Allow identity, ensure dimensions is returned, & use pre-commit.ci (

#103)

Update tests with valid entity using 'identity'.
Ensure "identity" is respected everywhere.

Ensure "dimensions" is always returned.

Pre-commit is now run through pre-commit.ci.

.github/workflows/ci_tests.yml

@@ -16,7 +16,7 @@ jobs:
       install_extras: "[dev]"
 
       # pre-commit
-      python_version_pre-commit: "3.10"
+      run_pre-commit: false
 
       # pylint & safety
       python_version_pylint_safety: "3.10"

.pre-commit-config.yaml

@@ -1,7 +1,16 @@
-# To install the git pre-commit hook run:
-#   pre-commit install
-# To update the pre-commit hooks run:
-#   pre-commit autoupdate
+# pre-commit.ci
+ci:
+  autofix_commit_msg: |
+      [pre-commit.ci] auto fixes from pre-commit hooks
+
+      For more information, see https://pre-commit.ci
+  autofix_prs: false
+  autoupdate_branch: 'main'
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: 'weekly'
+  submodules: false
+
+# hooks
 repos:
   # pre-commit-hooks supplies a multitude of small hooks
   # To get an overview of them all as well as the ones used here, please see

entities_service/cli/_utils/generics.py

@@ -119,7 +119,7 @@ def get_namespace_name_version(entity: Entity | dict[str, Any]) -> tuple[str, st
     The version is reversed to sort it in descending order (utilizing StrReversor).
     """
     if isinstance(entity, dict):
-        uri = entity.get("uri", None) or (
+        uri = entity.get("uri", entity.get("identity", None)) or (
             f"{entity.get('namespace', '')}/{entity.get('version', '')}"
             f"/{entity.get('name', '')}"
         )

entities_service/main.py

@@ -19,6 +19,7 @@
 from entities_service.service.config import CONFIG
 from entities_service.service.logger import setup_logger
 from entities_service.service.routers import get_routers
+from entities_service.service.utils import _get_entity
 
 if TYPE_CHECKING:  # pragma: no cover
     from typing import Any
@@ -59,23 +60,6 @@ async def lifespan(_: FastAPI):
     APP.include_router(router)
 
 
-async def _get_entity(version: str, name: str, db: str | None = None) -> dict[str, Any]:
-    """Utility function for the endpoints to retrieve an entity."""
-    uri = f"{str(CONFIG.base_url).rstrip('/')}"
-
-    if db:
-        uri += f"/{db}"
-
-    uri += f"/{version}/{name}"
-
-    entity = get_backend(db=db).read(uri)
-
-    if entity is None:
-        raise ValueError(f"Could not find entity: uri={uri}")
-
-    return entity
-
-
 @APP.get(
     "/{version}/{name}",
     response_model=Entity,

entities_service/models/soft.py

@@ -174,6 +174,7 @@ class SOFTEntity(BaseModel):
                 "The universal identifier for the entity. This MUST start with the base"
                 " URL."
             ),
+            validation_alias=AliasChoices("identity", "uri"),
         ),
     ] = None
     description: Annotated[str, Field(description="Description of the entity.")] = ""
@@ -244,7 +245,7 @@ def _check_cross_dependent_fields(cls, data: Any) -> Any:
         if (
             isinstance(data, dict)
             and any(data.get(_) is None for _ in ("name", "version", "namespace"))
-            and data.get("uri") is None
+            and data.get("uri", data.get("identity")) is None
         ):
             error_message = (
                 "Either `name`, `version`, and `namespace` or `uri` must be set.\n"
@@ -254,13 +255,14 @@ def _check_cross_dependent_fields(cls, data: Any) -> Any:
         if (
             isinstance(data, dict)
             and all(data.get(_) is not None for _ in ("name", "version", "namespace"))
-            and data.get("uri") is not None
-            and data["uri"] != f"{data['namespace']}/{data['version']}/{data['name']}"
+            and data.get("uri", data.get("identity")) is not None
+            and data.get("uri", data.get("identity", ""))
+            != f"{data['namespace']}/{data['version']}/{data['name']}"
         ):
             # Ensure that `uri` is consistent with `name`, `version`, and `namespace`.
             diff = "\n  ".join(
                 difflib.ndiff(
-                    [data["uri"]],
+                    [data.get("uri", data.get("identity", ""))],
                     [f"{data['namespace']}/{data['version']}/{data['name']}"],
                 )
             )
@@ -269,4 +271,5 @@ def _check_cross_dependent_fields(cls, data: Any) -> Any:
                 f"`namespace`:\n\n  {diff}\n\n"
             )
             raise ValueError(error_message)
+
         return data

