entitysdk 0.2.5__tar.gz → 0.3.0__tar.gz

{entitysdk-0.2.5/src/entitysdk.egg-info → entitysdk-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.2.5
+Version: 0.3.0
 Summary: Python library for interacting with the entitycore service
 Author-email: Open Brain Institute <info@openbraininstitute.org>
 Maintainer-email: Open Brain Institute <info@openbraininstitute.org>

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/client.py

@@ -14,7 +14,11 @@ from entitysdk.models.core import Identifiable
 from entitysdk.result import IteratorResult
 from entitysdk.token_manager import TokenManager
 from entitysdk.types import ID, DeploymentEnvironment
-from entitysdk.util import build_api_url
+from entitysdk.util import (
+    build_api_url,
+    create_intermediate_directories,
+    validate_filename_extension_consistency,
+)
 
 
 class Client:
@@ -314,7 +318,7 @@ class Client:
         *,
         entity_id: ID,
         entity_type: type[Identifiable],
-        asset_id: str,
+        asset_id: ID,
         project_context: ProjectContext | None = None,
         token: str | None = None,
     ) -> bytes:
@@ -353,7 +357,7 @@ class Client:
         *,
         entity_id: ID,
         entity_type: type[Identifiable],
-        asset_id: str,
+        asset_id: ID,
         output_path: os.PathLike,
         project_context: ProjectContext | None = None,
         token: str | None = None,
@@ -364,26 +368,37 @@ class Client:
             entity_id: Id of the entity.
             entity_type: Type of the entity.
             asset_id: Id of the asset.
-            output_path: Path to save the file to.
+            output_path: Either be a file path to write the file to or an output directory.
             project_context: Optional project context.
             token: Authorization access token.
         """
-        url = (
-            route.get_assets_endpoint(
-                api_url=self.api_url,
-                entity_type=entity_type,
-                entity_id=entity_id,
-                asset_id=asset_id,
-            )
-            + "/download"
+        asset_endpoint = route.get_assets_endpoint(
+            api_url=self.api_url,
+            entity_type=entity_type,
+            entity_id=entity_id,
+            asset_id=asset_id,
         )
         token = self._get_token(override_token=token)
         context = self._optional_user_context(override_context=project_context)
+        asset = core.get_entity(
+            asset_endpoint,
+            entity_type=Asset,
+            token=token,
+            project_context=context,
+            http_client=self._http_client,
+        )
+        path: Path = Path(output_path)
+        path = (
+            path / asset.path
+            if path.is_dir()
+            else validate_filename_extension_consistency(path, Path(asset.path).suffix)
+        )
+        create_intermediate_directories(path)
         return core.download_asset_file(
-            url=url,
+            url=f"{asset_endpoint}/download",
             token=token,
             project_context=context,
-            output_path=Path(output_path),
+            output_path=path,
             http_client=self._http_client,
         )
 

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/core.py

@@ -3,6 +3,7 @@
 import io
 from collections.abc import Iterator
 from pathlib import Path
+from typing import TypeVar
 
 import httpx
 
@@ -13,6 +14,8 @@ from entitysdk.models.core import Identifiable
 from entitysdk.result import IteratorResult
 from entitysdk.util import make_db_api_request, stream_paginated_request
 
+TIdentifiable = TypeVar("TIdentifiable", bound=Identifiable)
+
 
 def search_entities(
     url: str,
@@ -55,11 +58,11 @@ def search_entities(
 def get_entity(
     url: str,
     *,
-    entity_type: type[Identifiable],
+    entity_type: type[TIdentifiable],
     project_context: ProjectContext | None = None,
     token: str,
     http_client: httpx.Client | None = None,
-) -> Identifiable:
+) -> TIdentifiable:
     """Instantiate entity with model ``entity_type`` from resource id."""
     response = make_db_api_request(
         url=url,

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/models/__init__.py

@@ -10,9 +10,11 @@ from entitysdk.models.emodel import EModel
 from entitysdk.models.ion_channel_model import IonChannelModel, NeuronBlock, UseIon
 from entitysdk.models.license import License
 from entitysdk.models.memodel import MEModel
+from entitysdk.models.memodelcalibrationresult import MEModelCalibrationResult
 from entitysdk.models.morphology import ReconstructionMorphology
 from entitysdk.models.mtype import MTypeClass
 from entitysdk.models.taxonomy import Species, Strain, Taxonomy
+from entitysdk.models.validation_result import ValidationResult
 
