Feature/add location oid type

.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

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 !!!
 

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 <[email protected]>"]
 maintainers = ["Geoff Low <[email protected]>"]
@@ -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" },
@@ -33,19 +31,21 @@ click = "*"
 faker = "*"
 urllib3 = "*"
 
+[tool.poetry.group.dev]
+optional = true
 
 [tool.poetry.group.dev.dependencies]
 httpretty = "*"
 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"
+

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)

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)
 
 

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'
+

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):
         """

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

rwslib/tests/test_builders.py → 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'))

rwslib/tests/test_builders_admindata.py → 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]))