fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/publications/periodical.py

@@ -0,0 +1,53 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.publications import Periodical as OMPeriodical
+from fairgraph import KGObject
+
+
+class Periodical(KGObject, OMPeriodical):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/Periodical"
+    default_space = "livepapers"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_parts",
+            "openminds.v4.publications.PublicationVolume",
+            "isPartOf",
+            reverse="is_part_of",
+            multiple=True,
+            description="reverse of 'is_part_of'",
+        ),
+    ]
+    existence_query_properties = ("abbreviation",)
+
+    def __init__(
+        self,
+        name=None,
+        abbreviation=None,
+        digital_identifier=None,
+        has_parts=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,
+            abbreviation=abbreviation,
+            digital_identifier=digital_identifier,
+            has_parts=has_parts,
+        )

fairgraph/openminds/publications/publication_issue.py

@@ -0,0 +1,44 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.publications import PublicationIssue as OMPublicationIssue
+from fairgraph import KGObject
+
+
+class PublicationIssue(KGObject, OMPublicationIssue):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/PublicationIssue"
+    default_space = "livepapers"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_parts",
+            "openminds.v4.publications.ScholarlyArticle",
+            "isPartOf",
+            reverse="is_part_of",
+            multiple=True,
+            description="reverse of 'is_part_of'",
+        ),
+    ]
+    existence_query_properties = ("is_part_of", "issue_number")
+
+    def __init__(
+        self, has_parts=None, is_part_of=None, issue_number=None, id=None, data=None, space=None, release_status=None
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            has_parts=has_parts,
+            is_part_of=is_part_of,
+            issue_number=issue_number,
+        )

fairgraph/openminds/publications/publication_volume.py

@@ -0,0 +1,44 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.publications import PublicationVolume as OMPublicationVolume
+from fairgraph import KGObject
+
+
+class PublicationVolume(KGObject, OMPublicationVolume):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/PublicationVolume"
+    default_space = "livepapers"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "has_parts",
+            ["openminds.v4.publications.PublicationIssue", "openminds.v4.publications.ScholarlyArticle"],
+            "isPartOf",
+            reverse="is_part_of",
+            multiple=True,
+            description="reverse of 'is_part_of'",
+        ),
+    ]
+    existence_query_properties = ("is_part_of", "volume_number")
+
+    def __init__(
+        self, has_parts=None, is_part_of=None, volume_number=None, id=None, data=None, space=None, release_status=None
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            has_parts=has_parts,
+            is_part_of=is_part_of,
+            volume_number=volume_number,
+        )

fairgraph/openminds/publications/scholarly_article.py

@@ -0,0 +1,146 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.publications import ScholarlyArticle as OMScholarlyArticle
+from fairgraph import KGObject
+
+from fairgraph.utility import as_list
+from .publication_issue import PublicationIssue
+from .periodical import Periodical
+from datetime import date
+from openminds import IRI
+
+
+class ScholarlyArticle(KGObject, OMScholarlyArticle):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/ScholarlyArticle"
+    default_space = "livepapers"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "related_to",
+            [
+                "openminds.v4.computation.ValidationTestVersion",
+                "openminds.v4.computation.WorkflowRecipeVersion",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "relatedPublication",
+            reverse="related_publications",
+            multiple=True,
+            description="reverse of 'related_publications'",
+        ),
+    ]
+    existence_query_properties = ("name",)
+
+    def __init__(
+        self,
+        name=None,
+        abstract=None,
+        authors=None,
+        cited_publications=None,
+        copyright=None,
+        creation_date=None,
+        custodians=None,
+        digital_identifier=None,
+        editors=None,
+        funding=None,
+        iri=None,
+        is_part_of=None,
+        keywords=None,
+        license=None,
+        modification_date=None,
+        pagination=None,
+        publication_date=None,
+        publisher=None,
+        related_to=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,
+            abstract=abstract,
+            authors=authors,
+            cited_publications=cited_publications,
+            copyright=copyright,
+            creation_date=creation_date,
+            custodians=custodians,
+            digital_identifier=digital_identifier,
+            editors=editors,
+            funding=funding,
+            iri=iri,
+            is_part_of=is_part_of,
+            keywords=keywords,
+            license=license,
+            modification_date=modification_date,
+            pagination=pagination,
+            publication_date=publication_date,
+            publisher=publisher,
+            related_to=related_to,
+            version_identifier=version_identifier,
+        )
+
+    def get_journal(self, client, with_volume=False, with_issue=False):
+        journal = volume = issue = None
+        if self.is_part_of:
+            issue_or_volume = self.is_part_of.resolve(
+                client, release_status=self.release_status, follow_links={"is_part_of": {}}
+            )
+            if isinstance(issue_or_volume, PublicationIssue):
+                volume = issue_or_volume.is_part_of
+                issue = issue_or_volume
+            else:
+                volume = issue_or_volume
+                issue = None
+            journal = volume.is_part_of
+            assert isinstance(journal, Periodical)
+        retval = [journal]
+        if with_volume:
+            retval.append(volume)
+        if with_issue:
+            retval.append(issue)
+        if not with_volume and not with_issue:
+            return journal
+        else:
+            return tuple(retval)
+
+    def get_citation_string(self, client):
+        # Eyal, G., Verhoog, M. B., Testa-Silva, G., Deitcher, Y., Lodder, '
+        #     -              'J. C., Benavides-Piccione, R., ... & Segev, I. (2016). Unique '
+        #     -              'membrane properties and enhanced signal processing in human '
+        #     -              'neocortical neurons. Elife, 5, e16553.
+        self.resolve(client, follow_links={"is_part_of": {}, "authors": {}})
+        authors = as_list(self.authors)
+        if len(authors) == 1:
+            author_str = authors[0].full_name
+        elif len(authors) > 1:
+            author_str = ", ".join(au.full_name for au in authors[:-1])
+            author_str += " & " + self.authors[-1].full_name
+        journal, volume, issue = self.get_journal(client, with_volume=True, with_issue=True)
+        title = self.name
+        if title and title[-1] != ".":
+            title += "."
+        journal_name = journal.name if journal else ""
+        volume_number = f"{volume.volume_number}: " if (volume and volume.volume_number != "placeholder") else ""
+        return f"{author_str} ({self.publication_date.year}). {title} {journal_name}, {volume_number}{self.pagination or ''}."

