entitysdk 0.1.1__tar.gz → 0.2.0__tar.gz

{entitysdk-0.1.1/src/entitysdk.egg-info → entitysdk-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.1.1
+Version: 0.2.0
 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-0.1.1 → entitysdk-0.2.0}/examples/morphology.ipynb

@@ -134,7 +134,7 @@
     "    strain=strain,\n",
     "    brain_region=brain_region,\n",
     "    location=brain_location,\n",
-    "    legacy_id=\"temp\",\n",
+    "    legacy_id=None,\n",
     ")"
    ]
   },

{entitysdk-0.1.1 → entitysdk-0.2.0}/examples/searching.ipynb

@@ -13,7 +13,8 @@
     "\n",
     "from entitysdk.client import Client\n",
     "from entitysdk.common import ProjectContext\n",
-    "from entitysdk.models.contribution import Organization, Person, Role\n",
+    "from entitysdk.models.agent import Organization, Person\n",
+    "from entitysdk.models.contribution import Role\n",
     "from entitysdk.models.morphology import (\n",
     "    ReconstructionMorphology,\n",
     "    Species,\n",

{entitysdk-0.1.1 → entitysdk-0.2.0}/src/entitysdk/client.py

@@ -13,7 +13,8 @@ from entitysdk.models.asset import Asset, LocalAssetMetadata
 from entitysdk.models.core import Identifiable
 from entitysdk.result import IteratorResult
 from entitysdk.token_manager import TokenManager
-from entitysdk.typedef import ID
+from entitysdk.typedef import ID, DeploymentEnvironment
+from entitysdk.util import build_api_url
 
 
 class Client:
@@ -21,10 +22,11 @@ class Client:
 
     def __init__(
         self,
-        api_url: str,
+        api_url: str | None = None,
         project_context: ProjectContext | None = None,
         http_client: httpx.Client | None = None,
         token_manager: TokenManager | None = None,
+        environment: DeploymentEnvironment | str | None = None,
     ) -> None:
         """Initialize client.
 
@@ -33,12 +35,39 @@ class Client:
             project_context: Project context.
             http_client: Optional HTTP client to use.
             token_manager: Optional token manager to use.
+            environment: Deployment environent.
         """
-        self.api_url = api_url.rstrip("/")
+        try:
+            environment = DeploymentEnvironment(environment) if environment else None
+        except ValueError:
+            raise EntitySDKError(
+                f"'{environment}' is not a valid DeploymentEnvironment. "
+                f"Choose one of: {[str(env) for env in DeploymentEnvironment]}"
+            ) from None
+
+        self.api_url = self._handle_api_url(
+            api_url=api_url,
+            environment=environment,
+        )
         self.project_context = project_context
         self._http_client = http_client or httpx.Client()
         self._token_manager = token_manager
 
+    @staticmethod
+    def _handle_api_url(api_url: str | None, environment: DeploymentEnvironment | None) -> str:
+        """Return or create api url."""
+        match (api_url, environment):
+            case (str(), None):
+                return api_url
+            case (None, DeploymentEnvironment()):
+                return build_api_url(environment=environment)
+            case (None, None):
+                raise EntitySDKError("Neither api_url nor environment have been defined.")
+            case (str(), DeploymentEnvironment()):
+                raise EntitySDKError("Either the api_url or environment must be defined, not both.")
+            case _:
+                raise EntitySDKError("Either api_url or environment is of the wrong type.")
+
     def _get_token(self, override_token: str | None = None) -> str:
         """Get a token either from an override or from the token manager.
 

entitysdk-0.2.0/src/entitysdk/common.py

@@ -0,0 +1,45 @@
+"""Common stuff."""
+
+import re
+from typing import Self
+from uuid import UUID
+
+from pydantic import BaseModel
+
+from entitysdk.exception import EntitySDKError
+from entitysdk.typedef import DeploymentEnvironment
+
+UUID_RE = "[0-9a-f]{8}(?:-[0-9a-f]{4}){3}-[0-9a-f]{12}"
+
+
+VLAB_URL_PATTERN = re.compile(
+    r"^https:\/\/(?P<env>staging|www)\.openbraininstitute\.org"
+    rf"\/app\/virtual-lab\/lab\/(?P<vlab>{UUID_RE})"
+    rf"\/project\/(?P<proj>{UUID_RE})(?:\/.*)?$"
+)
+
+
+class ProjectContext(BaseModel):
+    """Project context."""
+
+    project_id: UUID
+    virtual_lab_id: UUID
+    environment: DeploymentEnvironment | None = None
+
+    @classmethod
+    def from_vlab_url(cls, url: str) -> Self:
+        """Construct a ProjectContext from a virtual lab url."""
+        result = VLAB_URL_PATTERN.match(url)
+
+        if not result:
+            raise EntitySDKError(f"Badly formed vlab url: {url}")
+
+        env = {
+            "www": DeploymentEnvironment.production,
+            "staging": DeploymentEnvironment.staging,
+        }[result.group("env")]
+
+        vlab_id = UUID(result.group("vlab"))
+        proj_id = UUID(result.group("proj"))
+
+        return cls(project_id=proj_id, virtual_lab_id=vlab_id, environment=env)

