fairgraph 0.13.0__py3-none-any.whl

fairgraph/openminds/core/data/file.py

@@ -0,0 +1,275 @@
+"""
+Structured information on a file instance that is accessible via a URL.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import File as OMFile
+from fairgraph import KGObject
+
+import os
+import mimetypes
+from pathlib import Path
+from urllib.request import urlretrieve
+from urllib.parse import quote, urlparse, urlunparse
+from .hash import Hash
+from .content_type import ContentType
+from ..miscellaneous.quantitative_value import QuantitativeValue
+from ...controlled_terms.unit_of_measurement import UnitOfMeasurement
+from fairgraph.utility import accepted_terms_of_use, sha1sum
+
+mimetypes.init()
+from openminds import IRI
+
+
+class File(KGObject, OMFile):
+    """
+    Structured information on a file instance that is accessible via a URL.
+    """
+
+    type_ = "https://openminds.om-i.org/types/File"
+    default_space = "files"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.core.BehavioralProtocol",
+                "openminds.v4.core.Protocol",
+                "openminds.v4.ephys.ElectrodeArrayUsage",
+                "openminds.v4.ephys.ElectrodeUsage",
+                "openminds.v4.ephys.PipetteUsage",
+                "openminds.v4.specimen_prep.SlicingDeviceUsage",
+            ],
+            ["describedIn", "metadataLocation"],
+            reverse=["described_in", "metadata_locations"],
+            multiple=True,
+            description="reverse of described_in, metadata_locations",
+        ),
+        Property(
+            "fully_documents",
+            [
+                "openminds.v4.core.MetaDataModelVersion",
+                "openminds.v4.core.SoftwareVersion",
+                "openminds.v4.core.WebServiceVersion",
+                "openminds.v4.publications.LivePaperVersion",
+                "openminds.v4.sands.BrainAtlasVersion",
+                "openminds.v4.sands.CommonCoordinateSpaceVersion",
+            ],
+            "fullDocumentation",
+            reverse="full_documentation",
+            multiple=True,
+            description="reverse of 'full_documentation'",
+        ),
+        Property(
+            "has_copies",
+            "openminds.v4.computation.LocalFile",
+            "copyOf",
+            reverse="copy_of",
+            multiple=True,
+            description="reverse of 'copy_of'",
+        ),
+        Property(
+            "is_also_part_of",
+            "openminds.v4.computation.WorkflowRecipeVersion",
+            "hasPart",
+            reverse="has_parts",
+            multiple=True,
+            description="reverse of 'has_parts'",
+        ),
+        Property(
+            "is_configuration_of",
+            "openminds.v4.computation.WorkflowExecution",
+            "configuration",
+            reverse="configuration",
+            multiple=True,
+            description="reverse of 'configuration'",
+        ),
+        Property(
+            "is_default_image_for",
+            "openminds.v4.sands.CustomCoordinateSpace",
+            "defaultImage",
+            reverse="default_images",
+            multiple=True,
+            description="reverse of 'default_images'",
+        ),
+        Property(
+            "is_input_to",
+            "openminds.v4.core.DatasetVersion",
+            "inputData",
+            reverse="input_data",
+            multiple=True,
+            description="reverse of 'input_data'",
+        ),
+        Property(
+            "is_location_of",
+            ["openminds.v4.ephys.Recording", "openminds.v4.sands.ParcellationTerminologyVersion"],
+            "dataLocation",
+            reverse="data_location",
+            multiple=True,
+            description="reverse of 'data_location'",
+        ),
+        Property(
+            "is_output_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",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.ProtocolExecution",
+                "openminds.v4.ephys.RecordingActivity",
+                "openminds.v4.stimulation.StimulationActivity",
+            ],
+            ["output", "outputData"],
+            reverse=["output_data", "outputs"],
+            multiple=True,
+            description="reverse of output_data, outputs",
+        ),
+        Property(
+            "is_preview_of",
+            "openminds.v4.core.ServiceLink",
+            "previewImage",
+            reverse="preview_image",
+            multiple=True,
+            description="reverse of 'preview_image'",
+        ),