entities_service/service/backend/mongodb.py

@@ -419,7 +419,7 @@ def _single_uri_query(self, uri: str) -> dict[str, Any]:
     def _prepare_entity(self, entity: Entity | dict[str, Any]) -> dict[str, Any]:
         """Clean and prepare the entity for interactions with the MongoDB backend."""
         if isinstance(entity, dict):
-            uri = entity.get("uri", None) or (
+            uri = entity.get("uri", entity.get("identity", None)) or (
                 f"{entity.get('namespace', '')}/{entity.get('version', '')}"
                 f"/{entity.get('name', '')}"
             )

entities_service/service/routers/admin.py

@@ -19,6 +19,7 @@
 from entities_service.service.backend import get_backend
 from entities_service.service.config import CONFIG
 from entities_service.service.security import verify_token
+from entities_service.service.utils import _add_dimensions
 
 if TYPE_CHECKING:  # pragma: no cover
     from typing import Any
@@ -83,6 +84,12 @@ async def create_entities(
             CONFIG.backend, auth_level="write", db=namespace
         )
 
+        LOGGER.debug(
+            "Creating %s entities in namespace '%s'",
+            len(namespaced_entities),
+            namespace,
+        )
+
         try:
             created_namespaced_entities = namespaced_entities_backend.create(
                 namespaced_entities
@@ -97,7 +104,7 @@ async def create_entities(
                     "Already created entities: uris=%s",
                     ", ".join(
                         (
-                            entity.get("uri", "")
+                            entity.get("uri", entity.get("identity", ""))
                             or (
                                 f"{entity.get('namespace', '')}"
                                 f"/{entity.get('version', '')}"
@@ -123,6 +130,9 @@ async def create_entities(
         ):
             raise write_fail_exception
 
+        # Ensure the returned entities have the dimensions key
+        await _add_dimensions(created_namespaced_entities)
+
         if isinstance(created_namespaced_entities, dict):
             created_entities.append(created_namespaced_entities)
         else:

entities_service/service/utils.py

@@ -0,0 +1,50 @@
+"""Utility functions for the service."""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from entities_service.service.backend import get_backend
+from entities_service.service.config import CONFIG
+
+if TYPE_CHECKING:  # pragma: no cover
+    from typing import Any
+
+
+async def _add_dimensions(entity: dict[str, Any] | list[dict[str, Any]]) -> None:
+    """Utility function for the endpoints to add dimensions to an entity."""
+    if isinstance(entity, list):
+        for entity_ in entity:
+            await _add_dimensions(entity_)
+        return
+
+    if "dimensions" not in entity:
+        # SOFT5
+        if isinstance(entity["properties"], list):
+            entity["dimensions"] = []
+
+        # SOFT7
+        elif isinstance(entity["properties"], dict):
+            entity["dimensions"] = {}
+
+        else:
+            raise ValueError(f"Invalid entity: uri={entity['uri']}")
+
+
+async def _get_entity(version: str, name: str, db: str | None = None) -> dict[str, Any]:
+    """Utility function for the endpoints to retrieve an entity."""
+    uri = f"{str(CONFIG.base_url).rstrip('/')}"
+
+    if db:
+        uri += f"/{db}"
+
+    uri += f"/{version}/{name}"
+
+    entity = get_backend(db=db).read(uri)
+
+    if entity is None:
+        raise ValueError(f"Could not find entity: uri={uri}")
+
+    await _add_dimensions(entity)
+
+    return entity

tests/cli/commands/test_upload.py

@@ -60,7 +60,11 @@ def test_upload_filepath(
     core_namespace = str(CONFIG.base_url).rstrip("/")
     current_namespace = f"{core_namespace}/{namespace}" if namespace else core_namespace
 
