Merge branch 'release/0.3.73' into main

README.rst

@@ -8,8 +8,41 @@ Add classes for the Informed Consent form and process.
 Installation
 ============
 
-Register your consent model, its version and period of validity, with ``site_consents``. ``site_consents`` will ``autodiscover`` ``consents.py`` in any app listed in ``INSTALLED_APPS``. For now we just create a version 1 consent. In ``consents.py`` add something like this:
+Declare the consent model:
 
+.. code-block:: python
+
+    class SubjectConsent(
+        ConsentModelMixin,
+        SiteModelMixin,
+        UpdatesOrCreatesRegistrationModelMixin,
+        NonUniqueSubjectIdentifierModelMixin,
+        IdentityFieldsMixin,
+        PersonalFieldsMixin,
+        SampleCollectionFieldsMixin,
+        ReviewFieldsMixin,
+        VulnerabilityFieldsMixin,
+        SearchSlugModelMixin,
+        BaseUuidModel,
+    ):
+
+        """A model completed by the user that captures the ICF."""
+
+        subject_identifier_cls = SubjectIdentifier
+
+        subject_screening_model = "effect_screening.subjectscreening"
+
+        objects = SubjectConsentManager()
+        on_site = CurrentSiteManager()
+        consent = ConsentManager()
+        history = HistoricalRecords()
+
+        class Meta(ConsentModelMixin.Meta, BaseUuidModel.Meta):
+            pass
+
+Declare at least one ``ConsentDefinition`` that references your consent model.
+
+``ConsentDefinitions`` are declared in the root of your app in module ``consents.py``. A typical declaration looks something like this:
 
 .. code-block:: python
 
@@ -20,17 +53,18 @@ Register your consent model, its version and period of validity, with ``site_con
     from edc_consent.site_consents import site_consents
     from edc_constants.constants import MALE, FEMALE
 
-    subjectconsent_v1 = ConsentDefinition(
+    consent_v1 = ConsentDefinition(
         'edc_example.subjectconsent',
         version='1',
         start=datetime(2013, 10, 15, tzinfo=ZoneInfo("UTC")),
-        end=datetime(2016, 10, 15, tzinfo=ZoneInfo("UTC")),
+        end=datetime(2016, 10, 15, 23, 59, 999999, tzinfo=ZoneInfo("UTC")),
         age_min=16,
         age_is_adult=18,
         age_max=64,
         gender=[MALE, FEMALE])
 
-    site_consents.register(subjectconsent_v1)
+    site_consents.register(consent_v1)
+
 
 add to settings:
 
@@ -42,8 +76,124 @@ add to settings:
         ...
     ]
 
