entitysdk 0.7.0__tar.gz → 0.7.1__tar.gz

{entitysdk-0.7.0/src/entitysdk.egg-info → entitysdk-0.7.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.7.0
+Version: 0.7.1
 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-0.7.0 → entitysdk-0.7.1}/pyproject.toml

@@ -46,6 +46,7 @@ addopts = [
 [tool.ruff]
 line-length = 100
 target-version = "py311"
+include = ["pyproject.toml", "src/**/*.py", "tests/**/*.py", "examples/**/*.py"]
 
 [tool.ruff.lint]
 select = [

{entitysdk-0.7.0 → entitysdk-0.7.1}/src/entitysdk/client.py

@@ -1,5 +1,6 @@
 """Identifiable SDK client."""
 
+import concurrent.futures
 import io
 import os
 from pathlib import Path
@@ -216,7 +217,7 @@ class Client:
         file_content_type: str,
         file_name: str | None = None,
         file_metadata: dict | None = None,
-        asset_label: str | None = None,
+        asset_label: str,
         project_context: ProjectContext | None = None,
     ) -> Asset:
         """Upload asset to an existing entity's endpoint from a file path."""
@@ -252,7 +253,7 @@ class Client:
         file_name: str,
         file_content_type: str,
         file_metadata: dict | None = None,
-        asset_label: str | None = None,
+        asset_label: str,
         project_context: ProjectContext | None = None,
     ) -> Asset:
         """Upload asset to an existing entity's endpoint from a file-like object."""
@@ -286,7 +287,7 @@ class Client:
         name: str,
         paths: dict[os.PathLike, os.PathLike],
         metadata: dict | None = None,
-        label: str | None = None,
+        label: str,
         project_context: ProjectContext | None = None,
     ) -> Asset:
         """Attach directory to an entity from with a group of paths."""
@@ -349,8 +350,9 @@ class Client:
         output_path: os.PathLike,
         project_context: ProjectContext | None = None,
         ignore_directory_name: bool = False,
+        max_concurrent: int = 1,
     ) -> list[Path]:
-        """List directory existing entity's endpoint from a directory path."""
+        """Download directory of assets."""
         output_path = Path(output_path)
 
         if output_path.exists() and output_path.is_file():
@@ -386,9 +388,8 @@ class Client:
             project_context=project_context,
         )
 
-        paths = []
-        for path in contents.files:
-            paths.append(
+        if max_concurrent == 1:
+            paths = [
                 self.download_file(
                     entity_id=entity_id,
                     entity_type=entity_type,
@@ -397,7 +398,24 @@ class Client:
                     asset_path=path,
                     project_context=context,
                 )
-            )
+                for path in contents.files
+            ]
+        else:
+            with concurrent.futures.ThreadPoolExecutor(max_workers=max_concurrent) as executor:
+                futures = [
+                    executor.submit(
+                        self.download_file,
+                        entity_id=entity_id,
+                        entity_type=entity_type,
+                        asset_id=asset if asset else asset_id,
+                        output_path=output_path / path,
+                        asset_path=path,
+                        project_context=context,
+                    )
+                    for path in contents.files
+                ]
+                result = concurrent.futures.wait(futures)
+                paths = [res.result() for res in result.done]
 
         return paths
 
@@ -597,7 +615,7 @@ class Client:
 
         Note: This operation is not atomic. Deletion can succeed and upload can fail.
         """
-        self.delete_asset(
+        deleted_asset = self.delete_asset(
             entity_id=entity_id,
             entity_type=entity_type,
             asset_id=asset_id,
@@ -611,4 +629,5 @@ class Client:
             file_name=file_name,
             file_metadata=file_metadata,
             project_context=project_context,
+            asset_label=deleted_asset.label,
         )

{entitysdk-0.7.0 → entitysdk-0.7.1}/src/entitysdk/core.py

@@ -187,7 +187,7 @@ def upload_asset_directory(
     name: str,
     paths: dict[Path, Path],
     metadata: dict | None = None,
-    label: str | None = None,
+    label: str,
     project_context: ProjectContext,
     token: str,
     http_client: httpx.Client | None = None,