+        Property(
+            "is_reference_for",
+            "openminds.v4.computation.ValidationTestVersion",
+            "referenceData",
+            reverse="reference_data",
+            multiple=True,
+            description="reverse of 'reference_data'",
+        ),
+        Property(
+            "is_source_data_of",
+            "openminds.v4.core.FileArchive",
+            "sourceData",
+            reverse="source_data",
+            multiple=True,
+            description="reverse of 'source_data'",
+        ),
+        Property(
+            "is_used_to_group",
+            "openminds.v4.core.FileBundle",
+            "groupedBy",
+            reverse="grouped_by",
+            multiple=True,
+            description="reverse of 'grouped_by'",
+        ),
+        Property(
+            "specifies",
+            [
+                "openminds.v4.sands.AtlasAnnotation",
+                "openminds.v4.sands.CustomAnnotation",
+                "openminds.v4.stimulation.EphysStimulus",
+            ],
+            "specification",
+            reverse="specification",
+            multiple=True,
+            description="reverse of 'specification'",
+        ),
+    ]
+    aliases = {"hash": "hashes"}
+    existence_query_properties = ("iri", "hashes")
+
+    def __init__(
+        self,
+        name=None,
+        content_description=None,
+        data_types=None,
+        describes=None,
+        file_repository=None,
+        format=None,
+        fully_documents=None,
+        has_copies=None,
+        hash=None,
+        hashes=None,
+        iri=None,
+        is_also_part_of=None,
+        is_configuration_of=None,
+        is_default_image_for=None,
+        is_input_to=None,
+        is_location_of=None,
+        is_output_of=None,
+        is_part_of=None,
+        is_preview_of=None,
+        is_reference_for=None,
+        is_source_data_of=None,
+        is_used_to_group=None,
+        special_usage_role=None,
+        specifies=None,
+        storage_size=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,
+            content_description=content_description,
+            data_types=data_types,
+            describes=describes,
+            file_repository=file_repository,
+            format=format,
+            fully_documents=fully_documents,
+            has_copies=has_copies,
+            hash=hash,
+            hashes=hashes,
+            iri=iri,
+            is_also_part_of=is_also_part_of,
+            is_configuration_of=is_configuration_of,
+            is_default_image_for=is_default_image_for,
+            is_input_to=is_input_to,
+            is_location_of=is_location_of,
+            is_output_of=is_output_of,
+            is_part_of=is_part_of,
+            is_preview_of=is_preview_of,
+            is_reference_for=is_reference_for,
+            is_source_data_of=is_source_data_of,
+            is_used_to_group=is_used_to_group,
+            special_usage_role=special_usage_role,
+            specifies=specifies,
+            storage_size=storage_size,
+        )
+
+    @classmethod
+    def from_local_file(cls, relative_path):
+        obj = cls(
+            name=relative_path,
+            storage_size=QuantitativeValue(
+                value=float(os.stat(relative_path).st_size), unit=UnitOfMeasurement(name="bytes")
+            ),
+            hashes=Hash(algorithm="SHA1", digest=sha1sum(relative_path)),
+            format=ContentType(name=mimetypes.guess_type(relative_path)[0]),
+            # todo: query ContentTypes since that contains additional, EBRAINS-specific content types
+        )
+        return obj
+
+    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):
+            local_path = Path(local_path)
+            if local_path.is_dir():
+                local_filename = local_path / self.name
+            else:
+                local_filename = local_path
+                local_filename.parent.mkdir(parents=True, exist_ok=True)
+            url_parts = urlparse(self.iri.value)
+            url_parts = url_parts._replace(path=quote(url_parts.path))
+            url = urlunparse(url_parts)
+            local_filename, headers = urlretrieve(url, local_filename)
+            # todo: check hash value of downloaded file
+            # todo: if local_path isn't an existing directory but looks like a directory name
+            #       rather than a filename, create that directory and save a file called self.name
+            #       within it
+            return local_filename