+On bootup ``site_consents`` will ``autodiscover`` the ``consents.py`` and register the ``ConsentDefinition``.
+
+Now create an instance of the ``SubjectConsent`` model, ``subject_consent``. When the instance is saved, the model will find the ``ConsentDefinition`` with a validity period that includes ``subject_consent.consent_datetime`` and update ``subject_consent.version`` with the value of ``consent_definition.version``.
+In this case, for ``consent_datetime`` equal to ``datetime(2013, 10, 16, tzinfo=ZoneInfo("UTC"))``, the model will find ``consent_v1``.
+If the ``consent_datetime`` is outside of the date boundary, for example datetime(2017, 1, 1, tzinfo=ZoneInfo("UTC")), the model will not find a
+``ConsentDefinition`` and an exception will be raised (``ConsentDefinitionNotFound``).
+
+Add a second ``ConsentDefinition`` to ``your consents.py`` for version 2:
+
+.. code-block:: python
+
+    consent_v1 = ConsentDefinition(...)
+
+    consent_v2 = ConsentDefinition(
+        'edc_example.subjectconsent',
+        version='2',
+        start=datetime(2016, 10, 16, 0,0,0, tzinfo=ZoneInfo("UTC")),
+        end=datetime(2020, 10, 15, 23, 59, 999999, tzinfo=ZoneInfo("UTC")),
+        age_min=16,
+        age_is_adult=18,
+        age_max=64,
+        gender=[MALE, FEMALE])
+
+    site_consents.register(consent_v1)
+    site_consents.register(consent_v2)
+
+
+Now resave the instance from above with ``consent_datetime = datetime(2017, 1, 1, tzinfo=ZoneInfo("UTC"))``. The model will find
+``consent_v2`` and update ``subject_consent.version = consent_v2.version`` which in this case is "2".
+
+``edc_consent`` is coupled with ``edc_visit_schedule``. In fact, a data collection schedule is declared with one or more ``ConsentDefinitions``. CRFs and Requisitions listed in a schedule may only be submitted if the subject has consented.
+
+.. code-block:: python
+
+    schedule = Schedule(
+        name=SCHEDULE,
+        verbose_name="Day 1 to Month 6 Follow-up",
+        onschedule_model="effect_prn.onschedule",
+        offschedule_model="effect_prn.endofstudy",
+        consent_definitions=[consent_v1, consent_v2],
+    )
+
+When a CRF is saved, the CRF model will check the ``schedule`` to find the ``ConsentDefinition`` with a validity period that contains the ``crf.report_datetime``. Using the located ``ConsentDefinitions``, the CRF model will confirm the subject has a saved ``subject_consent`` with this ``consent_definition.version``.
+
+When there is more than one ``ConsentDefinition`` but still just one ``SubjectConsent`` model, declaring proxy models
+provides some clarity and allows the ``ModelForm`` and ``ModelAdmin`` classes to be customized.
+
+.. code-block:: python
+
+    class SubjectConsentV1(SubjectConsent):
+
+        class Meta:
+            proxy = True
+            verbose_name = "Consent V1"
+            verbose_name_plural = "Consent V1"
+
+
+    class SubjectConsentV2(SubjectConsent):
+
+        class Meta:
+            proxy = True
+            verbose_name = "Consent V2"
+            verbose_name_plural = "Consent V2"
+
+
+.. code-block:: python
+
+    consent_v1 = ConsentDefinition(
+        'edc_example.subjectconsentv1',
+        version='1', ...)
+
+    consent_v2 = ConsentDefinition(
+        'edc_example.subjectconsentv2',
+        version='2', ...)
+
+    site_consents.register(consent_v1)
+    site_consents.register(consent_v2)
+
+Now each model can use a custom ``ModelAdmin`` class.
+
+The ConsentDefinitions above assume that consent version 1 is completed for a subject
+consenting on or before 2016/10/15 and version 2 for those consenting after 2016/10/15.
+
+Sometimes when version 2 is introduced, those subjects who consented for version 1 need
+to update their version 1 consent to version 2. For example, a question may have been added
+in version 2 to allow a subject to opt-out of having their specimens put into longterm
+storage. The subjects who are already consented under version 1 need to indicate their
+preference as well by submitting a version 2 consent. (To make things simple, we would
+programatically carry-over and validate duplicate data from the subject's version 1 consent.)
+
+To allow this, we would add ``update_versions`` to the version 2 ``ConsentDefinition``.
+
+.. code-block:: python
+
+    consent_v1 = ConsentDefinition(
+        'edc_example.subjectconsentv1',
+        version='1', ...)
+
+    consent_v2 = ConsentDefinition(
+        'edc_example.subjectconsentv2',
+        version='2',
+        update_versions=[UpdateVersion(consent_v1.version, consent_v1.end)],
+
+    site_consents.register(consent_v1)
+    site_consents.register(consent_v2)
+
+As the trial continues past 2016/10/15, there will three categories of subjects:
+
+* Subjects who completed version 1 only
+* Subjects who completed version 1 and version 2
+* Subjects who completed version 2 only
+
+If the report date is after 2016/10/15, data entry for "Subjects who completed version 1 only"
+will be blocked until the version 2 consent is submitted.
+
+
+
 
- Below needs to be updated
 
 Features
 ========
@@ -65,56 +215,24 @@ TODO
 Usage
 =====
 
-Then declare the consent model:
 
-.. code-block:: python
-
-    class SubjectConsent(
-        ConsentModelMixin,
-        SiteModelMixin,
-        UpdatesOrCreatesRegistrationModelMixin,
-        NonUniqueSubjectIdentifierModelMixin,
-        IdentityFieldsMixin,
-        PersonalFieldsMixin,
-        SampleCollectionFieldsMixin,
-        ReviewFieldsMixin,
-        VulnerabilityFieldsMixin,
-        SearchSlugModelMixin,
-        BaseUuidModel,
-    ):
-
-        """A model completed by the user that captures the ICF."""
-
-        subject_identifier_cls = SubjectIdentifier
-
-        subject_screening_model = "effect_screening.subjectscreening"
-
-        objects = SubjectConsentManager()
-        on_site = CurrentSiteManager()
-        consent = ConsentManager()
-        history = HistoricalRecords()
-
-        class Meta(ConsentModelMixin.Meta, BaseUuidModel.Meta):
-            pass
 
 Declare the ModelForm:
 
 .. code-block:: python
 
-    class MyConsentForm(BaseConsentForm):
+    class SubjectConsentForm(BaseConsentForm):
 
         class Meta:
-            model = MyConsent
+            model = SubjectConsent
 
 
-Now that you have a consent model class, identify and declare the models that will require this consent:
+Now that you have a consent model class, declare the models that will require this consent:
 
 .. code-block:: python
 
     class Questionnaire(RequiresConsentMixin, models.Model):
 
-        consent_model = MyConsent  # or tuple (app_label, model_name)
-
         report_datetime = models.DateTimeField(default=timezone.now)
 
         question1 = models.CharField(max_length=10)
@@ -132,28 +250,23 @@ Now that you have a consent model class, identify and declare the models that wi
         app_label = 'my_app'
         verbose_name = 'My Questionnaire'
 
-Notice above the first two class attributes, namely:
-
-* consent_model: this is the consent model class that was declared above;
-* report_datetime: a required field used to lookup the correct consent version from ConsentType and to find, together with ``subject_identifier``,  a valid instance of ``MyConsent``;
-
-Also note the property ``subject_identifier``.
 
