meta-edc 0.2.24__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_subject/models/followup_vitals.py

@@ -1,5 +1,5 @@
 from django.db import models
-from edc_model import models as edc_models
+from edc_model.models import BaseUuidModel
 from edc_vitals.model_mixins import (
     BloodPressureModelMixin,
     SimpleBloodPressureModelMixin,
@@ -14,9 +14,8 @@ class FollowupVitals(
     BloodPressureModelMixin,
     SimpleBloodPressureModelMixin,
     CrfModelMixin,
-    edc_models.BaseUuidModel,
+    BaseUuidModel,
 ):
-
     # TODO: Grading for blood pressure?? sokoine See DAIDS
     # TODO: Add action item modelmixin, grading like blood results
 
@@ -26,6 +25,6 @@ class FollowupVitals(
         choices=WEIGHT_DETERMINATION,
     )
 
-    class Meta(CrfModelMixin.Meta, edc_models.BaseUuidModel.Meta):
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Clinic follow up: Vitals"
         verbose_name_plural = "Clinic follow ups: Vitals"

meta_subject/models/glucose.py

@@ -1,31 +1,49 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 from edc_constants.choices import YES_NO
-from edc_glucose.model_mixins import FastingModelMixin, FbgModelMixin, OgttModelMixin
-from edc_model import models as edc_models
+from edc_glucose.model_mixin_factories import (
+    fasting_model_mixin_factory,
+    fbg_model_mixin_factory,
+    ogtt_model_mixin_factory,
+)
+from edc_model.models import BaseUuidModel
+from edc_utils import formatted_date
 
+from ..choices import ENDPOINT_CHOICES
+from ..constants import AMENDMENT_DATE
 from ..model_mixins import CrfModelMixin
 
 
 class Glucose(
     CrfModelMixin,
-    FastingModelMixin,
-    FbgModelMixin,
-    OgttModelMixin,
-    edc_models.BaseUuidModel,
+    fasting_model_mixin_factory(
+        None,
+        fasting=models.CharField(
+            verbose_name="Has the participant fasted?",
+            max_length=15,
+            choices=YES_NO,
+            default="",
+            blank=False,
+            help_text="As reported by patient",
+        ),
+    ),
+    fbg_model_mixin_factory("fbg"),
+    ogtt_model_mixin_factory("ogtt"),
+    BaseUuidModel,
 ):
-    # TODO: diagnosis of diabetes is OGTT 11.1mmol / L ONLY. Triggers EoS form
-    # TODO: move IFG to bloogresultglu. Use this form for OGTT only 27/01/2021
+    """A user model to capture both FBG/RBG and OGTT
 
-    """A user model to capture IFG and OGTT"""
+    See also GlucoseFbg.
+    """
 
     fbg_performed = models.CharField(
-        verbose_name="Was the IFG test performed?",
+        verbose_name="Was the FBG test performed?",
         max_length=15,
         choices=YES_NO,
     )
 
     fbg_not_performed_reason = models.CharField(
-        verbose_name="If NO, provide reason", max_length=150, null=True, blank=True
+        verbose_name="If NO, provide reason", max_length=150, default="", blank=True
     )
 
     ogtt_performed = models.CharField(
@@ -35,9 +53,26 @@ class Glucose(
     )
 
     ogtt_not_performed_reason = models.CharField(
-        verbose_name="If NO, provide reason", max_length=150, null=True, blank=True
+        verbose_name="If NO, provide reason", max_length=150, default="", blank=True
     )
 
