entitysdk 0.2.0__tar.gz → 0.2.2__tar.gz

{entitysdk-0.2.0/src/entitysdk.egg-info → entitysdk-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.2.0
+Version: 0.2.2
 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>
@@ -39,6 +39,21 @@ entitysdk is a Python library for interacting with the [entitycore service][enti
 ```bash
 pip install entitysdk
 ```
+
+## Obtaining a valid access token
+
+An access token can be retrieved easily using the obi-auth helper library.
+
+```bash
+pip install obi-auth
+```
+
+```python
+from obi_auth import get_token
+
+access_token = get_token(environment="staging")
+```
+
 ## Quick Start
 
 ```python
@@ -49,11 +64,11 @@ from entitysdk.models.morphology import ReconstructionMorphology
 
 # Initialize client
 client = Client(
-    api_url="http://api.example.com",
     project_context=ProjectContext(
         project_id=UUID("your-project-id"),
         virtual_lab_id=UUID("your-lab-id")
     )
+    environment="staging"
 )
 
 # Search for morphologies

{entitysdk-0.2.0 → entitysdk-0.2.2}/README.md

@@ -18,6 +18,21 @@ entitysdk is a Python library for interacting with the [entitycore service][enti
 ```bash
 pip install entitysdk
 ```
+
+## Obtaining a valid access token
+
+An access token can be retrieved easily using the obi-auth helper library.
+
+```bash
+pip install obi-auth
+```
+
+```python
+from obi_auth import get_token
+
+access_token = get_token(environment="staging")
+```
+
 ## Quick Start
 
 ```python
@@ -28,11 +43,11 @@ from entitysdk.models.morphology import ReconstructionMorphology
 
 # Initialize client
 client = Client(
-    api_url="http://api.example.com",
     project_context=ProjectContext(
         project_id=UUID("your-project-id"),
         virtual_lab_id=UUID("your-lab-id")
     )
+    environment="staging"
 )
 
 # Search for morphologies

entitysdk-0.2.0/examples/searching.ipynb → entitysdk-0.2.2/examples/01_searching.ipynb

@@ -28,7 +28,13 @@
     "    project_id=\"0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6\",\n",
     ")\n",
     "client = Client(api_url=entitycore_api_url, project_context=project_context)\n",
-    "token = os.getenv(\"ACCESS_TOKEN\", \"XXX\")"
+    "token = os.getenv(\"ACCESS_TOKEN\", \"XXX\")\n",
+    "\n",
+    "# uncomment for staging\n",
+    "# from obi_auth import get_token\n",
+    "\n",
+    "# token = get_token(environment=\"staging\")\n",
+    "# client = Client(environment=\"staging\")"
    ]
   },
   {
@@ -239,7 +245,7 @@
    "id": "fae8506b-9cbc-433b-a17d-6ce3d84bcf4c",
    "metadata": {},
    "source": [
-    "## Find morphologies of a specifix mtype id"
+    "## Find morphologies by mtype"
    ]
   },
   {
@@ -282,7 +288,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.10"
   }
  },
  "nbformat": 4,

entitysdk-0.2.0/examples/morphology.ipynb → entitysdk-0.2.2/examples/02_morphology.ipynb