entitysdk-0.2.0/src/entitysdk/config.py

@@ -0,0 +1,37 @@
+"""Configuration for this library."""
+
+from typing import Annotated
+
+from pydantic import Field
+from pydantic_settings import BaseSettings
+
+
+class Settings(BaseSettings):
+    """Constants for this library."""
+
+    page_size: Annotated[
+        int | None,
+        Field(
+            alias="ENTITYSDK_PAGE_SIZE",
+            description="Default pagination page size, or None to use server default.",
+        ),
+    ] = None
+
+    staging_api_url: Annotated[
+        str,
+        Field(
+            alias="ENTITYSDK_STAGING_API_URL",
+            description="Default staging entitycore API url.",
+        ),
+    ] = "https://staging.openbraininstitute.org/api/entitycore"
+
+    production_api_url: Annotated[
+        str,
+        Field(
+            alias="ENTITYSDK_PRODUCTION_API_URL",
+            description="Default production entitycore API url.",
+        ),
+    ] = "https://www.openbraininstitute.org/api/entitycore"
+
+
+settings = Settings()

{entitysdk-0.1.1 → entitysdk-0.2.0}/src/entitysdk/models/agent.py

@@ -66,3 +66,6 @@ class Organization(Agent):
             description="The alternative name of the organization.",
         ),
     ] = None
+
+
+AgentUnion = Annotated[Person | Organization, Field(discriminator="type")]

{entitysdk-0.1.1 → entitysdk-0.2.0}/src/entitysdk/models/contribution.py

@@ -4,7 +4,7 @@ from typing import Annotated
 
 from pydantic import Field
 
-from entitysdk.models.agent import Organization, Person
+from entitysdk.models.agent import AgentUnion
 from entitysdk.models.core import Identifiable
 from entitysdk.models.entity import Entity
 
@@ -30,9 +30,8 @@ class Contribution(Identifiable):
     """Contribution model."""
 
     agent: Annotated[
-        Person | Organization,
+        AgentUnion,
         Field(
-            discriminator="type",
             description="The agent of the contribution.",
         ),
     ]

{entitysdk-0.1.1 → entitysdk-0.2.0}/src/entitysdk/models/entity.py

@@ -5,7 +5,7 @@ from uuid import UUID
 
 from pydantic import Field
 
-from entitysdk.models.agent import Agent
+from entitysdk.models.agent import AgentUnion
 from entitysdk.models.core import Identifiable
 
 
@@ -13,11 +13,11 @@ class Entity(Identifiable):
     """Entity is a model with id and authorization."""
 
     createdBy: Annotated[
-        Agent | None,
+        AgentUnion | None,
         Field(description="The agent that created this entity."),
     ] = None
     updatedBy: Annotated[
-        Agent | None,
+        AgentUnion | None,
         Field(
             description="The agent that updated this entity.",
         ),

{entitysdk-0.1.1 → entitysdk-0.2.0}/src/entitysdk/models/morphology.py

@@ -190,13 +190,6 @@ class ReconstructionMorphology(HasAssets, Entity):
             description="The description of the morphology.",
         ),
     ]
-    pref_label: Annotated[
-        str | None,
-        Field(
-            examples=["layer 5 Pyramidal Cell"],
-            description="The preferred label of the morphology.",
-        ),
-    ] = None
     species: Annotated[
         Species,
         Field(
@@ -227,3 +220,4 @@ class ReconstructionMorphology(HasAssets, Entity):
             description="The mtype classes of the morphology.",
         ),
     ] = None
+    legacy_id: list[str] | None = None

entitysdk-0.2.0/src/entitysdk/typedef.py

@@ -0,0 +1,13 @@
+"""Type definitions."""
+
+import uuid
+from enum import StrEnum
+
+ID = uuid.UUID
+
+
+class DeploymentEnvironment(StrEnum):
+    """Deployment environment."""
+
+    staging = "staging"
+    production = "production"

