Fix status code for missing IVA ID

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
 
 ENV PYTHONUNBUFFERED 1
 

.pre-commit-config.yaml

@@ -45,7 +45,7 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.2
+    rev: v0.4.9
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.pyproject_generation/pyproject_custom.toml

@@ -1,11 +1,11 @@
 [project]
 name = "ars"
-version = "2.0.1"
+version = "2.0.2"
 description = "Access Request Service"
 dependencies = [
-    "ghga-event-schemas~=3.1.0",
-    "ghga-service-commons[api,auth]>=3.1.3",
-    "hexkit[mongodb,akafka]>=3.0.0",
+    "ghga-event-schemas~=3.3.0",
+    "ghga-service-commons[api,auth]>=3.1.5",
+    "hexkit[mongodb,akafka]>=3.2.2",
     "httpx>=0.27",
     "typer>=0.12",
 ]

.template/static_files.txt

@@ -15,6 +15,8 @@
 
 scripts/script_utils/__init__.py
 scripts/script_utils/cli.py
+scripts/script_utils/deps.py
+scripts/script_utils/lock_deps.py
 
 scripts/__init__.py
 scripts/update_all.py

README.md

@@ -16,21 +16,21 @@ We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/access-request-service):
 ```bash
-docker pull ghga/access-request-service:2.0.1
+docker pull ghga/access-request-service:2.0.2
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/access-request-service:2.0.1 .
+docker build -t ghga/access-request-service:2.0.2 .
 ```
 
 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/access-request-service:2.0.1 --help
+docker run -p 8080:8080 ghga/access-request-service:2.0.2 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:

lock/requirements-dev-template.in

@@ -29,4 +29,4 @@ setuptools>=69.5
 # required since switch to pyproject.toml and pip-tools
 tomli_w>=1.0
 
-uv>=0.1.39
+uv>=0.1.44

openapi.yaml

@@ -159,7 +159,7 @@ components:
 info:
   description: A service managing access requests for the GHGA Data Portal
   title: Access Request Service
-  version: 2.0.1
+  version: 2.0.2
 openapi: 3.1.0
 paths:
   /access-requests:

pyproject.toml

@@ -21,12 +21,12 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "ars"
-version = "2.0.1"
+version = "2.0.2"
 description = "Access Request Service"
 dependencies = [
-    "ghga-event-schemas~=3.1.0",
-    "ghga-service-commons[api,auth]>=3.1.3",
-    "hexkit[mongodb,akafka]>=3.0.0",
+    "ghga-event-schemas~=3.3.0",
+    "ghga-service-commons[api,auth]>=3.1.5",
+    "hexkit[mongodb,akafka]>=3.2.2",
     "httpx>=0.27",
     "typer>=0.12",
 ]

scripts/check_license.py

@@ -40,7 +40,7 @@
     ".git",
     ".github",
     ".flake8",
-    ".gitignore" ".pre-commit-config.yaml",
+    ".gitignore",
     ".mypy_cache",
     ".mypy.ini",
     ".pylintrc",
@@ -115,8 +115,8 @@
 See the License for the specific language governing permissions and
 limitations under the License."""
 
-# A list of all chars that may be used to introduce a comment:
-COMMENT_CHARS = ["#"]
+# A list of strings that may be used to introduce a line comment:
+LINE_COMMENTS = ["#"]
 
 AUTHOR = """Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 for the German Human Genome-Phenome Archive (GHGA)"""
@@ -202,24 +202,25 @@ def get_target_files(
         file_
         for file_ in all_files
         if not (
-            any([file_.is_relative_to(excl) for excl in exclude_normalized])
-            or any([str(file_).endswith(ending) for ending in exclude_endings])
-            or any([re.match(pattern, str(file_)) for pattern in exclude_pattern])
+            any(file_.is_relative_to(excl) for excl in exclude_normalized)
+            or any(str(file_).endswith(ending) for ending in exclude_endings)
+            or any(re.match(pattern, str(file_)) for pattern in exclude_pattern)
         )
     ]
     return target_files
 
 
-def normalized_line(line: str, chars_to_trim: list[str] = COMMENT_CHARS) -> str:
-    norm_line = line.strip()
+def normalized_line(line: str, line_comments: list[str] = LINE_COMMENTS) -> str:
+    line = line.strip()
+    for line_comment in line_comments:
+        line_without_comment = line.removeprefix(line_comment)
+        if line_without_comment != line:
+            line = line_without_comment.lstrip()
+            break
+    return line
 
-    for char in chars_to_trim:
-        norm_line = norm_line.strip(char)
 
-    return norm_line.strip("\n").strip("\t").strip()
-
-
-def normalized_text(text: str, chars_to_trim: list[str] = COMMENT_CHARS) -> str:
+def normalized_text(text: str, line_comments: list[str] = LINE_COMMENTS) -> str:
     "Normalize a license header text."
     lines = text.split("\n")
 