-* subject_identifier: a required property that knows how to find the ``subject_identifier`` for the instance of ``Questionnaire``.
+* report_datetime: a required field used to lookup the correct ``ConsentDefinition`` and to find, together with ``subject_identifier``,  a valid instance of ``SubjectConsent``;
+* subject_identifier: a required field or may be a property that knows how to find the ``subject_identifier`` for the instance of ``Questionnaire``.
 
 Once all is declared you need to:
 
-* define the consent version and validity period for the consent version in ``ConsentType``;
+* define the consent version and validity period for the consent version in ``ConsentDefinition``;
 * add a Quota for the consent model.
 
 As subjects are identified:
 
 * add a consent
 * add the models (e.g. ``Questionnaire``)
 
-If a consent version cannot be found given the consent model class and report_datetime a ``ConsentTypeError`` is raised.
+If a consent version cannot be found given the consent model class and report_datetime a ``ConsentDefinitionError`` is raised.
 
-If a consent for this subject_identifier cannot be found that matches the ``ConsentType`` a ``NotConsentedError`` is raised.
+If a consent for this subject_identifier cannot be found that matches the ``ConsentDefinition`` a ``NotConsentedError`` is raised.
 
 Specimen Consent
 ================
@@ -227,12 +340,12 @@ Common senarios
 Tracking the consent version with collected data
 ++++++++++++++++++++++++++++++++++++++++++++++++
 
-All model data is tagged with the consent version identified in ``ConsentType`` for the consent model class and report_datetime.
+All model data is tagged with the consent version identified in ``ConsentDefinition`` for the consent model class and report_datetime.
 
 Reconsenting consented subjects when the consent changes
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
-The consent model is unique on subject_identifier, identity and version. If a new consent version is added to ``ConsentType``, a new consent will be required for each subject as data is reported within the validity period of the new consent.
+The consent model is unique on subject_identifier, identity and version. If a new consent version is added to ``ConsentDefinition``, a new consent will be required for each subject as data is reported within the validity period of the new consent.
 
 Some care must be taken to ensure that the consent model is queried with an understanding of the unique constraint.
 

consent_app/apps.py

@@ -0,0 +1,7 @@
+from django.apps import AppConfig as DjangoAppConfig
+
+
+class AppConfig(DjangoAppConfig):
+    name = "consent_app"
+    verbose_name = "Edc Consent test app"
+    include_in_administration_section = False

edc_consent/baker_recipes.py → consent_app/baker_recipes.py

@@ -5,7 +5,7 @@
 from faker import Faker
 from model_bakery.recipe import Recipe, seq
 
-from .tests.models import SubjectConsent
+from .models import SubjectConsent, SubjectConsentV3
 
 fake = Faker()
 
@@ -34,3 +34,29 @@
     consent_signature=YES,
     site=Site.objects.get_current(),
 )
+
+subjectconsentv3 = Recipe(
+    SubjectConsentV3,
+    consent_datetime=get_utcnow,
+    dob=get_utcnow() - relativedelta(years=25),
+    first_name=fake.first_name,
+    last_name=fake.last_name,
+    # note, passes for model but won't pass validation in modelform clean()
+    initials="AA",
+    gender=MALE,
+    # will raise IntegrityError if multiple made without _quantity
+    identity=seq("12315678"),
+    # will raise IntegrityError if multiple made without _quantity
+    confirm_identity=seq("12315678"),
+    identity_type="passport",
+    is_dob_estimated="-",
+    language="en",
+    is_literate=YES,
+    is_incarcerated=NO,
+    study_questions=YES,
+    consent_reviewed=YES,
+    consent_copy=YES,
+    assessment_score=YES,
+    consent_signature=YES,
+    site=Site.objects.get_current(),
+)

edc_consent/tests/models.py → consent_app/models.py

@@ -17,15 +17,10 @@
     ReviewFieldsMixin,
     VulnerabilityFieldsMixin,
 )
-from edc_consent.model_mixins import (
-    ConsentDefinitionModelMixin,
-    ConsentModelMixin,
-    RequiresConsentFieldsModelMixin,
-)
+from edc_consent.model_mixins import ConsentModelMixin, RequiresConsentFieldsModelMixin
 
 
-class SubjectScreening(SiteModelMixin, ConsentDefinitionModelMixin, BaseUuidModel):
-    consent_definition = None
+class SubjectScreening(SiteModelMixin, BaseUuidModel):
 
     screening_identifier = models.CharField(max_length=25, unique=True)
 
@@ -74,6 +69,26 @@ class Meta(ConsentModelMixin.Meta):
         pass
 
 
+class SubjectConsentV1(SubjectConsent):
+    class Meta:
+        proxy = True
+
+
+class SubjectConsentV2(SubjectConsent):
+    class Meta:
+        proxy = True
+
+
+class SubjectConsentV3(SubjectConsent):
+    class Meta:
+        proxy = True
+
+
+class SubjectConsentUpdateToV3(SubjectConsent):
+    class Meta:
+        proxy = True
+
+
 class SubjectReconsent(
     ConsentModelMixin,
     SiteModelMixin,