 __all__ = [
     "Asset",
@@ -24,6 +26,7 @@ __all__ = [
     "IonChannelModel",
     "License",
     "MEModel",
+    "MEModelCalibrationResult",
     "MTypeClass",
     "NeuronBlock",
     "Organization",
@@ -34,4 +37,5 @@ __all__ = [
     "Strain",
     "Taxonomy",
     "UseIon",
+    "ValidationResult",
 ]

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/models/asset.py

@@ -13,13 +13,13 @@ class Asset(Identifiable):
     path: Annotated[
         str,
         Field(
-            description="The path of the asset.",
+            description="The relative path of the asset.",
         ),
     ]
     full_path: Annotated[
         str,
         Field(
-            description="The full path of the asset.",
+            description="The full s3 path of the asset.",
         ),
     ]
     is_directory: Annotated[

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/models/entity.py

@@ -46,12 +46,12 @@ class Entity(Identifiable, HasAssets):
         ),
     ] = None
     authorized_public: Annotated[
-        bool | None,
+        bool,
         Field(
             examples=[True, False],
             description="Whether the resource is authorized to be public.",
         ),
-    ] = None
+    ] = False
     authorized_project_id: Annotated[
         ID | None,
         Field(

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/models/memodel.py

@@ -8,6 +8,7 @@ from entitysdk.models.contribution import Contribution
 from entitysdk.models.emodel import EModel
 from entitysdk.models.entity import Entity
 from entitysdk.models.etype import ETypeClass
+from entitysdk.models.memodelcalibrationresult import MEModelCalibrationResult
 from entitysdk.models.morphology import (
     BrainRegion,
     License,
@@ -93,4 +94,10 @@ class MEModel(Entity):
             description="The mtype classes of the memodel.",
         ),
     ] = None
+    calibration_result: Annotated[
+        MEModelCalibrationResult | None,
+        Field(
+            description="The calibration result of the memodel.",
+        ),
+    ] = None
     legacy_id: list[str] | None = None

entitysdk-0.3.0/src/entitysdk/models/memodelcalibrationresult.py

@@ -0,0 +1,42 @@
+"""ME-Model Calibration Result."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.entity import Entity
+from entitysdk.types import ID
+
+
+class MEModelCalibrationResult(Entity):
+    """ME-Model calibration result."""
+
+    holding_current: Annotated[
+        float,
+        Field(
+            description="The holding current to apply to the simulatable neuron, in nA.",
+            example=-0.016,
+        ),
+    ]
+    threshold_current: Annotated[
+        float,
+        Field(
+            description="The minimal amount of current needed to make "
+            "the simulatable neuron spike, in nA.",
+            example=0.1,
+        ),
+    ]
+    rin: Annotated[
+        float | None,
+        Field(
+            description="The input resistance of the simulatable neuron, in MOhm.",
+            example=0.1,
+        ),
+    ] = None
+    calibrated_entity_id: Annotated[
+        ID,
+        Field(
+            description="ID of the calibrated entity.",
+            example="85663316-a7ff-4107-9eb9-236de8868c5c",
+        ),
+    ]

entitysdk-0.3.0/src/entitysdk/models/validation_result.py

@@ -0,0 +1,34 @@
+"""Validation result."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.entity import Entity
+from entitysdk.types import ID
+
+
+class ValidationResult(Entity):
+    """Validation result."""
+
+    passed: Annotated[
+        bool,
+        Field(
+            description="True if the validation passed, False otherwise.",
+            example=True,
+        ),
+    ]
+    name: Annotated[
+        str,
+        Field(
+            description="Name of the validation.",
+            example="Neuron spiking validation",
+        ),
+    ]
+    validated_entity_id: Annotated[
+        ID,
+        Field(
+            description="ID of the validated entity.",
+            example="85663316-a7ff-4107-9eb9-236de8868c5c",
+        ),
+    ]

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/route.py

@@ -11,8 +11,13 @@ _ROUTES = {
     "BrainRegion": "brain-region",
     "Contribution": "contribution",
     "ElectricalCellRecording": "electrical-cell-recording",
+    "EModel": "emodel",
     "Entity": "entity",
+    "Ion": "ion",
+    "IonChannelModel": "ion-channel-model",
     "License": "license",
+    "MEModel": "memodel",
+    "MEModelCalibrationResult": "memodel-calibration-result",
     "MTypeClass": "mtype",
     "Organization": "organization",
     "Person": "person",
@@ -21,10 +26,7 @@ _ROUTES = {
     "Species": "species",
     "Strain": "strain",
     "Taxonomy": "taxonomy",
-    "IonChannelModel": "ion-channel-model",
-    "Ion": "ion",
-    "EModel": "emodel",
-    "MEModel": "memodel",
+    "ValidationResult": "validation-result",
 }
 