@@ -231,7 +232,7 @@ def normalized_text(text: str, chars_to_trim: list[str] = COMMENT_CHARS) -> str:
         if stripped_line.startswith("#!"):
             continue
 
-        norm_line = normalized_line(stripped_line)
+        norm_line = normalized_line(stripped_line, line_comments=line_comments)
 
         # exclude empty lines:
         if norm_line == "":
@@ -249,30 +250,25 @@ def format_copyright_template(copyright_template: str, author: str) -> str:
     return normalized_text(copyright_template.replace("{author}", author))
 
 
-def is_commented_line(line: str, comment_chars: list[str] = COMMENT_CHARS) -> bool:
+def is_commented_line(line: str, line_comments: list[str] = LINE_COMMENTS) -> bool:
     """Checks whether a line is a comment."""
-    line_stripped = line.strip()
-    for comment_char in comment_chars:
-        if line_stripped.startswith(comment_char):
-            return True
-
-    return False
+    return line.lstrip().startswith(tuple(line_comments))
 
 
 def is_empty_line(line: str) -> bool:
     """Checks whether a line is empty."""
-    return line.strip("\n").strip("\t").strip() == ""
+    return not line.strip()
 
 
-def get_header(file_path: Path, comment_chars: list[str] = COMMENT_CHARS):
+def get_header(file_path: Path, line_comments: list[str] = LINE_COMMENTS):
     """Extracts the header from a file and normalizes it."""
     header_lines: list[str] = []
 
     try:
         with open(file_path) as file:
             for line in file:
                 if is_commented_line(
-                    line, comment_chars=comment_chars
+                    line, line_comments=line_comments
                 ) or is_empty_line(line):
                     header_lines.append(line)
                 else:
@@ -282,7 +278,7 @@ def get_header(file_path: Path, comment_chars: list[str] = COMMENT_CHARS):
 
     # normalize the lines:
     header = "".join(header_lines)
-    return normalized_text(header, chars_to_trim=comment_chars)
+    return normalized_text(header, line_comments=line_comments)
 
 
 def validate_year_string(year_string: str, min_year: int = MIN_YEAR) -> bool:
@@ -317,7 +313,7 @@ def check_copyright_notice(
     global_copyright: GlobalCopyrightNotice,
     copyright_template: str = COPYRIGHT_TEMPLATE,
     author: str = AUTHOR,
-    comment_chars: list[str] = COMMENT_CHARS,
+    line_comments: list[str] = LINE_COMMENTS,
     min_year: int = MIN_YEAR,
 ) -> bool:
     """Checks the specified copyright text against a template.
@@ -385,7 +381,7 @@ def check_file_headers(
     exclude: list[str] = EXCLUDE,
     exclude_endings: list[str] = EXCLUDE_ENDINGS,
     exclude_pattern: list[str] = EXCLUDE_PATTERN,
-    comment_chars: list[str] = COMMENT_CHARS,
+    line_comments: list[str] = LINE_COMMENTS,
     min_year: int = MIN_YEAR,
 ) -> tuple[list[Path], list[Path]]:
     """Check files for presence of a license header and verify that
@@ -429,13 +425,13 @@ def check_file_headers(
 
     for target_file in target_files:
         try:
-            header = get_header(target_file, comment_chars=comment_chars)
+            header = get_header(target_file, line_comments=line_comments)
             if check_copyright_notice(
                 copyright=header,
                 global_copyright=global_copyright,
                 copyright_template=copyright_template,
                 author=author,
-                comment_chars=comment_chars,
+                line_comments=line_comments,
                 min_year=min_year,
             ):
                 passed_files.append(target_file)
@@ -453,7 +449,7 @@ def check_license_file(
     global_copyright: GlobalCopyrightNotice,
     copyright_template: str = COPYRIGHT_TEMPLATE,
     author: str = AUTHOR,
-    comment_chars: list[str] = COMMENT_CHARS,
+    line_comments: list[str] = LINE_COMMENTS,
     min_year: int = MIN_YEAR,
 ) -> bool:
     """Currently only checks if the copyright notice in the
@@ -495,7 +491,7 @@ def check_license_file(
         global_copyright=global_copyright,
         copyright_template=copyright_template,
         author=author,
-        comment_chars=comment_chars,
+        line_comments=line_comments,
         min_year=min_year,
     )
 

scripts/script_utils/deps.py

@@ -15,12 +15,12 @@
 #
 """Contains utils for working with dependencies, lock files, etc."""
 
