entitysdk 0.6.0__tar.gz → 0.6.2__tar.gz

{entitysdk-0.6.0/src/entitysdk.egg-info → entitysdk-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.6.0
+Version: 0.6.2
 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-0.6.0 → entitysdk-0.6.2}/examples/02_morphology.ipynb

@@ -276,7 +276,8 @@
     "        entity_id=registered.id,\n",
     "        entity_type=ReconstructionMorphology,\n",
     "        file_path=file1,\n",
-    "        file_content_type=\"application/h5\",\n",
+    "        file_content_type=\"application/x-hdf5\",\n",
+    "        asset_label=\"hdf5\",\n",
     "    )\n",
     "    rprint(asset1)\n",
     "\n",
@@ -289,6 +290,7 @@
     "        file_content=buffer,\n",
     "        file_name=\"buffer.h5\",\n",
     "        file_content_type=\"application/swc\",\n",
+    "        asset_label=\"swc\",\n",
     "    )\n",
     "    rprint(asset2)"
    ]
@@ -408,8 +410,22 @@
   }
  ],
  "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-0.6.0 → entitysdk-0.6.2}/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-0.6.2/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-0.6.2}/src/entitysdk/client.py

@@ -214,6 +214,7 @@ class Client:
         file_content_type: str,
         file_name: str | None = None,
         file_metadata: dict | None = None,
+        asset_label: str | None = None,
         project_context: ProjectContext | None = None,
     ) -> Asset:
         """Upload asset to an existing entity's endpoint from a file path."""
@@ -229,6 +230,7 @@ class Client:
             file_name=file_name or path.name,
             content_type=file_content_type,
             metadata=file_metadata,
+            label=asset_label,
         )
         return core.upload_asset_file(
             url=url,
@@ -248,6 +250,7 @@ class Client:
         file_name: str,
         file_content_type: str,
         file_metadata: dict | None = None,
+        asset_label: str | None = None,
         project_context: ProjectContext | None = None,
     ) -> Asset:
         """Upload asset to an existing entity's endpoint from a file-like object."""
@@ -261,6 +264,7 @@ class Client:
             file_name=file_name,
             content_type=file_content_type,
             metadata=file_metadata or {},
+            label=asset_label,
         )
         context = self._required_user_context(override_context=project_context)
         return core.upload_asset_content(

{entitysdk-0.6.0 → entitysdk-0.6.2}/src/entitysdk/core.py

@@ -1,6 +1,7 @@
 """Core SDK operations."""
 
 import io
+import logging
 import os
 from collections.abc import Iterator
 from pathlib import Path
@@ -10,11 +11,13 @@ import httpx
 
 from entitysdk import serdes
 from entitysdk.common import ProjectContext
+from entitysdk.exception import EntitySDKError
 from entitysdk.models.asset import Asset, DetailedFileList, LocalAssetMetadata
 from entitysdk.models.core import Identifiable
 from entitysdk.result import IteratorResult
 from entitysdk.util import make_db_api_request, stream_paginated_request
 
+L = logging.getLogger(__name__)
 TIdentifiable = TypeVar("TIdentifiable", bound=Identifiable)
 
 
@@ -170,6 +173,7 @@ def upload_asset_content(
         url=url,
         method="POST",
         files=files,
+        data={"label": asset_metadata.label} if asset_metadata.label else None,
         project_context=project_context,
         token=token,
         http_client=http_client,
@@ -192,7 +196,7 @@ def upload_asset_directory(
     for concrete_path in paths.values():
         if not concrete_path.exists():
             msg = f"Path {concrete_path} does not exist"
-            raise Exception(msg)
+            raise EntitySDKError(msg)
 
     response = make_db_api_request(
         url=url,
@@ -214,11 +218,20 @@ def upload_asset_directory(
         failed = {}
         for path, url in to_upload.items():
             with open(paths[Path(path)], "rb") as fd:
-                response = http_client.request(
-                    method="PUT", url=url, content=fd, follow_redirects=True
-                )
-            if response.status_code != 200:
-                failed[path] = url
+                try:
+                    response = http_client.request(
+                        method="PUT",
+                        url=url,
+                        content=fd,
+                        follow_redirects=True,
+                        timeout=20,
+                    )
+                except httpx.HTTPError:
+                    L.exception("Upload failed, will retry again")
+                    failed[path] = url
+                else:
+                    if response.status_code != 200:
+                        failed[path] = url
         return failed
 
     to_upload = js["files"]
@@ -228,7 +241,7 @@ def upload_asset_directory(
             break
 
     if to_upload:
-        raise Exception(f"Uploading these files failed: {to_upload}")
+        raise EntitySDKError(f"Uploading these files failed: {to_upload}")
 
     return serdes.deserialize_model(js["asset"], Asset)
 

{entitysdk-0.6.0 → entitysdk-0.6.2}/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-0.6.2}/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-0.6.0 → entitysdk-0.6.2}/src/entitysdk/models/asset.py