{entitysdk-0.1.1 → entitysdk-0.2.0}/src/entitysdk/util.py

@@ -10,6 +10,7 @@ from entitysdk.common import ProjectContext
 from entitysdk.config import settings
 from entitysdk.exception import EntitySDKError
 from entitysdk.models.response import ListResponse
+from entitysdk.typedef import DeploymentEnvironment
 
 
 def make_db_api_request(
@@ -126,3 +127,11 @@ def stream_paginated_request(
             if number_of_items >= limit:
                 return
         page += 1
+
+
+def build_api_url(environment: DeploymentEnvironment) -> str:
+    """Return API url for the respective deployment environment."""
+    return {
+        DeploymentEnvironment.staging: settings.staging_api_url,
+        DeploymentEnvironment.production: settings.production_api_url,
+    }[environment]

{entitysdk-0.1.1 → entitysdk-0.2.0/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.1.1
+Version: 0.2.0
 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-0.1.1 → entitysdk-0.2.0}/src/entitysdk.egg-info/SOURCES.txt

@@ -46,6 +46,7 @@ tests/unit/__init__.py
 tests/unit/conftest.py
 tests/unit/test_base.py
 tests/unit/test_client.py
+tests/unit/test_common.py
 tests/unit/test_config.py
 tests/unit/test_result.py
 tests/unit/test_route.py
@@ -53,9 +54,10 @@ tests/unit/test_serdes.py
 tests/unit/test_token_manager.py
 tests/unit/test_util.py
 tests/unit/util.py
-tests/unit/data/.gitignore
 tests/unit/models/__init__.py
 tests/unit/models/test_agent.py
 tests/unit/models/test_asset.py
 tests/unit/models/test_contribution.py
-tests/unit/models/test_morphology.py
+tests/unit/models/test_morphology.py
+tests/unit/models/data/.gitignore
+tests/unit/models/data/reconstruction_morphology.json