-    class Meta(CrfModelMixin.Meta, edc_models.BaseUuidModel.Meta):
-        verbose_name = "Glucose (IFG, OGTT)"
-        verbose_name_plural = "Glucose (IFG, OGTT)"
+    endpoint_today = models.CharField(
+        verbose_name="Has the participant reached a study endpoint today?",
+        max_length=25,
+        choices=ENDPOINT_CHOICES,
+        default=NOT_APPLICABLE,
+        help_text=(
+            f"Response is applicable if reporting after {formatted_date(AMENDMENT_DATE)} "
+            "and both the FBG and OGTT were performed"
+        ),
+    )
+
+    repeat_fbg_date = models.DateField(
+        "If required, date particpant to repeat FBG",
+        null=True,
+        blank=True,
+    )
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Glucose (FBG/RBG, OGTT)"
+        verbose_name_plural = "Glucose (FBG/RBG, OGTT)"

meta_subject/models/glucose_fbg.py

@@ -0,0 +1,74 @@
+from clinicedc_constants import NO, NOT_APPLICABLE
+from django.db import models
+from edc_constants.choices import YES_NO
+from edc_glucose.model_mixin_factories import (
+    fasting_model_mixin_factory,
+    fbg_model_mixin_factory,
+)
+from edc_model.models import BaseUuidModel
+from edc_utils import formatted_date
+
+from ..choices import ENDPOINT_CHOICES
+from ..constants import AMENDMENT_DATE
+from ..model_mixins import CrfModelMixin
+
+
+class GlucoseFbg(
+    CrfModelMixin,
+    fasting_model_mixin_factory(
+        None,
+        fasting=models.CharField(
+            verbose_name="Has the participant fasted?",
+            max_length=15,
+            choices=YES_NO,
+            null=True,
+            blank=False,
+            help_text="As reported by patient",
+        ),
+    ),
+    fbg_model_mixin_factory("fbg"),
+    BaseUuidModel,
+):
+    fbg_performed = models.CharField(
+        verbose_name="Was the FBG test performed?",
+        max_length=15,
+        choices=YES_NO,
+    )
+
+    fbg_not_performed_reason = models.CharField(
+        verbose_name="If NO, provide reason",
+        max_length=150,
+        default="",
+        blank=True,
+    )
+
+    fasting_duration_estimated = models.CharField(
+        max_length=15,
+        default=NO,
+        editable=False,
+        help_text=(
+            "Set to YES for existing values before duration "
+            "question was added to the form, otherwise NO"
+        ),
+    )
+
+    endpoint_today = models.CharField(
+        verbose_name="Has the participant reached a study endpoint today?",
+        max_length=25,
+        choices=ENDPOINT_CHOICES,
+        default=NOT_APPLICABLE,
+        help_text=(
+            f"Response is applicable if reporting after {formatted_date(AMENDMENT_DATE)} "
+            "and both the FBG and OGTT were performed"
+        ),
+    )
+
+    repeat_fbg_date = models.DateField(
+        null=True,
+        blank=True,
+        help_text="Date should be within 1 week of report date",
+    )
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Glucose (FBG)"
+        verbose_name_plural = "Glucose (FBG)"

meta_subject/models/glucose_review.py

@@ -0,0 +1,15 @@
+from django.db import models
+from edc_model.models import BaseUuidModel
+
+from ..model_mixins import CrfModelMixin
+
+
+class RepeatFbgRequest(CrfModelMixin, BaseUuidModel):
+    """A model completed by the user to schedule a repeat FBG
+    to determine if participant meets endpoint criteria.
+    """
+
+    next_fbg_date = models.DateField("Date particpant will attend to repeat FBG")
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        pass

meta_subject/models/health_economics/__init__.py

@@ -0,0 +1,5 @@
+from .health_economics import HealthEconomics
+from .health_economics_simple import HealthEconomicsSimple
+from .health_economics_update import HealthEconomicsUpdate
+
+__all__ = ["HealthEconomics", "HealthEconomicsSimple", "HealthEconomicsUpdate"]

meta_subject/models/{health_economics.py → health_economics/health_economics.py}

@@ -1,20 +1,19 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
 from edc_constants.choices import YES_NO, YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE
-from edc_model import models as edc_models
+from edc_model.models import BaseUuidModel
 