@@ -46,7 +46,14 @@
     "    project_id=\"0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6\",\n",
     ")\n",
     "client = Client(api_url=entitycore_api_url, project_context=project_context)\n",
-    "token = os.getenv(\"ACCESS_TOKEN\", \"XXX\")"
+    "token = os.getenv(\"ACCESS_TOKEN\", \"XXX\")\n",
+    "\n",
+    "# uncomment for staging\n",
+    "# from obi_auth import get_token\n",
+    "# token = get_token(environment=\"staging\")\n",
+    "# Replace this with your vlab project url in staging\n",
+    "# project_context = ProjectContext.from_vlab_url(\"https://staging.openbraininstitute.org/app/virtual-lab/lab/594fd60d-7a38-436f-939d-500feaa13bba/project/ff89ca07-6613-4922-9ab0-2637221db8b5/home\")\n",
+    "# client = Client(environment=\"staging\", project_context=project_context)"
    ]
   },
   {
@@ -92,13 +99,35 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "45d75d53-71f1-4213-8355-4937c1e27558",
+   "id": "e5dde536-0c58-4d42-a834-1b1a0ec17e9d",
    "metadata": {},
    "outputs": [],
    "source": [
     "rprint(strain)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5d42a174-9737-4477-830a-3dc908dea925",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "brain_region = client.search_entity(\n",
+    "    entity_type=BrainRegion, query={\"annotation_value\": 68}, token=token\n",
+    ").one()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "282200cd-ad0c-4bb3-bc21-88de85289179",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(brain_region)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "a0193055-3448-4d1c-99cc-4d953727ef4e",
@@ -114,19 +143,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# No GET endpoint yet for brain-region\n",
-    "\n",
     "brain_location = BrainLocation(\n",
     "    x=4101.52490234375,\n",
     "    y=1173.8499755859375,\n",
     "    z=4744.60009765625,\n",
     ")\n",
-    "brain_region = BrainRegion(\n",
-    "    id=68,\n",
-    "    name=\"Frontal pole, layer 1\",\n",
-    "    acronym=\"FRP1\",\n",
-    "    children=[],\n",
-    ")\n",
     "morphology = ReconstructionMorphology(\n",
     "    name=\"my-morph\",\n",
     "    description=\"A morphology\",\n",
@@ -153,7 +174,25 @@
    "id": "83fb7e5e-73b5-4227-aa22-90bb789b0907",
    "metadata": {},
    "source": [
-    "## Register morphology and upload assets"
+    "## Register morphology"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2e32a168",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "registered = client.register_entity(entity=morphology, token=token)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c0d500bd",
+   "metadata": {},
+   "source": [
+    "## Upload assets"
    ]
   },
   {
@@ -163,8 +202,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "registered = client.register_entity(entity=morphology, token=token)\n",
-    "\n",
     "with tempfile.TemporaryDirectory() as tdir:\n",
     "    file1 = Path(tdir, \"morph.h5\")\n",
     "    file1.write_text(\"h5\")\n",
@@ -428,7 +465,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.10"
   }
  },
  "nbformat": 4,

entitysdk-0.2.0/examples/contribution.ipynb → entitysdk-0.2.2/examples/03_contribution.ipynb

@@ -23,7 +23,14 @@
     "    project_id=\"0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6\",\n",
     ")\n",
     "client = Client(api_url=entitycore_api_url, project_context=project_context)\n",
-    "token = os.getenv(\"ACCESS_TOKEN\", \"XXX\")"
+    "token = os.getenv(\"ACCESS_TOKEN\", \"XXX\")\n",
+    "\n",
+    "# uncomment for staging\n",
+    "# from obi_auth import get_token\n",
+    "# token = get_token(environment=\"staging\")\n",
+    "# Replace this with your vlab project url in staging\n",
+    "# project_context = ProjectContext.from_vlab_url(\"https://staging.openbraininstitute.org/app/virtual-lab/lab/594fd60d-7a38-436f-939d-500feaa13bba/project/ff89ca07-6613-4922-9ab0-2637221db8b5/home\")\n",
+    "# client = Client(environment=\"staging\", project_context=project_context)"
    ]
   },
   {
@@ -82,7 +89,7 @@
    "outputs": [],
    "source": [
     "morphology = client.search_entity(\n",
-    "    entity_type=ReconstructionMorphology, token=token, limit=1\n",
+    "    entity_type=ReconstructionMorphology, token=token, limit=1, query={\"name__ilike\": \"my-morph\"}\n",
     ").first()"
    ]
   },
@@ -135,6 +142,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# Note: It will fail if registered twice\n",
+    "# because there is a uniqueness constraint on (agent, morphology_id)\n",
     "registered = client.register_entity(entity=contribution, token=token)"
    ]
   },
@@ -193,7 +202,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.10"
   }
  },
  "nbformat": 4,

{entitysdk-0.2.0 → entitysdk-0.2.2}/src/entitysdk/models/asset.py

@@ -22,12 +22,6 @@ class Asset(Identifiable):
             description="The full path of the asset.",
         ),
     ]
-    bucket_name: Annotated[
-        str,
-        Field(
-            description="The name of the s3 bucket.",
-        ),
-    ]
     is_directory: Annotated[
         bool,
         Field(

entitysdk-0.2.2/src/entitysdk/models/brain_region.py

@@ -0,0 +1,36 @@
+"""BrainRegion model."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.core import Identifiable
+from entitysdk.typedef import ID
+
+
+class BrainRegion(Identifiable):
+    """BrainRegion model."""
+
+    name: Annotated[
+        str,
+        Field(
+            examples=["Thalamus"],
+            description="The name of the brain region.",
+        ),
+    ]
+    annotation_value: Annotated[
+        int, Field(examples=[997], description="The annotation voxel value.")
+    ]
+    acronym: Annotated[
+        str,
+        Field(
+            examples=["TH"],
+            description="The acronym of the brain region.",
+        ),
+    ]
+    parent_structure_id: Annotated[
+        ID, Field(examples=[], description="The parent region structure UUID.")
+    ]
+    hierarchy_id: Annotated[
+        ID, Field(examples=[], description="The brain hierarchy that includes this brain region.")
+    ]

