entitysdk 0.6.1__tar.gz → 0.6.2__tar.gz

{entitysdk-0.6.1/src/entitysdk.egg-info → entitysdk-0.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.6.1
+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-0.6.1 → 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-0.6.1 → 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-0.6.1 → 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-0.6.1 → 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-0.6.1 → 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-0.6.1 → entitysdk-0.6.2/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.6.1
+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-0.6.1 → 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-0.6.1 → 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
@@ -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,