Utility CLI for DLite Entities Service

.github/workflows/ci_tests.yml

@@ -82,6 +82,7 @@ jobs:
             --name "entity-service" \
             --network "host" \
             --volume "${PWD}:/app" \
+            --user "$(id -u):$(id -g)" \
             entity-service
           sleep 5
 
@@ -94,7 +95,7 @@ jobs:
       - name: Run tests
         run: |
           {
-            pytest -vv --live-backend
+            pytest -vv --live-backend --cov-report=xml
           } || {
             echo "Failed! Here's the Docker logs for the service:" &&
             docker logs entity-service &&
@@ -105,6 +106,17 @@ jobs:
             exit 1
           }
 
+      - name: Upload coverage
+        if: github.repository_owner == 'SINTEF'
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
+          env_vars: OS,PYTHON
+          flags: docker
+        env:
+          OS: ubuntu-latest
+          PYTHON: '3.10'
+
   pytest:
     runs-on: ubuntu-latest
 
@@ -137,6 +149,7 @@ jobs:
         with:
           fail_ci_if_error: true
           env_vars: OS,PYTHON
+          flags: local
         env:
           OS: ubuntu-latest
           PYTHON: ${{ matrix.python_version }}

.pre-commit-config.yaml

@@ -62,7 +62,7 @@ repos:
     rev: v1.7.0
     hooks:
     - id: mypy
-      exclude: ^docs/example/.*$$
+      exclude: ^(docs/example|tests)/.*$
       additional_dependencies:
         - pydantic>=2
         - types-requests

dlite_entities_service/main.py

@@ -9,10 +9,10 @@
 from fastapi import FastAPI, HTTPException, Path, status
 
 from dlite_entities_service import __version__
-from dlite_entities_service.backend import ENTITIES_COLLECTION
-from dlite_entities_service.config import CONFIG
-from dlite_entities_service.logger import setup_logger
 from dlite_entities_service.models import VersionedSOFTEntity
+from dlite_entities_service.service.backend import ENTITIES_COLLECTION
+from dlite_entities_service.service.config import CONFIG
+from dlite_entities_service.service.logger import setup_logger
 
 if TYPE_CHECKING:  # pragma: no cover
     from typing import Any

dlite_entities_service/models/soft5.py

@@ -6,7 +6,7 @@
 from pydantic import BaseModel, Field, field_validator, model_validator
 from pydantic.networks import AnyHttpUrl
 
-from dlite_entities_service.config import CONFIG
+from dlite_entities_service.service.config import CONFIG
 
 
 class SOFT5Dimension(BaseModel):

dlite_entities_service/models/soft7.py

@@ -6,7 +6,7 @@
 from pydantic import BaseModel, Field, field_validator, model_validator
 from pydantic.networks import AnyHttpUrl
 
-from dlite_entities_service.config import CONFIG
+from dlite_entities_service.service.config import CONFIG
 
 
 class SOFT7Property(BaseModel):

dlite_entities_service/service/backend.py

@@ -0,0 +1,43 @@
+"""Backend implementation."""
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
+from pymongo import MongoClient
+from pymongo.errors import WriteConcernError, WriteError
+
+from dlite_entities_service.service.config import CONFIG
+
+if TYPE_CHECKING:  # pragma: no cover
+    from pymongo.collection import Collection
+
+
+AnyWriteError = (WriteError, WriteConcernError)
+"""Any write error exception."""
+
+
+def get_collection(
+    uri: str | None = None, username: str | None = None, password: str | None = None
+) -> Collection:
+    """Get the MongoDB collection for entities."""
+    client_kwargs = {
+        "username": username or CONFIG.mongo_user,
+        "password": password
+        or (
+            CONFIG.mongo_password.get_secret_value()
+            if CONFIG.mongo_password is not None
+            else None
+        ),
+    }
+    for key, value in list(client_kwargs.items()):
+        if value is None:
+            client_kwargs.pop(key, None)
+
+    mongo_client = MongoClient(
+        uri or str(CONFIG.mongo_uri),
+        **client_kwargs,
+    )
+    return mongo_client.dlite.entities
+
+
+ENTITIES_COLLECTION = get_collection()

dlite_entities_service/logger.py → dlite_entities_service/service/logger.py

@@ -44,7 +44,7 @@ def disable_logging():
 def _get_service_logger_handlers() -> list[logging.Handler]:
     """Return a list of handlers for the service logger."""
     # Create logs directory
-    root_dir = Path(__file__).resolve().parent.parent.resolve()
+    root_dir = Path(__file__).resolve().parent.parent.parent.resolve()
     logs_dir = root_dir / "logs"
     logs_dir.mkdir(exist_ok=True)
 

dlite_entities_service/utils_cli/__init__.py

@@ -0,0 +1,5 @@
+"""Utility CLI
+
+This module contains a CLI with utilities that may be useful when dealing with the
+DLite entities service, it's data (backend), and possibly more.
+"""

dlite_entities_service/utils_cli/_utils/global_settings.py

@@ -0,0 +1,92 @@
+"""Global settings for the CLI."""
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Optional
+
+try:
+    import typer
+except ImportError as exc:
+    raise ImportError(
+        "Please install the DLite entities service utility CLI with 'pip install "
+        f"{Path(__file__).resolve().parent.parent.parent.parent.resolve()}[cli]'"
+    ) from exc
+
+from rich import print  # pylint: disable=redefined-builtin
+
+from dlite_entities_service import __version__
+
+STATUS = {"use_service_dotenv": False}
+
+# Type Aliases
+OptionalBool = Optional[bool]
+
+
+def print_version(value: bool) -> None:
+    """Print version and exit."""
+    if value:
+        print(f"dlite-entities-service version: {__version__}")
+        raise typer.Exit()
+
+
+def global_options(
+    _: OptionalBool = typer.Option(
+        None,
+        "--version",
+        help="Show version and exit",
+        is_eager=True,
+        callback=print_version,
+    ),
+    use_service_dotenv: bool = typer.Option(
+        False,
+        "--use-service-dotenv/--use-cli-dotenv",
+        help=(
+            "Use the .env file also used for the DLite Entities Service or one "
+            "only for the CLI."
+        ),
+        is_flag=True,
+        rich_help_panel="Global options",
+    ),
+    as_json: bool = typer.Option(
+        False,
+        "--json",
+        help=(
+            "Print output as JSON. (Muting mutually exclusive with --yaml/--yml "
+            "and --json-one-line.)"
+        ),
+        is_flag=True,
+        rich_help_panel="Global options",
+    ),
+    as_json_one_line: bool = typer.Option(
+        False,
+        "--json-one-line",
+        help=(
+            "Print output as JSON without new lines. (Muting mutually exclusive "
+            "with --yaml/--yml and --json.)"
+        ),
+        is_flag=True,
+        rich_help_panel="Global options",
+    ),
+    as_yaml: bool = typer.Option(
+        False,
+        "--yaml",
+        "--yml",
+        help=(
+            "Print output as YAML. (Mutually exclusive with --json and "
+            "--json-one-line.)"
+        ),
+        is_flag=True,
+        rich_help_panel="Global options",
+    ),
+) -> None:
+    """Global options for the CLI."""
+    STATUS["use_service_dotenv"] = use_service_dotenv
+
+    if sum(int(_) for _ in [as_json, as_json_one_line, as_yaml]) > 1:
+        raise typer.BadParameter(
+            "Cannot use --json, --yaml/--yml, and --json-one-line together in any "
+            "combination."
+        )
+    STATUS["as_json"] = as_json
+    STATUS["as_json_one_line"] = as_json_one_line
+    STATUS["as_yaml"] = as_yaml