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

meta_subject/models/blood_results/blood_results_lft.py

@@ -1,4 +1,6 @@
-from edc_lab.model_mixins import CrfWithRequisitionModelMixin
+from django.db import models
+from edc_crf.model_mixins import CrfStatusModelMixin
+from edc_lab.model_mixins import CrfWithRequisitionModelMixin, requisition_fk_options
 from edc_lab_panel.panels import lft_panel
 from edc_lab_results import BLOOD_RESULTS_LFT_ACTION
 from edc_lab_results.model_mixins import (
@@ -25,12 +27,16 @@ class BloodResultsLft(
     GgtModelMixin,
     CrfWithRequisitionModelMixin,
     BloodResultsModelMixin,
+    CrfStatusModelMixin,
     BaseUuidModel,
 ):
     action_name = BLOOD_RESULTS_LFT_ACTION
-    tracking_identifier_prefix = "LF"
     lab_panel = lft_panel
 
+    requisition = models.ForeignKey(
+        limit_choices_to={"panel__name": lft_panel.name}, **requisition_fk_options
+    )
+
     class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Blood Result: LFT"
         verbose_name_plural = "Blood Results: LFT"

meta_subject/models/blood_results/{blood_results_lipid.py → blood_results_lipids.py}

@@ -1,6 +1,8 @@
-from edc_lab.model_mixins import CrfWithRequisitionModelMixin
+from django.db import models
+from edc_crf.model_mixins import CrfStatusModelMixin
+from edc_lab.model_mixins import CrfWithRequisitionModelMixin, requisition_fk_options
 from edc_lab_panel.panels import lipids_panel
-from edc_lab_results import BLOOD_RESULTS_LIPID_ACTION
+from edc_lab_results import BLOOD_RESULTS_LIPIDS_ACTION
 from edc_lab_results.model_mixins import (
     BloodResultsModelMixin,
     CholModelMixin,
@@ -13,7 +15,7 @@ from edc_model.models import BaseUuidModel
 from ...model_mixins import CrfWithActionModelMixin
 
 
-class BloodResultsLipid(
+class BloodResultsLipids(
     CrfWithActionModelMixin,
     HdlModelMixin,
     LdlModelMixin,
@@ -21,12 +23,17 @@ class BloodResultsLipid(
     CholModelMixin,
     CrfWithRequisitionModelMixin,
     BloodResultsModelMixin,
+    CrfStatusModelMixin,
     BaseUuidModel,
 ):
-    action_name = BLOOD_RESULTS_LIPID_ACTION
+    action_name = BLOOD_RESULTS_LIPIDS_ACTION
     tracking_identifier_prefix = "LP"
     lab_panel = lipids_panel
 
+    requisition = models.ForeignKey(
+        limit_choices_to={"panel__name": lipids_panel.name}, **requisition_fk_options
+    )
+
     class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Blood Result: Lipids"
         verbose_name_plural = "Blood Results: Lipids"

meta_subject/models/blood_results/blood_results_rft.py

@@ -1,6 +1,7 @@
 from django.db import models
+from edc_crf.model_mixins import CrfStatusModelMixin
 from edc_egfr.model_mixins import EgfrModelMixin
-from edc_lab.model_mixins import CrfWithRequisitionModelMixin
+from edc_lab.model_mixins import CrfWithRequisitionModelMixin, requisition_fk_options
 from edc_lab_panel.panels import rft_panel
 from edc_lab_results import BLOOD_RESULTS_RFT_ACTION
 from edc_lab_results.model_mixins import (
@@ -22,12 +23,17 @@ class BloodResultsRft(
     UricAcidModelMixin,
     CrfWithRequisitionModelMixin,
     BloodResultsModelMixin,
+    CrfStatusModelMixin,
     BaseUuidModel,
 ):
     action_name = BLOOD_RESULTS_RFT_ACTION
     lab_panel = rft_panel
     egfr_formula_name = "ckd-epi"
 
+    requisition = models.ForeignKey(
+        limit_choices_to={"panel__name": rft_panel.name}, **requisition_fk_options
+    )
+
     old_egfr_value = models.DecimalField(
         decimal_places=4,
         max_digits=8,

meta_subject/models/complications.py

@@ -1,14 +1,12 @@
 from django.db import models
 from edc_constants.choices import NORMAL_ABNORMAL, PRESENT_ABSENT, YES_NO
-from edc_data_manager.modeladmin_mixins import DataManagerModelAdminMixin
 from edc_model import models as edc_models
 
 from ..choices import FUNDOSCOPY_CHOICES
 from ..model_mixins import CrfModelMixin
 
