entitysdk 0.6.0__tar.gz → 0.6.1__tar.gz

{entitysdk-0.6.0/src/entitysdk.egg-info → entitysdk-0.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.6.0
+Version: 0.6.1
 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-0.6.0 → entitysdk-0.6.1}/examples/03_circuit.ipynb

@@ -8,8 +8,11 @@
    "outputs": [],
    "source": [
     "import os\n",
+    "import tempfile\n",
+    "from pathlib import Path\n",
     "\n",
     "from rich import print as rprint\n",
+    "from utils import create_mock_circuit_dir\n",
     "\n",
     "from entitysdk import Client, ProjectContext, models\n",
     "\n",
@@ -109,44 +112,135 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8bf620b4-fafc-4476-a719-bbe6e7a821bf",
+   "id": "c3ff25a9-fc61-4c19-8949-140c1dd33af7",
    "metadata": {},
    "source": [
-    "## Fetch Circuit"
+    "## Upload directory"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bed0af2c-ae46-41b0-ba77-485daef0a87b",
+   "id": "3dccd413-f91b-42b1-8efe-56d01f68ddd0",
    "metadata": {},
    "outputs": [],
    "source": [
-    "fetched = client.get_entity(entity_id=registered_circuit.id, entity_type=models.Circuit)"
+    "with tempfile.TemporaryDirectory() as tdir:\n",
+    "    # create a hierarchy of files to upload\n",
+    "    create_mock_circuit_dir(tdir)\n",
+    "\n",
+    "    files = {str(path.relative_to(tdir)): path for path in Path(tdir).rglob(\"*\") if path.is_file()}\n",
+    "\n",
+    "    directory_asset = client.upload_directory(\n",
+    "        entity_id=registered_circuit.id,\n",
+    "        entity_type=models.Circuit,\n",
+    "        name=\"circuit\",\n",
+    "        paths=files,\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6ad6ce94-ad74-4710-b274-1883fdeb41f5",
+   "metadata": {},
+   "source": [
+    "## List directory"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ee27c8b5-dfa5-4fa5-ac2f-6cf158057bcf",
+   "id": "3b0d302e-46fe-4d97-b221-99833975eede",
    "metadata": {},
    "outputs": [],
    "source": [
-    "rprint(fetched)"
+    "files = client.list_directory(\n",
+    "    entity_id=registered_circuit.id, entity_type=models.Circuit, asset_id=directory_asset.id\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "749b85d2-dbce-455b-9ade-fec7e17f7208",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(files)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "aad97379-3010-42c9-9fc5-f30101163f1c",
+   "metadata": {},
+   "source": [
+    "## Download directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ace27230-6dfa-4bc6-8b2c-33998a22a111",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with tempfile.TemporaryDirectory() as tdir:\n",
+    "    client.download_directory(\n",
+    "        entity_id=registered_circuit.id,\n",
+    "        entity_type=models.Circuit,\n",
+    "        asset_id=directory_asset.id,\n",
+    "        output_path=Path(tdir),\n",
+    "    )\n",
+    "    files = {str(path.relative_to(tdir)): path for path in Path(tdir).rglob(\"*\") if path.is_file()}\n",
+    "    rprint(files)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8bf620b4-fafc-4476-a719-bbe6e7a821bf",
+   "metadata": {},
+   "source": [
+    "## Fetch Circuit"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f359b797-02ad-4358-bef7-ad3f3008d323",
+   "id": "bed0af2c-ae46-41b0-ba77-485daef0a87b",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "fetched = client.get_entity(entity_id=registered_circuit.id, entity_type=models.Circuit)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ee27c8b5-dfa5-4fa5-ac2f-6cf158057bcf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rprint(fetched)"
+   ]
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.10"
   }
  },
  "nbformat": 4,

entitysdk-0.6.1/examples/utils.py

@@ -0,0 +1,13 @@
+"""Helpers."""
+
+from pathlib import Path
+
+
+def create_mock_circuit_dir(output_dir: Path):
+    """Create a mock hierarchy that looks like a circuit."""
+    output_dir = Path(output_dir)
+    output_dir.mkdir(exist_ok=True)
+    (output_dir / "circuit_config.json").touch()
+    (output_dir / "sonata").mkdir()
+    (output_dir / "sonata" / "nodes.h5").touch()
+    (output_dir / "sonata" / "edges.h5").touch()

{entitysdk-0.6.0 → entitysdk-0.6.1}/src/entitysdk/downloaders/ion_channel_model.py