entitysdk-0.2.0/tests/unit/models/data/reconstruction_morphology.json

@@ -0,0 +1,174 @@
+{
+  "id": "9720aa4a-0cd1-4f10-b6ad-04deb8f997b6",
+  "update_date": "2024-10-29T13:36:30.827776Z",
+  "creation_date": "2024-09-10T14:25:03.707956Z",
+  "createdBy": null,
+  "updatedBy": null,
+  "authorized_public": true,
+  "authorized_project_id": "0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6",
+  "assets": [
+    {
+      "id": "a90bab5c-8529-4829-99fc-e90a270e8b30",
+      "update_date": null,
+      "creation_date": null,
+      "path": "mpg150211_A_idA.swc",
+      "full_path": "public/a98b7abc-fc46-4700-9e3d-37137812c730/0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6/assets/reconstruction_morphology/9720aa4a-0cd1-4f10-b6ad-04deb8f997b6/mpg150211_A_idA.swc",
+      "bucket_name": "entitycore-data-dev",
+      "is_directory": false,
+      "content_type": "application/swc",
+      "size": 561221,
+      "sha256_digest": "8b850eface3e7b881db62c361dc5da62be008ca81501c406a59646bf7075c95b",
+      "status": "created",
+      "meta": {
+        "legacy": {
+          "@id": "https://bbp.epfl.ch/data/public/morphologies/42315b31-081f-4d40-8b94-b72dbd16c99e",
+          "name": "mpg150211_A_idA.swc",
+          "@type": "DataDownload",
+          "digest": {
+            "value": "8b850eface3e7b881db62c361dc5da62be008ca81501c406a59646bf7075c95b",
+            "algorithm": "SHA-256"
+          },
+          "atLocation": {
+            "@type": "Location",
+            "store": {
+              "@id": "nxv:diskStorageDefault",
+              "_rev": 1,
+              "@type": "DiskStorage"
+            }
+          },
+          "contentUrl": "https://bbp.epfl.ch/nexus/v1/files/public/morphologies/https:%2F%2Fbbp.epfl.ch%2Fdata%2Fpublic%2Fmorphologies%2F42315b31-081f-4d40-8b94-b72dbd16c99e",
+          "contentSize": {
+            "value": 561221,
+            "unitCode": "bytes"
+          },
+          "encodingFormat": "application/swc"
+        }
+      }
+    },
+    {
+      "id": "56394210-d2fb-4755-990c-8083a97a46fd",
+      "update_date": null,
+      "creation_date": null,
+      "path": "mpg150211_A_idA.ASC",
+      "full_path": "public/a98b7abc-fc46-4700-9e3d-37137812c730/0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6/assets/reconstruction_morphology/9720aa4a-0cd1-4f10-b6ad-04deb8f997b6/mpg150211_A_idA.ASC",
+      "bucket_name": "entitycore-data-dev",
+      "is_directory": false,
+      "content_type": "application/asc",
+      "size": 525332,
+      "sha256_digest": "bf00878444539ead825f2d451cdf6f87072526f9a82c87de35fca5563ae5596b",
+      "status": "created",
+      "meta": {
+        "legacy": {
+          "@id": "https://bbp.epfl.ch/data/public/morphologies/7f422a37-48f0-4ea4-8760-f1481403d51f",
+          "name": "mpg150211_A_idA.ASC",
+          "@type": "DataDownload",
+          "digest": {
+            "value": "bf00878444539ead825f2d451cdf6f87072526f9a82c87de35fca5563ae5596b",
+            "algorithm": "SHA-256"
+          },
+          "atLocation": {
+            "@type": "Location",
+            "store": {
+              "@id": "nxv:diskStorageDefault",
+              "_rev": 1,
+              "@type": "DiskStorage"
+            }
+          },
+          "contentUrl": "https://bbp.epfl.ch/nexus/v1/files/public/morphologies/https:%2F%2Fbbp.epfl.ch%2Fdata%2Fpublic%2Fmorphologies%2F7f422a37-48f0-4ea4-8760-f1481403d51f",
+          "contentSize": {
+            "value": 525332,
+            "unitCode": "bytes"
+          },
+          "encodingFormat": "application/asc"
+        }
+      }
+    }
+  ],
+  "name": "mpg150211_A_idA",
+  "location": null,
+  "brain_region": {
+    "id": 407,
+    "update_date": "2025-03-29T16:48:20.636283Z",
+    "creation_date": "2025-03-29T16:48:20.636283Z",
+    "createdBy": null,
+    "updatedBy": null,
+    "authorized_public": null,
+    "authorized_project_id": null,
+    "name": "Field CA1, pyramidal layer",
+    "acronym": "CA1sp",
+    "children": []
+  },
+  "description": "Neuronal morphology of excitatory neuron cell 'mpg150211_A_idA' in Field CA1, pyramidal layer of cell type SR_PC. A neuron that releases excitatory neurotransmitters. This neuron doesn't have axon, has a basal dendrite and apical dendrite.",
+  "species": {
+    "id": "0895fa61-fa6d-4674-9014-7300f9edf8da",
+    "update_date": "2025-03-29T16:48:36.175090Z",
+    "creation_date": "2025-03-29T16:48:36.175090Z",
+    "createdBy": null,
+    "updatedBy": null,
+    "authorized_public": null,
+    "authorized_project_id": null,
+    "name": "Mus musculus",
+    "taxonomy_id": "NCBITaxon:10090"
+  },
+  "strain": null,
+  "license": null,
+  "contributions": [
+    {
+      "id": "79987156-9f97-4095-b69e-6b4e5ca213bb",
+      "update_date": "2025-03-29T16:49:12.446844Z",
+      "creation_date": "2025-03-29T16:49:12.446844Z",
+      "agent": {
+        "id": "eda92bb4-560b-4ad2-9c4b-4649bb254e83",
+        "update_date": "2024-04-22T14:40:13.122739Z",
+        "creation_date": "2021-03-17T16:59:51.555000Z",
+        "type": "person",
+        "pref_label": "Maurizio Pezzoli Gonzalez",
+        "givenName": "Maurizio",
+        "familyName": "Pezzoli Gonzalez"
+      },
+      "role": {
+        "id": "8b06e557-277b-4b0c-a439-bfb02d41927c",
+        "update_date": "2025-03-29T16:48:36.192831Z",
+        "creation_date": "2025-03-29T16:48:36.192831Z",
+        "name": "unspecified",
+        "role_id": "unspecified"
+      },
+      "entity": null
+    },
+    {
+      "id": "7f43ce20-e63d-48c1-bc73-dabb38ee181b",
+      "update_date": "2025-03-29T16:49:12.449364Z",
+      "creation_date": "2025-03-29T16:49:12.449364Z",
+      "agent": {
+        "id": "f27cfa11-d1bc-4a14-b651-174bb53674ff",
+        "update_date": "2021-04-14T09:51:14.062000Z",
+        "creation_date": "2021-04-14T09:51:14.062000Z",
+        "type": "organization",
+        "pref_label": "École Polytechnique Fédérale de Lausanne",
+        "alternative_name": ""
+      },
+      "role": {
+        "id": "8b06e557-277b-4b0c-a439-bfb02d41927c",
+        "update_date": "2025-03-29T16:48:36.192831Z",
+        "creation_date": "2025-03-29T16:48:36.192831Z",
+        "name": "unspecified",
+        "role_id": "unspecified"
+      },
+      "entity": null
+    }
+  ],
+  "mtypes": [
+    {
+      "id": "b2221a58-008a-45a6-8464-7159c324c985",
+      "update_date": "2021-09-06T15:47:05.039000Z",
+      "creation_date": "2021-09-06T15:47:04.890000Z",
+      "createdBy": null,
+      "updatedBy": null,
+      "authorized_public": null,
+      "authorized_project_id": null,
+      "pref_label": "SR_PC",
+      "definition": "",
+      "alt_label": ""
+    }
+  ]
+}