-from ..choices import (
+from ...choices import (
     ACTIVITY_CHOICES,
     CHILDCARE_CHOICES,
     PAYEE_CHOICES,
     TRANSPORT_CHOICES,
 )
-from ..model_mixins import CrfModelMixin
+from ...model_mixins import CrfModelMixin
 
 
-class HealthEconomics(CrfModelMixin, edc_models.BaseUuidModel):
-
+class HealthEconomics(CrfModelMixin, BaseUuidModel):
     """Not used"""
 
     occupation = models.CharField(
@@ -80,17 +79,17 @@ class HealthEconomics(CrfModelMixin, edc_models.BaseUuidModel):
     )
 
     is_highest_earner = models.CharField(
-        verbose_name=("Are you the person who earns the highest income in your household?"),
+        verbose_name="Are you the person who earns the highest income in your household?",
         max_length=15,
         choices=YES_NO,
     )
 
     highest_earner = models.CharField(
         verbose_name=(
-            "If NO, what is the profession of the person " "who earns the highest income?"
+            "If NO, what is the profession of the person who earns the highest income?"
         ),
         max_length=50,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -100,7 +99,7 @@ class HealthEconomics(CrfModelMixin, edc_models.BaseUuidModel):
     )
 
     accomodation_per_month = models.IntegerField(
-        verbose_name=("How much do you/your family spend on rent and utilities in a month?"),
+        verbose_name="How much do you/your family spend on rent and utilities in a month?",
         help_text="in Shilling",
     )
 
@@ -181,7 +180,7 @@ class HealthEconomics(CrfModelMixin, edc_models.BaseUuidModel):
     )
 
     expenditure_other_detail = models.TextField(
-        verbose_name="If YES, what was the activity", null=True, blank=True
+        verbose_name="If YES, what was the activity", default="", blank=True
     )
 
     expenditure_other = models.IntegerField(
@@ -201,7 +200,7 @@ class HealthEconomics(CrfModelMixin, edc_models.BaseUuidModel):
     )
 
     healthcare_expenditure_month = models.IntegerField(
-        verbose_name=("How much in total has been spent on your healthcare in the last month?")
+        verbose_name="How much in total has been spent on your healthcare in the last month?"
     )
 
     routine_activities = models.CharField(
@@ -211,7 +210,7 @@ class HealthEconomics(CrfModelMixin, edc_models.BaseUuidModel):
     )
 
     routine_activities_other = models.CharField(
-        verbose_name="If OTHER, please specify", max_length=50, null=True, blank=True
+        verbose_name="If OTHER, please specify", max_length=50, default="", blank=True
     )
 
     off_work_days = models.DecimalField(
@@ -315,6 +314,6 @@ class HealthEconomics(CrfModelMixin, edc_models.BaseUuidModel):
         help_text="in Shilling",
     )
 
-    class Meta(CrfModelMixin.Meta, edc_models.BaseUuidModel.Meta):
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Health Economics (M2)"
         verbose_name_plural = "Health Economics (M2)"

meta_subject/models/{health_economics_simple.py → health_economics/health_economics_simple.py}

@@ -1,13 +1,12 @@
 from django.db import models
 from edc_constants.choices import MARITAL_STATUS
-from edc_he.model_mixins import HealthEconomicsEducationModelMixin
+from edc_he.model_mixins import EducationModelMixin
 from edc_model.models import BaseUuidModel
 
-from ..model_mixins import CrfModelMixin
+from ...model_mixins import CrfModelMixin
 