 
-class Complications(DataManagerModelAdminMixin, CrfModelMixin, edc_models.BaseUuidModel):
-
+class Complications(CrfModelMixin, edc_models.BaseUuidModel):
     cataracts = models.CharField(
         verbose_name="Presence of cataracts", max_length=15, choices=YES_NO
     )

meta_subject/models/complications_glycemia.py

@@ -1,6 +1,6 @@
 from django.db import models
 from edc_constants.choices import NORMAL_ABNORMAL_NOEXAM
-from edc_model import models as edc_models
+from edc_model.models import BaseUuidModel
 
 from ..choices import (
     FUNDOSCOPY_CHOICES,
@@ -11,8 +11,7 @@ from ..choices import (
 from ..model_mixins import CrfModelMixin
 
 
-class ComplicationsGlycemia(CrfModelMixin, edc_models.BaseUuidModel):
-
+class ComplicationsGlycemia(CrfModelMixin, BaseUuidModel):
     """Not used"""
 
     # eye examination
@@ -207,6 +206,6 @@ class ComplicationsGlycemia(CrfModelMixin, edc_models.BaseUuidModel):
         choices=YES_NO_NO_EXAM,
     )
 
-    class Meta(CrfModelMixin.Meta, edc_models.BaseUuidModel.Meta):
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Complications (Raised Glycemia)"
         verbose_name_plural = "Complications (Raised Glycemia)"

meta_subject/models/concomitant_medication.py

@@ -4,7 +4,6 @@ from ..model_mixins import CrfModelMixin
 
 
 class ConcomitantMedication(CrfModelMixin, BaseUuidModel):
-
     # prescription
     # days
     # dosage

meta_subject/models/delivery.py

@@ -1,12 +1,12 @@
 # TODO: urine_bhcg form (probably not necessary)
 # TODO: if pos, take of study drug and estimate
 #  delivery date for the pregnancy outcomes form. See Form 25/26
+from clinicedc_constants import NOT_APPLICABLE, PATIENT, YES
 from django.apps import apps as django_apps
 from django.core.validators import MaxValueValidator, MinValueValidator
 from django.db import models
 from django_crypto_fields.fields import EncryptedTextField
 from edc_constants.choices import YES_NO, YES_NO_NA
-from edc_constants.constants import NOT_APPLICABLE, PATIENT, YES
 from edc_model.models import BaseUuidModel
 from edc_model.validators import datetime_not_future
 from edc_model_fields.fields import OtherCharField
@@ -38,8 +38,6 @@ class Delivery(
 
     action_name = DELIVERY_ACTION
 
-    tracking_identifier_prefix = "DL"
-
     report_datetime = models.DateTimeField(
         verbose_name="Report Date and Time", default=get_utcnow
     )
@@ -54,7 +52,7 @@ class Delivery(
 
     info_not_available_reason = models.TextField(
         verbose_name="If the report was not available, please explain?",
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -112,7 +110,7 @@ class Delivery(
             "please give name of the facility"
         ),
         max_length=150,
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -162,4 +160,4 @@ class Delivery(
     class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Delivery"
         verbose_name_plural = "Delivery"
-        unique_together = ["subject_visit", "delivery_datetime"]
+        unique_together = ("subject_visit", "delivery_datetime")

meta_subject/models/diabetes/__init__.py

@@ -0,0 +1,4 @@
+from .dm_endpoint import DmEndpoint
+from .dm_followup import DmFollowup
+
+__all__ = ["DmEndpoint", "DmFollowup"]

