meta-edc 1.1.10__py3-none-any.whl → 1.1.13__py3-none-any.whl

meta_subject/form_validators/dm_followup_form_validator.py

@@ -11,7 +11,6 @@ from meta_prn.models import DmReferral
 
 class DmFollowupFormValidator(CrfFormValidator):
     def clean(self):
-
         # referral_date must be before report datetime
         if (
             self.report_datetime
@@ -228,8 +227,10 @@ class DmFollowupFormValidator(CrfFormValidator):
             and self.cleaned_data.get("on_dm_medications") == YES
         ):
             confirmed = self.cleaned_data.get("visual_score_confirmed")
-            if confirmed is not None:
-                if int(self.cleaned_data.get("visual_score_slider", "0")) != confirmed:
-                    raise forms.ValidationError(
-                        {"visual_score_confirmed": "Does not match visual score above."}
-                    )
+            if (
+                confirmed is not None
+                and int(self.cleaned_data.get("visual_score_slider", "0")) != confirmed
+            ):
+                raise forms.ValidationError(
+                    {"visual_score_confirmed": "Does not match visual score above."}
+                )

meta_subject/form_validators/glucose_form_validator.py

@@ -70,13 +70,11 @@ class GlucoseFormValidator(FbgOgttFormValidatorMixin, CrfFormValidator):
 
     def is_endpoint(self):
         value = NO
-        if self.cleaned_data.get("fbg_value") >= Decimal("7.0") and self.cleaned_data.get(
+        if (self.cleaned_data.get("fbg_value") >= Decimal("7.0") and self.cleaned_data.get(
             "ogtt_value"
-        ) >= Decimal("11.1"):
-            value = YES
-        elif self.cleaned_data.get("fbg_value") < Decimal("7.0") and self.cleaned_data.get(
+        ) >= Decimal("11.1")) or (self.cleaned_data.get("fbg_value") < Decimal("7.0") and self.cleaned_data.get(
             "ogtt_value"
-        ) >= Decimal("11.1"):
+        ) >= Decimal("11.1")):
             value = YES
         elif self.cleaned_data.get("fbg_value") >= Decimal("7.0") and self.cleaned_data.get(
             "ogtt_value"

meta_subject/forms/__init__.py

@@ -35,3 +35,44 @@ from .subject_visit_form import SubjectVisitForm
 from .subject_visit_missed_form import SubjectVisitMissedForm
 from .urine_dipstick_test_form import UrineDipstickTestForm
 from .urine_pregnancy_form import UrinePregnancyForm
+
+__all__ = [
+    "BirthOutcomesForm",
+    "BloodResultsFbcForm",
+    "BloodResultsHba1cForm",
+    "BloodResultsInsForm",
+    "BloodResultsInsForm",
+    "BloodResultsLftForm",
+    "BloodResultsLipidsForm",
+    "BloodResultsRftForm",
+    "ComplicationsGlycemiaForm",
+    "ConcomitantMedicationForm",
+    "DeliveryForm",
+    "DmEndpointForm",
+    "DmFollowupForm",
+    "EgfrDropNotificationForm",
+    "Eq5d3lForm",
+    "FollowupExaminationForm",
+    "FollowupVitalsForm",
+    "GlucoseFbgForm",
+    "GlucoseForm",
+    "HealthEconomicsSimpleForm",
+    "HealthEconomicsUpdateForm",
+    "HepatitisTestForm",
+    "MalariaTestForm",
+    "MedicationAdherenceForm",
+    "MnsiForm",
+    "NextAppointmentForm",
+    "OtherArvRegimensDetailForm",
+    "OtherArvRegimensForm",
+    "PatientHistoryForm",
+    "PhysicalExamForm",
+    "PregnancyUpdateForm",
+    "Sf12Form",
+    "StudyMedicationForm",
+    "SubjectRequisitionForm",
+    "SubjectVisitForm",
+    "SubjectVisitMissedForm",
+    "UrineDipstickTestForm",
+    "UrinePregnancyForm",
+]