entitysdk-0.2.2/src/entitysdk/models/ion_channel_model.py

@@ -0,0 +1,158 @@
+"""Ion channel model."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.mixin import HasAssets
+from entitysdk.models.base import BaseModel
+from entitysdk.models.contribution import Contribution
+from entitysdk.models.entity import Entity
+from entitysdk.models.morphology import BrainRegion, License, Species, Strain
+
+
+class UseIon(BaseModel):
+    """Specifies how an ion is used in the mod file (USEION behavior)."""
+
+    ion_name: Annotated[
+        str,
+        Field(
+            description="The name of the ion involved.",
+            examples="Ca",
+        ),
+    ]
+    read: Annotated[
+        list[str] | None,
+        Field(
+            description="Variables listed in the READ statement for this ion.",
+            examples=["eca", "ica"],
+        ),
+    ]
+    write: Annotated[
+        list[str] | None,
+        Field(
+            description="Variables listed in the WRITE statement for this ion.",
+            examples=["ica"],
+        ),
+    ]
+    valence: Annotated[
+        int | None,
+        Field(
+            description="VALENCE of the ion, if specified.",
+            examples=2,
+        ),
+    ]
+    main_ion: Annotated[
+        bool | None,
+        Field(
+            description="Whether this ion is the main ion for the mechanism.",
+            examples=True,
+        ),
+    ] = None
+
+
+class NeuronBlock(BaseModel):
+    """Variables declared in the NEURON block of the mod file."""
+
+    global_: Annotated[
+        list[dict[str, str | None]] | None,
+        Field(
+            description="Variables listed in the GLOBAL statement, with associated units.",
+            examples=[{"celsius": "degree C"}],
+        ),
+    ] = None
+    range: Annotated[
+        list[dict[str, str | None]] | None,
+        Field(
+            description="Variables listed in the RANGE statement, with associated units.",
+            examples=[{"gCa_HVAbar": "S/cm2"}, {"ica": "mA/cm2"}],
+        ),
+    ] = None
+    useion: Annotated[
+        list[UseIon] | None,
+        Field(
+            description="Ion-specific READ/WRITE/VALENCE declarations from USEION.",
+        ),
+    ] = None
+    nonspecific: Annotated[
+        list[dict[str, str | None]] | None,
+        Field(
+            description="Variables listed in NONSPECIFIC_CURRENT statements.",
+            examples=[{"ihcn": "mA/cm2"}],
+        ),
+    ] = None
+
+
+class IonChannelModel(HasAssets, Entity):
+    """Ion channel mechanism model."""
+
+    name: Annotated[
+        str,
+        Field(
+            description="The name of the ion channel model "
+            "(e.g., the SUFFIX or POINT_PROCESS name).",
+            examples="Ca_HVA",
+        ),
+    ]
+    nmodl_suffix: Annotated[
+        str,
+        Field(
+            description="The SUFFIX of the ion channel model as defined in the NMODL file ",
+            examples="Ca_HVA",
+        ),
+    ]
+    description: Annotated[
+        str,
+        Field(
+            description="A description of the ion channel mechanism.",
+            examples="High-voltage activated calcium channel",
+        ),
+    ]
+    species: Annotated[
+        Species,
+        Field(description="The species for which the mechanism applies."),
+    ]
+    strain: Annotated[
+        Strain | None,
+        Field(description="The specific strain of the species, if applicable."),
+    ] = None
+    brain_region: Annotated[
+        BrainRegion,
+        Field(description="The brain region where the mechanism is used or applies."),
+    ]
+    license: Annotated[
+        License | None,
+        Field(description="License under which the mechanism is distributed."),
+    ] = None
+    contributions: Annotated[
+        list[Contribution] | None,
+        Field(description="List of contributions related to this mechanism."),
+    ] = None
+    is_ljp_corrected: Annotated[
+        bool,
+        Field(
+            description="Whether the mechanism is corrected for liquid junction potential.",
+        ),
+    ] = False
+    is_temperature_dependent: Annotated[
+        bool,
+        Field(
+            description="Whether the mechanism includes temperature dependence "
+            "(e.g. via q10 factor).",
+        ),
+    ]
+    temperature_celsius: Annotated[
+        int,
+        Field(description="The temperature at which the mechanism has been built to work on."),
+    ]
+    is_stochastic: Annotated[
+        bool | None,
+        Field(
+            description="Whether the mechanism has stochastic behavior.",
+        ),
+    ] = False
+    neuron_block: Annotated[
+        NeuronBlock,
+        Field(description="Variables declared in the NEURON block of the mod file."),
+    ]
+    legacy_id: list[str] | None = None