 
-class HealthEconomicsSimple(HealthEconomicsEducationModelMixin, CrfModelMixin, BaseUuidModel):
-
+class HealthEconomicsSimple(EducationModelMixin, CrfModelMixin, BaseUuidModel):
     occupation = models.CharField(
         verbose_name="What is your occupation/profession?", max_length=50
     )

meta_subject/models/health_economics/health_economics_update.py

@@ -0,0 +1,97 @@
+from clinicedc_constants import NOT_APPLICABLE
+from django.core.validators import MaxValueValidator, MinValueValidator
+from django.db import models
+from django.utils.translation import gettext as _
+from edc_constants.choices import YES_NO
+from edc_crf.model_mixins import SingletonCrfModelMixin
+from edc_he.choices import RELATIONSHIP_CHOICES, STATUS
+from edc_he.model_mixin_factories import income_model_mixin_factory
+from edc_he.model_mixins import HouseholdModelMixin
+from edc_model.models import BaseUuidModel
+from edc_model_fields.fields import OtherCharField
+
+from ...model_mixins import CrfModelMixin
+
+
+class HealthEconomicsUpdate(
+    HouseholdModelMixin,
+    income_model_mixin_factory(
+        field_data={
+            "avg_income": _(
+                "Thinking over the last 12 months, can you tell me "
+                "what the average earnings of the household have been?"
+            ),
+        }
+    ),
+    SingletonCrfModelMixin,
+    CrfModelMixin,
+    BaseUuidModel,
+):
+    """A user model to learn about the household, wealth and
+    opportunities in the community
+
+    Introduced 22 FEB 2024
+    """
+
+    hoh = models.CharField(
+        verbose_name=_("Are you the household head?"),
+        max_length=15,
+        choices=YES_NO,
+        help_text=_(
+            "By head of the household we mean the main decision "
+            "maker in the household. The head can be either male or "
+            "female. If two people are equal decision-makers, take "
+            "the older person."
+        ),
+    )
+
+    relationship_to_hoh = models.CharField(
+        verbose_name=_("If No, what is your relationship to the household head?"),
+        max_length=25,
+        choices=RELATIONSHIP_CHOICES,
+        default=NOT_APPLICABLE,
+        help_text=_("Not applicable if patient is head of household"),
+    )
+
+    relationship_to_hoh_other = OtherCharField(
+        verbose_name=_("If OTHER relationship, specify ..."),
+    )
+
+    rooms = models.IntegerField(
+        verbose_name=_(
+            "How many rooms does your dwelling have in total, without counting "
+            "the bathrooms/ toilets or hallways/passageways?"
+        ),
+        validators=[MinValueValidator(1), MaxValueValidator(30)],
+    )
+
+    bedrooms = models.IntegerField(
+        verbose_name=_("How many rooms are used for sleeping in your dwelling?"),
+        validators=[MinValueValidator(0), MaxValueValidator(30)],
+    )
+
+    beds = models.IntegerField(
+        verbose_name=_("How many beds does your dwelling have in total?"),
+        validators=[MinValueValidator(0), MaxValueValidator(30)],
+    )
+
+    external_dependents = models.IntegerField(
+        verbose_name=_(
+            "Outside of this household, how many other people depend on this "
+            "household's income?"
+        ),
+        validators=[MinValueValidator(0), MaxValueValidator(15)],
+        help_text=_(
+            "Insert '0' if no dependents other than the members in the household roster"
+        ),
+    )
+
+    financial_status = models.CharField(
+        verbose_name=_("Would you say your household's financial situation is?"),
+        max_length=25,
+        choices=STATUS,
+    )
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Health Economics: Baseline"
+        verbose_name_plural = "Health Economics: Baseline"

meta_subject/models/hepatitis_test.py

@@ -8,7 +8,6 @@ from ..model_mixins import CrfModelMixin
 
 
 class HepatitisTest(CrfModelMixin, BaseUuidModel):
-
     # Hepatitis B Surface Antigen Test
     hbsag_performed = models.CharField(
         verbose_name="Was Hepatitis B Surface Antigen test performed?",
@@ -21,7 +20,7 @@ class HepatitisTest(CrfModelMixin, BaseUuidModel):
         verbose_name=mark_safe("<u>HbSAg</u>"),  # nosec B308
         max_length=15,
         choices=POS_NEG,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -44,7 +43,7 @@ class HepatitisTest(CrfModelMixin, BaseUuidModel):
         verbose_name=mark_safe("<u>HCV</u>"),  # nosec B308
         max_length=15,
         choices=POS_NEG,
-        null=True,
+        default="",
         blank=True,
     )
 