 

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk/util.py

@@ -3,6 +3,7 @@
 import sys
 from collections.abc import Iterator
 from json import dumps
+from pathlib import Path
 
 import httpx
 
@@ -135,3 +136,15 @@ def build_api_url(environment: DeploymentEnvironment) -> str:
         DeploymentEnvironment.staging: settings.staging_api_url,
         DeploymentEnvironment.production: settings.production_api_url,
     }[environment]
+
+
+def validate_filename_extension_consistency(path: Path, expected_extension: str) -> Path:
+    """Validate file path extension against expected extension."""
+    if path.suffix.lower() == expected_extension.lower():
+        return path
+    raise EntitySDKError(f"File path {path} does not have expected extension {expected_extension}.")
+
+
+def create_intermediate_directories(path: Path) -> None:
+    """Create intermediate directories in a path."""
+    path.parent.mkdir(parents=True, exist_ok=True)

{entitysdk-0.2.5 → entitysdk-0.3.0/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.2.5
+Version: 0.3.0
 Summary: Python library for interacting with the entitycore service
 Author-email: Open Brain Institute <info@openbraininstitute.org>
 Maintainer-email: Open Brain Institute <info@openbraininstitute.org>

{entitysdk-0.2.5 → entitysdk-0.3.0}/src/entitysdk.egg-info/SOURCES.txt

@@ -43,11 +43,13 @@ src/entitysdk/models/etype.py
 src/entitysdk/models/ion_channel_model.py
 src/entitysdk/models/license.py
 src/entitysdk/models/memodel.py
+src/entitysdk/models/memodelcalibrationresult.py
 src/entitysdk/models/morphology.py
 src/entitysdk/models/mtype.py
 src/entitysdk/models/response.py
 src/entitysdk/models/subject.py
 src/entitysdk/models/taxonomy.py
+src/entitysdk/models/validation_result.py
 tests/__init__.py
 tests/integration/__init__.py
 tests/integration/conftest.py
@@ -72,8 +74,12 @@ tests/unit/models/test_contribution.py
 tests/unit/models/test_electrical_cell_recording.py
 tests/unit/models/test_init.py
 tests/unit/models/test_ion_channel_model.py
+tests/unit/models/test_memodel_calibration_result.py
 tests/unit/models/test_morphology.py
+tests/unit/models/test_validation_result.py
 tests/unit/models/data/.gitignore
 tests/unit/models/data/electrical_cell_recording.json
 tests/unit/models/data/ion_channel_model.json
-tests/unit/models/data/reconstruction_morphology.json
+tests/unit/models/data/memodel_calibration_result.json
+tests/unit/models/data/reconstruction_morphology.json
+tests/unit/models/data/validation_result.json

{entitysdk-0.2.5 → entitysdk-0.3.0}/tests/integration/test_searching.py

@@ -7,6 +7,7 @@ from entitysdk.models import (
     IonChannelModel,
     License,
     MEModel,
+    MEModelCalibrationResult,
     MTypeClass,
     Organization,
     Person,
@@ -14,6 +15,7 @@ from entitysdk.models import (
     Role,
     Species,
     Strain,
+    ValidationResult,
 )
 
 
@@ -33,6 +35,8 @@ from entitysdk.models import (
         EModel,
         MEModel,
         ElectricalCellRecording,
+        ValidationResult,
+        MEModelCalibrationResult,
     ],
 )
 def test_is_searchable(entity_type, client):

{entitysdk-0.2.5 → entitysdk-0.3.0}/tests/unit/models/data/electrical_cell_recording.json

@@ -97,7 +97,8 @@
       "name": "GenericStep",
       "description": "",
       "injection_type": "current_clamp",
-      "shape": "step"
+      "shape": "step",
+      "authorized_public": false
     },
     {
       "type": "electrical_recording_stimulus",
@@ -107,7 +108,8 @@
       "name": "GenericStep",
       "description": "",
       "injection_type": "current_clamp",
-      "shape": "step"
+      "shape": "step",
+      "authorized_public": false
     },
     {
       "type": "electrical_recording_stimulus",
@@ -117,7 +119,8 @@
       "name": "GenericStep",
       "description": "",
       "injection_type": "current_clamp",
-      "shape": "step"
+      "shape": "step",
+      "authorized_public": false
     }
   ]
 }

