fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/sands/atlas/brain_atlas_version.py

@@ -0,0 +1,213 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import BrainAtlasVersion as OMBrainAtlasVersion
+from fairgraph import KGObject
+
+from urllib.request import urlretrieve
+from pathlib import Path
+from ....utility import accepted_terms_of_use
+from datetime import date
+from openminds import IRI
+
+
+class BrainAtlasVersion(KGObject, OMBrainAtlasVersion):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/BrainAtlasVersion"
+    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.computation.DataAnalysis",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.ProtocolExecution",
+            ],
+            ["input", "inputData"],
+            reverse=["input_data", "inputs"],
+            multiple=True,
+            description="reverse of input_data, inputs",
+        ),
+        Property(
+            "is_old_version_of",
+            "openminds.v4.sands.BrainAtlasVersion",
+            "isNewVersionOf",
+            reverse="is_new_version_of",
+            multiple=True,
+            description="reverse of 'is_new_version_of'",
+        ),
+        Property(
+            "is_part_of",
+            [
+                "openminds.v4.core.Project",
+                "openminds.v4.core.ResearchProductGroup",
+                "openminds.v4.core.SoftwareVersion",
+            ],
+            "hasPart",
+            reverse="has_parts",
+            multiple=True,
+            description="reverse of 'has_parts'",
+        ),
+        Property(
+            "is_version_of",
+            "openminds.v4.sands.BrainAtlas",
+            "hasVersion",
+            reverse="has_versions",
+            multiple=True,
+            description="reverse of 'has_versions'",
+        ),
+        Property(
+            "learning_resources",
+            "openminds.v4.publications.LearningResource",
+            "about",
+            reverse="about",
+            multiple=True,
+            description="reverse of 'about'",
+        ),
+    ]
+    aliases = {"name": "full_name", "alias": "short_name"}
+    existence_query_properties = ("short_name", "version_identifier")
+
+    def __init__(
+        self,
+        name=None,
+        alias=None,
+        abbreviation=None,
+        accessibility=None,
+        authors=None,
+        comments=None,
+        coordinate_space=None,
+        copyright=None,
+        custodians=None,
+        description=None,
+        digital_identifier=None,
+        full_documentation=None,
+        full_name=None,
+        funding=None,
+        has_terminology=None,
+        homepage=None,
+        how_to_cite=None,
+        is_alternative_version_of=None,
+        is_input_to=None,
+        is_new_version_of=None,
+        is_old_version_of=None,
+        is_part_of=None,
+        is_version_of=None,
+        keywords=None,
+        learning_resources=None,
+        license=None,
+        major_version_identifier=None,
+        ontology_identifier=None,
+        other_contributions=None,
+        related_publications=None,
+        release_date=None,
+        repository=None,
+        short_name=None,
+        support_channels=None,
+        type=None,
+        used_specimens=None,
+        version_identifier=None,
+        version_innovation=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,
+            accessibility=accessibility,
+            authors=authors,
+            comments=comments,
+            coordinate_space=coordinate_space,
+            copyright=copyright,
+            custodians=custodians,
+            description=description,
+            digital_identifier=digital_identifier,
+            full_documentation=full_documentation,
+            full_name=full_name,
+            funding=funding,
+            has_terminology=has_terminology,
+            homepage=homepage,
+            how_to_cite=how_to_cite,
+            is_alternative_version_of=is_alternative_version_of,
+            is_input_to=is_input_to,
+            is_new_version_of=is_new_version_of,
+            is_old_version_of=is_old_version_of,
+            is_part_of=is_part_of,
+            is_version_of=is_version_of,
+            keywords=keywords,
+            learning_resources=learning_resources,
+            license=license,
+            major_version_identifier=major_version_identifier,
+            ontology_identifier=ontology_identifier,
+            other_contributions=other_contributions,
+            related_publications=related_publications,
+            release_date=release_date,
+            repository=repository,
+            short_name=short_name,
+            support_channels=support_channels,
+            type=type,
+            used_specimens=used_specimens,
+            version_identifier=version_identifier,
+            version_innovation=version_innovation,
+        )
+
+    def download(self, local_path, client, accept_terms_of_use=False):
+        if accepted_terms_of_use(client, accept_terms_of_use=accept_terms_of_use):
+            repo = self.repository.resolve(client, release_status=self.release_status or None)
+            if repo.iri.value.startswith("https://object.cscs.ch/v1/AUTH") or repo.iri.value.startswith(
+                "https://data-proxy.ebrains.eu/api/v1/public"
+            ):
+                zip_archive_url = f"https://data.kg.ebrains.eu/zip?container={repo.iri.value}"
+            else:
+                raise NotImplementedError("Download not yet implemented for this repository type")
+            if local_path.endswith(".zip"):
+                local_filename = Path(local_path)
+            else:
+                local_filename = Path(local_path) / (zip_archive_url.split("/")[-1] + ".zip")
+            local_filename.parent.mkdir(parents=True, exist_ok=True)
+            local_filename, headers = urlretrieve(zip_archive_url, local_filename)
+            return local_filename, repo.iri.value
+
+    def _get_inherited_property(self, property_name, client, release_status="released"):
+        value = getattr(self, property_name)
+        if value:
+            return value
+        else:
+            parent = self.is_version_of.resolve(client, release_status=release_status)
+            return getattr(parent, property_name)
+
+    def get_full_name(self, client, release_status="released"):
+        return self._get_inherited_property("full_name", client, release_status)
+
+    def get_short_name(self, client, release_status="released"):
+        return self._get_inherited_property("short_name", client, release_status)
+
+    def get_description(self, client, release_status="released"):
+        return self._get_inherited_property("description", client, release_status)
+
+    def get_authors(self, client, release_status="released"):
+        return self._get_inherited_property("authors", client, release_status)