{entitysdk-0.7.0 → entitysdk-0.7.1}/src/entitysdk/models/asset.py

@@ -65,7 +65,7 @@ class Asset(Identifiable):
         dict,
         Field(description="Asset json metadata."),
     ] = {}
-    label: Annotated[str | None, Field(description="Optional asset label.")] = None
+    label: Annotated[str, Field(description="Asset label.")]
 
 
 class LocalAssetMetadata(BaseModel):
@@ -96,7 +96,7 @@ class LocalAssetMetadata(BaseModel):
             description="The metadata of the asset.",
         ),
     ] = None
-    label: Annotated[str | None, Field(description="Optional asset label.")] = None
+    label: Annotated[str, Field(description="Optional asset label.")]
 
 
 class DetailedFile(BaseModel):

{entitysdk-0.7.0 → entitysdk-0.7.1}/src/entitysdk/staging/circuit.py

@@ -22,6 +22,7 @@ def stage_circuit(client: Client, *, model: Circuit, output_dir: Path) -> Path:
         selection={
             "content_type": "application/vnd.directory",
             "is_directory": True,
+            "label": "sonata_circuit",
         },
     ).one()
 

{entitysdk-0.7.0 → entitysdk-0.7.1/src/entitysdk.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: entitysdk
-Version: 0.7.0
+Version: 0.7.1
 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-0.7.0 → entitysdk-0.7.1}/tests/unit/downloaders/test_emodel.py

@@ -11,6 +11,7 @@ def _mock_asset_response(asset_id):
         "full_path": "foo.hoc",
         "is_directory": False,
         "content_type": "application/hoc",
+        "label": "neuron_hoc",
         "size": 100,
         "status": "created",
         "meta": {},

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/downloaders/test_ion_channel_model.py

@@ -11,6 +11,7 @@ def _mock_asset_response(asset_id):
         "full_path": "foo.mod",
         "is_directory": False,
         "content_type": "application/mod",
+        "label": "neuron_mechanisms",
         "size": 100,
         "status": "created",
         "meta": {},

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/downloaders/test_memodel.py

@@ -16,6 +16,7 @@ def _mock_morph_asset_response(asset_id):
         "full_path": "foo.asc",
         "is_directory": False,
         "content_type": "application/asc",
+        "label": "morphology",
         "size": 100,
         "status": "created",
         "meta": {},
@@ -31,6 +32,7 @@ def _mock_ic_asset_response(asset_id):
         "full_path": "foo.mod",
         "is_directory": False,
         "content_type": "application/mod",
+        "label": "neuron_mechanisms",
         "size": 100,
         "status": "created",
         "meta": {},
@@ -46,6 +48,7 @@ def _mock_emodel_asset_response(asset_id):
         "full_path": "foo.hoc",
         "is_directory": False,
         "content_type": "application/hoc",
+        "label": "neuron_hoc",
         "size": 100,
         "status": "created",
         "meta": {},

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/downloaders/test_morphology.py

@@ -14,6 +14,7 @@ def _mock_asset_response(asset_id):
         "full_path": "foo.asc",
         "is_directory": False,
         "content_type": "application/asc",
+        "label": "morphology",
         "size": 100,
         "status": "created",
         "meta": {},

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/models/data/electrical_cell_recording.json

@@ -60,6 +60,7 @@
       "content_type": "application/nwb",
       "size": 1657656,
       "sha256_digest": "696ffb1e4eb24839c53407d1d5beee030316ef61648bea5a6e15eae6486fd813",
+      "label": "electrical_cell_recording",
       "meta": {
         "legacy": {
           "name": "S1FL_L5_DBC_cIR_4.nwb",

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/models/data/ion_channel_model.json

@@ -84,7 +84,8 @@
       "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",
+      "content_type": "application/mod",
+      "label": "neuron_mechanisms",
       "size": 561221,
       "sha256_digest": "8b850eface3e7b881db62c361dc5da62be008ca81501c406a59646bf7075c95b",
       "status": "created",