entitysdk-0.2.0/tests/unit/models/test_agent.py

@@ -0,0 +1,66 @@
+from entitysdk.models import agent as test_module
+from entitysdk.models.core import Identifiable
+
+from ..util import MOCK_UUID
+
+
+def test_person_entity():
+    agent = test_module.Person(
+        givenName="foo",
+        familyName="bar",
+        pref_label="test",
+        type="person",
+    )
+    assert agent.givenName == "foo"
+    assert agent.familyName == "bar"
+    assert agent.pref_label == "test"
+    assert agent.type == "person"
+
+
+def test_organization_entity():
+    organization = test_module.Organization(
+        pref_label="foo",
+        alternative_name="bar",
+        type="organization",
+    )
+    assert organization.pref_label == "foo"
+    assert organization.alternative_name == "bar"
+    assert organization.type == "organization"
+
+
+def test_agent_discriminated_union():
+    class A(Identifiable):
+        agent: test_module.AgentUnion | None = None
+
+    res = A.model_validate(
+        {
+            "id": MOCK_UUID,
+        }
+    )
+    assert res.id == MOCK_UUID
+
+    res = A.model_validate(
+        {
+            "id": MOCK_UUID,
+            "agent": {
+                "type": "organization",
+                "pref_label": "foo",
+            },
+        }
+    )
+    assert res.id == MOCK_UUID
+    assert isinstance(res.agent, test_module.Organization)
+
+    res = A.model_validate(
+        {
+            "id": MOCK_UUID,
+            "agent": {
+                "type": "person",
+                "pref_label": "foo",
+                "givenName": "John",
+                "familyName": "Smith",
+            },
+        }
+    )
+    assert res.id == MOCK_UUID
+    assert isinstance(res.agent, test_module.Person)

{entitysdk-0.1.1 → entitysdk-0.2.0}/tests/unit/models/test_contribution.py

@@ -36,3 +36,21 @@ def test_contribution(role):
 
     assert res.agent == organization
     assert res.role == role
+
+    res = test_module.Contribution.model_validate(
+        {
+            "agent": person.model_dump(mode="json"),
+            "role": role.model_dump(mode="json"),
+        }
+    )
+    assert res.agent == person
+    assert res.role == role
+
+    res = test_module.Contribution.model_validate(
+        {
+            "agent": organization.model_dump(mode="json"),
+            "role": role.model_dump(mode="json"),
+        }
+    )
+    assert res.agent == organization
+    assert res.role == role

