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

meta_screening/model_mixins/__init__.py

@@ -3,3 +3,11 @@ from .eligibility_model_mixin import EligibilityModelMixin
 from .part_one_fields_model_mixin import PartOneFieldsModelMixin
 from .part_three_fields_model_mixin import PartThreeFieldsModelMixin
 from .part_two_fields_model_mixin import PartTwoFieldsModelMixin
+
+__all__ = [
+    "CalculatedModelMixin",
+    "EligibilityModelMixin",
+    "PartOneFieldsModelMixin",
+    "PartThreeFieldsModelMixin",
+    "PartTwoFieldsModelMixin",
+]

meta_screening/model_mixins/calculated_model_mixin.py

@@ -1,15 +1,14 @@
+from clinicedc_constants import MILLIMOLES_PER_LITER, TBD
 from django.db import models
 from edc_constants.choices import YES_NO_TBD
-from edc_constants.constants import TBD
-from edc_reportable.units import MICROMOLES_PER_LITER_DISPLAY, MILLIMOLES_PER_LITER
+from edc_reportable.units import MICROMOLES_PER_LITER_DISPLAY
 
 
 class CalculatedModelMixin(models.Model):
-
     # calculated
     calculated_egfr_value = models.DecimalField(
         verbose_name="eGFR",
-        max_digits=8,
+        max_digits=10,
         decimal_places=4,
         null=True,
         help_text="mL/min/1.73m2 (system calculated)",
@@ -18,7 +17,7 @@ class CalculatedModelMixin(models.Model):
     # converted if necessary
     converted_creatinine_value = models.DecimalField(
         verbose_name="Serum creatinine",
-        max_digits=8,
+        max_digits=10,
         decimal_places=4,
         null=True,
         help_text=f"{MICROMOLES_PER_LITER_DISPLAY} (system converted)",
@@ -27,7 +26,7 @@ class CalculatedModelMixin(models.Model):
     # converted if necessary
     converted_fbg_value = models.DecimalField(
         verbose_name="FBG level",
-        max_digits=8,
+        max_digits=10,
         decimal_places=4,
         null=True,
         help_text=f"{MILLIMOLES_PER_LITER} (system converted)",
@@ -35,7 +34,7 @@ class CalculatedModelMixin(models.Model):
 
     converted_fbg2_value = models.DecimalField(
         verbose_name="Repeat FBG level",
-        max_digits=8,
+        max_digits=10,
         decimal_places=4,
         null=True,
         help_text=f"{MILLIMOLES_PER_LITER} (system converted)",
@@ -44,7 +43,7 @@ class CalculatedModelMixin(models.Model):
     # converted if necessary
     converted_ogtt_value = models.DecimalField(
         verbose_name="OGTT (2-hours)",
-        max_digits=8,
+        max_digits=10,
         decimal_places=4,
         null=True,
         help_text=f"{MILLIMOLES_PER_LITER} (system converted)",
@@ -53,7 +52,7 @@ class CalculatedModelMixin(models.Model):
     # converted if necessary
     converted_ogtt2_value = models.DecimalField(
         verbose_name="Repeat OGTT (2-hours)",
-        max_digits=8,
+        max_digits=10,
         decimal_places=4,
         null=True,
         help_text=f"{MILLIMOLES_PER_LITER} (system converted)",

meta_screening/model_mixins/creatinine_fields_model_mixin.py

@@ -1,13 +1,11 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
-from django.utils.html import format_html
-from edc_constants.constants import NOT_APPLICABLE
 from edc_lab.choices import SERUM_CREATININE_UNITS_NA
 
 
 class CreatinineModelFieldsMixin(models.Model):
-
     creatinine_value = models.DecimalField(
-        verbose_name=format_html("Creatinine {}", "<B>level</B>"),
+        verbose_name="Creatinine level",
         max_digits=8,
         decimal_places=2,
         null=True,

meta_screening/model_mixins/eligibility_model_mixin.py

@@ -1,6 +1,6 @@
+from clinicedc_constants import TBD
 from django.db import models
 from edc_constants.choices import YES_NO_TBD
-from edc_constants.constants import TBD
 from edc_screening.model_mixins import (
     EligibilityModelMixin as BaseEligibilityModelMixin,
 )
@@ -9,7 +9,6 @@ from ..eligibility import MetaEligibility
 
 
 class EligibilityModelMixin(BaseEligibilityModelMixin):
-
     eligibility_cls = MetaEligibility
 
     eligible_part_one = models.CharField(
@@ -20,7 +19,7 @@ class EligibilityModelMixin(BaseEligibilityModelMixin):
         help_text="system calculated value",
     )
 