{entitysdk-0.2.0 → entitysdk-0.2.2}/src/entitysdk/models/morphology.py

@@ -5,6 +5,7 @@ from typing import Annotated
 from pydantic import Field
 
 from entitysdk.mixin import HasAssets
+from entitysdk.models.brain_region import BrainRegion
 from entitysdk.models.contribution import Contribution
 from entitysdk.models.core import Struct
 from entitysdk.models.entity import Entity
@@ -38,40 +39,6 @@ class License(Entity):
     ]
 
 
-class BrainRegion(Entity):
-    """BrainRegion model."""
-
-    id: Annotated[
-        int,
-        Field(
-            examples=[1, 2],
-            description="The region's id.",
-        ),
-    ]  # type: ignore
-
-    name: Annotated[
-        str,
-        Field(
-            examples=["Prefrontal Cortex"],
-            description="The name of the brain region.",
-        ),
-    ]
-    acronym: Annotated[
-        str,
-        Field(
-            examples=["PFC"],
-            description="The acronym of the brain region.",
-        ),
-    ]
-    children: Annotated[
-        list[int],
-        Field(
-            examples=[1, 2],
-            description="The children of the brain region hierarchy.",
-        ),
-    ]
-
-
 class BrainLocation(Struct):
     """BrainLocation model."""
 

{entitysdk-0.2.0 → entitysdk-0.2.2}/src/entitysdk/route.py

@@ -20,6 +20,8 @@ _ROUTES = {
     "Species": "species",
     "Strain": "strain",
     "Taxonomy": "taxonomy",
+    "IonChannelModel": "ion-channel-model",
+    "Ion": "ion",
 }
 
 

