diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e62d059..6a486de 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -11,13 +11,13 @@ on: jobs: tests: name: "Python ${{ matrix.python-version }}" - runs-on: "ubuntu-latest" + runs-on: ubuntu-latest env: - USING_COVERAGE: '3.7,3.8,3.10' + USING_COVERAGE: '3.7,3.8,3.10,3.11,3.12' strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] + python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v3 @@ -60,7 +60,7 @@ jobs: # Install dependencies. `--no-root` means "install all dependencies but not the project # itself", which is what you want to avoid caching _your_ code. The `if` statement # ensures this only runs on a cache miss. - - run: poetry install --no-interaction --no-root + - run: poetry install --no-interaction --no-root --with dev if: steps.cache-deps.outputs.cache-hit != 'true' # Now install _your_ project. This isn't necessary for many types of projects -- particularly diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 61b9574..6e1dd5c 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -9,14 +9,14 @@ Developer Setup ``` git clone https://github.com/mdsol/rwslib ``` -2. Create a Virtual Env for the Local instance +2. Install poetry and start a shell ```bash - $ python -m venv venv - $ source venv/bin/activate + $ pip install poetry + $ poetry shell ``` 3. Install the development dependencies ```bash - $ pip install -r requirements-dev.txt + $ poetry install --with dev ``` 4. Enjoy !!! diff --git a/poetry.lock b/poetry.lock index eb7aa45..249258c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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"sha256:ce42d816b81b68506614c11e8937d3aa9e41007ceb50bfdcb0749b921bf646c7"}, - {file = "pytz-2023.3.post1.tar.gz", hash = "sha256:7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b"}, + {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"}, + {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"}, ] [[package]] @@ -786,22 +866,6 @@ urllib3 = ">=1.21.1,<3" socks = ["PySocks (>=1.5.6,!=1.5.7)"] use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] -[[package]] -name = "setuptools" -version = "68.2.2" -description = "Easily download, build, install, upgrade, and uninstall Python packages" -optional = false -python-versions = ">=3.8" -files = [ - {file = "setuptools-68.2.2-py3-none-any.whl", hash = "sha256:b454a35605876da60632df1a60f736524eb73cc47bbc9f3f1ef1b644de74fd2a"}, - {file = "setuptools-68.2.2.tar.gz", hash = "sha256:4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87"}, -] - -[package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"] -testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] -testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"] - [[package]] name = "six" version = "1.16.0" @@ -963,17 +1027,6 @@ files = [ lint = ["docutils-stubs", "flake8", "mypy"] test = ["pytest"] -[[package]] -name = "toml" -version = "0.10.2" -description = "Python Library for Tom's Obvious, Minimal Language" -optional = false -python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" -files = [ - {file = "toml-0.10.2-py2.py3-none-any.whl", hash = "sha256:806143ae5bfb6a3c6e736a764057db0e6a0e05e338b5630894a5f779cabb4f9b"}, - {file = "toml-0.10.2.tar.gz", hash = "sha256:b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f"}, -] - [[package]] name = "tomli" version = "2.0.1" @@ -1014,25 +1067,6 @@ virtualenv = ">=20.24.1" docs = ["furo (>=2023.5.20)", "sphinx (>=7.0.1)", "sphinx-argparse-cli (>=1.11.1)", "sphinx-autodoc-typehints (>=1.23.3,!=1.23.4)", "sphinx-copybutton (>=0.5.2)", "sphinx-inline-tabs (>=2023.4.21)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] testing = ["build[virtualenv] (>=0.10)", "covdefaults (>=2.3)", "detect-test-pollution (>=1.1.1)", "devpi-process (>=0.3.1)", "diff-cover (>=7.7)", "distlib (>=0.3.7)", "flaky (>=3.7)", "hatch-vcs (>=0.3)", "hatchling (>=1.17.1)", "psutil (>=5.9.5)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)", "pytest-xdist (>=3.3.1)", "re-assert (>=1.1)", "time-machine (>=2.10)", "wheel (>=0.40)"] -[[package]] -name = "tox-poetry" -version = "0.4.1" -description = "Tox poetry plugin" -optional = false -python-versions = "*" -files = [ - {file = "tox-poetry-0.4.1.tar.gz", hash = "sha256:2395808e1ce487b5894c10f2202e14702bfa6d6909c0d1e525170d14809ac7ef"}, - {file = "tox_poetry-0.4.1-py2.py3-none-any.whl", hash = "sha256:11d9cd4e51d4cd9484b3ba63f2650ab4cfb4096e5f0682ecf561ddfc3c8e8c92"}, -] - -[package.dependencies] -pluggy = "*" -toml = "*" -tox = {version = ">=3.7.0", markers = "python_version >= \"3\""} - -[package.extras] -test = ["coverage", "pycodestyle", "pylint", "pytest"] - [[package]] name = "typing-extensions" version = "4.7.1" @@ -1063,23 +1097,23 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "virtualenv" -version = "20.24.6" +version = "20.26.3" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.24.6-py3-none-any.whl", hash = "sha256:520d056652454c5098a00c0f073611ccbea4c79089331f60bf9d7ba247bb7381"}, - {file = "virtualenv-20.24.6.tar.gz", hash = "sha256:02ece4f56fbf939dbbc33c0715159951d6bf14aaf5457b092e4548e1382455af"}, + {file = "virtualenv-20.26.3-py3-none-any.whl", hash = "sha256:8cc4a31139e796e9a7de2cd5cf2489de1217193116a8fd42328f1bd65f434589"}, + {file = "virtualenv-20.26.3.tar.gz", hash = "sha256:4c43a2a236279d9ea36a0d76f98d84bd6ca94ac4e0f4a3b9d46d05e10fea542a"}, ] [package.dependencies] distlib = ">=0.3.7,<1" filelock = ">=3.12.2,<4" importlib-metadata = {version = ">=6.6", markers = "python_version < \"3.8\""} -platformdirs = ">=3.9.1,<4" +platformdirs = ">=3.9.1,<5" [package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] [[package]] @@ -1100,4 +1134,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" python-versions = ">=3.7.0,<4" -content-hash = "2845a4da507d6fa037d8680dd59597e8094bcbbc1471d58b2c78b6793eb6b017" +content-hash = "540c0b830aba95632cfb45ae47542178d9fe3d15a670c596912ec00c5ebabc9c" diff --git a/pyproject.toml b/pyproject.toml index ced63d2..fd2acec 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "rwslib" -version = "1.2.11" +version = "1.2.12" description = "Rave Web Services for Python" authors = ["Ian Sparks "] maintainers = ["Geoff Low "] @@ -14,11 +14,9 @@ classifiers = [ 'Natural Language :: English', 'License :: OSI Approved :: MIT License', 'Programming Language :: Python', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10', 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', ] packages = [ { include = "rwslib" }, @@ -33,6 +31,8 @@ click = "*" faker = "*" urllib3 = "*" +[tool.poetry.group.dev] +optional = true [tool.poetry.group.dev.dependencies] httpretty = "*" @@ -40,12 +40,12 @@ mock = "*" coverage = "*" pytest = "*" tox = "*" -tox-poetry = "*" [tool.poetry.group.docs.dependencies] Sphinx = "^5.1.1" sphinx-pyproject = "^0.3.0" [build-system] -requires = ["poetry-core"] +requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" + diff --git a/rwslib/builders/clinicaldata.py b/rwslib/builders/clinicaldata.py index d52dfc2..29ba2f9 100644 --- a/rwslib/builders/clinicaldata.py +++ b/rwslib/builders/clinicaldata.py @@ -1,4 +1,6 @@ # -*- coding: utf-8 -*- +from typing import Optional + from rwslib.builders.common import ( ODMElement, TransactionalElement, @@ -8,7 +10,7 @@ ) from rwslib.builders.modm import LastUpdateMixin, MilestoneMixin from rwslib.builders.metadata import MeasurementUnitRef -from rwslib.builders.constants import ProtocolDeviationStatus, QueryStatusType +from rwslib.builders.constants import ProtocolDeviationStatus, QueryStatusType, LocationOIDType from rwslib.builders.common import Unset from collections import OrderedDict @@ -77,6 +79,7 @@ def __init__( subject_key, subject_key_type="SubjectName", transaction_type="Update", + location_oid_type: Optional[LocationOIDType] = None, ): """ :param str site_location_oid: :class:`SiteLocation` OID @@ -98,6 +101,8 @@ def __init__( self.signature = None #: :class:`SiteRef` self.siteref = None + #: :class:`LocationOIDType` + self.location_oid_type = location_oid_type def build(self, builder): """Build XML by appending to builder""" @@ -120,8 +125,8 @@ def build(self, builder): if self.siteref: self.siteref.build(builder) else: - builder.start("SiteRef", {"LocationOID": self.sitelocationoid}) - builder.end("SiteRef") + _siteref = SiteRef(self.sitelocationoid, self.location_oid_type) + _siteref.build(builder) for event in self.study_events: event.build(builder) @@ -993,17 +998,66 @@ class SiteRef(ODMElement, LastUpdateMixin): .. note:: The `mdsol:LocationOIDType` attribute should be used to indicate the type of `LocationOID` """ - def __init__(self, oid): + def __init__(self, + oid, + location_oid_type: Optional[LocationOIDType] = None, + site_number: Optional[str] = None, + study_site_name: Optional[str] = None, + site_uuid: Optional[str] = None, + location_name: Optional[str] = None, + study_env_site_number: Optional[str] = None, + previous_location_oid: Optional[str] = None, + shared_location_oid: Optional[str] = None, + previous_shared_location_oid: Optional[str] = None, + subject_created_at_site: Optional[str] = None,): """ :param str oid: OID for referenced :class:`Location` + :param LocationOIDType location_oid_type: Type for the oid + :param site_number: Site number + :param study_site_name: Study site name + :param site_uuid: Site UUID + :param location_name: Location name + :param study_env_site_number: Study environment site number + :param previous_location_oid: Previous location OID + :param shared_location_oid: Shared location OID + :param previous_shared_location_oid: Previous shared location OID + :param subject_created_at_site: Subject created at site """ self.oid = oid + self.location_oid_type = location_oid_type + self.site_number = site_number + self.study_site_name = study_site_name + self.site_uuid = site_uuid + self.location_name = location_name + self.study_env_site_number = study_env_site_number + self.previous_location_oid = previous_location_oid + self.shared_location_oid = shared_location_oid + self.previous_shared_location_oid = previous_shared_location_oid + self.subject_created_at_site = subject_created_at_site def build(self, builder): """ Build XML by appending to builder """ params = dict(LocationOID=self.oid) + if self.location_oid_type: + params["mdsol:LocationOIDType"] = self.location_oid_type.value + elif self.site_uuid: + params["mdsol:SiteUUID"] = self.site_uuid + elif self.site_number: + params["mdsol:SiteNumber"] = self.site_number + elif self.study_site_name: + params["mdsol:StudySiteName"] = self.study_site_name + elif self.study_env_site_number: + params["mdsol:StudyEnvSiteNumber"] = self.study_env_site_number + if self.location_name: + params["mdsol:LocationName"] = self.location_name + if self.previous_location_oid: + params["mdsol:PreviousLocationOID"] = self.previous_location_oid + if self.shared_location_oid: + params["mdsol:SharedLocationOID"] = self.shared_location_oid + if self.subject_created_at_site: + params["mdsol:SubjectCreatedAtSite"] = self.subject_created_at_site # mixins self.mixin() self.mixin_params(params) diff --git a/rwslib/builders/common.py b/rwslib/builders/common.py index eabeabf..d716db1 100644 --- a/rwslib/builders/common.py +++ b/rwslib/builders/common.py @@ -1,7 +1,7 @@ # -*- coding: utf-8 -*- - +import platform from string import ascii_letters -from datetime import datetime +import datetime from xml.etree import cElementTree as ET @@ -13,11 +13,21 @@ # ----------------------------------------------------------------------------------------------------------------------- # Utilities +def get_utc_date() -> datetime.datetime: + """ + Returns the UTC date as datetime.datetime object. + """ + version = platform.python_version_tuple() + if int(version[1]) < 11: + utc_date = datetime.datetime.utcnow() + else: + utc_date = datetime.datetime.now(datetime.UTC) + return utc_date def now_to_iso8601(): """Returns NOW date/time as a UTC date/time formated as iso8601 string""" - utc_date = datetime.utcnow() + utc_date = get_utc_date() return dt_to_iso8601(utc_date) diff --git a/rwslib/builders/constants.py b/rwslib/builders/constants.py index 781bdc1..5ae2ae7 100644 --- a/rwslib/builders/constants.py +++ b/rwslib/builders/constants.py @@ -329,3 +329,14 @@ class GranularityType(enum.Enum): AllClinicalData = 'AllClinicalData' SingleSite = 'SingleSite' SingleSubject = 'SingleSubject' + + +class LocationOIDType(enum.Enum): + """ + Location OID Type Enumeration + Applies to a :class:`SiteRef` + """ + SiteUUID = 'SiteUUID' + SiteNumber = 'SiteNumber' + StudyEnvSiteNumber = 'StudyEnvSiteNumber' + diff --git a/rwslib/builders/modm.py b/rwslib/builders/modm.py index 8d6eee0..9b4a3ad 100644 --- a/rwslib/builders/modm.py +++ b/rwslib/builders/modm.py @@ -5,6 +5,8 @@ import datetime import enum +from rwslib.builders.common import get_utc_date + class MODMExtensionRegistry(enum.Enum): """ @@ -167,7 +169,7 @@ def set_update_time(self, update_time=None): if update_time and isinstance(update_time, (datetime.datetime,)): self.last_update_time = update_time else: - self.last_update_time = datetime.datetime.utcnow() + self.last_update_time = get_utc_date() def mixin_params(self, params): """ diff --git a/rwslib/tests/__init__.py b/rwslib/tests/__init__.py deleted file mode 100644 index 369f8f6..0000000 --- a/rwslib/tests/__init__.py +++ /dev/null @@ -1,12 +0,0 @@ -# -*- coding: utf-8 -*- - -__author__ = 'glow' - -import unittest - - -def all_tests(): - suite = unittest.TestSuite() - loader = unittest.TestLoader() - suite.addTests(loader.discover('rwslib.tests')) - return