@@ -93,6 +93,7 @@ class LocalAssetMetadata(BaseModel):
             description="The metadata of the asset.",
         ),
     ] = None
+    label: Annotated[str | None, Field(description="Optional asset label.")] = None
 
 
 class DetailedFile(BaseModel):

entitysdk-0.6.2/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-0.6.2}/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-0.6.2}/src/entitysdk/util.py

@@ -19,6 +19,7 @@ def make_db_api_request(
     *,
     method: str,
     json: dict | None = None,
+    data: dict | None = None,
     parameters: dict | None = None,
     files: dict | None = None,
     project_context: ProjectContext | None = None,
@@ -42,6 +43,7 @@ def make_db_api_request(
             headers=headers,
             json=json,
             files=files,
+            data=data,
             params=parameters,
             follow_redirects=True,
         )
@@ -53,6 +55,7 @@ def make_db_api_request(
     except httpx.HTTPStatusError as e:
         message = (
             f"HTTP error {response.status_code} for {method} {url}\n"
+            f"data       : {data}\n"
             f"json       : {dumps(json, indent=2)}\n"
             f"params     : {parameters}\n"
             f"response   : {response.text}"

{entitysdk-0.6.0 → entitysdk-0.6.2/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.6.0
+Version: 0.6.2
 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-0.6.0 → entitysdk-0.6.2}/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-0.6.2}/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-0.6.2}/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-0.6.2}/tests/unit/models/test_asset.py

@@ -39,4 +39,5 @@ def test_local_asset_metadata():
         "file_name": "file_name",
         "content_type": "text/plain",
         "metadata": {"key": "value"},
+        "label": None,
     }

{entitysdk-0.6.0 → entitysdk-0.6.2}/tests/unit/test_client.py

@@ -4,6 +4,7 @@ import uuid
 from pathlib import Path
 from unittest.mock import patch
 
+import httpx
 import pytest
 
 from entitysdk.client import Client
@@ -145,6 +146,14 @@ def test_client_upload_file(
         method="POST",
         url=f"{api_url}/entity/{entity_id}/assets",
         match_headers=request_headers,
+        match_files={
+            "file": (
+                "foo",
+                b"foo",
+                "text/plain",
+            )
+        },
+        match_data={"label": "swc"},
         json=_mock_asset_response(asset_id),
     )
 
@@ -158,6 +167,7 @@ def test_client_upload_file(
         file_path=path,
         file_content_type="text/plain",
         file_metadata={"key": "value"},
+        asset_label="swc",
     )
 
     assert res.id == asset_id
@@ -179,6 +189,7 @@ def test_client_upload_content(client, httpx_mock, api_url, request_headers):
                 "text/plain",
             )
         },
+        match_data={"label": "swc"},
         json=_mock_asset_response(asset_id),
     )
     res = client.upload_content(
@@ -188,6 +199,7 @@ def test_client_upload_content(client, httpx_mock, api_url, request_headers):
         file_content=buffer,
         file_content_type="text/plain",
         file_metadata={"key": "value"},
+        asset_label="swc",
     )
 
     assert res.id == asset_id
@@ -555,7 +567,7 @@ 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"},
             ]
@@ -767,6 +779,45 @@ def test_upload_directory_by_paths(
     )
     assert res == Asset.model_validate(asset)
 
+    httpx_mock.add_response(
+        method="POST",
+        url=f"{api_url}/entity/{entity_id}/assets/directory/upload",
+        match_headers=request_headers,
+        json={
+            "asset": asset,
+            "files": {
+                "foo/bar/baz/subdir0/file1.txt": "http://upload_url0",
+            },
+        },
+    )
+
+    # have read error / exception
+    httpx_mock.add_exception(
+        httpx.ReadTimeout("Unable to read within timeout"),
+        method="PUT",
+        url="http://upload_url0",
+    )
+    httpx_mock.add_exception(
+        httpx.ReadTimeout("Unable to read within timeout"),
+        method="PUT",
+        url="http://upload_url0",
+    )
+    httpx_mock.add_exception(
+        httpx.ReadTimeout("Unable to read within timeout"),
+        method="PUT",
+        url="http://upload_url0",
+    )
+
+    with pytest.raises(EntitySDKError, match="Uploading these files failed"):
+        client.upload_directory(
+            entity_id=entity_id,
+            entity_type=Entity,
+            name="test-directory",
+            paths=paths,
+            label=None,
+            metadata=None,
+        )
+
     # have s3 upload fail:
     httpx_mock.add_response(
         method="POST",
@@ -784,7 +835,7 @@ def test_upload_directory_by_paths(
     httpx_mock.add_response(method="PUT", url="http://upload_url0", status_code=404)
     httpx_mock.add_response(method="PUT", url="http://upload_url0", status_code=404)
 
-    with pytest.raises(Exception, match="Uploading these files failed"):
+    with pytest.raises(EntitySDKError, match="Uploading these files failed"):
         client.upload_directory(
             entity_id=entity_id,
             entity_type=Entity,