meta-edc 0.3.39__py3-none-any.whl → 1.4.0__py3-none-any.whl

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/metadata_rules.py

@@ -160,3 +160,17 @@ class Eq53dlRuleGroup(CrfRuleGroup):
     class Meta:
         app_label = "meta_subject"
         source_model = "meta_subject.subjectvisit"
+
+
+@register()
+class NextAppointmentRuleGroup(CrfRuleGroup):
+    next_appt = CrfRule(
+        predicate=pc.next_appt_required,
+        consequence=REQUIRED,
+        alternative=NOT_REQUIRED,
+        target_models=["nextappointment"],
+    )
+
+    class Meta:
+        app_label = "meta_subject"
+        source_model = "meta_subject.subjectvisit"

meta_subject/metadata_rules/predicates.py

@@ -1,9 +1,10 @@
 from datetime import datetime
 from zoneinfo import ZoneInfo
 
+from clinicedc_constants import YES
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
-from edc_constants.constants import YES
+from edc_appointment.constants import NEW_APPT
 from edc_lab_panel.panels import hba1c_panel, insulin_panel
 from edc_metadata.metadata_rules import PersistantSingletonMixin
 from edc_sites.site import sites
@@ -70,20 +71,21 @@ class Predicates(PersistantSingletonMixin):
     app_label = "meta_subject"
 
     @staticmethod
-    def glucose_required(visit, **kwargs):
-        if visit.visit_code in [MONTH12, MONTH24, MONTH36, MONTH48]:
-            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_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_required(visit, **kwargs):  # noqa: ARG004
+        return visit.visit_code in [MONTH12, MONTH24, MONTH36, MONTH48]
+
+    @staticmethod
+    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)
@@ -94,7 +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.
         """
@@ -110,7 +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.
         """
@@ -126,7 +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 (
@@ -143,7 +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 (
@@ -159,7 +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
@@ -183,7 +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.
 
@@ -205,7 +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
@@ -213,9 +215,10 @@ class Predicates(PersistantSingletonMixin):
         """
         model_cls = django_apps.get_model(f"{self.app_label}.mnsi")
         required = True
-        if visit.visit_code_sequence != 0:
-            required = False
-        elif visit.visit_code not in [
+
+        if self.offschedule_today(visit):
+            return True
+        if visit.visit_code_sequence != 0 or visit.visit_code not in [
             MONTH1,
             MONTH3,
             MONTH6,
@@ -248,18 +251,34 @@ 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 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 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 offschedule_today(self, visit):
+        try:
+            obj = django_apps.get_model(f"{self.app_label}.nextappointment").objects.get(
+                subject_visit=visit
+            )
+        except ObjectDoesNotExist:
+            pass
+        else:
+            if obj.offschedule_today == YES:
+                return True
+        return False