meta_subject/models/hiv_exit_review.py

@@ -0,0 +1,44 @@
+from clinicedc_constants import NULL_STRING, YES
+from django.db import models
+from edc_constants.choices import YES_NO
+from edc_crf.model_mixins import SingletonCrfModelMixin
+from edc_model.models import BaseUuidModel
+
+from meta_lists.models import ArvRegimens
+
+from ..model_mixins import ArvReviewModelMixin, CrfModelMixin
+
+
+class HivExitReview(SingletonCrfModelMixin, ArvReviewModelMixin, CrfModelMixin, BaseUuidModel):
+    available = models.CharField(
+        verbose_name="Are HIV test result and treatment information available?",
+        max_length=25,
+        default=YES,
+        choices=YES_NO,
+    )
+
+    not_available_reason = models.TextField(
+        verbose_name="If not available, please explain ...",
+        default=NULL_STRING,
+        blank=True,
+    )
+
+    current_arv_regimen = models.ForeignKey(
+        ArvRegimens,
+        on_delete=models.PROTECT,
+        related_name="last_arv_regimen",
+        verbose_name="Which antiretroviral therapy regimen is the patient currently on?",
+        null=True,
+        blank=True,
+    )
+
+    comment = models.TextField(
+        verbose_name="Any other comment?",
+        default=NULL_STRING,
+        blank=True,
+        help_text="May be left blank.",
+    )
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "HIV Exit Review"
+        verbose_name_plural = "HIV Exit Review"

meta_subject/models/malaria_test.py

@@ -1,37 +1,9 @@
-from django.db import models
-from edc_constants.choices import PRESENT_ABSENT_NA, YES_NO
-from edc_constants.constants import NOT_APPLICABLE
+from edc_microscopy.model_mixins import MalariaTestModelMixin
 from edc_model.models import BaseUuidModel
 
-from ..choices import MALARIA_TEST_CHOICES
 from ..model_mixins import CrfModelMixin
 
 
-class MalariaTest(CrfModelMixin, BaseUuidModel):
-
-    performed = models.CharField(
-        verbose_name="Was the malaria test performed?",
-        max_length=15,
-        choices=YES_NO,
-    )
-
-    not_performed_reason = models.CharField(
-        verbose_name="If NO, provide reason", max_length=150, null=True, blank=True
-    )
-
-    diagnostic_type = models.CharField(
-        verbose_name="Diagnostic test used",
-        max_length=15,
-        choices=MALARIA_TEST_CHOICES,
-        default=NOT_APPLICABLE,
-    )
-
-    result = models.CharField(
-        verbose_name="Result",
-        max_length=25,
-        choices=PRESENT_ABSENT_NA,
-        default=NOT_APPLICABLE,
-    )
-
-    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+class MalariaTest(MalariaTestModelMixin, CrfModelMixin, BaseUuidModel):
+    class Meta(MalariaTestModelMixin.Meta, CrfModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Malaria Test"

meta_subject/models/next_appointment.py

@@ -0,0 +1,15 @@
+from __future__ import annotations
+
+from edc_appointment.model_mixins import NextAppointmentCrfModelMixin
+from edc_model.models import BaseUuidModel
+
+from ..model_mixins import CrfModelMixin
+
+__all__ = ["NextAppointment"]
+
+
+class NextAppointment(NextAppointmentCrfModelMixin, CrfModelMixin, BaseUuidModel):
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Next Appointment"
+        verbose_name_plural = "Next Appointments"
+        indexes = CrfModelMixin.Meta.indexes + BaseUuidModel.Meta.indexes

meta_subject/models/off_study_drug.py

@@ -8,7 +8,6 @@ from ..model_mixins import CrfModelMixin
 
 
 class OffStudyMedication(CrfModelMixin, BaseUuidModel):
-
     last_dose_date = models.DateField(
         verbose_name="Date of last known dose",
         validators=[date_not_before_study_start, date_not_future],