meta_subject/forms/blood_results/__init__.py

@@ -4,3 +4,12 @@ from .blood_results_ins_form import BloodResultsInsForm
 from .blood_results_lft_form import BloodResultsLftForm
 from .blood_results_lipids_form import BloodResultsLipidsForm
 from .blood_results_rft_form import BloodResultsRftForm
+
+__all__ = [
+    "BloodResultsFbcForm",
+    "BloodResultsHba1cForm",
+    "BloodResultsInsForm",
+    "BloodResultsLftForm",
+    "BloodResultsLipidsForm",
+    "BloodResultsRftForm",
+]

meta_subject/forms/blood_results/blood_results_rft_form.py

@@ -30,7 +30,6 @@ class BloodResultsRftFormValidator(
         if self.cleaned_data.get("creatinine_value") and self.cleaned_data.get(
             "creatinine_units"
         ):
-
             if is_baseline(self.related_visit):
                 baseline_egfr_value = None
             else:
@@ -83,7 +82,7 @@ class BloodResultsRftForm(ActionItemCrfFormMixin, CrfModelFormMixin, forms.Model
     class Meta(ActionItemCrfFormMixin.Meta):
         model = BloodResultsRft
         fields = "__all__"
-        help_texts = {
+        help_texts = {  # noqa: RUF012
             "action_identifier": "(read-only)",
             "egfr_value": mark_safe(  # nosec B308
                 "Calculated using 2009 CKD-EPI Creatinine. "

meta_subject/forms/diabetes/__init__.py

@@ -1,2 +1,4 @@
 from .dm_endpoint_form import DmEndpointForm
 from .dm_followup_form import DmFollowupForm
+
+__all__ = ["DmEndpointForm", "DmFollowupForm"]

meta_subject/forms/diabetes/dm_followup_form.py

@@ -17,8 +17,8 @@ class DmFollowupForm(CrfModelFormMixin, ActionItemCrfFormMixin, forms.ModelForm)
     class Meta:
         model = DmFollowup
         fields = "__all__"
-        help_text = {"action_identifier": "(read-only)"}
-        widgets = {
+        help_text = {"action_identifier": "(read-only)"}  # noqa: RUF012
+        widgets = {  # noqa: RUF012
             "action_identifier": forms.TextInput(
                 attrs={"required": False, "readonly": "readonly"}
             ),

meta_subject/forms/followup_vitals_form.py

@@ -9,7 +9,6 @@ from ..models import FollowupVitals
 
 class FollowupVitalsFormValidator(CrfFormValidator):
     def clean(self):
-
         self.required_if(
             YES, field="waist_circumference_measured", field_required="waist_circumference"
         )
@@ -17,13 +16,9 @@ class FollowupVitalsFormValidator(CrfFormValidator):
         visit_code = (
             f"{self.related_visit.visit_code}.{self.related_visit.visit_code_sequence}"
         )
-        require_waist_circumference_comment = (
-            True
-            if (
-                visit_code in [f"{MONTH36}.0", f"{MONTH48}.0"]
-                or self.cleaned_data.get("waist_circumference_measured") == YES
-            )
-            else False
+        require_waist_circumference_comment = bool(
+            visit_code in [f"{MONTH36}.0", f"{MONTH48}.0"]
+            or self.cleaned_data.get("waist_circumference_measured") == YES
         )
 
         if (

meta_subject/forms/health_economics/__init__.py

@@ -1,2 +1,4 @@
 from .health_economics_simple_form import HealthEconomicsSimpleForm
 from .health_economics_update_form import HealthEconomicsUpdateForm
+
+__all__ = ["HealthEconomicsSimpleForm", "HealthEconomicsUpdateForm"]

meta_subject/forms/next_appointment_form.py

@@ -18,17 +18,16 @@ class NextAppointmentCrfFormValidator(
 
 
 class NextAppointmentForm(CrfModelFormMixin, forms.ModelForm):
-
     form_validator_cls = NextAppointmentCrfFormValidator
 
     class Meta:
         model = NextAppointment
         fields = "__all__"
-        labels = {
+        labels = {  # noqa: RUF012
             "appt_date": "Next scheduled appointment date",
             "visitschedule": "Next scheduled appointment",
         }
-        help_texts = {
+        help_texts = {  # noqa: RUF012
             "appt_date": (
                 "Default recommended. If changed, should be within "
                 "the window period of the next appointment"