fairgraph/openminds/sands/atlas/common_coordinate_space.py

@@ -0,0 +1,121 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import CommonCoordinateSpace as OMCommonCoordinateSpace
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class CommonCoordinateSpace(KGObject, OMCommonCoordinateSpace):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/CommonCoordinateSpace"
+    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(
+            "is_used_to_group",
+            "openminds.v4.core.FileBundle",
+            "groupedBy",
+            reverse="grouped_by",
+            multiple=True,
+            description="reverse of 'grouped_by'",
+        ),
+        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 = ("short_name", "version_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_versions=None,
+        homepage=None,
+        how_to_cite=None,
+        is_input_to=None,
+        is_part_of=None,
+        is_used_to_group=None,
+        learning_resources=None,
+        ontology_identifiers=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_versions=has_versions,
+            homepage=homepage,
+            how_to_cite=how_to_cite,
+            is_input_to=is_input_to,
+            is_part_of=is_part_of,
+            is_used_to_group=is_used_to_group,
+            learning_resources=learning_resources,
+            ontology_identifiers=ontology_identifiers,
+            short_name=short_name,
+            used_species=used_species,
+            versions=versions,
+        )

fairgraph/openminds/sands/atlas/common_coordinate_space_version.py

@@ -0,0 +1,243 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.sands import CommonCoordinateSpaceVersion as OMCommonCoordinateSpaceVersion
+from fairgraph import KGObject
+
+from urllib.request import urlretrieve
+from pathlib import Path
+from ....utility import accepted_terms_of_use
+from datetime import date
+from openminds import IRI
+
+
+class CommonCoordinateSpaceVersion(KGObject, OMCommonCoordinateSpaceVersion):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/CommonCoordinateSpaceVersion"
+    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_coordinate_space_of",
+            ["openminds.v4.sands.BrainAtlasVersion", "openminds.v4.sands.CustomAnnotation"],
+            "coordinateSpace",
+            reverse="coordinate_space",
+            multiple=True,
+            description="reverse of 'coordinate_space'",
+        ),
+        Property(
+            "is_input_to",
+            [
+                "openminds.v4.computation.DataAnalysis",
+                "openminds.v4.core.DatasetVersion",
+                "openminds.v4.core.ProtocolExecution",
+            ],
+            ["input", "inputData"],
+            reverse=["input_data", "inputs"],
+            multiple=True,
+            description="reverse of input_data, inputs",
+        ),
+        Property(
+            "is_old_version_of",
+            "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            "isNewVersionOf",
+            reverse="is_new_version_of",
+            multiple=True,
+            description="reverse of 'is_new_version_of'",
+        ),
+        Property(
+            "is_part_of",
+            [
+                "openminds.v4.core.Project",
+                "openminds.v4.core.ResearchProductGroup",
+                "openminds.v4.core.SoftwareVersion",
+            ],
+            "hasPart",
+            reverse="has_parts",
+            multiple=True,
+            description="reverse of 'has_parts'",
+        ),
+        Property(
+            "is_used_to_group",
+            "openminds.v4.core.FileBundle",
+            "groupedBy",
+            reverse="grouped_by",
+            multiple=True,
+            description="reverse of 'grouped_by'",
+        ),
+        Property(
+            "is_version_of",
+            "openminds.v4.sands.CommonCoordinateSpace",
+            "hasVersion",
+            reverse="has_versions",
+            multiple=True,
+            description="reverse of 'has_versions'",
+        ),
+        Property(
+            "learning_resources",
+            "openminds.v4.publications.LearningResource",
+            "about",
+            reverse="about",
+            multiple=True,
+            description="reverse of 'about'",
+        ),
+    ]
+    aliases = {"name": "full_name", "alias": "short_name"}
+    existence_query_properties = (
+        "accessibility",
+        "anatomical_axes_orientation",
+        "axes_origins",
+        "full_documentation",
+        "native_unit",
+        "release_date",
+        "short_name",
+        "version_identifier",
+        "version_innovation",
+    )
+
+    def __init__(
+        self,
+        name=None,
+        alias=None,
+        abbreviation=None,
