entitysdk 0.1.0__tar.gz → 0.1.2__tar.gz

{entitysdk-0.1.0/src/entitysdk.egg-info → entitysdk-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.1.0
+Version: 0.1.2
 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-0.1.0 → entitysdk-0.1.2}/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-0.1.0 → entitysdk-0.1.2}/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-0.1.0 → entitysdk-0.1.2}/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-0.1.0 → entitysdk-0.1.2}/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-0.1.0 → entitysdk-0.1.2}/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-0.1.0 → entitysdk-0.1.2}/src/entitysdk/models/morphology.py

@@ -227,3 +227,4 @@ class ReconstructionMorphology(HasAssets, Entity):
             description="The mtype classes of the morphology.",
         ),
     ] = None
+    legacy_id: list[str] | None = None

{entitysdk-0.1.0 → entitysdk-0.1.2}/src/entitysdk/util.py

@@ -31,7 +31,7 @@ def make_db_api_request(
 
     if project_context:
         headers["project-id"] = str(project_context.project_id)
-        headers["virtual-lab-id"] = str(project_context.project_id)
+        headers["virtual-lab-id"] = str(project_context.virtual_lab_id)
 
     try:
         response = http_client.request(

{entitysdk-0.1.0 → entitysdk-0.1.2/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.1.0
+Version: 0.1.2
 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-0.1.0 → entitysdk-0.1.2}/src/entitysdk.egg-info/SOURCES.txt

@@ -53,9 +53,10 @@ 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-0.1.0 → entitysdk-0.1.2}/tests/unit/conftest.py

@@ -4,6 +4,7 @@ import pytest
 
 from entitysdk.client import Client
 from entitysdk.common import ProjectContext
+from tests.unit.util import PROJECT_ID, VIRTUAL_LAB_ID
 
 
 @pytest.fixture(scope="session")
@@ -14,8 +15,8 @@ def api_url():
 @pytest.fixture(scope="session")
 def project_context():
     return ProjectContext(
-        project_id=uuid.UUID("103d7868-147e-4f07-af0d-71d8568f575c"),
-        virtual_lab_id=uuid.UUID("103d7868-147e-4f07-af0d-71d8568f575c"),
+        project_id=PROJECT_ID,
+        virtual_lab_id=VIRTUAL_LAB_ID,
     )
 
 

entitysdk-0.1.2/tests/unit/models/data/reconstruction_morphology.json

@@ -0,0 +1,175 @@
+{
+  "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.",
+  "pref_label": null,
+  "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-0.1.2/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-0.1.0 → entitysdk-0.1.2}/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-0.1.2/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-0.1.2/tests/unit/util.py

@@ -0,0 +1,5 @@
+import uuid
+
+MOCK_UUID = uuid.UUID("12341234-1234-1234-1234-123412341234")
+VIRTUAL_LAB_ID = uuid.UUID("ac9b42ed-22b9-4c9d-9dcb-cdd604c6ebf0")
+PROJECT_ID = uuid.UUID("bf0c75df-7dea-43b2-9a11-fcf994f87ccd")

entitysdk-0.1.0/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-0.1.0/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
-
-
-@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": "103d7868-147e-4f07-af0d-71d8568f575c",
-        "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"

entitysdk-0.1.0/tests/unit/util.py

@@ -1,3 +0,0 @@
-import uuid
-
-MOCK_UUID = uuid.UUID("12341234-1234-1234-1234-123412341234")