-    reasons_ineligible_part_one = models.TextField(max_length=150, null=True, editable=False)
+    reasons_ineligible_part_one = models.TextField(max_length=150, default="", editable=False)
 
     eligible_part_two = models.CharField(
         max_length=15,
@@ -30,7 +29,7 @@ class EligibilityModelMixin(BaseEligibilityModelMixin):
         help_text="system calculated value",
     )
 
-    reasons_ineligible_part_two = models.TextField(max_length=150, null=True, editable=False)
+    reasons_ineligible_part_two = models.TextField(max_length=150, default="", editable=False)
 
     eligible_part_three = models.CharField(
         max_length=15,
@@ -40,7 +39,9 @@ class EligibilityModelMixin(BaseEligibilityModelMixin):
         help_text="system calculated value",
     )
 
-    reasons_ineligible_part_three = models.TextField(max_length=150, null=True, editable=False)
+    reasons_ineligible_part_three = models.TextField(
+        max_length=150, default="", editable=False
+    )
 
     def get_report_datetime_for_eligibility_datetime(self):
         return self.part_three_report_datetime

meta_screening/model_mixins/part_one_fields_model_mixin.py

@@ -1,21 +1,19 @@
+from clinicedc_constants import YES
 from django.db import models
-from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 from django_crypto_fields.fields import EncryptedCharField
 from edc_constants.choices import SELECTION_METHOD, YES_NO, YES_NO_NA, YESDEFAULT_NO
-from edc_constants.constants import YES
 
 from ..choices import ETHNICITY
 from ..constants import PREG_YES_NO_NA
 
 
 class PartOneFieldsModelMixin(models.Model):
-
     screening_consent = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Has the subject given his/her verbal consent to be screened for "
             "the <u>META Phase 3</u> trial?"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO,
     )
@@ -27,10 +25,10 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     meta_phase_two = models.CharField(
-        verbose_name=format_html("Was the subject enrolled in the <u>META Phase 2</u> trial?"),
+        verbose_name=mark_safe("Was the subject enrolled in the <u>META Phase 2</u> trial?"),  # nosec B308
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -45,9 +43,9 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     art_six_months = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Has the patient been on anti-retroviral therapy for <u>at least 6 months</u>"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO_NA,
     )
@@ -60,10 +58,10 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     vl_undetectable = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Does the patient have a viral load measure of less than 1000 copies per ml "
             "taken <u>within the last 12 months</u>"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO_NA,
     )
@@ -76,24 +74,24 @@ class PartOneFieldsModelMixin(models.Model):
 
     staying_nearby_6 = models.CharField(
         verbose_name=(
-            "Is the patient planning to remain in the catchment area " "for at least 6 months"
+            "Is the patient planning to remain in the catchment area for at least 6 months"
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text="META PHASE_TWO ONLY",
         editable=False,
     )
 
     staying_nearby_12 = models.CharField(
-        verbose_name=format_html(
+        verbose_name=mark_safe(
             "Is the patient planning to remain in the catchment area "
             "for <u>at least 12 months</u>"
-        ),
+        ),  # nosec B308
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -102,18 +100,16 @@ class PartOneFieldsModelMixin(models.Model):
     )
 
     continue_part_two = models.CharField(
-        verbose_name=mark_safe(  # nosec B308
-            "Continue with <U>part two</U> of the screening process?"
-        ),
+        verbose_name=mark_safe("Continue with <U>part two</U> of the screening process?"),  # nosec B308
         max_length=15,
         choices=YESDEFAULT_NO,
         default=YES,
-        help_text=mark_safe(  # nosec B308
+        help_text=mark_safe(
             "<B>Important</B>: This response will be be automatically "
             "set to YES if:<BR><BR>"
             "- the participant meets the eligibility criteria for part one, or;<BR><BR>"
             "- the eligibility criteria for part two is already complete.<BR>"
-        ),
+        ),  # nosec B308
     )
 
     class Meta:

meta_screening/model_mixins/part_three_fields_model_mixin.py

@@ -1,14 +1,9 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.contrib import admin
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
-from edc_constants.choices import (
-    NO,
-    YES_NO,
-    YES_NO_NA,
-    YES_NO_PENDING_NA_GLUCOSE_SCREENING,
-)
-from edc_constants.constants import NOT_APPLICABLE
-from edc_glucose.model_mixins import (
+from edc_constants.choices import NO, YES_NO, YES_NO_PENDING_NA_GLUCOSE_SCREENING
+from edc_glucose.model_mixin_factories import (
     fasting_model_mixin_factory,
     fbg_model_mixin_factory,
     ogtt_model_mixin_factory,
@@ -23,24 +18,6 @@ from edc_vitals.model_mixins import (
 from .creatinine_fields_model_mixin import CreatinineModelFieldsMixin
 
