Update hexit and small improvements (#30)

.static_files

@@ -16,6 +16,7 @@ scripts/script_utils/__init__.py
 scripts/script_utils/cli.py
 
 scripts/__init__.py
+scripts/update_all.py
 scripts/license_checker.py
 scripts/get_package_name.py
 scripts/update_config_docs.py

README.md

@@ -62,21 +62,21 @@ We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/metldata):
 ```bash
-docker pull ghga/metldata:0.3.6
+docker pull ghga/metldata:0.3.7
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/metldata:0.3.6 .
+docker build -t ghga/metldata:0.3.7 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/metldata:0.3.6 --help
+docker run -p 8080:8080 ghga/metldata:0.3.7 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:

metldata/__init__.py

@@ -15,4 +15,4 @@
 
 """Short description of package"""  # Please adapt to package
 
-__version__ = "0.3.6"
+__version__ = "0.3.7"

metldata/model_utils/essentials.py

@@ -22,7 +22,6 @@
 import json
 from contextlib import contextmanager
 from copy import copy, deepcopy
-from functools import lru_cache
 from pathlib import Path
 from tempfile import NamedTemporaryFile
 from typing import Any, Generator
@@ -36,16 +35,11 @@
 ROOT_CLASS = "Submission"
 
 
-@lru_cache
-def schema_view_from_model(model: MetadataModel) -> SchemaView:
-    """Get a schema view instance from the metadata model."""
-
-    return ExportableSchemaView(model)
-
-
 class MetadataModel(SchemaDefinition):
     """A dataclass for describing metadata models."""
 
+    _schema_view = None
+
     @classmethod
     def init_from_path(cls, model_path: Path) -> MetadataModel:
         """Initialize from a model file in yaml format."""
@@ -58,13 +52,19 @@ def init_from_path(cls, model_path: Path) -> MetadataModel:
     @property
     def schema_view(self) -> ExportableSchemaView:
         """Get a schema view instance from the metadata model."""
+        schema_view = self._schema_view
+        if schema_view is None:
+            schema_view = ExportableSchemaView(self)
+            self._schema_view = schema_view
+        return schema_view
 
-        return schema_view_from_model(self)
-
-    def copy(self) -> MetadataModel:
-        """Copy the model."""
-
-        return deepcopy(self)
+    def __deepcopy__(self, memo: Any):
+        """Return a deep copy of the model."""
+        schema_view = self._schema_view
+        self._schema_view = None
+        copied_model = deepcopy(super())
+        self._schema_view = schema_view
+        return copied_model
 
     def __eq__(self, other: object):
         """For comparisons."""
@@ -141,11 +141,6 @@ def temporary_yaml_path(self) -> Generator[Path, None, None]:
             file.flush()
             yield Path(file.name)
 
-    def __hash__(self):
-        """Return a hash of the model."""
-
-        return hash(self.as_json())
-
 
 class ExportableSchemaView(SchemaView):
     """Extend the SchemaView by adding a method for exporting a MetadataModel."""

metldata/transform/handling.py

@@ -32,7 +32,7 @@
 )
 
 
-class WorkflowConfigMissmatchError(RuntimeError):
+class WorkflowConfigMismatchError(RuntimeError):
     """Raised when the provided workflow config does not match the config class of the
     workflow definition.
     """
@@ -140,11 +140,11 @@ def check_workflow_config(
     definition.
 
     Raises:
-        WorkflowConfigMissmatchError:
+        WorkflowConfigMismatchError:
     """
 
     if workflow_config.schema_json() == workflow_definition.schema_json():
-        raise WorkflowConfigMissmatchError(
+        raise WorkflowConfigMismatchError(
             workflow_definition=workflow_definition, workflow_config=workflow_config
         )
 

scripts/update_all.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python3
+
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""Run all update scripts that are present in the repository in the correct order"""
+
+try:
+    from scripts.update_template_files import main as update_template
+except ImportError:
+    pass
+else:
+    print("Pulling in updates from template repository")