{entitysdk-0.2.0 → entitysdk-0.2.2/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.2.0
+Version: 0.2.2
 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>
@@ -39,6 +39,21 @@ entitysdk is a Python library for interacting with the [entitycore service][enti
 ```bash
 pip install entitysdk
 ```
+
+## Obtaining a valid access token
+
+An access token can be retrieved easily using the obi-auth helper library.
+
+```bash
+pip install obi-auth
+```
+
+```python
+from obi_auth import get_token
+
+access_token = get_token(environment="staging")
+```
+
 ## Quick Start
 
 ```python
@@ -49,11 +64,11 @@ from entitysdk.models.morphology import ReconstructionMorphology
 
 # Initialize client
 client = Client(
-    api_url="http://api.example.com",
     project_context=ProjectContext(
         project_id=UUID("your-project-id"),
         virtual_lab_id=UUID("your-lab-id")
     )
+    environment="staging"
 )
 
 # Search for morphologies

{entitysdk-0.2.0 → entitysdk-0.2.2}/src/entitysdk.egg-info/SOURCES.txt

@@ -7,9 +7,9 @@ pyproject.toml
 tox.ini
 .github/workflows/sdist.yml
 .github/workflows/tox.yml
-examples/contribution.ipynb
-examples/morphology.ipynb
-examples/searching.ipynb
+examples/01_searching.ipynb
+examples/02_morphology.ipynb
+examples/03_contribution.ipynb
 src/entitysdk/__init__.py
 src/entitysdk/client.py
 src/entitysdk/common.py
@@ -32,9 +32,11 @@ src/entitysdk/models/__init__.py
 src/entitysdk/models/agent.py
 src/entitysdk/models/asset.py
 src/entitysdk/models/base.py
+src/entitysdk/models/brain_region.py
 src/entitysdk/models/contribution.py
 src/entitysdk/models/core.py
 src/entitysdk/models/entity.py
+src/entitysdk/models/ion_channel_model.py
 src/entitysdk/models/morphology.py
 src/entitysdk/models/mtype.py
 src/entitysdk/models/response.py
@@ -57,7 +59,10 @@ tests/unit/util.py
 tests/unit/models/__init__.py
 tests/unit/models/test_agent.py
 tests/unit/models/test_asset.py
+tests/unit/models/test_brain_region.py
 tests/unit/models/test_contribution.py
+tests/unit/models/test_ion_channel_model.py
 tests/unit/models/test_morphology.py
 tests/unit/models/data/.gitignore
+tests/unit/models/data/ion_channel_model.json
 tests/unit/models/data/reconstruction_morphology.json

entitysdk-0.2.2/tests/unit/models/data/ion_channel_model.json

@@ -0,0 +1,114 @@
+{
+  "id": "b8f38c7f-2675-4c6a-a394-f3a60a9a3e6f",
+  "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": "c73ac3a5-3b7d-41bc-92e7-9f9309a49300",
+  "name": "Ca_HVA",
+  "nmodl_suffix": "Ca_HVA",
+  "brain_region": {
+    "id": "38553ac8-7d71-4591-bfee-2fc72e2dffdf",
+    "update_date": "2025-05-09T13:32:18.034672Z",
+    "creation_date": "2025-05-09T13:32:18.034672Z",
+    "name": "Accessory abducens nucleus",
+    "annotation_value": 568,
+    "acronym": "ACVI",
+    "parent_structure_id": "596305b3-71b2-41e4-afd3-b9f2e90f79f8",
+    "hierarchy_id": "e3e70682-c209-4cac-a29f-6fbed82c07cd"
+  },
+  "description": "High-voltage activated calcium channel",
+  "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": "Rattus norvegicus",
+    "taxonomy_id": "NCBITaxon:10116"
+  },
+  "strain": null,
+  "license": null,
+  "contributions": [
+    {
+      "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
+    }
+  ],
+  "is_ljp_corrected": false,
+  "is_temperature_dependent": true,
+  "temperature_celsius": 36,
+  "is_stochastic": true,
+  "neuron_block": {
+    "global_": [
+      {"gna": "S/cm2"},
+      {"gk": "S/cm2"}
+    ],
+    "range": [
+      {"gCa_HVAbar": "S/cm2"},
+      {"ica": "mA/cm2"}
+    ],
+    "useion": [
+      {
+        "ion_name": "Ca",
+        "read": ["eca"],
+        "write": ["ica"],
+        "valence": 2,
+        "main_ion": true
+      }
+    ],
+    "nonspecific": [{"ihcn": "mA/cm2"}]
+  },
+  "assets": [
+    {
+      "id": "a90bab5c-8529-4829-99fc-e90a270e8b30",
+      "path": "Ca_HVA.mod",
+      "full_path": "public/a98b7abc-fc46-4700-9e3d-37137812c730/0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6/assets/ion_channel_model/9720aa4a-0cd1-4f10-b6ad-04deb8f997b6/Ca_HVA.mod",
+      "is_directory": false,
+      "content_type": "application/swc",
+      "size": 561221,
+      "sha256_digest": "8b850eface3e7b881db62c361dc5da62be008ca81501c406a59646bf7075c95b",
+      "status": "created",
+      "creation_date": null,
+      "update_date": null,
+      "meta": {
+        "legacy": {
+          "@id": "https://bbp.epfl.ch/data/public/morphologies/42315b31-081f-4d40-8b94-b72dbd16c99e",
+          "name": "Ca_HVA.mod",
+          "@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/mod"
+        }
+      }
+    }
+  ]
+}

{entitysdk-0.2.0 → entitysdk-0.2.2}/tests/unit/models/data/reconstruction_morphology.json

@@ -13,7 +13,6 @@
       "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,