+        accessibility=None,
+        anatomical_axes_orientation=None,
+        authors=None,
+        axes_origins=None,
+        comments=None,
+        copyright=None,
+        custodians=None,
+        default_images=None,
+        description=None,
+        digital_identifier=None,
+        full_documentation=None,
+        full_name=None,
+        funding=None,
+        homepage=None,
+        how_to_cite=None,
+        is_alternative_version_of=None,
+        is_coordinate_space_of=None,
+        is_input_to=None,
+        is_new_version_of=None,
+        is_old_version_of=None,
+        is_part_of=None,
+        is_used_to_group=None,
+        is_version_of=None,
+        keywords=None,
+        learning_resources=None,
+        license=None,
+        native_unit=None,
+        ontology_identifiers=None,
+        other_contributions=None,
+        related_publications=None,
+        release_date=None,
+        repository=None,
+        short_name=None,
+        support_channels=None,
+        used_specimens=None,
+        version_identifier=None,
+        version_innovation=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,
+            accessibility=accessibility,
+            anatomical_axes_orientation=anatomical_axes_orientation,
+            authors=authors,
+            axes_origins=axes_origins,
+            comments=comments,
+            copyright=copyright,
+            custodians=custodians,
+            default_images=default_images,
+            description=description,
+            digital_identifier=digital_identifier,
+            full_documentation=full_documentation,
+            full_name=full_name,
+            funding=funding,
+            homepage=homepage,
+            how_to_cite=how_to_cite,
+            is_alternative_version_of=is_alternative_version_of,
+            is_coordinate_space_of=is_coordinate_space_of,
+            is_input_to=is_input_to,
+            is_new_version_of=is_new_version_of,
+            is_old_version_of=is_old_version_of,
+            is_part_of=is_part_of,
+            is_used_to_group=is_used_to_group,
+            is_version_of=is_version_of,
+            keywords=keywords,
+            learning_resources=learning_resources,
+            license=license,
+            native_unit=native_unit,
+            ontology_identifiers=ontology_identifiers,
+            other_contributions=other_contributions,
+            related_publications=related_publications,
+            release_date=release_date,
+            repository=repository,
+            short_name=short_name,
+            support_channels=support_channels,
+            used_specimens=used_specimens,
+            version_identifier=version_identifier,
+            version_innovation=version_innovation,
+        )
+
+    def download(self, local_path, client, accept_terms_of_use=False):
+        if accepted_terms_of_use(client, accept_terms_of_use=accept_terms_of_use):
+            repo = self.repository.resolve(client, release_status=self.release_status or None)
+            if repo.iri.value.startswith("https://object.cscs.ch/v1/AUTH") or repo.iri.value.startswith(
+                "https://data-proxy.ebrains.eu/api/v1/public"
+            ):
+                zip_archive_url = f"https://data.kg.ebrains.eu/zip?container={repo.iri.value}"
+            else:
+                raise NotImplementedError("Download not yet implemented for this repository type")
+            if local_path.endswith(".zip"):
+                local_filename = Path(local_path)
+            else:
+                local_filename = Path(local_path) / (zip_archive_url.split("/")[-1] + ".zip")
+            local_filename.parent.mkdir(parents=True, exist_ok=True)
+            local_filename, headers = urlretrieve(zip_archive_url, local_filename)
+            return local_filename, repo.iri.value
+
+    def _get_inherited_property(self, property_name, client, release_status="released"):
+        value = getattr(self, property_name)
+        if value:
+            return value
+        else:
+            parent = self.is_version_of.resolve(client, release_status=release_status)
+            return getattr(parent, property_name)
+
+    def get_full_name(self, client, release_status="released"):
+        return self._get_inherited_property("full_name", client, release_status)
+
+    def get_short_name(self, client, release_status="released"):
+        return self._get_inherited_property("short_name", client, release_status)
+
+    def get_description(self, client, release_status="released"):
+        return self._get_inherited_property("description", client, release_status)
+
+    def get_authors(self, client, release_status="released"):
+        return self._get_inherited_property("authors", client, release_status)