+    update_template()
+
+try:
+    from scripts.update_config_docs import main as update_config
+except ImportError:
+    pass
+else:
+    print("Updating config docs")
+    update_config()
+
+try:
+    from scripts.update_openapi_docs import main as update_openapi
+except ImportError:
+    pass
+else:
+    print("Updating OpenAPI docs")
+    update_openapi()
+
+try:
+    from scripts.update_readme import main as update_readme
+except ImportError:
+    pass
+else:
+    print("Updating README")
+    update_readme()

setup.cfg

@@ -35,10 +35,11 @@ zip_safe = False
 include_package_data = True
 packages = find:
 install_requires =
-    hexkit[mongodb]==0.10.0
-    ghga-service-commons[api,auth]==0.4.2
+    hexkit[mongodb]==0.10.2
+    ghga-service-commons[api,auth]==0.4.3
     typer==0.7.0
-    linkml-runtime==1.4.2
+    linkml==1.5.6
+    linkml-runtime==1.5.5
     linkml-validator==0.4.5
 
 python_requires = >= 3.9

tests/artifact_rest/test_api_factory.py

@@ -22,13 +22,15 @@
 from fastapi import FastAPI
 from ghga_service_commons.api.testing import AsyncTestClient
 from hexkit.protocols.dao import DaoFactoryProtocol
-from hexkit.providers.mongodb.testutils import mongodb_fixture  # noqa: F401
-from hexkit.providers.mongodb.testutils import MongoDbFixture
 
 from metldata.artifacts_rest.api_factory import rest_api_factory
 from metldata.artifacts_rest.artifact_info import ArtifactInfo
 from tests.artifact_rest.test_load_artifacts import load_example_artifact_resources
 from tests.fixtures.artifact_info import EXAMPLE_ARTIFACT_INFOS, MINIMAL_ARTIFACT_INFO
+from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
+    MongoDbFixture,
+    mongodb_fixture,
+)
 
 
 @pytest.mark.asyncio
@@ -48,7 +50,9 @@ async def get_example_app_client(
 
 
 @pytest.mark.asyncio
-async def test_artifacts_info_endpoint(mongodb_fixture: MongoDbFixture):  # noqa: F811
+async def test_artifacts_info_endpoint(
+    mongodb_fixture: MongoDbFixture,  # noqa: F811
+):
     """Test happy path of using the artifacts info endpoint."""
 
     expected_infos = EXAMPLE_ARTIFACT_INFOS
@@ -99,7 +103,8 @@ async def test_get_artifact_resource_endpoint(
     class_name = "File"
     resource_id = "test_sample_01_R1"
     async with await get_example_app_client(
-        dao_factory=mongodb_fixture.dao_factory, artifact_infos=[MINIMAL_ARTIFACT_INFO]
+        dao_factory=mongodb_fixture.dao_factory,
+        artifact_infos=[MINIMAL_ARTIFACT_INFO],
     ) as client:
         response = await client.get(
             f"/artifacts/{artifact_name}/classes/{class_name}/resources/{resource_id}"

tests/artifact_rest/test_load_artifacts.py

@@ -18,14 +18,16 @@
 
 import pytest
 from hexkit.protocols.dao import DaoFactoryProtocol
-from hexkit.providers.mongodb.testutils import mongodb_fixture  # noqa: F401
-from hexkit.providers.mongodb.testutils import MongoDbFixture
 
 from metldata.artifacts_rest.artifact_dao import ArtifactDaoCollection
 from metldata.artifacts_rest.load_resources import load_artifact_resources
 from metldata.artifacts_rest.models import ArtifactResource
 from tests.fixtures.artifact_info import MINIMAL_ARTIFACT_INFO
 from tests.fixtures.metadata import VALID_MINIMAL_METADATA_EXAMPLE
+from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
+    MongoDbFixture,
+    mongodb_fixture,
+)
 
 
 async def load_example_artifact_resources(
@@ -51,7 +53,9 @@ async def load_example_artifact_resources(
 
 
 @pytest.mark.asyncio
-async def test_load_artifact_resources(mongodb_fixture: MongoDbFixture):  # noqa: F811
+async def test_load_artifact_resources(
+    mongodb_fixture: MongoDbFixture,  # noqa: F811
+):
     """Test happy path of using load_artifact_resources function."""
 
     dao_collection = await load_example_artifact_resources(

tests/artifact_rest/test_query_resources.py

@@ -17,16 +17,20 @@
 """Test the query_resource module."""
 
 import pytest
-from hexkit.providers.mongodb.testutils import mongodb_fixture  # noqa: F401
-from hexkit.providers.mongodb.testutils import MongoDbFixture
 