meta_subject/forms/slider_widget.py

@@ -22,4 +22,4 @@ class SliderWidget(Input):
         return context
 
     class Media:
-        css = {"all": ("meta_subject/slider.css",)}
+        css = {"all": ("meta_subject/slider.css",)}  # noqa: RUF012

meta_subject/forms/study_medication_form.py

@@ -28,14 +28,17 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
         except AttributeError:
             self.raise_validation_error("Subject visit is required", INVALID_ERROR)
         else:
-            if subject_visit.visit_code == DAY1 and subject_visit.visit_code_sequence == 0:
-                if (
+            if (
+                subject_visit.visit_code == DAY1
+                and subject_visit.visit_code_sequence == 0
+                and (
                     self.cleaned_data.get("dosage_guideline")
                     and self.cleaned_data.get("dosage_guideline").dose != 1000
-                ):
-                    raise forms.ValidationError(
-                        {"dosage_guideline": "Invalid. Expected 1000mg/day at baseline"}
-                    )
+                )
+            ):
+                raise forms.ValidationError(
+                    {"dosage_guideline": "Invalid. Expected 1000mg/day at baseline"}
+                )
 
     def validate_stock_codes_are_dispensed(self):
         if self.cleaned_data.get("stock_codes"):
@@ -59,7 +62,7 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
                             self.subject_identifier
                         ),
                     )
-                except ObjectDoesNotExist:
+                except ObjectDoesNotExist as e:
                     raise forms.ValidationError(
                         {
                             "stock_codes": (
@@ -68,7 +71,7 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
                                 "Please check the bottle or check with your pharmacist."
                             )
                         }
-                    )
+                    ) from e
 
 
 class StudyMedicationForm(CrfModelFormMixin, forms.ModelForm):

meta_subject/management/commands/create_missing_refills.py

@@ -39,14 +39,14 @@ def create_missing_rx_refills():
     print_messages(messages)
 
 
-def save_or_raise(obj, messages: list[str] = None):
+def save_or_raise(obj, messages: list[str] | None = None):
     try:
         obj.save()
     except NextStudyMedicationError as e:
         messages.append(f"NextStudyMedicationError: {e}")
     except ObjectDoesNotExist as e:
         messages.append(
-            f"ObjectDoesNotExist: {obj.subject_identifier}, {obj.related_visit}, {str(e)}"
+            f"ObjectDoesNotExist: {obj.subject_identifier}, {obj.related_visit}, {e!s}"
         )
     except StudyMedicationError as e:
         messages.append(f"StudyMedicationError: {e}")
@@ -65,5 +65,5 @@ def print_messages(messages: list[str]):
 
 
 class Command(BaseCommand):
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         create_missing_rx_refills()

meta_subject/management/commands/create_missing_rx.py

@@ -39,5 +39,5 @@ def create_missing_rx():
 
 
 class Command(BaseCommand):
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         create_missing_rx()

meta_subject/management/commands/missed.py

@@ -46,21 +46,21 @@ def get_missed_visit_codes(subject_identifier: str) -> list[str]:
     """Return visit codes from SubjectVisitMissed
     reports for this subject.
     """
-    codes = []
-    for missed_obj in SubjectVisitMissed.objects.filter(
-        subject_visit__subject_identifier=subject_identifier
-    ).order_by("report_datetime"):
-        codes.append(missed_obj.subject_visit.visit_code)
-    return codes
+    return [
+        missed_obj.subject_visit.visit_code
+        for missed_obj in SubjectVisitMissed.objects.filter(
+            subject_visit__subject_identifier=subject_identifier
+        ).order_by("report_datetime")
+    ]
 
 
 def get_missed_visit_codes_from_subject_visit(subject_identifier: str) -> list[str]:
-    codes = []
-    for missed_obj in SubjectVisit.objects.filter(
-        subject_identifier=subject_identifier, reason=MISSED_VISIT
-    ).order_by("report_datetime"):
-        codes.append(missed_obj.visit_code)
-    return codes
+    return [
+        missed_obj.visit_code
+        for missed_obj in SubjectVisit.objects.filter(
+            subject_identifier=subject_identifier, reason=MISSED_VISIT
+        ).order_by("report_datetime")
+    ]
 