-    assert "uri" in raw_entity
+    id_key = "uri" if "uri" in raw_entity else "identity"
+    assert id_key in raw_entity
+
+    # Match raw_entity to a backend entity (always use 'uri')
+    raw_entity["uri"] = raw_entity.pop(id_key)
 
     if namespace:
         # Update the entity's namespace to the current namespace
@@ -82,7 +86,7 @@ def test_upload_filepath(
 
     # Mock response for "Check if entity already exists"
     httpx_mock.add_response(
-        url=raw_entity["uri"],
+        url=raw_entity[id_key],
         status_code=404,  # not found
     )
 
@@ -176,11 +180,13 @@ def test_upload_directory(
         directory = tmp_path / "valid_entities"
         directory.mkdir(parents=True, exist_ok=True)
         for index, raw_entity in enumerate(raw_entities):
+            id_key = "uri" if "uri" in raw_entity else "identity"
+
             # Update the entity's namespace to the current namespace
             if "namespace" in raw_entity:
                 raw_entity["namespace"] = current_namespace
-            if "uri" in raw_entity:
-                raw_entity["uri"] = raw_entity["uri"].replace(
+            if id_key in raw_entity:
+                raw_entity[id_key] = raw_entity[id_key].replace(
                     f"{core_namespace}/", f"{current_namespace}/"
                 )
 
@@ -196,9 +202,9 @@ def test_upload_directory(
 
     # Mock response for "Check if entity already exists"
     for raw_entity in raw_entities:
-        assert "uri" in raw_entity
+        assert any(_ in raw_entity for _ in ("uri", "identity"))
         httpx_mock.add_response(
-            url=raw_entity["uri"],
+            url=raw_entity.get("uri", raw_entity.get("identity")),
             status_code=404,  # not found
         )
 
@@ -322,14 +328,16 @@ def test_existing_entity_different_content(
     core_namespace = str(CONFIG.base_url).rstrip("/")
     current_namespace = f"{core_namespace}/{namespace}" if namespace else core_namespace
 
+    assert "uri" in raw_entity
+
     if namespace:
         # Update the entity's namespace to the current namespace
         if "namespace" in raw_entity:
             raw_entity["namespace"] = current_namespace
-        if "uri" in raw_entity:
-            raw_entity["uri"] = raw_entity["uri"].replace(
-                f"{core_namespace}/", f"{current_namespace}/"
-            )
+
+        raw_entity["uri"] = raw_entity["uri"].replace(
+            f"{core_namespace}/", f"{current_namespace}/"
+        )
 
         # Write the updated entity to file
         directory = tmp_path / "valid_entities"
@@ -345,7 +353,6 @@ def test_existing_entity_different_content(
     )
 
     # Mock response for "Check if entity already exists"
-    assert "uri" in raw_entity
     httpx_mock.add_response(
         url=raw_entity["uri"],
         status_code=200,  # ok
@@ -549,14 +556,16 @@ def test_existing_entity_errors(
     core_namespace = str(CONFIG.base_url).rstrip("/")
     current_namespace = f"{core_namespace}/{namespace}" if namespace else core_namespace
 
+    assert "uri" in raw_entity
+
     if namespace:
         # Update the entity's namespace to the current namespace
         if "namespace" in raw_entity:
             raw_entity["namespace"] = current_namespace
-        if "uri" in raw_entity:
-            raw_entity["uri"] = raw_entity["uri"].replace(
-                f"{core_namespace}/", f"{current_namespace}/"
-            )
+
+        raw_entity["uri"] = raw_entity["uri"].replace(
+            f"{core_namespace}/", f"{current_namespace}/"
+        )
 
         # Write the updated entity to file
         directory = tmp_path / "valid_entities"
@@ -572,7 +581,6 @@ def test_existing_entity_errors(
     )
 
     # Mock response for "Check if entity already exists"
-    assert "uri" in raw_entity
     httpx_mock.add_response(
         url=raw_entity["uri"],
         status_code=200,  # ok
@@ -859,7 +867,9 @@ def test_using_stdin(
 
     valid_entities_dir = static_dir / "valid_entities"
     entity_uris: list[str] = [
-        json.loads(filepath.read_text())["uri"]
+        json.loads(filepath.read_text()).get(
+            "uri", json.loads(filepath.read_text()).get("identity")
+        )
         for filepath in valid_entities_dir.glob("*.json")
     ]