entitysdk-0.2.0/tests/unit/models/test_morphology.py

@@ -0,0 +1,62 @@
+import json
+from pathlib import Path
+
+import pytest
+
+from entitysdk.models.morphology import (
+    ReconstructionMorphology,
+)
+
+from ..util import MOCK_UUID
+
+DATA_DIR = Path(__file__).parent / "data"
+
+
+@pytest.fixture
+def json_morphology_expanded():
+    return json.loads(Path(DATA_DIR / "reconstruction_morphology.json").read_bytes())
+
+
+@pytest.fixture
+def morphology(json_morphology_expanded):
+    return ReconstructionMorphology.model_validate(json_morphology_expanded)
+
+
+def test_read_reconstruction_morphology(client, httpx_mock, auth_token, json_morphology_expanded):
+    httpx_mock.add_response(method="GET", json=json_morphology_expanded)
+    entity = client.get_entity(
+        entity_id=MOCK_UUID,
+        entity_type=ReconstructionMorphology,
+        token=auth_token,
+        with_assets=False,
+    )
+    assert entity.model_dump(mode="json") == json_morphology_expanded | {"legacy_id": None}
+
+
+def test_register_reconstruction_morphology(
+    client, httpx_mock, auth_token, morphology, json_morphology_expanded
+):
+    httpx_mock.add_response(
+        method="POST", json=morphology.model_dump(mode="json") | {"id": str(MOCK_UUID)}
+    )
+    registered = client.register_entity(entity=morphology, token=auth_token)
+    expected_json = json_morphology_expanded.copy() | {"id": str(MOCK_UUID)}
+    assert registered.model_dump(mode="json") == expected_json | {"legacy_id": None}
+
+
+def test_update_reconstruction_morphology(
+    client, httpx_mock, auth_token, morphology, json_morphology_expanded
+):
+    httpx_mock.add_response(
+        method="PATCH",
+        json=morphology.model_dump(mode="json") | {"name": "foo"},
+    )
+    updated = client.update_entity(
+        entity_id=morphology.id,
+        entity_type=ReconstructionMorphology,
+        attrs_or_entity={"name": "foo"},
+        token=auth_token,
+    )
+
+    expected_json = json_morphology_expanded.copy() | {"name": "foo"}
+    assert updated.model_dump(mode="json") == expected_json | {"legacy_id": None}

{entitysdk-0.1.1 → entitysdk-0.2.0}/tests/unit/test_client.py

@@ -1,13 +1,43 @@
 import io
+import re
 import uuid
 from unittest.mock import patch
 
 import pytest
 
 from entitysdk.client import Client
+from entitysdk.config import settings
 from entitysdk.exception import EntitySDKError
 from entitysdk.mixin import HasAssets
 from entitysdk.models.entity import Entity
+from entitysdk.typedef import DeploymentEnvironment
+
+
+def test_client_api_url():
+    client = Client(api_url="foo")
+    assert client.api_url == "foo"
+
+    client = Client(api_url=None, environment="staging")
+    assert client.api_url == settings.staging_api_url
+
+    client = Client(api_url=None, environment="production")
+    assert client.api_url == settings.production_api_url
+
+    with pytest.raises(
+        EntitySDKError, match="Either the api_url or environment must be defined, not both."
+    ):
+        Client(api_url="foo", environment="staging")
+
+    with pytest.raises(EntitySDKError, match="Neither api_url nor environment have been defined."):
+        Client()
+
+    with pytest.raises(EntitySDKError, match="Either api_url or environment is of the wrong type."):
+        Client(api_url=int)
+
+    str_envs = [str(env) for env in DeploymentEnvironment]
+    expected = f"'foo' is not a valid DeploymentEnvironment. Choose one of: {str_envs}"
+    with pytest.raises(EntitySDKError, match=re.escape(expected)):
+        Client(environment="foo")
 
 
 def test_client_get_token():