 
-class FastingModelMixin(
-    fasting_model_mixin_factory(),
-    fasting_model_mixin_factory(
-        "repeat",
-        repeat_fasting=models.CharField(
-            verbose_name="Has the participant fasted?",
-            max_length=15,
-            choices=YES_NO_NA,
-            blank=False,
-            default=NOT_APPLICABLE,
-            help_text="As reported by patient",
-        ),
-    ),
-):
-    class Meta:
-        abstract = True
-
-
 class FbgModelMixin(
     fbg_model_mixin_factory(
         "fbg",
@@ -95,7 +72,18 @@ class OgttModelMixin(
 
 
 class PartThreeFieldsModelMixin(
-    FastingModelMixin,
+    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",
+        ),
+    ),
+    fasting_model_mixin_factory("repeat"),
     FbgModelMixin,
     OgttModelMixin,
     CreatinineModelFieldsMixin,
@@ -104,17 +92,15 @@ class PartThreeFieldsModelMixin(
     WeightHeightBmiModelMixin,
     models.Model,
 ):
-
     repeat_glucose_opinion = models.CharField(
         verbose_name=(
-            "In opinion of the clinician, " "should the glucose measurements be repeated?"
+            "In opinion of the clinician, should the glucose measurements be repeated?"
         ),
         max_length=15,
         choices=YES_NO,
         default=NO,
         help_text=(
-            "If repeated, must be at least 3 days "
-            "after the first glucose measures (FBG, OGTT)"
+            "If repeated, must be at least 3 days after the first glucose measures (FBG, OGTT)"
         ),
     )
 
@@ -137,7 +123,7 @@ class PartThreeFieldsModelMixin(
         verbose_name="Units (creatinine)",
         max_length=15,
         choices=SERUM_CREATININE_UNITS,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -193,5 +179,5 @@ class PartThreeFieldsModelMixin(
     def p3_repeat_appt(self):
         return self.repeat_appt_datetime
 
-    class Meta:
+    class Meta:  # noqa: DJ012
         abstract = True

meta_screening/model_mixins/part_two_fields_model_mixin.py

@@ -1,14 +1,13 @@
+from clinicedc_constants import NO, NOT_APPLICABLE
 from django.contrib import admin
 from django.db import models
 from edc_constants.choices import POS_NEG_NA, YES_NO, YES_NO_NA
-from edc_constants.constants import NO, NOT_APPLICABLE
 
 from ..choices import YES_NO_NOT_ELIGIBLE, YES_PENDING_NA
 from ..constants import PREG_YES_NO_NA
 
 
 class PartTwoFieldsModelMixin(models.Model):
-
     part_two_report_datetime = models.DateTimeField(
         verbose_name="Part 2 report date and time",
         null=True,
@@ -41,7 +40,7 @@ class PartTwoFieldsModelMixin(models.Model):
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -49,7 +48,7 @@ class PartTwoFieldsModelMixin(models.Model):
         verbose_name="Is there clinical evidence of liver disease",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text=(
             "Evidence of chronic liver disease: Jaundice, pruritus, "
@@ -63,7 +62,7 @@ class PartTwoFieldsModelMixin(models.Model):
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text=(
             "Evidence of alcoholism or acute alcohol intoxication: "
@@ -78,7 +77,7 @@ class PartTwoFieldsModelMixin(models.Model):
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text="lactic acidosis and/or diabetic ketoacidosis",
     )
@@ -89,7 +88,7 @@ class PartTwoFieldsModelMixin(models.Model):
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -99,7 +98,7 @@ class PartTwoFieldsModelMixin(models.Model):
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text=(
             "Including: decompensated heart failure, respiratory failure, "
@@ -114,7 +113,7 @@ class PartTwoFieldsModelMixin(models.Model):
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -125,7 +124,7 @@ class PartTwoFieldsModelMixin(models.Model):
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text=(
             "For example: Magnesium stearate, sodium carboxymethylcellulose, hypromellose"
@@ -136,7 +135,7 @@ class PartTwoFieldsModelMixin(models.Model):
         verbose_name="Is the patient known to have diabetes?",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -144,7 +143,7 @@ class PartTwoFieldsModelMixin(models.Model):
         verbose_name="Is the patient known to be taking anti-diabetic medications?",
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
     )
 