entitysdk-0.3.0/tests/unit/models/data/memodel_calibration_result.json

@@ -0,0 +1,8 @@
+{
+    "authorized_public": false,
+    "id" : "cfecab84-b37c-4fa0-adaa-86457d660061",
+    "holding_current" : 0.0,
+    "threshold_current" : 0.06554153953301577,
+    "rin" : 100.03205800593804,
+    "calibrated_entity_id" : "54004e96-cef0-4f1c-8c89-d9cdf7b94e43"
+}

entitysdk-0.3.0/tests/unit/models/data/validation_result.json

@@ -0,0 +1,7 @@
+{
+    "authorized_public": false,
+	"id" : "6fa52c8b-e9df-4f10-bdee-07c9af59a5ba",
+	"passed" : true,
+	"name" : "Simulatable Neuron Spiking Validation",
+	"validated_entity_id" : "54004e96-cef0-4f1c-8c89-d9cdf7b94e43"
+}

entitysdk-0.3.0/tests/unit/models/test_memodel_calibration_result.py

@@ -0,0 +1,42 @@
+import json
+from pathlib import Path
+
+import pytest
+
+from entitysdk.models import MEModelCalibrationResult
+
+from ..util import MOCK_UUID
+
+DATA_DIR = Path(__file__).parent / "data"
+
+Model = MEModelCalibrationResult
+
+
+@pytest.fixture
+def json_data():
+    return json.loads(Path(DATA_DIR / "memodel_calibration_result.json").read_bytes())
+
+
+@pytest.fixture
+def model(json_data):
+    return Model.model_validate(json_data)
+
+
+def test_read(client, httpx_mock, auth_token, json_data):
+    httpx_mock.add_response(method="GET", json=json_data)
+    entity = client.get_entity(
+        entity_id=MOCK_UUID,
+        entity_type=Model,
+        token=auth_token,
+        with_assets=False,
+    )
+    assert entity.model_dump(mode="json", exclude_none=True) == json_data
+
+
+def test_register(client, httpx_mock, auth_token, model, json_data):
+    httpx_mock.add_response(
+        method="POST", json=model.model_dump(mode="json") | {"id": str(MOCK_UUID)}
+    )
+    registered = client.register_entity(entity=model, token=auth_token)
+    expected_json = json_data | {"id": str(MOCK_UUID)}
+    assert registered.model_dump(mode="json", exclude_none=True) == expected_json

entitysdk-0.3.0/tests/unit/models/test_validation_result.py

@@ -0,0 +1,42 @@
+import json
+from pathlib import Path
+
+import pytest
+
+from entitysdk.models import ValidationResult
+
+from ..util import MOCK_UUID
+
+DATA_DIR = Path(__file__).parent / "data"
+
+Model = ValidationResult
+
+
+@pytest.fixture
+def json_data():
+    return json.loads(Path(DATA_DIR / "validation_result.json").read_bytes())
+
+
+@pytest.fixture
+def model(json_data):
+    return Model.model_validate(json_data)
+
+
+def test_read(client, httpx_mock, auth_token, json_data):
+    httpx_mock.add_response(method="GET", json=json_data)
+    entity = client.get_entity(
+        entity_id=MOCK_UUID,
+        entity_type=Model,
+        token=auth_token,
+        with_assets=False,
+    )
+    assert entity.model_dump(mode="json", exclude_none=True) == json_data
+
+
+def test_register(client, httpx_mock, auth_token, model, json_data):
+    httpx_mock.add_response(
+        method="POST", json=model.model_dump(mode="json") | {"id": str(MOCK_UUID)}
+    )
+    registered = client.register_entity(entity=model, token=auth_token)
+    expected_json = json_data | {"id": str(MOCK_UUID)}
+    assert registered.model_dump(mode="json", exclude_none=True) == expected_json

{entitysdk-0.2.5 → entitysdk-0.3.0}/tests/unit/test_client.py

@@ -1,6 +1,7 @@
 import io
 import re
 import uuid
+from pathlib import Path
 from unittest.mock import patch
 
 import pytest
@@ -237,7 +238,7 @@ def test_client_download_content(
     assert res == b"foo"
 
 
-def test_client_download_file(
+def test_client_download_file__output_file(
     tmp_path,
     client,
     httpx_mock,
@@ -249,6 +250,12 @@ def test_client_download_file(
     entity_id = uuid.uuid4()
     asset_id = uuid.uuid4()
 
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset_id}",
+        match_headers=request_headers,
+        json=_mock_asset_response(asset_id) | {"path": "foo.h5"},
+    )
     httpx_mock.add_response(
         method="GET",
         url=f"{api_url}/entity/{entity_id}/assets/{asset_id}/download",
@@ -268,6 +275,140 @@ def test_client_download_file(
     assert output_path.read_bytes() == b"foo"
 
