",
+            "coordinator",
+            reverse="coordinators",
+            multiple=True,
+            description="reverse of 'coordinators'",
+        ),
+        Property(
+            "developed",
+            [
+                "openminds.v4.computation.ValidationTest",
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipe",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.MetaDataModel",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.Model",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.Software",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebService",
+                "openminds.v4.core.WebServiceVersion",
+            ],
+            "developer",
+            reverse="developers",
+            multiple=True,
+            description="reverse of 'developers'",
+        ),
+        Property(
+            "funded",
+            "openminds.v4.core.Funding",
+            "funder",
+            reverse="funder",
+            multiple=True,
+            description="reverse of 'funder'",
+        ),
+        Property(
+            "has_children",
+            "openminds.v4.core.Organization",
+            "hasParent",
+            reverse="has_parents",
+            multiple=True,
+            description="reverse of 'has_parents'",
+        ),
+        Property(
+            "has_members",
+            "openminds.v4.core.Affiliation",
+            "memberOf",
+            reverse="member_of",
+            multiple=True,
+            description="reverse of 'member_of'",
+        ),
+        Property(
+            "hosts",
+            ["openminds.v4.core.FileRepository", "openminds.v4.publications.LivePaperResourceItem"],
+            "hostedBy",
+            reverse="hosted_by",
+            multiple=True,
+            description="reverse of 'hosted_by'",
+        ),
+        Property(
+            "is_custodian_of",
+            [
+                "openminds.v4.core.Dataset",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.publications.LivePaper",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.sands.BrainAtlas",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpace",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "custodian",
+            reverse="custodians",
+            multiple=True,
+            description="reverse of 'custodians'",
+        ),
+        Property(
+            "is_owner_of",
+            [
+                "openminds.v4.ephys.Electrode",
+                "openminds.v4.ephys.ElectrodeArray",
+                "openminds.v4.ephys.Pipette",
+                "openminds.v4.specimen_prep.SlicingDevice",
+            ],
+            "owner",
+            reverse="owners",
+            multiple=True,
+            description="reverse of 'owners'",
+        ),
+        Property(
+            "is_provider_of",
+            "openminds.v4.chemicals.ProductSource",
+            "provider",
+            reverse="provider",
+            multiple=True,
+            description="reverse of 'provider'",
+        ),
+        Property(
+            "manufactured",
+            "openminds.v4.core.Setup",
+            "manufacturer",
+            reverse="manufacturers",
+            multiple=True,
+            description="reverse of 'manufacturers'",
+        ),
+        Property(
+            "published",
+            [
+                "openminds.v4.publications.Book",
+                "openminds.v4.publications.Chapter",
+                "openminds.v4.publications.LearningResource",
+                "openminds.v4.publications.ScholarlyArticle",
+            ],
+            "publisher",
+            reverse="publisher",
+            multiple=True,
+            description="reverse of 'publisher'",
+        ),
+    ]
+    aliases = {"name": "full_name", "alias": "short_name"}
+    existence_query_properties = ("full_name",)
+
+    def __init__(
+        self,
+        name=None,
+        alias=None,
+        affiliations=None,
+        coordinated_projects=None,
+        developed=None,
+        digital_identifiers=None,
+        full_name=None,
+        funded=None,
+        has_children=None,
+        has_members=None,
+        has_parents=None,
+        homepage=None,
+        hosts=None,
+        is_custodian_of=None,
+        is_owner_of=None,
+        is_provider_of=None,
+        manufactured=None,
+        published=None,
+        short_name=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,
+            alias=alias,
+            affiliations=affiliations,
+            coordinated_projects=coordinated_projects,
+            developed=developed,
+            digital_identifiers=digital_identifiers,
+            full_name=full_name,
+            funded=funded,
+            has_children=has_children,
+            has_members=has_members,
+            has_parents=has_parents,
+            homepage=homepage,
+            hosts=hosts,
+            is_custodian_of=is_custodian_of,
+            is_owner_of=is_owner_of,
+            is_provider_of=is_provider_of,
+            manufactured=manufactured,
+            published=published,
+            short_name=short_name,
+        )