fairgraph/openminds/core/data/file_archive.py

@@ -0,0 +1,71 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import FileArchive as OMFileArchive
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class FileArchive(KGObject, OMFileArchive):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/FileArchive"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "is_location_of",
+            "openminds.v4.core.ServiceLink",
+            "dataLocation",
+            reverse="data_location",
+            multiple=True,
+            description="reverse of 'data_location'",
+        ),
+        Property(
+            "is_output_of",
+            [
+                "openminds.v4.computation.DataAnalysis",
+                "openminds.v4.computation.GenericComputation",
+                "openminds.v4.computation.Simulation",
+                "openminds.v4.computation.Visualization",
+            ],
+            "output",
+            reverse="outputs",
+            multiple=True,
+            description="reverse of 'outputs'",
+        ),
+    ]
+    existence_query_properties = ("iri", "format")
+
+    def __init__(
+        self,
+        format=None,
+        iri=None,
+        is_location_of=None,
+        is_output_of=None,
+        source_data=None,
+        id=None,
+        data=None,
+        space=None,
+        release_status=None,
+    ):
+        return KGObject.__init__(
+            self,
+            id=id,
+            space=space,
+            release_status=release_status,
+            data=data,
+            format=format,
+            iri=iri,
+            is_location_of=is_location_of,
+            is_output_of=is_output_of,
+            source_data=source_data,
+        )

fairgraph/openminds/core/data/file_bundle.py

@@ -0,0 +1,150 @@
+"""
+Structured information on a bundle of file instances.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import FileBundle as OMFileBundle
+from fairgraph import KGObject
+
+
+class FileBundle(KGObject, OMFileBundle):
+    """
+    Structured information on a bundle of file instances.
+    """
+
+    type_ = "https://openminds.om-i.org/types/FileBundle"
+    default_space = "files"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "describes",
+            [
+                "openminds.v4.ephys.ElectrodeArrayUsage",
+                "openminds.v4.ephys.ElectrodeUsage",
+                "openminds.v4.ephys.PipetteUsage",
+                "openminds.v4.specimen_prep.SlicingDeviceUsage",
+            ],
+            "metadataLocation",
+            reverse="metadata_locations",
+            multiple=True,
+            description="reverse of 'metadata_locations'",
+        ),
+        Property(
+            "has_parts",
+            ["openminds.v4.core.File", "openminds.v4.core.FileBundle"],
+            "isPartOf",
+            reverse="is_part_of",
+            multiple=True,
+            description="reverse of 'is_part_of'",
+        ),
+        Property(
+            "is_also_part_of",
+            "openminds.v4.computation.WorkflowRecipeVersion",
+            "hasPart",
+            reverse="has_parts",
+            multiple=True,
+            description="reverse of 'has_parts'",
+        ),
+        Property(
+            "is_input_to",
+            "openminds.v4.core.DatasetVersion",
+            "inputData",
+            reverse="input_data",
+            multiple=True,
+            description="reverse of 'input_data'",
+        ),
+        Property(
+            "is_location_of",
+            ["openminds.v4.core.ServiceLink", "openminds.v4.ephys.Recording"],
+            "dataLocation",
+            reverse="data_location",
+            multiple=True,
+            description="reverse of 'data_location'",
+        ),
+        Property(
+            "is_output_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",
+                "openminds.v4.core.ModelVersion",
+                "openminds.v4.core.ProtocolExecution",
+                "openminds.v4.ephys.RecordingActivity",
+                "openminds.v4.stimulation.StimulationActivity",
+            ],
+            ["output", "outputData"],
+            reverse=["output_data", "outputs"],
+            multiple=True,
+            description="reverse of output_data, outputs",
+        ),
+        Property(
+            "is_reference_for",
+            "openminds.v4.computation.ValidationTestVersion",
+            "referenceData",
+            reverse="reference_data",
+            multiple=True,
+            description="reverse of 'reference_data'",
+        ),
+        Property(
+            "specifies",
+            "openminds.v4.stimulation.EphysStimulus",
+            "specification",
+            reverse="specifications",
+            multiple=True,
+            description="reverse of 'specifications'",
+        ),
+    ]
+    existence_query_properties = ("is_part_of", "name")
+
+    def __init__(
+        self,
+        name=None,
+        content_description=None,
+        describes=None,
+        format=None,
+        grouped_by=None,
+        grouping_types=None,
+        has_parts=None,
+        hash=None,
+        is_also_part_of=None,
+        is_input_to=None,
+        is_location_of=None,
+        is_output_of=None,
+        is_part_of=None,
+        is_reference_for=None,
+        specifies=None,
+        storage_size=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,
+            content_description=content_description,
+            describes=describes,
+            format=format,
+            grouped_by=grouped_by,
+            grouping_types=grouping_types,
+            has_parts=has_parts,
+            hash=hash,
+            is_also_part_of=is_also_part_of,
+            is_input_to=is_input_to,
+            is_location_of=is_location_of,
+            is_output_of=is_output_of,
+            is_part_of=is_part_of,
+            is_reference_for=is_reference_for,
+            specifies=specifies,
+            storage_size=storage_size,
+        )