entitysdk-0.2.0/tests/unit/test_common.py

@@ -0,0 +1,89 @@
+import pytest
+
+from entitysdk import common as test_module
+from entitysdk.exception import EntitySDKError
+from entitysdk.typedef import DeploymentEnvironment
+
+VLAB_ID = "ff888f05-f314-4702-8a92-b86f754270bb"
+PROJ_ID = "f373e771-3a2f-4f45-ab59-0955efd7b1f4"
+
+
+@pytest.mark.parametrize(
+    ("url", "expected"),
+    [
+        (
+            f"https://staging.openbraininstitute.org/app/virtual-lab/lab/{VLAB_ID}/project/{PROJ_ID}/home",
+            test_module.ProjectContext(
+                virtual_lab_id=VLAB_ID,
+                project_id=PROJ_ID,
+                environment=DeploymentEnvironment.staging,
+            ),
+        ),
+        (
+            f"https://staging.openbraininstitute.org/app/virtual-lab/lab/{VLAB_ID}/project/{PROJ_ID}",
+            test_module.ProjectContext(
+                virtual_lab_id=VLAB_ID,
+                project_id=PROJ_ID,
+                environment=DeploymentEnvironment.staging,
+            ),
+        ),
+        (
+            f"https://www.openbraininstitute.org/app/virtual-lab/lab/{VLAB_ID}/project/{PROJ_ID}/home",
+            test_module.ProjectContext(
+                virtual_lab_id=VLAB_ID,
+                project_id=PROJ_ID,
+                environment=DeploymentEnvironment.production,
+            ),
+        ),
+        (
+            f"https://www.openbraininstitute.org/app/virtual-lab/lab/{VLAB_ID}/project/{PROJ_ID}",
+            test_module.ProjectContext(
+                virtual_lab_id=VLAB_ID,
+                project_id=PROJ_ID,
+                environment=DeploymentEnvironment.production,
+            ),
+        ),
+    ],
+)
+def test_project_context__from_vlab_url(url, expected):
+    res = test_module.ProjectContext.from_vlab_url(url)
+    assert res == expected
+
+
+@pytest.mark.parametrize(
+    ("url", "expected_error", "expected_msg"),
+    [
+        ("asdf", EntitySDKError, "Badly formed vlab url"),
+        ("https://", EntitySDKError, "Badly formed vlab url"),
+        ("https://openbraininstitute.org", EntitySDKError, "Badly formed vlab url"),
+        ("https://staging.openbraininstitute.org", EntitySDKError, "Badly formed vlab url"),
+        (
+            "https://staging.openbraininstitute.org/app/virtual-lab/lab/foo",
+            EntitySDKError,
+            "Badly formed vlab url",
+        ),
+        (
+            "https://staging.openbraininstitute.org/app/virtual-lab/lab/foo/project/bar",
+            EntitySDKError,
+            "Badly formed vlab url",
+        ),
+        (
+            f"https://dev.openbraininstitute.org/app/virtual-lab/lab/{VLAB_ID}/project/{PROJ_ID}",
+            EntitySDKError,
+            "Badly formed vlab url",
+        ),
+        (
+            f"https://dev.openbraininstitute.org/app/virtual-lab/lab/foo/project/{PROJ_ID}",
+            EntitySDKError,
+            "Badly formed vlab url",
+        ),
+        (
+            f"https://dev.openbraininstitute.org/app/virtual-lab/lab/{VLAB_ID}/project/bar",
+            EntitySDKError,
+            "Badly formed vlab url",
+        ),
+    ],
+)
+def test_project_context__from_vlab_url__raises(url, expected_error, expected_msg):
+    with pytest.raises(expected_error, match=expected_msg):
+        test_module.ProjectContext.from_vlab_url(url)

entitysdk-0.1.1/src/entitysdk/common.py

@@ -1,12 +0,0 @@
-"""Common stuff."""
-
-from dataclasses import dataclass
-from uuid import UUID
-
-
-@dataclass
-class ProjectContext:
-    """Project context."""
-
-    project_id: UUID
-    virtual_lab_id: UUID

entitysdk-0.1.1/src/entitysdk/config.py

@@ -1,21 +0,0 @@
-"""Configuration for this library."""
-
-from typing import Annotated
-
-from pydantic import Field
-from pydantic_settings import BaseSettings
-
-
-class Settings(BaseSettings):
-    """Constants for this library."""
-
-    page_size: Annotated[
-        int | None,
-        Field(
-            alias="ENTITYSDK_PAGE_SIZE",
-            description="Default pagination page size, or None to use server default.",
-        ),
-    ] = None
-
-
-settings = Settings()

entitysdk-0.1.1/src/entitysdk/typedef.py

@@ -1,5 +0,0 @@
-"""Type definitions."""
-
-import uuid
-
-ID = uuid.UUID

entitysdk-0.1.1/tests/unit/models/test_agent.py

@@ -1,25 +0,0 @@
-from entitysdk.models import agent as test_module
-
-
-def test_person_entity():
-    agent = test_module.Person(
-        givenName="foo",
-        familyName="bar",
-        pref_label="test",
-        type="person",
-    )
-    assert agent.givenName == "foo"
-    assert agent.familyName == "bar"
-    assert agent.pref_label == "test"
-    assert agent.type == "person"
-
-
-def test_organization_entity():
-    organization = test_module.Organization(
-        pref_label="foo",
-        alternative_name="bar",
-        type="organization",
-    )
-    assert organization.pref_label == "foo"
-    assert organization.alternative_name == "bar"
-    assert organization.type == "organization"