@@ -51,7 +50,6 @@
       "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,
@@ -87,16 +85,14 @@
   "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": []
+    "id": "38553ac8-7d71-4591-bfee-2fc72e2dffdf",
+    "update_date": "2025-05-09T13:32:18.034672Z",
+    "creation_date": "2025-05-09T13:32:18.034672Z",
+    "name": "Accessory abducens nucleus",
+    "annotation_value": 568,
+    "acronym": "ACVI",
+    "parent_structure_id": "596305b3-71b2-41e4-afd3-b9f2e90f79f8",
+    "hierarchy_id": "e3e70682-c209-4cac-a29f-6fbed82c07cd"
   },
   "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": {

{entitysdk-0.2.0 → entitysdk-0.2.2}/tests/unit/models/test_asset.py

@@ -8,7 +8,6 @@ def test_asset():
         id=MOCK_UUID,
         path="path/to/asset",
         full_path="full/path/to/asset",
-        bucket_name="bucket_name",
         is_directory=False,
         content_type="text/plain",
         size=100,
@@ -20,7 +19,6 @@ def test_asset():
         "id": MOCK_UUID,
         "path": "path/to/asset",
         "full_path": "full/path/to/asset",
-        "bucket_name": "bucket_name",
         "is_directory": False,
         "content_type": "text/plain",
         "size": 100,

entitysdk-0.2.2/tests/unit/models/test_brain_region.py

@@ -0,0 +1,22 @@
+import pytest
+
+from entitysdk.models.brain_region import BrainRegion
+
+
+@pytest.fixture
+def json_data():
+    return {
+        "id": "38553ac8-7d71-4591-bfee-2fc72e2dffdf",
+        "update_date": "2025-05-09T13:32:18.034672Z",
+        "creation_date": "2025-05-09T13:32:18.034672Z",
+        "name": "Accessory abducens nucleus",
+        "annotation_value": 568,
+        "acronym": "ACVI",
+        "parent_structure_id": "596305b3-71b2-41e4-afd3-b9f2e90f79f8",
+        "hierarchy_id": "e3e70682-c209-4cac-a29f-6fbed82c07cd",
+    }
+
+
+def test_model(json_data):
+    res = BrainRegion.model_validate(json_data)
+    assert res.model_dump(mode="json") == json_data

entitysdk-0.2.2/tests/unit/models/test_ion_channel_model.py

@@ -0,0 +1,60 @@
+import json
+from pathlib import Path
+
+import pytest
+
+from entitysdk.models.ion_channel_model import IonChannelModel
+
+from ..util import MOCK_UUID
+
+DATA_DIR = Path(__file__).parent / "data"
+
+
+@pytest.fixture
+def json_ion_channel_expanded():
+    return json.loads(Path(DATA_DIR / "ion_channel_model.json").read_bytes())
+
+
+@pytest.fixture
+def ion_channel_model(json_ion_channel_expanded):
+    return IonChannelModel.model_validate(json_ion_channel_expanded)
+
+
+def test_read_ion_channel_model(client, httpx_mock, auth_token, json_ion_channel_expanded):
+    httpx_mock.add_response(method="GET", json=json_ion_channel_expanded)
+    entity = client.get_entity(
+        entity_id=MOCK_UUID,
+        entity_type=IonChannelModel,
+        token=auth_token,
+        with_assets=False,
+    )
+    assert entity.model_dump(mode="json") == json_ion_channel_expanded | {"legacy_id": None}
+
+
+def test_register_ion_channel_model(
+    client, httpx_mock, auth_token, ion_channel_model, json_ion_channel_expanded
+):
+    httpx_mock.add_response(
+        method="POST", json=ion_channel_model.model_dump(mode="json") | {"id": str(MOCK_UUID)}
+    )
+    registered = client.register_entity(entity=ion_channel_model, token=auth_token)
+    expected_json = json_ion_channel_expanded.copy() | {"id": str(MOCK_UUID)}
+    assert registered.model_dump(mode="json") == expected_json | {"legacy_id": None}
+
+
+def test_update_ion_channel_model(
+    client, httpx_mock, auth_token, ion_channel_model, json_ion_channel_expanded
+):
+    httpx_mock.add_response(
+        method="PATCH",
+        json=ion_channel_model.model_dump(mode="json") | {"name": "foo"},
+    )
+    updated = client.update_entity(
+        entity_id=ion_channel_model.id,
+        entity_type=IonChannelModel,
+        attrs_or_entity={"name": "foo"},
+        token=auth_token,
+    )
+
+    expected_json = json_ion_channel_expanded.copy() | {"name": "foo"}
+    assert updated.model_dump(mode="json") == expected_json | {"legacy_id": None}

{entitysdk-0.2.0 → entitysdk-0.2.2}/tests/unit/test_client.py

@@ -133,7 +133,6 @@ def _mock_asset_response(asset_id):
         "id": str(asset_id),
         "path": "path/to/asset",
         "full_path": "full/path/to/asset",
-        "bucket_name": "bucket_name",
         "is_directory": False,
         "content_type": "text/plain",
         "size": 100,
@@ -315,7 +314,6 @@ def _mock_asset_delete_response(asset_id):
     return {
         "path": "buffer.h5",
         "full_path": "private/103d7868/103d7868/assets/reconstruction_morphology/8703/buffer.h5",
-        "bucket_name": "obi-private",
         "is_directory": False,
         "content_type": "application/swc",
         "size": 18,