fairgraph/openminds/core/data/file_path_pattern.py

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

fairgraph/openminds/core/data/file_repository.py

@@ -0,0 +1,99 @@
+"""
+Structured information on a file repository.
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import FileRepository as OMFileRepository
+from fairgraph import KGObject
+
+
+from openminds import IRI
+
+
+class FileRepository(KGObject, OMFileRepository):
+    """
+    Structured information on a file repository.
+    """
+
+    type_ = "https://openminds.om-i.org/types/FileRepository"
+    default_space = "dataset"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "contains_content_of",
+            [
+                "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",
+            ],
+            "repository",
+            reverse="repository",
+            multiple=True,
+            description="reverse of 'repository'",
+        ),
+        Property(
+            "files",
+            "openminds.v4.core.File",
+            "fileRepository",
+            reverse="file_repository",
+            multiple=True,
+            description="reverse of 'file_repository'",
+        ),
+        Property(
+            "has_parts",
+            "openminds.v4.core.FileBundle",
+            "isPartOf",
+            reverse="is_part_of",
+            multiple=True,
+            description="reverse of 'is_part_of'",
+        ),
+    ]
+    existence_query_properties = ("iri",)
+
+    def __init__(
+        self,
+        name=None,
+        contains_content_of=None,
+        content_type_patterns=None,
+        files=None,
+        format=None,
+        has_parts=None,
+        hash=None,
+        hosted_by=None,
+        iri=None,
+        storage_size=None,
+        structure_pattern=None,
+        type=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,
+            contains_content_of=contains_content_of,
+            content_type_patterns=content_type_patterns,
+            files=files,
+            format=format,
+            has_parts=has_parts,
+            hash=hash,
+            hosted_by=hosted_by,
+            iri=iri,
+            storage_size=storage_size,
+            structure_pattern=structure_pattern,
+            type=type,
+        )

fairgraph/openminds/core/data/file_repository_structure.py

@@ -0,0 +1,51 @@
+"""
+<description not available>
+"""
+
+# this file was auto-generated
+
+from openminds.properties import Property
+from openminds.v4.core import FileRepositoryStructure as OMFileRepositoryStructure
+from fairgraph import KGObject
+
+
+class FileRepositoryStructure(KGObject, OMFileRepositoryStructure):
+    """
+    <description not available>
+    """
+
+    type_ = "https://openminds.om-i.org/types/FileRepositoryStructure"
+    default_space = "files"
+    # forward properties are defined in the parent class (in openMINDS-Python)
+    reverse_properties = [
+        Property(
+            "structures",
+            "openminds.v4.core.FileRepository",
+            "structurePattern",
+            reverse="structure_pattern",
+            multiple=True,
+            description="reverse of 'structure_pattern'",
+        ),
+    ]
+    existence_query_properties = ("lookup_label",)
+
+    def __init__(
+        self,
+        lookup_label=None,
+        file_path_patterns=None,
+        structures=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,
+            file_path_patterns=file_path_patterns,
+            structures=structures,
+        )

fairgraph/openminds/core/data/hash.py

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