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/models/data/reconstruction_morphology.json

@@ -17,6 +17,7 @@
       "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",
       "is_directory": false,
       "content_type": "application/swc",
+      "label": "morphology",
       "size": 561221,
       "sha256_digest": "8b850eface3e7b881db62c361dc5da62be008ca81501c406a59646bf7075c95b",
       "status": "created",
@@ -55,6 +56,7 @@
       "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",
       "is_directory": false,
       "content_type": "application/asc",
+      "label": "morphology",
       "size": 525332,
       "sha256_digest": "bf00878444539ead825f2d451cdf6f87072526f9a82c87de35fca5563ae5596b",
       "status": "created",

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/models/test_asset.py

@@ -8,6 +8,7 @@ def test_asset():
         id=MOCK_UUID,
         path="path/to/asset",
         full_path="full/path/to/asset",
+        label="mock",
         is_directory=False,
         content_type="text/plain",
         size=100,
@@ -25,7 +26,7 @@ def test_asset():
         "status": None,
         "sha256_digest": None,
         "meta": {},
-        "label": None,
+        "label": "mock",
     }
 
 
@@ -34,10 +35,11 @@ def test_local_asset_metadata():
         file_name="file_name",
         content_type="text/plain",
         metadata={"key": "value"},
+        label="mock",
     )
     assert res.model_dump() == {
         "file_name": "file_name",
         "content_type": "text/plain",
         "metadata": {"key": "value"},
-        "label": None,
+        "label": "mock",
     }

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/staging/conftest.py

@@ -60,7 +60,7 @@ def circuit(subject, brain_region):
             Asset(
                 id=uuid.uuid4(),
                 content_type="application/vnd.directory",
-                label="circuit",
+                label="sonata_circuit",
                 size=0,
                 path="circuit",
                 full_path="/circuit",

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/test_client.py

@@ -129,6 +129,7 @@ def _mock_asset_response(asset_id):
         "status": "created",
         "meta": {},
         "sha256_digest": "sha256_digest",
+        "label": "morphology",
     }
 
 
@@ -146,14 +147,8 @@ 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"},
+        match_files={"file": ("foo", b"foo", "application/swc")},
+        match_data={"label": "morphology"},
         json=_mock_asset_response(asset_id),
     )
 
@@ -165,9 +160,9 @@ def test_client_upload_file(
         entity_type=Entity,
         file_name="foo",
         file_path=path,
-        file_content_type="text/plain",
+        file_content_type="application/swc",
         file_metadata={"key": "value"},
-        asset_label="swc",
+        asset_label="morphology",
     )
 
     assert res.id == asset_id
@@ -182,24 +177,18 @@ def test_client_upload_content(client, httpx_mock, api_url, request_headers):
         method="POST",
         url=f"{api_url}/entity/{entity_id}/assets",
         match_headers=request_headers,
-        match_files={
-            "file": (
-                "foo.txt",
-                buffer,
-                "text/plain",
-            )
-        },
-        match_data={"label": "swc"},
+        match_files={"file": ("foo.swc", buffer, "application/swc")},
+        match_data={"label": "morphology"},
         json=_mock_asset_response(asset_id),
     )
     res = client.upload_content(
         entity_id=entity_id,
         entity_type=Entity,
-        file_name="foo.txt",
+        file_name="foo.swc",
         file_content=buffer,
-        file_content_type="text/plain",
+        file_content_type="application/swc",
         file_metadata={"key": "value"},
-        asset_label="swc",
+        asset_label="morphology",
     )
 