+import tomllib
 from copy import deepcopy
 from pathlib import Path
 from typing import Any
 
 import stringcase
-import tomli
 
 
 def exclude_from_dependency_list(*, package_name: str, dependencies: list) -> list:
@@ -69,7 +69,7 @@ def remove_self_dependencies(pyproject: dict) -> dict:
 def get_modified_pyproject(pyproject_toml_path: Path) -> dict[str, Any]:
     """Get a copy of pyproject.toml with any self-referencing dependencies removed."""
     with open(pyproject_toml_path, "rb") as pyproject_toml:
-        pyproject = tomli.load(pyproject_toml)
+        pyproject = tomllib.load(pyproject_toml)
 
     modified_pyproject = remove_self_dependencies(pyproject)
     return modified_pyproject

src/ars/adapters/inbound/fastapi_/routes.py

@@ -157,7 +157,10 @@ async def patch_access_request(
         raise HTTPException(status_code=403, detail=str(exc)) from exc
     except repository.AccessRequestNotFoundError as exc:
         raise HTTPException(status_code=404, detail=str(exc)) from exc
-    except repository.AccessRequestInvalidState as exc:
+    except (
+        repository.AccessRequestInvalidState,
+        repository.AccessRequestMissingIva,
+    ) as exc:
         raise HTTPException(status_code=422, detail=str(exc)) from exc
     except Exception as exc:
         log.error("Could not modify access request: %s", exc)

tests/conftest.py

@@ -16,22 +16,13 @@
 
 """Setup for testing the access request service."""
 
-import pytest
-from hexkit.providers.akafka.testutils import get_kafka_fixture
-from hexkit.providers.mongodb.testutils import get_mongodb_fixture
-
-from .fixtures import JointFixture, get_joint_fixture
-
-
-@pytest.fixture(autouse=True)
-def reset_state(joint_fixture: JointFixture):
-    """Clear joint_fixture state before tests.
-
-    This is a function-level fixture because it needs to run in each test.
-    """
-    joint_fixture.mongodb.empty_collections()
-
-
-kafka_fixture = get_kafka_fixture("session")
-mongodb_fixture = get_mongodb_fixture("session")
-joint_fixture = get_joint_fixture("session")
+from hexkit.providers.akafka.testutils import (  # noqa: F401
+    kafka_container_fixture,
+    kafka_fixture,
+)
+from hexkit.providers.mongodb.testutils import (  # noqa: F401
+    mongodb_container_fixture,
+    mongodb_fixture,
+)
+
+from .fixtures import joint_fixture  # noqa: F401

tests/fixtures/__init__.py

@@ -24,7 +24,6 @@
     generate_jwk,
     sign_and_serialize_token,
 )
-from hexkit.custom_types import PytestScope
 from hexkit.providers.akafka.testutils import KafkaFixture
 from hexkit.providers.mongodb.testutils import MongoDbFixture
 from pytest import fixture
@@ -38,7 +37,7 @@
     "AUTH_CLAIMS_STEWARD",
     "fixture_auth_headers_doe",
     "fixture_auth_headers_steward",
-    "get_joint_fixture",
+    "joint_fixture",
     "JointFixture",
     "headers_for_token",
 ]
@@ -91,8 +90,9 @@ class JointFixture(NamedTuple):
     rest_client: AsyncTestClient
 
 
-async def joint_fixture_function(
-    mongodb_fixture: MongoDbFixture, kafka_fixture: KafkaFixture
+@pytest_asyncio.fixture()
+async def joint_fixture(
+    mongodb: MongoDbFixture, kafka: KafkaFixture
 ) -> AsyncGenerator[JointFixture, None]:
     """A fixture that embeds all other fixtures for API-level integration testing
 
@@ -101,8 +101,8 @@ async def joint_fixture_function(
     config = Config(
         auth_key=AUTH_KEY_PAIR.export_public(),  # pyright: ignore
         download_access_url="http://access",
-        **kafka_fixture.config.model_dump(),
-        **mongodb_fixture.config.model_dump(),
+        **kafka.config.model_dump(),
+        **mongodb.config.model_dump(),
     )
     async with prepare_core(config=config) as core:
         async with (
@@ -111,12 +111,7 @@ async def joint_fixture_function(
             async with AsyncTestClient(app=app) as rest_client:
                 yield JointFixture(
                     config=config,
-                    kafka=kafka_fixture,
-                    mongodb=mongodb_fixture,
+                    kafka=kafka,
+                    mongodb=mongodb,
                     rest_client=rest_client,
                 )
-
-
-def get_joint_fixture(scope: PytestScope = "function"):
-    """Produce a joint fixture with desired scope"""
-    return pytest_asyncio.fixture(joint_fixture_function, scope=scope)

tests/test_access_grants.py

@@ -27,7 +27,7 @@
 
 from ars.adapters.outbound.http import AccessGrantsAdapter, AccessGrantsConfig
 
-pytestmark = pytest.mark.asyncio(scope="session")
+pytestmark = pytest.mark.asyncio()
 
 
 DOWNLOAD_ACCESS_URL = "http://test-access:1234"