@@ -192,9 +191,9 @@ class PartTwoFieldsModelMixin(models.Model):
         choices=YES_PENDING_NA,
         default=NOT_APPLICABLE,
         help_text=(
-            "Only applicable if the patient missed the appointment for the second stage "
-            "of screening (P3), several attempts have been made to contact the patient, "
-            "and the patient has not started P3. See above"
+            "Only applicable if the patient missed the appointment for the second "
+            "stage of screening (P3), several attempts have been made to contact the "
+            "patient, and the patient has not started P3. See above"
         ),
     )
 
@@ -202,12 +201,14 @@ class PartTwoFieldsModelMixin(models.Model):
         verbose_name="Date decision made",
         null=True,
         blank=True,
-        help_text="Must be after the appointment date for the second stage of screening (P3)",
+        help_text=(
+            "Must be after the appointment date for the second stage of screening (P3)"
+        ),
     )
 
     p3_ltfu_comment = models.TextField(
         verbose_name="Provide any additional comments on this decision (or leave blank)",
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -215,5 +216,5 @@ class PartTwoFieldsModelMixin(models.Model):
     def p3_appt(self):
         return self.appt_datetime
 
-    class Meta:
+    class Meta:  # noqa: DJ012
         abstract = True

meta_screening/models/__init__.py

@@ -1,5 +1,14 @@
-from .icp_referral import IcpReferral
+# from .icp_referral import IcpReferral
 from .proxy_models import ScreeningPartOne, ScreeningPartThree, ScreeningPartTwo
 from .signals import update_p3_ltfu_on_post_save
 from .subject_refusal import SubjectRefusal
 from .subject_screening import SubjectScreening
+
+__all__ = [
+    "ScreeningPartOne",
+    "ScreeningPartThree",
+    "ScreeningPartTwo",
+    "SubjectRefusal",
+    "SubjectScreening",
+    "update_p3_ltfu_on_post_save",
+]

meta_screening/models/icp_referral.py

@@ -3,7 +3,8 @@ from django.db import models
 from django_crypto_fields.fields import EncryptedCharField
 from edc_constants.choices import GENDER, YES_NO, YES_NO_NA
 from edc_model.models import BaseUuidModel, HistoricalRecords
-from edc_sites.models import CurrentSiteManager, SiteModelMixin
+from edc_sites.managers import CurrentSiteManager
+from edc_sites.model_mixins import SiteModelMixin
 from edc_utils.date import get_utcnow
 
 from ..choices import ETHNICITY
@@ -20,7 +21,7 @@ class IcpReferralManager(models.Manager):
 
 
 class IcpReferral(SiteModelMixin, BaseUuidModel):
-    """ "Not used"""
+    """Not used"""
 
     subject_screening = models.OneToOneField(
         SubjectScreening, null=True, on_delete=models.PROTECT
@@ -90,28 +91,28 @@ class IcpReferral(SiteModelMixin, BaseUuidModel):
 
     referred_datetime = models.DateTimeField(null=True, help_text="Date and time of referral")
 
-    referral_reasons = models.TextField(null=True)
-
-    on_site = CurrentSiteManager()
+    referral_reasons = models.TextField(default="")
 
     objects = IcpReferralManager()
 
+    on_site = CurrentSiteManager()
+
     history = HistoricalRecords(inherit=True)
 
     def save(self, *args, **kwargs):
         try:
             SubjectScreening.objects.get(screening_identifier=self.screening_identifier)
-        except ObjectDoesNotExist:
+        except ObjectDoesNotExist as e:
             raise IcpReferralError(
                 f"Invalid META screening identifier. Got {self.screening_identifier}"
-            )
+            ) from e
         super().save(*args, **kwargs)
 
     def __str__(self):
         return f"{self.screening_identifier} {self.gender} {self.age_in_years}"
 
     def natural_key(self):
-        return (self.screening_identifier,)  # noqa
+        return (self.screening_identifier,)
 
     class Meta:
         pass

meta_screening/models/proxy_models.py

@@ -1,4 +1,6 @@
-from edc_constants.constants import NO, TBD, YES
+from clinicedc_constants import NO, TBD, YES
+
+from meta_consent.consents import consent_v1
 