 from metldata.artifacts_rest.query_resources import query_artifact_resource
 from tests.artifact_rest.test_load_artifacts import load_example_artifact_resources
 from tests.fixtures.artifact_info import MINIMAL_ARTIFACT_INFO
+from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
+    MongoDbFixture,
+    mongodb_fixture,
+)
 
 
 @pytest.mark.asyncio
-async def test_query_artifact_resource(mongodb_fixture: MongoDbFixture):  # noqa: F811
+async def test_query_artifact_resource(
+    mongodb_fixture: MongoDbFixture,  # noqa: F811
+):
     """Test happy path of using the query_artifact_resource function."""
 
     # load example resources and prepare client:

tests/conftest.py

@@ -0,0 +1,24 @@
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+""""Shared fixtures"""
+
+from hexkit.providers.mongodb.testutils import get_mongodb_fixture
+from hexkit.providers.testing.utils import get_event_loop
+
+event_loop = get_event_loop(scope="session")
+
+mongodb_session = get_mongodb_fixture(scope="session")

tests/fixtures/event_handling.py

@@ -29,7 +29,7 @@
 )
 
 
-class EventExpectationMissmatch(RuntimeError):
+class EventExpectationMismatch(RuntimeError):
     """Raised when expected events where not found."""
 
     def __init__(self, expected_events: set[str], consumed_events: set[str]):
@@ -49,7 +49,7 @@ def expect_events(self, expected_events: list[Event]) -> None:
         """Check if the events expected to be published can be consumed.
 
         Raises:
-            EventExpectationMissmatch: If the expected events are not consumed.
+            EventExpectationMismatch: If the expected events are not consumed.
         """
 
         topics = sorted({event.topic for event in expected_events})
@@ -66,7 +66,7 @@ def expect_events(self, expected_events: list[Event]) -> None:
         expected_event_jsons = {event.json() for event in expected_events}
 
         if expected_event_jsons != observed_event_jsons:
-            raise EventExpectationMissmatch(
+            raise EventExpectationMismatch(
                 expected_events=observed_event_jsons,
                 consumed_events=expected_event_jsons,
             )

tests/fixtures/mongodb.py

@@ -0,0 +1,29 @@
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# for the German Human Genome-Phenome Archive (GHGA)
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+"""Fixture for using the MongoDB."""
+
+from hexkit.providers.mongodb.testutils import MongoDbFixture
+from pytest import fixture
+
+
+@fixture
+def mongodb_fixture(  # pylint: disable=redefined-outer-name
+    mongodb_session: MongoDbFixture,
+) -> MongoDbFixture:
+    """Fixture that gets an empty MongoDB."""
+    mongodb_session.empty_collections()
+    return mongodb_session

tests/load/test_main.py

@@ -19,15 +19,17 @@
 import pytest
 from ghga_service_commons.api.testing import AsyncTestClient
 from hexkit.protocols.dao import ResourceNotFoundError
-from hexkit.providers.mongodb.testutils import mongodb_fixture  # noqa: F401
-from hexkit.providers.mongodb.testutils import MongoDbFixture
 
 from metldata.artifacts_rest.artifact_dao import ArtifactDaoCollection
 from metldata.artifacts_rest.models import ArtifactInfo
 from metldata.load.auth import generate_token, generate_token_and_hash
 from metldata.load.config import ArtifactLoaderAPIConfig
 from metldata.load.main import get_app
 from tests.fixtures.artifact_info import EXAMPLE_ARTIFACT_INFOS
+from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
+    MongoDbFixture,
+    mongodb_fixture,
+)
 from tests.fixtures.workflows import EXAMPLE_ARTIFACTS
 
 
@@ -81,7 +83,8 @@ async def test_load_artifacts_endpoint_happy(
     }
 
     dao_collection = await ArtifactDaoCollection.construct(
-        dao_factory=mongodb_fixture.dao_factory, artifact_infos=EXAMPLE_ARTIFACT_INFOS
+        dao_factory=mongodb_fixture.dao_factory,
+        artifact_infos=EXAMPLE_ARTIFACT_INFOS,
     )
     dao = await dao_collection.get_dao(
         artifact_name=expected_artifact_name, class_name=expected_resource_class