suite diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..2a06a4f --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,21 @@ +import pytest +import os + + +@pytest.fixture(scope="class") +def car_message(request): + with open( + os.path.join( + os.path.dirname(__file__), "fixtures", "car_message.xml" + ), 'r' + ) as fh: + content = fh.read() + request.cls.car_message = content + + +@pytest.fixture(scope="class") +def double_byte_chars(request): + with open(os.path.join( + os.path.dirname(__file__), "fixtures", "test_double_byte_chars.xml"), "r+b") as fh: + content = fh.read() + request.cls.double_byte_chars = content diff --git a/rwslib/tests/fixtures/car_message.xml b/tests/fixtures/car_message.xml similarity index 100% rename from rwslib/tests/fixtures/car_message.xml rename to tests/fixtures/car_message.xml diff --git a/rwslib/tests/fixtures/test_double_byte_chars.xml b/tests/fixtures/test_double_byte_chars.xml similarity index 100% rename from rwslib/tests/fixtures/test_double_byte_chars.xml rename to tests/fixtures/test_double_byte_chars.xml diff --git a/tests/rwslib/__init__.py b/tests/rwslib/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/rwslib/builders/__init__.py b/tests/rwslib/builders/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rwslib/tests/test_builders.py b/tests/rwslib/builders/test_builders.py similarity index 96% rename from rwslib/tests/test_builders.py rename to tests/rwslib/builders/test_builders.py index 99f2f36..6cd6f89 100644 --- a/rwslib/tests/test_builders.py +++ b/tests/rwslib/builders/test_builders.py @@ -4,13 +4,13 @@ from mock import patch -from rwslib.tests.common import obj_to_doc +from ..common import obj_to_doc __author__ = 'isparks' import unittest -from rwslib.builders.common import bool_to_yes_no, bool_to_true_false, ODMElement +from rwslib.builders.common import bool_to_yes_no, bool_to_true_false, ODMElement, get_utc_date from rwslib.builders.clinicaldata import UserRef, LocationRef, ClinicalData, SubjectData from rwslib.builders.metadata import Study from rwslib.builders.admindata import AdminData @@ -123,7 +123,7 @@ def test_creation_datetime(self): tested_1 = obj_to_doc(obj=obj_1) with patch('rwslib.builders.common.datetime') as mock_dt: # offset the time to ensure we don't overlap - mock_dt.utcnow.return_value = datetime.datetime.utcnow() + datetime.timedelta(seconds=61) + mock_dt.utcnow.return_value = get_utc_date() + datetime.timedelta(seconds=61) obj_2 = ODM("Test User", fileoid="1235", source_system="Battlestar", source_system_version="1.04") tested_2 = obj_to_doc(obj=obj_2) self.assertEqual(tested_1.get('Originator'), tested_2.get('Originator')) diff --git a/rwslib/tests/test_builders_admindata.py b/tests/rwslib/builders/test_builders_admindata.py similarity index 86% rename from rwslib/tests/test_builders_admindata.py rename to tests/rwslib/builders/test_builders_admindata.py index 9def9a2..1a0e62f 100644 --- a/rwslib/tests/test_builders_admindata.py +++ b/tests/rwslib/builders/test_builders_admindata.py @@ -1,12 +1,13 @@ # -*- coding: utf-8 -*- import datetime +from rwslib.builders.common import get_utc_date from rwslib.builders.constants import LocationType, UserType __author__ = 'glow' import unittest -from rwslib.tests.common import obj_to_doc +from ..common import obj_to_doc from rwslib.builders.admindata import AdminData, User, FirstName, LastName, Location, DisplayName, MetaDataVersionRef @@ -125,33 +126,40 @@ def test_create_user_with_display_nae(self): self.assertEqual("DisplayName", list(tested)[0].tag) self.assertEqual("Henrik", list(tested)[0].text) + class TestMetaDataVersionRef(unittest.TestCase): def test_create_a_version_ref(self): """We create a MetaDataVersionRef""" - obj = MetaDataVersionRef("Mediflex(Prod)", "1024", datetime.datetime.utcnow()) + _utc_date = get_utc_date() + obj = MetaDataVersionRef("Mediflex(Prod)", "1024", _utc_date) tested = obj_to_doc(obj) self.assertEqual("MetaDataVersionRef", tested.tag) self.assertEqual("Mediflex(Prod)", tested.get('StudyOID')) self.assertEqual("1024", tested.get('MetaDataVersionOID')) - self.assertTrue(tested.get('EffectiveDate').startswith(datetime.date.today().isoformat())) + _effective_date = tested.get('EffectiveDate') + self.assertIsNotNone(_effective_date) + _ref_date = get_utc_date().isoformat().split('T')[0] + self.assertTrue(_effective_date.startswith(_ref_date)) def test_create_a_version_ref_and_attach_to_location(self): """We create a MetaDataVersionRef""" - this = MetaDataVersionRef("Mediflex(Prod)", "1024", datetime.datetime.utcnow() - datetime.timedelta(days=7)) - that = MetaDataVersionRef("Mediflex(Prod)", "1025", datetime.datetime.utcnow()) + this = MetaDataVersionRef("Mediflex(Prod)", + "1024", get_utc_date() - datetime.timedelta(days=7)) + that = MetaDataVersionRef("Mediflex(Prod)", "1025", get_utc_date()) obj = Location('Site01', 'Site 1') obj << this - obj << that + obj << that tested = obj_to_doc(obj) self.assertEqual("Location", tested.tag) self.assertTrue(len(list(tested)) == 2) _this = list(tested)[0] self.assertEqual("Mediflex(Prod)", _this.get('StudyOID')) self.assertEqual("1024", _this.get('MetaDataVersionOID')) - self.assertTrue(_this.get('EffectiveDate').startswith((datetime.date.today() - - datetime.timedelta(days=7)).isoformat())) + _ref_date = (get_utc_date() - datetime.timedelta(days=7)) + self.assertTrue(_this.get('EffectiveDate').startswith(_ref_date.isoformat().split('T')[0])) _that = list(tested)[1] self.assertEqual("Mediflex(Prod)", _that.get('StudyOID')) self.assertEqual("1025", _that.get('MetaDataVersionOID')) - self.assertTrue(_that.get('EffectiveDate').startswith(datetime.date.today().isoformat())) + _ref_date = get_utc_date() + self.assertTrue(_that.get('EffectiveDate').startswith(_ref_date.isoformat().split('T')[0])) diff --git a/rwslib/tests/test_builders_clinicaldata.py b/tests/rwslib/builders/test_builders_clinicaldata.py similarity index 95% rename from rwslib/tests/test_builders_clinicaldata.py rename to tests/rwslib/builders/test_builders_clinicaldata.py index 4cfa104..2af99a8 100644 --- a/rwslib/tests/test_builders_clinicaldata.py +++ b/tests/rwslib/builders/test_builders_clinicaldata.py @@ -5,7 +5,7 @@ import unittest from rwslib.builders import * -from rwslib.tests.common import obj_to_doc +from ..common import obj_to_doc from datetime import datetime @@ -202,6 +202,15 @@ def test_multiple_subject_data(self): doc = obj_to_doc(cd) self.assertEqual(2, len(doc)) + def test_multiple_subject_data_location_oid(self): + """Specify the LocationOID Type""" + cd = ClinicalData("Mediflex", "Prod") + cd << SubjectData("Site1", "Subject1", + location_oid_type=LocationOIDType.StudyEnvSiteNumber) + doc = obj_to_doc(cd) + site_ref = doc.find(".//SiteRef", namespaces={"odm": "http://www.cdisc.org/ns/odm/v1.3"}) + self.assertEqual('StudyEnvSiteNumber', site_ref.attrib["mdsol:LocationOIDType"]) + class TestStudyEventData(unittest.TestCase): """Test StudyEventData classes""" @@ -1310,7 +1319,7 @@ def test_add_to_audit(self): record = AuditRecord() record << UserRef("glow1") record << LocationRef("hillview") - record << DateTimeStamp(datetime.utcnow()) + record << DateTimeStamp(get_utc_date().isoformat()) record << SourceID("12345") tested = obj_to_doc(record) self.assertEqual("AuditRecord", tested.tag) @@ -1340,3 +1349,39 @@ def test_uuid_type(self): "E20DEF2D-0CD4-4B3A-B963-AC7D592CB85B", tested.get("LocationOID") ) self.assertEqual("SiteUUID", tested.get("mdsol:LocationOIDType")) + + def test_oid_type_init_site_uuid(self): + siteref = SiteRef(oid="E20DEF2D-0CD4-4B3A-B963-AC7D592CB85B", location_oid_type=LocationOIDType.SiteUUID) + tested = obj_to_doc(siteref) + self.assertEqual("SiteRef", tested.tag) + self.assertEqual( + "E20DEF2D-0CD4-4B3A-B963-AC7D592CB85B", tested.get("LocationOID") + ) + self.assertEqual("SiteUUID", tested.get("mdsol:LocationOIDType")) + + def test_oid_type_init_site_number(self): + siteref = SiteRef(oid="001", location_oid_type=LocationOIDType.SiteNumber) + tested = obj_to_doc(siteref) + self.assertEqual("SiteRef", tested.tag) + self.assertEqual( + "001", tested.get("LocationOID") + ) + self.assertEqual("SiteNumber", tested.get("mdsol:LocationOIDType")) + + def test_oid_type_init_study_env_site_number(self): + siteref = SiteRef(oid="01", location_oid_type=LocationOIDType.StudyEnvSiteNumber) + tested = obj_to_doc(siteref) + self.assertEqual("SiteRef", tested.tag) + self.assertEqual( + "01", tested.get("LocationOID") + ) + self.assertEqual("StudyEnvSiteNumber", tested.get("mdsol:LocationOIDType")) + + def test_oid_type_study_env_site_number(self): + siteref = SiteRef(oid="01", study_env_site_number="001") + tested = obj_to_doc(siteref) + self.assertEqual("SiteRef", tested.tag) + self.assertEqual( + "01", tested.get("LocationOID") + ) + self.assertEqual("001", tested.get("mdsol:StudyEnvSiteNumber")) diff --git a/rwslib/tests/test_builders_mdsol.py b/tests/rwslib/builders/test_builders_mdsol.py similarity index 99% rename from rwslib/tests/test_builders_mdsol.py rename