Merge pull request #31 from BAMresearch/29-testcases-jmp

Test changes and clean up

Author: LucasZimm

openbis_upload_helper/app/utils/utils.py

@@ -20,7 +20,6 @@
 from openbis_upload_helper.uploader.entry_points import get_entry_point_parsers
 
 
-
 def get_cipher_suite():
     """Return a Fernet instance using the configured secret key.
 

pyproject.toml

@@ -1,3 +1,79 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "setuptools-scm>=8.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "openbis_upload_helper"
+version = "0.1.0"
+description = "The openBIS Upload Helper is a tool to parse files and extract their relevant metadata into objects and vocabularies in openBIS."
+readme = "README.md"
+
+license = { text = "Not open source" }
+authors = [
+  { name = "Jose M. Pizarro", email = "jose.pizarro-blanco@bam.de" },
+]
+requires-python = ">=3.12.12"
+dependencies = [
+    "argon2-cffi==25.1.0",
+    "celery==5.6.0",
+    "crispy-bootstrap5==2025.6",
+    "django==5.2.9",
+    "django-allauth[mfa]==65.13.1",
+    "django-anymail[mailgun]==14.0",
+    "django-celery-beat==2.8.1",
+    "django-crispy-forms==2.5",
+    "django-environ==0.12.0",
+    "django-model-utils==5.0.0",
+    "django-redis==6.0.0",
+    "gunicorn==23.0.0",
+    "hiredis==3.3.0",
+    "pillow==12.0.0",
+    "psycopg[binary]==3.3.2",
+    "python-slugify==8.0.4",
+    "redis==7.1.0",
+    "sentry-sdk==2.48.0",
+    "uvicorn-worker==0.4.0",
+    "uvicorn[standard]==0.38.0",
+    "whitenoise==6.11.0",
+    "bam-masterdata>=0.8.4",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/BAMresearch/openbis-upload-helper"
+"Bug Tracker" = "https://github.com/BAMresearch/openbis-upload-helper/issues"
+
+[project.optional-dependencies]
+dev = [
+    "coverage==7.13.0",
+    "django-coverage-plugin==3.2.0",
+    "django-debug-toolbar==6.1.0",
+    "django-extensions==4.1",
+    "django-stubs[compatible-mypy]==5.2.8",
+    "djlint==1.36.4",
+    "factory-boy==3.3.2",
+    "ipdb==0.13.13",
+    "mypy==1.19.1",
+    "pre-commit==4.5.1",
+    "psycopg[binary]==3.3.2",
+    "pytest==9.0.2",
+    "pytest-cov",
+    "pytest-django==4.11.1",
+    "pytest-sugar==1.1.1",
+    "pytest-timeout",
+    "ruff==0.14.10",
+    "sphinx==9.0.4",
+    "sphinx-autobuild==2025.8.25",
+    "structlog==24.4.0",
+    "watchfiles==1.1.1",
+    "werkzeug[watchdog]==3.1.4",
+    "ruff",
+]
+parsers = [
+    "masterdata-parser-example@git+https://github.com/BAMresearch/masterdata-parser-example.git@main",
+]
+
+# "sigmabam2openbis@git+https://github.com/BAMresearch/sigmabam2openbis.git@main"
+
 # ==== pytest ====
 [tool.pytest.ini_options]
 minversion = "6.0"
@@ -6,8 +82,6 @@ python_files = [
     "tests.py",
     "test_*.py",
 ]
-DJANGO_SETTINGS_MODULE = "config.settings.test"
-
 