     assert res.id == asset_id
@@ -468,9 +457,10 @@ def test_client_get(
 def _mock_asset_delete_response(asset_id):
     return {
         "path": "buffer.h5",
-        "full_path": "private/103d7868/103d7868/assets/reconstruction_morphology/8703/buffer.h5",
+        "full_path": "private/103d7868/103d7868/assets/reconstruction_morphology/8703/buffer.swc",
         "is_directory": False,
         "content_type": "application/swc",
+        "label": "morphology",
         "size": 18,
         "sha256_digest": "47ddc1b6e05dcbfbd2db9dcec4a49d83c6f9f10ad595649bacdcb629671fd954",
         "meta": {},
@@ -682,6 +672,7 @@ def test_client_download_assets__entity(
                 full_path="/foo/asset1",
                 is_directory=False,
                 content_type="application/json",
+                label="cell_composition_summary",
                 size=1,
             ),
         ],
@@ -731,7 +722,7 @@ def test_upload_directory_by_paths(
             entity_type=Entity,
             name="test-directory",
             paths=paths,
-            label=None,
+            label="sonata_circuit",
             metadata=None,
         )
 
@@ -744,7 +735,7 @@ def test_upload_directory_by_paths(
         "full_path": "asdf",
         "id": "a370a57b-7211-4426-8046-970758ceaf68",
         "is_directory": True,
-        "label": None,
+        "label": "sonata_circuit",
         "meta": {},
         "path": "",
         "sha256_digest": None,
@@ -880,12 +871,14 @@ def test_client_list_directory(
     assert res.files[Path("a/b/foo.txt")].name == "a/b/foo.txt"
 
 
+@pytest.mark.parametrize("max_concurrent", [1, 4])
 def test_client_download_directory_ignore_directory(
     tmp_path,
     client,
     httpx_mock,
     api_url,
     request_headers,
+    max_concurrent,
 ):
     entity_id = uuid.uuid4()
     asset_id = uuid.uuid4()
@@ -924,17 +917,20 @@ def test_client_download_directory_ignore_directory(
         asset_id=asset_id,
         output_path=tmp_path,
         ignore_directory_name=True,
+        max_concurrent=max_concurrent,
     )
     assert len(res) == 1
     assert res[0] == (tmp_path / "foo.txt").absolute()
 
 
+@pytest.mark.parametrize("max_concurrent", [1, 4])
 def test_client_download_directory(
     tmp_path,
     client,
     httpx_mock,
     api_url,
     request_headers,
+    max_concurrent,
 ):
     entity_id = uuid.uuid4()
     asset_id = uuid.uuid4()
@@ -987,15 +983,18 @@ def test_client_download_directory(
             asset_id=asset_id,
             output_path=target,
             ignore_directory_name=False,
+            max_concurrent=max_concurrent,
         )
 
 
+@pytest.mark.parametrize("max_concurrent", [1, 4])
 def test_client_download_directory__asset(
     tmp_path,
     client,
     httpx_mock,
     api_url,
     request_headers,
+    max_concurrent,
 ):
     entity_id = uuid.uuid4()
     asset_id = uuid.uuid4()
@@ -1009,6 +1008,7 @@ def test_client_download_directory__asset(
         is_directory=True,
         size=0,
         content_type="application/vnd.directory",
+        label="sonata_circuit",
     )
 
     # for listing dirs
@@ -1037,6 +1037,7 @@ def test_client_download_directory__asset(
         asset_id=asset,
         output_path=tmp_path,
         ignore_directory_name=False,
+        max_concurrent=max_concurrent,
     )
     assert len(res) == 1
     assert res[0] == (tmp_path / "path_to_asset/foo.txt").absolute()

{entitysdk-0.7.0 → entitysdk-0.7.1}/tests/unit/utils/test_asset.py

@@ -17,6 +17,7 @@ def assets():
             is_directory=False,
             content_type="application/json",
             size=1,
+            label="json",
         ),
         Asset(
             id=uuid.uuid4(),
@@ -25,6 +26,7 @@ def assets():
             is_directory=False,
             content_type="application/csv",
             size=1,
+            label="csv",
         ),
         Asset(
             id=uuid.uuid4(),
@@ -33,6 +35,7 @@ def assets():
             is_directory=False,
             content_type="application/csv",
             size=1,
+            label="csv",
         ),
     ]