 
 def run():
@@ -70,9 +70,8 @@ def run():
         RegisteredSubject.objects.all().order_by("subject_identifier"), total=total
     ):
         missed_visit_codes = get_missed_visit_codes(obj.subject_identifier)
-        if len(missed_visit_codes) > 2:
-            if is_sublist(missed_visit_codes, visit_codes):
-                result.update({obj.subject_identifier: missed_visit_codes})
+        if len(missed_visit_codes) > 2 and is_sublist(missed_visit_codes, visit_codes):
+            result.update({obj.subject_identifier: missed_visit_codes})
     return result
 
 
@@ -83,9 +82,8 @@ def run2():
         RegisteredSubject.objects.all().order_by("subject_identifier"), total=total
     ):
         missed_visit_codes = get_missed_visit_codes_from_subject_visit(obj.subject_identifier)
-        if len(missed_visit_codes) > 2:
-            if is_sublist(missed_visit_codes, visit_codes):
-                result.update({obj.subject_identifier: missed_visit_codes})
+        if len(missed_visit_codes) > 2 and is_sublist(missed_visit_codes, visit_codes):
+            result.update({obj.subject_identifier: missed_visit_codes})
     return result
 
 
@@ -102,9 +100,8 @@ def new_appointments():
             timepoint_datetime__lte=get_utcnow(),
         ).order_by("timepoint_datetime"):
             codes.append(appointment.visit_code)
-            if len(codes) >= 2:
-                if is_sublist(codes, visit_codes):
-                    result.update({obj.subject_identifier: codes})
+            if len(codes) >= 2 and is_sublist(codes, visit_codes):
+                result.update({obj.subject_identifier: codes})
     return result
 
 
@@ -133,7 +130,7 @@ def new_appointments_within(months: int):
 class Result:
     """Used with run3."""
 
-    def __init__(
+    def __init__(  # noqa: PLR0913
         self,
         subject_identifier: str,
         sid: str,
@@ -166,7 +163,7 @@ class Result:
         self.visit_codes = codes
 
     def __str__(self):
-        return self.subject_identifier, self.visit_codes
+        return f"{self.subject_identifier} {self.visit_codes}"
 
     def formatted(self) -> str:
         """Copy/paste output into text file"""

meta_subject/metadata_rules/__init__.py

@@ -1 +1,3 @@
 from .metadata_rules import HealthEconomicsRuleGroup
+
+__all__ = ["HealthEconomicsRuleGroup"]

meta_subject/metadata_rules/predicates.py

@@ -71,26 +71,21 @@ class Predicates(PersistantSingletonMixin):
     app_label = "meta_subject"
 
     @staticmethod
-    def next_appt_required(visit, **kwargs):
-        if visit.appointment.next and visit.appointment.next.appt_status == NEW_APPT:
-            return True
-        return False
+    def next_appt_required(visit, **kwargs):  # noqa: ARG004
+        return visit.appointment.next and visit.appointment.next.appt_status == NEW_APPT
 
     @staticmethod
-    def glucose_required(visit, **kwargs):
-        if visit.visit_code in [MONTH12, MONTH24, MONTH36, MONTH48]:
-            return True
-        return False
+    def glucose_required(visit, **kwargs):  # noqa: ARG004
+        return visit.visit_code in [MONTH12, MONTH24, MONTH36, MONTH48]
 
     @staticmethod
-    def glucose_fbg_required(visit, **kwargs):
-        if visit.report_datetime >= datetime(2024, 3, 4, tzinfo=ZoneInfo("UTC")):
-            if visit.visit_code in [MONTH6, MONTH18, MONTH30, MONTH42]:
-                return True
-        return False
+    def glucose_fbg_required(visit, **kwargs):  # noqa: ARG004
+        return visit.report_datetime >= datetime(
+            2024, 3, 4, tzinfo=ZoneInfo("UTC")
+        ) and visit.visit_code in [MONTH6, MONTH18, MONTH30, MONTH42]
 