 # ==== Coverage ====
 [tool.coverage.run]
@@ -91,68 +165,27 @@ indent-width = 4
 
 [tool.ruff.lint]
 select = [
-    "F",
-    "E",
-    "W",
-    "C90",
-    "I",
-    "N",
-    "UP",
-    "YTT",
-    # "ANN", # flake8-annotations: we should support this in the future but 100+ errors atm
-    "ASYNC",
-    "S",
-    "BLE",
-    "FBT",
-    "B",
-    "A",
-    "COM",
-    "C4",
-    "DTZ",
-    "T10",
-    "DJ",
-    "EM",
-    "EXE",
-    "FA",
-    'ISC',
-    "ICN",
-    "G",
-    'INP',
-    'PIE',
-    "T20",
-    'PYI',
-    'PT',
-    "Q",
-    "RSE",
-    "RET",
-    "SLF",
-    "SLOT",
-    "SIM",
-    "TID",
-    "TC",
-    "INT",
-    # "ARG", # Unused function argument
-    "PTH",
-    "ERA",
-    "PD",
-    "PGH",
-    "PL",
-    "TRY",
-    "FLY",
-    # "NPY",
-    # "AIR",
-    "PERF",
-    # "FURB",
-    # "LOG",
-    "RUF",
+    "E", # pycodestyle
+    "PL", # pylint
+    "F", # Pyflakes
+    "UP", # pyupgrade
+    "I", # isort
 ]
 ignore = [
-    "S101", # Use of assert detected https://docs.astral.sh/ruff/rules/assert/
-    "RUF012", # Mutable class attributes should be annotated with `typing.ClassVar`
-    "SIM102", # sometimes it's better to nest
-    # of types for comparison.
-    # Deactivated because it can make the code slow:
-    # https://github.com/astral-sh/ruff/issues/7871
+    "F401", # Module imported but unused
+    "E501", # Line too long ({width} > {limit} characters)
+    "E701", # Multiple statements on one line (colon)
+    "E731", # Do not assign a lambda expression, use a def
+    "E402",  # Module level import not at top of file
+    "PLR0911", # Too many return statements
+    "PLR0912", # Too many branches
+    "PLR0913", # Too many arguments in function definition
+    "PLR0915", # Too many statements
+    "PLR2004", # Magic value used instead of constant
+    "PLW0603", # Using the global statement
+    "PLW2901", # redefined-loop-name
+    "PLR1714", # consider-using-in
+    "PLR5501", # else-if-used
 ]
 fixable = ["ALL"]
 # Allow unused variables when underscore-prefixed.
@@ -161,89 +194,7 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 [tool.ruff.lint.isort]
 force-single-line = true
 
-[dependency-groups]
-dev = [
-    "coverage==7.13.0",
-    "django-coverage-plugin==3.2.0",
-    "django-debug-toolbar==6.1.0",
-    "django-extensions==4.1",
-    "django-stubs[compatible-mypy]==5.2.8",
-    "djlint==1.36.4",
-    "factory-boy==3.3.2",
-    "ipdb==0.13.13",
-    "mypy==1.19.1",
-    "pre-commit==4.5.1",
-    "psycopg[binary]==3.3.2",
-    "pytest==9.0.2",
-    "pytest-django==4.11.1",
-    "pytest-sugar==1.1.1",
-    "ruff==0.14.10",
-    "sphinx==9.0.4",
-    "sphinx-autobuild==2025.8.25",
-    "watchfiles==1.1.1",
-    "werkzeug[watchdog]==3.1.4",
-]
-
-[project]
-name = "openbis_upload_helper"
-version = "0.1.0"
-description = "The openBIS Upload Helper is a tool to parse files and extract their relevant metadata into objects and vocabularies in openBIS."
-readme = "README.md"
-
-license = { text = "Not open source" }
-authors = [
-  { name = "Jose M. Pizarro", email = "jose.pizarro-blanco@bam.de" },
-]
-requires-python = ">=3.12.12"
-dependencies = [
-    "argon2-cffi==25.1.0",
-    "celery==5.6.0",
-    "crispy-bootstrap5==2025.6",
-    "django==5.2.9",
-    "django-allauth[mfa]==65.13.1",
-    "django-anymail[mailgun]==14.0",
-    "django-celery-beat==2.8.1",
-    "django-crispy-forms==2.5",
-    "django-environ==0.12.0",
-    "django-model-utils==5.0.0",
-    "django-redis==6.0.0",
-    "gunicorn==23.0.0",
-    "hiredis==3.3.0",
-    "pillow==12.0.0",
-    "psycopg[binary]==3.3.2",
-    "python-slugify==8.0.4",
-    "redis==7.1.0",
-    "sentry-sdk==2.48.0",
-    "uvicorn-worker==0.4.0",
-    "uvicorn[standard]==0.38.0",
-    "whitenoise==6.11.0",
-    "bam-masterdata>=0.8.4",
-]
-
-[build-system]
-requires = ["setuptools>=61.0.0", "setuptools-scm>=8.0"]
-build-backend = "setuptools.build_meta"
-
-[project.urls]
-"Homepage" = "https://github.com/BAMresearch/openbis-upload-helper"
-"Bug Tracker" = "https://github.com/BAMresearch/openbis-upload-helper/issues"
-
-[project.optional-dependencies]
-dev = [
-    "mypy==1.18.1",
-    "django-stubs",
-    "pytest",
-    "pytest-timeout",
-    "pytest-cov",
-    "structlog==24.4.0",
-]
-parsers = [
-    "masterdata-parser-example@git+https://github.com/BAMresearch/masterdata-parser-example.git@main",
-]
-
-# "sigmabam2openbis@git+https://github.com/BAMresearch/sigmabam2openbis.git@main"
-
-
+# this is entirely optional, you can remove this if you wish to
 [tool.ruff.format]
 # use double quotes for strings.
 quote-style = "double"