fairgraph/openminds/sands/__init__.py

@@ -0,0 +1,57 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import EmbeddedMetadata
+
+from .mathematical_shapes import Ellipse, Rectangle, Circle
+from .non_atlas import CustomCoordinateSpace, CustomAnnotation, CustomAnatomicalEntity
+from .miscellaneous import (
+    AnatomicalTargetPosition,
+    ViewerSpecification,
+    QualitativeRelationAssessment,
+    CoordinatePoint,
+    QuantitativeRelationAssessment,
+    SingleColor,
+)
+from .atlas import (
+    ParcellationEntity,
+    CommonCoordinateSpace,
+    BrainAtlas,
+    ParcellationTerminologyVersion,
+    ParcellationTerminology,
+    CommonCoordinateSpaceVersion,
+    AtlasAnnotation,
+    ParcellationEntityVersion,
+    BrainAtlasVersion,
+)
+
+
+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/sands/atlas/__init__.py

@@ -0,0 +1,9 @@
+from .atlas_annotation import AtlasAnnotation
+from .brain_atlas import BrainAtlas
+from .brain_atlas_version import BrainAtlasVersion
+from .common_coordinate_space import CommonCoordinateSpace
+from .common_coordinate_space_version import CommonCoordinateSpaceVersion
+from .parcellation_entity import ParcellationEntity
+from .parcellation_entity_version import ParcellationEntityVersion
+from .parcellation_terminology import ParcellationTerminology
+from .parcellation_terminology_version import ParcellationTerminologyVersion

fairgraph/openminds/sands/atlas/atlas_annotation.py

@@ -0,0 +1,52 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import AtlasAnnotation as OMAtlasAnnotation
+from fairgraph import EmbeddedMetadata
+
+
+class AtlasAnnotation(EmbeddedMetadata, OMAtlasAnnotation):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/AtlasAnnotation"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = []
+    existence_query_properties = ("criteria_quality_type", "criteria_type", "type")
+
+    def __init__(
+        self,
+        anchor_points=None,
+        criteria=None,
+        criteria_quality_type=None,
+        criteria_type=None,
+        inspired_by=None,
+        internal_identifier=None,
+        lateralities=None,
+        preferred_visualization=None,
+        specification=None,
+        type=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return EmbeddedMetadata.__init__(
+            self,
+            data=data,
+            anchor_points=anchor_points,
+            criteria=criteria,
+            criteria_quality_type=criteria_quality_type,
+            criteria_type=criteria_type,
+            inspired_by=inspired_by,
+            internal_identifier=internal_identifier,
+            lateralities=lateralities,
+            preferred_visualization=preferred_visualization,
+            specification=specification,
+            type=type,
+        )

fairgraph/openminds/sands/atlas/brain_atlas.py

@@ -0,0 +1,113 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import BrainAtlas as OMBrainAtlas
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class BrainAtlas(KGObject, OMBrainAtlas):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/BrainAtlas"
+    default_space = "atlas"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "comments",
+            "openminds.v4.core.Comment",
+            "about",
+            reverse="about",
+            multiple=True,
+            description="reverse of 'about'",
+        ),
+        Property(
+            "is_input_to",
+            "openminds.v4.core.DatasetVersion",
+            "inputData",
+            reverse="input_data",
+            multiple=True,
+            description="reverse of 'input_data'",
+        ),
+        Property(
+            "is_part_of",
+            ["openminds.v4.core.Project", "openminds.v4.core.ResearchProductGroup"],
+            "hasPart",
+            reverse="has_parts",
+            multiple=True,
+            description="reverse of 'has_parts'",
+        ),
+        Property(
+            "learning_resources",
+            "openminds.v4.publications.LearningResource",
+            "about",
+            reverse="about",
+            multiple=True,
+            description="reverse of 'about'",
+        ),
+    ]
+    aliases = {"name": "full_name", "versions": "has_versions", "alias": "short_name"}
+    existence_query_properties = ("digital_identifier",)
+
+    def __init__(
+        self,
+        name=None,
+        alias=None,
+        abbreviation=None,
+        authors=None,
+        comments=None,
+        custodians=None,
+        description=None,
+        digital_identifier=None,
+        full_name=None,
+        has_terminology=None,
+        has_versions=None,
+        homepage=None,
+        how_to_cite=None,
+        is_input_to=None,
+        is_part_of=None,
+        learning_resources=None,
+        ontology_identifier=None,
+        short_name=None,
+        used_species=None,
+        versions=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,
+            abbreviation=abbreviation,
+            authors=authors,
+            comments=comments,
+            custodians=custodians,
+            description=description,
+            digital_identifier=digital_identifier,
+            full_name=full_name,
+            has_terminology=has_terminology,
+            has_versions=has_versions,
+            homepage=homepage,
+            how_to_cite=how_to_cite,
+            is_input_to=is_input_to,
+            is_part_of=is_part_of,
+            learning_resources=learning_resources,
+            ontology_identifier=ontology_identifier,
+            short_name=short_name,
+            used_species=used_species,
+            versions=versions,
+        )