to tests/rwslib/builders/test_builders_mdsol.py index 3f6dbe6..0111647 100644 --- a/rwslib/tests/test_builders_mdsol.py +++ b/tests/rwslib/builders/test_builders_mdsol.py @@ -3,7 +3,7 @@ from rwslib.builders.constants import ProtocolDeviationStatus, QueryStatusType from rwslib.builders.clinicaldata import ItemData, MdsolProtocolDeviation, MdsolQuery -from rwslib.tests.common import obj_to_doc +from ..common import obj_to_doc class TestMdsolQuery(unittest.TestCase): diff --git a/rwslib/tests/test_builders_mdsol_modm.py b/tests/rwslib/builders/test_builders_mdsol_modm.py similarity index 98% rename from rwslib/tests/test_builders_mdsol_modm.py rename to tests/rwslib/builders/test_builders_mdsol_modm.py index 2d14da2..c1e556c 100644 --- a/rwslib/tests/test_builders_mdsol_modm.py +++ b/tests/rwslib/builders/test_builders_mdsol_modm.py @@ -6,11 +6,12 @@ from faker import Faker from rwslib.builders.admindata import Location +from rwslib.builders.common import get_utc_date from rwslib.builders.constants import QueryStatusType from rwslib.builders.clinicaldata import ClinicalData, FormData, ItemData, ItemGroupData, MdsolQuery, StudyEventData, \ SubjectData -from rwslib.tests.common import obj_to_doc +from ..common import obj_to_doc import datetime import unittest @@ -57,7 +58,7 @@ class TestMODMClinicalData(TestCase): def test_add_last_update_time(self): """We add a LastUpdateTime""" clindata = ClinicalData("Mediflex", "Prod", metadata_version_oid="1012") - now = datetime.datetime.utcnow() + now = get_utc_date() clindata.last_update_time = now tested = obj_to_doc(clindata) self.assertEqual(now.isoformat(), tested.get('mdsol:LastUpdateTime')) @@ -100,7 +101,7 @@ class TestMODMSubjectData(TestCase): def test_add_last_update_time(self): """We add a LastUpdateTime""" obj = SubjectData("Subject 1", "Site 1") - now = datetime.datetime.utcnow() + now = get_utc_date() obj.last_update_time = now tested = obj_to_doc(obj) self.assertEqual(now.isoformat(), tested.get('mdsol:LastUpdateTime')) @@ -158,7 +159,7 @@ class TestMODMStudyEventData(TestCase): def test_add_last_update_time(self): """We add a LastUpdateTime""" obj = StudyEventData("VISIT1") - now = datetime.datetime.utcnow() + now = get_utc_date() obj.last_update_time = now tested = obj_to_doc(obj) self.assertEqual("StudyEventData", tested.tag) @@ -233,7 +234,7 @@ class TestMODMFormData(TestCase): def test_add_last_update_time(self): """We add a LastUpdateTime""" obj = FormData(formoid="DM") - now = datetime.datetime.utcnow() + now = get_utc_date() obj.last_update_time = now tested = obj_to_doc(obj) self.assertEqual("FormData", tested.tag) @@ -305,7 +306,7 @@ class TestMODMItemGroupData(TestCase): def test_add_last_update_time(self): """We add a LastUpdateTime""" obj = ItemGroupData(itemgroupoid="DM") - now = datetime.datetime.utcnow() + now = get_utc_date() obj.last_update_time = now tested = obj_to_doc(obj) self.assertEqual("ItemGroupData", tested.tag) @@ -377,7 +378,7 @@ class TestMODMItemData(TestCase): def test_add_last_update_time(self): """We add a LastUpdateTime""" obj = ItemData(itemoid="BRTHDAT", value="12 DEC 1975") - now = datetime.datetime.utcnow() + now = get_utc_date() obj.last_update_time = now tested = obj_to_doc(obj) self.assertEqual("ItemData", tested.tag) @@ -428,7 +429,7 @@ def test_add_milestones(self): def test_add_item_uuid(self): """We add a mdsol:ItemUUID""" obj = ItemData(itemoid="BRTHDAT", value="12 DEC 1975") - now = datetime.datetime.utcnow() + now = get_utc_date() obj.last_update_time = now obj.add_attribute("ItemUUID", "85D4F9F0-9F49-42F3-A8E7-413DE85CC55E") tested = obj_to_doc(obj) @@ -439,7 +440,7 @@ def test_add_item_uuid(self): def test_gate_modm_attributes(self): """We add a mdsol:Nonsense""" obj = ItemData(itemoid="BRTHDAT", value="12 DEC 1975") - now = datetime.datetime.utcnow() + now = get_utc_date() obj.last_update_time = now with self.assertRaises(ValueError) as exc: obj.add_attribute("Nonsense", "85D4F9F0-9F49-42F3-A8E7-413DE85CC55E") diff --git a/rwslib/tests/test_builders_metadata.py b/tests/rwslib/builders/test_builders_metadata.py similarity index 99% rename from rwslib/tests/test_builders_metadata.py rename to tests/rwslib/builders/test_builders_metadata.py index 466fd8e..0eecefd 100644 --- a/rwslib/tests/test_builders_metadata.py +++ b/tests/rwslib/builders/test_builders_metadata.py @@ -8,7 +8,7 @@ from rwslib.builders.constants import DataType, LogicalRecordPositionType, StepType from rwslib.builders.clinicaldata import ItemData -from rwslib.tests.test_builders