tests/conftest.py

@@ -2,6 +2,7 @@
 import os
 from unittest.mock import MagicMock
 
+import django
 import pytest
 from bam_masterdata.logger import log_storage
 from bam_masterdata.metadata.definitions import ObjectTypeDef
@@ -27,6 +28,20 @@ def pytest_internalerror(excinfo):
         raise excinfo.value
 
 
+@pytest.fixture(scope="session", autouse=True)
+def configure_django_settings():
+    os.environ.setdefault("DJANGO_SETTINGS_MODULE", "config.settings.test")
+    if not settings.configured:
+        django.setup()
+    settings.ROOT_URLCONF = "openbis_upload_helper.app.urls"
+    settings.EMAIL_BACKEND = "django.core.mail.backends.locmem.EmailBackend"
+    # pytest-django clears django.core.mail.outbox automatically; ensure it exists
+    from django.core import mail  # noqa: PLC0415
+
+    if not hasattr(mail, "outbox"):
+        mail.outbox = []
+
+
 @pytest.fixture(autouse=True)
 def cleared_log_storage():
     """Fixture to clear the log storage before each test."""
@@ -335,3 +350,34 @@ def set_secret_encryption_key():
     settings.SECRET_ENCRYPTION_KEY = base64.urlsafe_b64encode(
         Fernet.generate_key(),
     ).decode()
+
+
+class DummySession(dict):
+    def __init__(self):
+        super().__init__()
+        self.flushed = False
+
+    def flush(self):
+        self.flushed = True
+        self.clear()
+
+
+@pytest.fixture
+def attach_session():
+    def _attach(request):
+        request.session = DummySession()
+        return request
+
+    return _attach
+
+
+@pytest.fixture
+def make_uploaded_file():
+    def _make(name="file.txt", content=b"x"):
+        uploaded_file = MagicMock()
+        uploaded_file.name = name
+        uploaded_file.size = len(content)
+        uploaded_file.chunks.return_value = [content]
+        return uploaded_file
+
+    return _make

tests/entry_points/test_load.py

@@ -1,7 +1,21 @@
+from types import SimpleNamespace
+from unittest.mock import patch
+
 from openbis_upload_helper.uploader.entry_points import get_entry_point_parsers
 
 
-def test_get_entry_point_parsers():
+@patch("importlib.metadata.entry_points")
+def test_get_entry_point_parsers(mock_entry_points):
+    mock_entry_points.return_value = [
+        SimpleNamespace(
+            name="masterdata_parser_example_entry_point",
+            load=lambda: {
+                "name": "MasterdataParserExample",
+                "description": "An example parser for masterdata.",
+                "parser_class": object(),
+            },
+        ),
+    ]
     parsers = get_entry_point_parsers()
     assert isinstance(parsers, dict)
     assert "masterdata_parser_example_entry_point" in parsers