entitysdk-0.1.1/tests/unit/models/test_morphology.py

@@ -1,138 +0,0 @@
-import pytest
-
-from entitysdk.models.morphology import (
-    BrainLocation,
-    BrainRegion,
-    ReconstructionMorphology,
-    Species,
-    Strain,
-)
-
-from ..util import MOCK_UUID, PROJECT_ID
-
-
-@pytest.fixture
-def species(random_uuid):
-    return Species(id=random_uuid, name="Mus musculus", taxonomy_id="NCBITaxon:10090")
-
-
-@pytest.fixture
-def strain(species, random_uuid):
-    return Strain(
-        name="Cux2-CreERT2",
-        taxonomy_id="http://bbp.epfl.ch/neurosciencegraph/ontologies/speciestaxonomy/RBS4I6tyfUBSDt1i0jXLpgN",
-        species_id=random_uuid,
-    )
-
-
-@pytest.fixture
-def brain_location(random_uuid):
-    return BrainLocation(
-        id=random_uuid,
-        x=4101.52490234375,
-        y=1173.8499755859375,
-        z=4744.60009765625,
-    )
-
-
-@pytest.fixture
-def brain_region():
-    return BrainRegion(
-        id=68,
-        name="Frontal pole, layer 1",
-        acronym="FRP1",
-        children=[],
-    )
-
-
-@pytest.fixture
-def morphology(species, strain, brain_region):
-    return ReconstructionMorphology(
-        name="my-morph",
-        description="my-description",
-        species=species,
-        strain=strain,
-        brain_region=brain_region,
-    )
-
-
-@pytest.fixture
-def json_morphology_expanded():
-    return {
-        "authorized_project_id": str(PROJECT_ID),
-        "authorized_public": False,
-        "license": {
-            "id": str(MOCK_UUID),
-            "creation_date": "2025-02-20T13:42:46.532333Z",
-            "update_date": "2025-02-20T13:42:46.532333Z",
-            "name": "https://creativecommons.org/licenses/by-nc-sa/4.0/",
-            "description": "Foo",
-            "label": "CC BY-NC-SA 4.0 Deed",
-        },
-        "id": str(MOCK_UUID),
-        "creation_date": "2025-02-20T13:44:50.111791Z",
-        "update_date": "2025-02-20T13:44:50.111791Z",
-        "name": "04446-04462-X10187-Y13578_final",
-        "description": "Bar",
-        "location": None,
-        "species": {
-            "id": str(MOCK_UUID),
-            "creation_date": "2025-02-20T13:42:56.228818Z",
-            "update_date": "2025-02-20T13:42:56.228818Z",
-            "name": "Mus musculus",
-            "taxonomy_id": "NCBITaxon:10090",
-        },
-        "strain": None,
-        "brain_region": {
-            "id": 1,
-            "creation_date": "2025-02-20T13:36:51.010167Z",
-            "update_date": "2025-02-20T13:36:51.010167Z",
-            "name": "Reticular nucleus of the thalamus",
-            "acronym": "RT",
-            "children": [],
-        },
-    }
-
-
-def test_read_reconstruction_morphology(client, httpx_mock, auth_token, json_morphology_expanded):
-    httpx_mock.add_response(method="GET", json=json_morphology_expanded)
-
-    entity = client.get_entity(
-        entity_id=MOCK_UUID,
-        entity_type=ReconstructionMorphology,
-        token=auth_token,
-        with_assets=False,
-    )
-
-    assert entity.id == MOCK_UUID
-
-
-def test_register_reconstruction_morphology(client, httpx_mock, auth_token, morphology):
-    httpx_mock.add_response(
-        method="POST", json=morphology.model_dump(mode="json") | {"id": str(MOCK_UUID)}
-    )
-
-    registered = client.register_entity(entity=morphology, token=auth_token)
-
-    assert registered.id == MOCK_UUID
-    assert registered.name == morphology.name
-
-
-def test_update_reconstruction_morphology(client, httpx_mock, auth_token, morphology):
-    morphology = morphology.evolve(id=1)
-    httpx_mock.add_response(
-        method="PATCH",
-        json=morphology.model_dump(mode="json") | {"id": str(MOCK_UUID), "name": "foo"},
-    )
-
-    updated = client.update_entity(
-        entity_id=MOCK_UUID,
-        entity_type=ReconstructionMorphology,
-        attrs_or_entity={
-            "name": "foo",
-        },
-        token=auth_token,
-    )
-
-    assert updated.id == MOCK_UUID
-    assert updated.name == "foo"