meta_subject/models/other_arv_regimens_detail.py

@@ -3,7 +3,7 @@ from edc_crf.model_mixins import CrfInlineModelMixin
 from edc_model.models import BaseUuidModel, HistoricalRecords
 from edc_model.validators import date_is_not_now, date_not_future
 from edc_model_fields.fields import OtherCharField
-from edc_sites.models import CurrentSiteManager
+from edc_sites.managers import CurrentSiteManager
 
 from meta_lists.models import ArvRegimens
 
@@ -11,7 +11,6 @@ from .other_arv_regimens import OtherArvRegimens
 
 
 class InlineModelManager(models.Manager):
-
     use_in_migrations = True
 
     def get_by_natural_key(
@@ -23,7 +22,6 @@ class InlineModelManager(models.Manager):
 
 
 class OtherArvRegimensDetail(CrfInlineModelMixin, BaseUuidModel):
-
     other_arv_regimens = models.ForeignKey(
         OtherArvRegimens,
         on_delete=models.PROTECT,
@@ -47,10 +45,10 @@ class OtherArvRegimensDetail(CrfInlineModelMixin, BaseUuidModel):
         blank=True,
     )
 
-    notes = models.CharField(verbose_name="Notes", max_length=100, null=True, blank=True)
+    notes = models.CharField(verbose_name="Notes", max_length=100, default="", blank=True)
 
-    on_site = CurrentSiteManager()
     objects = InlineModelManager()
+    on_site = CurrentSiteManager()
     history = HistoricalRecords(inherit=True)
 
     def natural_key(self) -> tuple:

meta_subject/models/patient_history.py

@@ -1,7 +1,7 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 from django.utils.safestring import mark_safe
 from edc_constants.choices import YES_NO, YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE
 from edc_model.models import BaseUuidModel
 from edc_model_fields.fields import OtherCharField
 
@@ -12,7 +12,6 @@ from ..model_mixins import ArvHistoryModelMixin, CrfModelMixin
 
 
 class PatientHistory(ArvHistoryModelMixin, CrfModelMixin, BaseUuidModel):
-
     symptoms = models.ManyToManyField(
         Symptoms, verbose_name="Do you have any of the following symptoms?"
     )
@@ -54,7 +53,7 @@ class PatientHistory(ArvHistoryModelMixin, CrfModelMixin, BaseUuidModel):
         verbose_name="Has the patient been diagnosed with dyslipidaemia?",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -78,7 +77,7 @@ class PatientHistory(ArvHistoryModelMixin, CrfModelMixin, BaseUuidModel):
     other_dyslipidaemia_rx = models.CharField(
         verbose_name="What medication is the patient currently taking for dyslipidaemia?",
         max_length=50,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -86,14 +85,14 @@ class PatientHistory(ArvHistoryModelMixin, CrfModelMixin, BaseUuidModel):
     concomitant_conditions = models.TextField(
         verbose_name="Does the patient have any other conditions not mentioned above?",
         max_length=250,
-        null=True,
+        default="",
         blank=True,
     )
     # PHASE_THREE_ONLY
     concomitant_medications = models.TextField(
         verbose_name="Is the patient taking any concomitant medications?",
         max_length=250,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -130,13 +129,12 @@ class PatientHistory(ArvHistoryModelMixin, CrfModelMixin, BaseUuidModel):
         verbose_name=mark_safe(  # nosec B308
             "If other symptom in the <u>past year</u>, please specify ..."
         ),
-        null=True,
         blank=True,
     )
 
     dm_in_family = models.CharField(
         verbose_name=(
-            "Has anyone in your immediate family " "ever been diagnosed with diabetes?"
+            "Has anyone in your immediate family ever been diagnosed with diabetes?"
         ),
         max_length=15,
         choices=YES_NO,