     @staticmethod
-    def pregnancy_notification_exists(visit, **kwargs):
+    def pregnancy_notification_exists(visit, **kwargs):  # noqa: ARG004
         model_cls = django_apps.get_model("meta_prn.pregnancynotification")
         try:
             model_cls.objects.get(subject_identifier=visit.subject_identifier, delivered=False)
@@ -101,7 +96,7 @@ class Predicates(PersistantSingletonMixin):
         return required
 
     @staticmethod
-    def hba1c_crf_required(visit, **kwargs) -> bool:
+    def hba1c_crf_required(visit, **kwargs) -> bool:  # noqa: ARG004
         """Require at baseline visit if not recorded on the
         screening form.
         """
@@ -117,7 +112,7 @@ class Predicates(PersistantSingletonMixin):
         return required
 
     @staticmethod
-    def hba1c_requisition_required(visit, **kwargs) -> bool:
+    def hba1c_requisition_required(visit, **kwargs) -> bool:  # noqa: ARG004
         """Require at baseline visit if not recorded on the
         screening form.
         """
@@ -133,7 +128,7 @@ class Predicates(PersistantSingletonMixin):
         return required
 
     @staticmethod
-    def insulin_crf_required(visit, **kwargs) -> bool:
+    def insulin_crf_required(visit, **kwargs) -> bool:  # noqa: ARG004
         """Require at baseline visit"""
         required = False
         if (
@@ -150,7 +145,7 @@ class Predicates(PersistantSingletonMixin):
         return required
 
     @staticmethod
-    def insulin_requisition_required(visit, **kwargs) -> bool:
+    def insulin_requisition_required(visit, **kwargs) -> bool:  # noqa: ARG004
         """Require at baseline visit"""
         required = False
         if (
@@ -166,7 +161,7 @@ class Predicates(PersistantSingletonMixin):
             required = True
         return required
 
-    def health_economics_required(self, visit, **kwargs) -> bool:
+    def health_economics_required(self, visit, **kwargs) -> bool:  # noqa: ARG002
         """Returns true if HE was not completed at week 2"""
 
         required = False
@@ -190,7 +185,7 @@ class Predicates(PersistantSingletonMixin):
                 required = True
         return required
 
-    def health_economics_update_required(self, visit, **kwargs) -> bool:
+    def health_economics_update_required(self, visit, **kwargs) -> bool:  # noqa: ARG002
         """Returns true if `healtheconomicsupdate` was not completed at
         month 3 or ever.
 
@@ -212,7 +207,7 @@ class Predicates(PersistantSingletonMixin):
             required = True
         return required
 
-    def mnsi_required(self, visit, **kwargs) -> bool:
+    def mnsi_required(self, visit, **kwargs) -> bool:  # noqa: ARG002
         """Returns True if:
         - MNSI assessment not performed in the 1, 3 or 6M visits
         - MNSI assessment not performed in the 36, 39, 42, 45M visits
@@ -223,9 +218,7 @@ class Predicates(PersistantSingletonMixin):
 
         if self.offschedule_today(visit):
             return True
-        elif visit.visit_code_sequence != 0:
-            required = False
-        elif visit.visit_code not in [
+        if visit.visit_code_sequence != 0 or visit.visit_code not in [
             MONTH1,
             MONTH3,
             MONTH6,
@@ -258,21 +251,21 @@ class Predicates(PersistantSingletonMixin):
                     break
         return required
 
-    def sf12_required(self, visit, **kwargs):
+    def sf12_required(self, visit, **kwargs):  # noqa: ARG002
         model = f"{self.app_label}.sf12"
-        if self.offschedule_today(visit):
-            return True
-        elif visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
+        if self.offschedule_today(visit) or (
+            visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]
+        ):
             return True
         return self.persistant_singleton_required(
             visit, model=model, exclude_visit_codes=[DAY1]
         )
 
-    def eq5d3l_required(self, visit, **kwargs):
+    def eq5d3l_required(self, visit, **kwargs):  # noqa: ARG002
         model = f"{self.app_label}.eq5d3l"
-        if self.offschedule_today(visit):
-            return True
-        elif visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
+        if self.offschedule_today(visit) or (
+            visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]
+        ):
             return True
         return self.persistant_singleton_required(
             visit, model=model, exclude_visit_codes=[DAY1]