import obj_to_doc +from ..common import obj_to_doc # Metadata object tests diff --git a/rwslib/tests/common.py b/tests/rwslib/common.py similarity index 99% rename from rwslib/tests/common.py rename to tests/rwslib/common.py index ab0f494..cd4ccf9 100644 --- a/rwslib/tests/common.py +++ b/tests/rwslib/common.py @@ -12,5 +12,3 @@ def obj_to_doc(obj, *args, **kwargs): builder = ET.TreeBuilder() obj.build(builder, *args, **kwargs) return builder.close() - - diff --git a/tests/rwslib/extras/__init__.py b/tests/rwslib/extras/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/rwslib/extras/audit_event/__init__.py b/tests/rwslib/extras/audit_event/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rwslib/tests/test_audit_event.py b/tests/rwslib/extras/audit_event/test_audit_event.py similarity index 93% rename from rwslib/tests/test_audit_event.py rename to tests/rwslib/extras/audit_event/test_audit_event.py index 6223ebd..6a6402f 100644 --- a/rwslib/tests/test_audit_event.py +++ b/tests/rwslib/extras/audit_event/test_audit_event.py @@ -1,6 +1,8 @@ from rwslib.extras.audit_event import parser import unittest import os +import pytest + class MockEventer: @@ -41,18 +43,16 @@ def eventlist(self): return self.__events.keys() +@pytest.mark.usefixtures("car_message") class TestAuditEvent(unittest.TestCase): """ Test Case for Audit Event Processor """ + def test_parses_audit_message(self): """parses an audit message from a CAR message""" - with open( - os.path.join(os.path.dirname(__file__), "fixtures", "car_message.xml") - ) as fh: - content = fh.read() eventer = MockEventer() - message = parser.parse(content, eventer) + message = parser.parse(self.car_message, eventer) # get the events self.assertTrue(len(eventer.eventlist) > 1) self.assertTrue("EnteredEmpty" in eventer.eventlist) @@ -61,26 +61,20 @@ def test_parses_audit_message(self): def test_parses_audit_message_entered(self): """parses an audit message, but only subscribe to Entered Events from a CAR message""" - with open( - os.path.join(os.path.dirname(__file__), "fixtures", "car_message.xml") - ) as fh: - content = fh.read() eventer = MockEventerEntered() - message = parser.parse(content, eventer) + message = parser.parse(self.car_message, eventer) # get the events self.assertTrue(len(eventer.eventlist) == 1) self.assertTrue("EnteredEmpty" not in eventer.eventlist) self.assertEqual(0, len(eventer.get_audit_subcategory_events("EnteredEmpty"))) self.assertEqual(501, len(eventer.get_audit_subcategory_events("Entered"))) + def test_parses_audit_message_subject_created(self): """parses an audit message, but only subscribe to Entered Events from a CAR message""" - with open( - os.path.join(os.path.dirname(__file__), "fixtures", "car_message.xml") - ) as fh: - content = fh.read() + eventer = MockEventer() - message = parser.parse(content, eventer) + message = parser.parse(self.car_message, eventer) # get the events self.assertEqual( 92, len(eventer.get_audit_subcategory_events("SubjectCreated")) diff --git a/rwslib/tests/test_parser.py b/tests/rwslib/extras/audit_event/test_parser.py similarity index 100% rename from rwslib/tests/test_parser.py rename to tests/rwslib/extras/audit_event/test_parser.py diff --git a/tests/rwslib/extras/rwscmd/__init__.py b/tests/rwslib/extras/rwscmd/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rwslib/tests/test_data_scrambler.py b/tests/rwslib/extras/rwscmd/test_data_scrambler.py similarity index 100% rename from rwslib/tests/test_data_scrambler.py rename to tests/rwslib/extras/rwscmd/test_data_scrambler.py diff --git a/rwslib/tests/test_rwscmd.py b/tests/rwslib/extras/rwscmd/test_rwscmd.py similarity index 100% rename from rwslib/tests/test_rwscmd.py rename to tests/rwslib/extras/rwscmd/test_rwscmd.py diff --git a/rwslib/tests/test_local_cv.py b/tests/rwslib/extras/test_local_cv.py similarity index 100% rename from rwslib/tests/test_local_cv.py rename to tests/rwslib/extras/test_local_cv.py diff --git a/tests/rwslib/rws_requests/__init__.py b/tests/rwslib/rws_requests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rwslib/tests/test_biostats_gateway.py b/tests/rwslib/rws_requests/test_biostats_gateway.py similarity index 100% rename from rwslib/tests/test_biostats_gateway.py rename to tests/rwslib/rws_requests/test_biostats_gateway.py diff --git a/rwslib/tests/test_odm_adapter.py b/tests/rwslib/rws_requests/test_odm_adapter.py similarity index 100% rename from rwslib/tests/test_odm_adapter.py rename to tests/rwslib/rws_requests/test_odm_adapter.py