@@ -22,7 +22,7 @@ def download_ion_channel_mechanism(
     output_dir = create_dir(output_dir)
     asset = client.download_assets(
         ion_channel_model,
-        selection={"content_type": "application/neuron-mod"},
+        selection={"content_type": "application/mod"},
         output_path=output_dir,
     ).one()
 

{entitysdk-0.6.0 → entitysdk-0.6.1}/src/entitysdk/models/__init__.py

@@ -4,6 +4,7 @@ from entitysdk.models.agent import Organization, Person
 from entitysdk.models.asset import Asset
 from entitysdk.models.brain_location import BrainLocation
 from entitysdk.models.brain_region import BrainRegion
+from entitysdk.models.brain_region_hierarchy import BrainRegionHierarchy
 from entitysdk.models.circuit import Circuit
 from entitysdk.models.classification import ETypeClassification, MTypeClassification
 from entitysdk.models.contribution import Contribution, Role
@@ -31,6 +32,7 @@ __all__ = [
     "Asset",
     "BrainLocation",
     "BrainRegion",
+    "BrainRegionHierarchy",
     "Circuit",
     "Contribution",
     "ElectricalCellRecording",

entitysdk-0.6.1/src/entitysdk/models/brain_region_hierarchy.py

@@ -0,0 +1,19 @@
+"""BrainRegionHierarchy model."""
+
+from typing import Annotated
+
+from pydantic import Field
+
+from entitysdk.models.core import Identifiable
+
+
+class BrainRegionHierarchy(Identifiable):
+    """BrainRegionHierarchy model."""
+
+    name: Annotated[
+        str,
+        Field(
+            examples=["Thalamus"],
+            description="The name of the brain region.",
+        ),
+    ]

{entitysdk-0.6.0 → entitysdk-0.6.1}/src/entitysdk/route.py

@@ -9,6 +9,7 @@ _ROUTES = {
     "Activity": "activity",
     "BrainLocation": "brain-location",
     "BrainRegion": "brain-region",
+    "BrainRegionHierarchy": "brain-region-hierarchy",
     "Circuit": "circuit",
     "Contribution": "contribution",
     "ElectricalCellRecording": "electrical-cell-recording",

{entitysdk-0.6.0 → entitysdk-0.6.1/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.6.0
+Version: 0.6.1
 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-0.6.0 → entitysdk-0.6.1}/src/entitysdk.egg-info/SOURCES.txt

@@ -11,6 +11,7 @@ examples/01_searching.ipynb
 examples/02_morphology.ipynb
 examples/03_circuit.ipynb
 examples/04_simulation_campaign.ipynb
+examples/utils.py
 src/entitysdk/__init__.py
 src/entitysdk/client.py
 src/entitysdk/common.py
@@ -41,6 +42,7 @@ src/entitysdk/models/asset.py
 src/entitysdk/models/base.py
 src/entitysdk/models/brain_location.py
 src/entitysdk/models/brain_region.py
+src/entitysdk/models/brain_region_hierarchy.py
 src/entitysdk/models/circuit.py
 src/entitysdk/models/classification.py
 src/entitysdk/models/contribution.py

{entitysdk-0.6.0 → entitysdk-0.6.1}/tests/unit/downloaders/test_ion_channel_model.py

@@ -10,7 +10,7 @@ def _mock_asset_response(asset_id):
         "path": "foo.mod",
         "full_path": "foo.mod",
         "is_directory": False,
-        "content_type": "application/neuron-mod",
+        "content_type": "application/mod",
         "size": 100,
         "status": "created",
         "meta": {},

{entitysdk-0.6.0 → entitysdk-0.6.1}/tests/unit/downloaders/test_memodel.py

@@ -30,7 +30,7 @@ def _mock_ic_asset_response(asset_id):
         "path": "foo.mod",
         "full_path": "foo.mod",
         "is_directory": False,
-        "content_type": "application/neuron-mod",
+        "content_type": "application/mod",
         "size": 100,
         "status": "created",
         "meta": {},

{entitysdk-0.6.0 → entitysdk-0.6.1}/tests/unit/test_client.py

@@ -555,7 +555,7 @@ def test_client_download_assets(
         | {
             "assets": [
                 _mock_asset_response(asset1_id)
-                | {"path": "foo/bar/bar.h5", "content_type": "application/hdf5"},
+                | {"path": "foo/bar/bar.h5", "content_type": "application/x-hdf5"},
                 _mock_asset_response(asset2_id)
                 | {"path": "foo/bar/bar.swc", "content_type": "application/swc"},
             ]