 
+def test_client_download_file__output_file__inconsistent_ext(
+    tmp_path,
+    client,
+    httpx_mock,
+    api_url,
+    project_context,
+    auth_token,
+    request_headers,
+):
+    """User must provide a path extension that is consitent with the asset path."""
+
+    entity_id = uuid.uuid4()
+    asset_id = uuid.uuid4()
+
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset_id}",
+        match_headers=request_headers,
+        json=_mock_asset_response(asset_id) | {"path": "foo.swc"},
+    )
+    output_path = tmp_path / "foo.h5"
+
+    with pytest.raises(
+        EntitySDKError, match=f"File path {output_path} does not have expected extension .swc."
+    ):
+        client.download_file(
+            entity_id=entity_id,
+            entity_type=Entity,
+            asset_id=asset_id,
+            output_path=output_path,
+            token=auth_token,
+        )
+
+
+def test_client_download_file__output_file__user_subdirectory_path(
+    tmp_path,
+    client,
+    httpx_mock,
+    api_url,
+    project_context,
+    auth_token,
+    request_headers,
+):
+    """User provides a nested output path that overrides the asset path."""
+
+    entity_id = uuid.uuid4()
+    asset_id = uuid.uuid4()
+
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset_id}",
+        match_headers=request_headers,
+        json=_mock_asset_response(asset_id) | {"path": "foo.h5"},
+    )
+
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset_id}/download",
+        match_headers=request_headers,
+        content=b"foo",
+    )
+
+    output_path = tmp_path / "foo" / "bar" / "bar.h5"
+
+    client.download_file(
+        entity_id=entity_id,
+        entity_type=Entity,
+        asset_id=asset_id,
+        output_path=output_path,
+        token=auth_token,
+    )
+    assert output_path.read_bytes() == b"foo"
+
+
+def test_client_download_file__asset_subdirectory_paths(
+    tmp_path,
+    client,
+    httpx_mock,
+    api_url,
+    project_context,
+    auth_token,
+    request_headers,
+):
+    """User provides directory, relative file paths from assets are written to it."""
+
+    entity_id = uuid.uuid4()
+    asset1_id = uuid.uuid4()
+    asset2_id = uuid.uuid4()
+
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset1_id}",
+        match_headers=request_headers,
+        json=_mock_asset_response(asset1_id) | {"path": "foo/bar/foo.h5"},
+    )
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset1_id}/download",
+        match_headers=request_headers,
+        content=b"foo",
+    )
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset2_id}",
+        match_headers=request_headers,
+        json=_mock_asset_response(asset2_id) | {"path": "foo/bar/bar.swc"},
+    )
+    httpx_mock.add_response(
+        method="GET",
+        url=f"{api_url}/entity/{entity_id}/assets/{asset2_id}/download",
+        match_headers=request_headers,
+        content=b"bar",
+    )
+    output_path = tmp_path
+
+    client.download_file(
+        entity_id=entity_id,
+        entity_type=Entity,
+        asset_id=asset1_id,
+        output_path=output_path,
+        token=auth_token,
+    )
+    client.download_file(
+        entity_id=entity_id,
+        entity_type=Entity,
+        asset_id=asset2_id,
+        output_path=output_path,
+        token=auth_token,
+    )
+
+    assert Path(output_path, "foo/bar/foo.h5").read_bytes() == b"foo"
+    assert Path(output_path, "foo/bar/bar.swc").read_bytes() == b"bar"
+
+
 @patch("entitysdk.route.get_route_name")
 def test_client_get(
     mock_route,

{entitysdk-0.2.5 → entitysdk-0.3.0}/tests/unit/test_util.py

@@ -430,3 +430,19 @@ def test_stream_paginated_request_with_unexpected_page_size(
         match="Unexpected response: payload.pagination.page_size=2 but it should be 123",
     ):
         next(it)
+
+
+def test_validate_filename_extension_consistency(tmp_path):
+    assert test_module.validate_filename_extension_consistency(tmp_path / "foo.txt", ".txt")
+    assert test_module.validate_filename_extension_consistency(tmp_path / "foo.txt", ".TXT")
+
+
+def test_create_intermediate_directories(tmp_path):
+    path = tmp_path / "foo" / "bar" / "foo.txt"
+
+    assert not path.parent.is_dir()
+
+    test_module.create_intermediate_directories(path)
+
+    assert path.parent.is_dir()
+    assert path.parent.parent.is_dir()