diff --git a/rwslib/tests/test_odmadapter.py b/tests/rwslib/rws_requests/test_odmadapter.py similarity index 100% rename from rwslib/tests/test_odmadapter.py rename to tests/rwslib/rws_requests/test_odmadapter.py diff --git a/rwslib/tests/test_rws_requests.py b/tests/rwslib/rws_requests/test_rws_requests.py similarity index 100% rename from rwslib/tests/test_rws_requests.py rename to tests/rwslib/rws_requests/test_rws_requests.py diff --git a/rwslib/tests/test_config_datasets.py b/tests/rwslib/test_config_datasets.py similarity index 100% rename from rwslib/tests/test_config_datasets.py rename to tests/rwslib/test_config_datasets.py diff --git a/rwslib/tests/test_context.py b/tests/rwslib/test_context.py similarity index 100% rename from rwslib/tests/test_context.py rename to tests/rwslib/test_context.py diff --git a/rwslib/tests/test_rwslib.py b/tests/rwslib/test_rwslib.py similarity index 97% rename from rwslib/tests/test_rwslib.py rename to tests/rwslib/test_rwslib.py index c66d1e6..0931189 100644 --- a/rwslib/tests/test_rwslib.py +++ b/tests/rwslib/test_rwslib.py @@ -1,7 +1,7 @@ -import os import unittest import httpretty +import pytest import requests from mock import mock @@ -117,7 +117,7 @@ def test_request_time(self): request_time = rave.request_time self.assertIs(type(request_time), float) - +@pytest.mark.usefixtures("double_byte_chars") class TestErrorResponse(unittest.TestCase): @httpretty.activate def test_503_error(self): @@ -433,18 +433,11 @@ def test_multibyte_character_encoding(self): Test the output is properly encoded, Rave sends text/xml, but the underlying library doesn't seem to detect the encoding correctly """ - with open( - os.path.join( - os.path.dirname(__file__), "fixtures", "test_double_byte_chars.xml" - ), - "r+b", - ) as fh: - content = fh.read() - httpretty.register_uri( + httpretty.register_uri( httpretty.GET, "https://training1.mdsol.com/RaveWebServices/studies/RWS_Training_Japan(PROD)/datasets/regular/SURGERY", status=200, - body=content, + body=self.double_byte_chars, content_type="text/xml" ) # Now my test @@ -453,7 +446,7 @@ def test_multibyte_character_encoding(self): StudyDatasetRequest("RWS_Training_Japan", "PROD", formoid="SURGERY") ) # these don't match as the encoding of the characters fails - self.assertNotEqual(content.decode('utf-8'), result) + self.assertNotEqual(self.double_byte_chars.decode('utf-8'), result) class UTF8StudyDatasetRequest(StudyDatasetRequest): """ @@ -467,7 +460,7 @@ def result(self, response): UTF8StudyDatasetRequest("RWS_Training_Japan", "PROD", formoid="SURGERY") ) # these match as the encoding enforcement makes it so - self.assertEqual(content.decode('utf-8'), result) + self.assertEqual(self.double_byte_chars.decode('utf-8'), result) if __name__ == "__main__": diff --git a/rwslib/tests/test_rwsobjects.py b/tests/rwslib/test_rwsobjects.py similarity index 100% rename from rwslib/tests/test_rwsobjects.py rename to tests/rwslib/test_rwsobjects.py diff --git a/tox.ini b/tox.ini index d62e11a..8ccfb4d 100644 --- a/tox.ini +++ b/tox.ini @@ -1,43 +1,54 @@ -# Tox (http://tox.testrun.org/) is a tool for running tests -# in multiple virtualenvs. This configuration file will run the -# test suite on all supported python versions. To use it, "pip install tox" -# and then run "tox" from this directory. - [tox] -isolated_build = true -envlist = clean, py37, py38, py39, py310, anaconda3, stats +envlist = clean, py{310,311,312}, anaconda3, coverage, stats recreate = true [testenv] -whitelist_externals = poetry -commands= - poetry install - poetry run coverage run -m pytest +allowlist_externals = poetry +commands_pre = + poetry install --no-root --sync --with dev +commands = + pytest tests --import-mode importlib +deps = + pytest + pytest-sugar + mock + httpretty + + +[testenv:coverage] +allowlist_externals = poetry +commands_pre = + poetry install --no-root --sync --with dev +commands = + coverage run -m pytest deps = pytest + pytest-sugar + mock + httpretty coverage [testenv:clean] +allowlist_externals = poetry, coverage commands= coverage erase [testenv:stats] +allowlist_externals = poetry, coverage commands= coverage report --include=rwslib/* --omit=*test* coverage html [gh-actions] python = - 3.6: py36 - 3.7: py37, docs - 3.8: py38, lint, manifest - 3.9: py39, lint, manifest 3.10: py310, lint, manifest + 3.11: py311, lint, manifest + 3.12: py312, lint, manifest pypy3: pypy3 [tool.coverage.run] omit = [".*", "*/site-packages/*"] [tool.coverage.report] -fail_under = 100 +fail_under = 80