 from .subject_screening import SubjectScreening
 
@@ -10,6 +12,8 @@ options = dict(
 
 
 class ScreeningPartOne(SubjectScreening):
+    consent_definition = consent_v1
+
     def save(self, *args, **kwargs):
         if self.eligible_part_one == YES:
             self.continue_part_two = YES
@@ -24,6 +28,8 @@ class ScreeningPartOne(SubjectScreening):
 
 
 class ScreeningPartTwo(SubjectScreening):
+    consent_definition = consent_v1
+
     class Meta:
         proxy = True
         verbose_name = "Subject Screening: Part Two"
@@ -31,6 +37,8 @@ class ScreeningPartTwo(SubjectScreening):
 
 
 class ScreeningPartThree(SubjectScreening):
+    consent_definition = consent_v1
+
     class Meta:
         proxy = True
         verbose_name = "Subject Screening: Part Three"

meta_screening/models/signals.py

@@ -1,6 +1,6 @@
+from clinicedc_constants import NOT_APPLICABLE, NULL_STRING
 from django.db.models.signals import post_save
 from django.dispatch import receiver
-from edc_constants.constants import NOT_APPLICABLE
 
 from .proxy_models import ScreeningPartThree
 
@@ -11,14 +11,13 @@ from .proxy_models import ScreeningPartThree
     sender=ScreeningPartThree,
     dispatch_uid="update_p3_ltfu_on_post_save",
 )
-def update_p3_ltfu_on_post_save(sender, instance, raw, created, **kwargs):
+def update_p3_ltfu_on_post_save(sender, instance, raw, created, **kwargs):  # noqa: ARG001
     """ """
-    if not raw:
-        if instance.p3_ltfu != NOT_APPLICABLE and instance.part_three_report_datetime:
-            msg = "[auto-updated p3 submitted]"
-            instance.p3_ltfu = NOT_APPLICABLE
-            instance.p3_ltfu_date = None
-            instance.p3_ltfu_comment = (
-                f"{msg} {instance.p3_ltfu_comment.replace(msg, '') or ''}".strip()
-            )
-            instance.save_base(update_fields=["p3_ltfu", "p3_ltfu_date", "p3_ltfu_comment"])
+    if not raw and instance.p3_ltfu != NOT_APPLICABLE and instance.part_three_report_datetime:
+        msg = "[auto-updated p3 submitted]"
+        instance.p3_ltfu = NOT_APPLICABLE
+        instance.p3_ltfu_date = None
+        instance.p3_ltfu_comment = (
+            f"{msg} {instance.p3_ltfu_comment.replace(msg, NULL_STRING) or NULL_STRING}"
+        ).strip()
+        instance.save_base(update_fields=["p3_ltfu", "p3_ltfu_date", "p3_ltfu_comment"])

meta_screening/models/subject_refusal.py

@@ -4,7 +4,8 @@ from edc_model.models import BaseUuidModel
 from edc_model.models.historical_records import HistoricalRecords
 from edc_model_fields.fields.other_charfield import OtherCharField
 from edc_search.model_mixins import SearchSlugManager
-from edc_sites.models import CurrentSiteManager, SiteModelMixin
+from edc_sites.managers import CurrentSiteManager
+from edc_sites.model_mixins import SiteModelMixin
 from edc_utils import get_utcnow
 
 from ..choices import REFUSAL_REASONS
@@ -17,7 +18,6 @@ class SubjectRefusalManager(SearchSlugManager, models.Manager):
 
 
 class SubjectRefusal(NonUniqueSubjectIdentifierModelMixin, SiteModelMixin, BaseUuidModel):
-
     subject_screening = models.ForeignKey(SubjectScreening, on_delete=models.PROTECT)
 
     subject_identifier = models.CharField(max_length=50, editable=False)
@@ -36,10 +36,10 @@ class SubjectRefusal(NonUniqueSubjectIdentifierModelMixin, SiteModelMixin, BaseU
 
     other_reason = OtherCharField()
 
-    on_site = CurrentSiteManager()
-
     objects = SubjectRefusalManager()
 
+    on_site = CurrentSiteManager()
+
     history = HistoricalRecords()
 
     def save(self, *args, **kwargs):
@@ -58,7 +58,7 @@ class SubjectRefusal(NonUniqueSubjectIdentifierModelMixin, SiteModelMixin, BaseU
         return (self.subject_identifier,)
 
     def get_search_slug_fields(self):
-        return ["screening_identifier", "subject_identifier"]
+        return "screening_identifier", "subject_identifier"
 
     class Meta:
         verbose_name = "Subject Refusal"