meta_subject/models/diabetes/dm_endpoint.py

@@ -0,0 +1,61 @@
+from clinicedc_constants import QUESTION_RETIRED
+from django.db import models
+from edc_constants.choices import YES_NO, YES_NO_RETIRED
+from edc_model.models import BaseUuidModel
+from edc_model_fields.fields import OtherCharField
+
+from ...model_mixins import CrfModelMixin
+
+
+class DmEndpoint(CrfModelMixin, BaseUuidModel):
+    """A user model to enrolled patient onto the DM Referral
+    Schedule.
+    """
+
+    endpoint_reached = models.CharField(
+        verbose_name="Was the patient referred because the diabetes endpoint was reached?",
+        max_length=15,
+        choices=YES_NO,
+        default="",
+        blank=False,
+        help_text="If YES, the EDC will check for the patient on the Endpoints report.",
+    )
+
+    # retired
+    dx_date = models.DateField(verbose_name="Date endpoint reached", null=True)
+
+    # retired
+    dx_initiated_by = models.CharField(
+        verbose_name="What initiated the diagnosis",
+        max_length=25,
+        default=QUESTION_RETIRED,
+    )
+
+    # retired
+    dx_initiated_by_other = OtherCharField(blank=True)
+
+    # retired
+    dx_tmg = models.CharField(
+        verbose_name="Was this case discussed with the TMG?",
+        max_length=25,
+        choices=YES_NO_RETIRED,
+        default=QUESTION_RETIRED,
+    )
+
+    # retired
+    dx_tmg_date = models.DateField(
+        verbose_name="If YES, provide the date of the TMG discussion", null=True, blank=True
+    )
+
+    # retired
+    dx_no_tmg_reason = models.TextField(
+        verbose_name="If NO, please explain why this case was not discussed with the TMG",
+        default="",
+        blank=True,
+    )
+
+    comments = models.TextField(verbose_name="Any other comments", default="", blank=True)
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Diabetes endpoint"
+        verbose_name_plural = "Diabetes endpoint"

meta_subject/models/diabetes/dm_followup.py

@@ -0,0 +1,215 @@
+from clinicedc_constants import NOT_APPLICABLE, QUESTION_RETIRED
+from django.core.validators import MaxValueValidator, MinValueValidator
+from django.db import models
+from django.utils.safestring import mark_safe
+from edc_action_item.models import ActionItem
+from edc_adherence.choices import MISSED_PILLS
+from edc_constants.choices import YES_NO, YES_NO_NA
+from edc_model.models import BaseUuidModel
+from edc_model_fields.fields import OtherCharField
+
+from meta_lists.models import (
+    Complications,
+    DmMedications,
+    DmTreatments,
+    HealthcareWorkers,
+    Investigations,
+    MissedReferralReasons,
+)
+
+from ...constants import DM_FOLLOWUP_ACTION
+from ...model_mixins import CrfWithActionModelMixin
+
+
+class DmFollowup(CrfWithActionModelMixin, BaseUuidModel):
+    action_name = DM_FOLLOWUP_ACTION
+
+    referral_date = models.DateField(
+        verbose_name="Date of referral to diabetes clinic",
+    )
+
+    # Diabetes clinic attendance
+    attended = models.CharField(
+        verbose_name=(
+            "Did you attend the diabetes clinic following referral from the META Trial"
+        ),
+        choices=YES_NO,
+        max_length=25,
+    )
+
+    missed_referral_reasons = models.ManyToManyField(
+        MissedReferralReasons,
+        verbose_name=(
+            "If 'No', please provide a reason for not seeking further care or follow up?"
+        ),
+        blank=True,
+    )
+
+    other_missed_referral_reason = OtherCharField(
+        verbose_name="If other 'reason for not seeking further care', please specify ...",
+        null=True,
+        blank=True,
+    )
+
+    not_attended_reason = models.TextField(
+        verbose_name=(
+            "If 'No', please provide a reason for not seeking further care or follow up?"
+        ),
+        default=QUESTION_RETIRED,
+        editable=False,
+    )
+
+    facility_attended = models.CharField(
+        verbose_name="If 'Yes', please give the name of the facility you attended",
+        max_length=50,
+        default="",
+        blank=True,
+    )
+
+    attended_date = models.DateField(
+        verbose_name="What was the date you attended the health facility named above?",
+        null=True,
+        blank=True,
+    )
+
+    healthcare_workers = models.ManyToManyField(
+        HealthcareWorkers,
+        verbose_name="What type of health care worker did you see?",
+        blank=True,
+    )
+
+    other_healthcare_workers = OtherCharField(
+        verbose_name="If other 'healthcare worker', please specify ...",
+        null=True,
+        blank=True,
+    )
+
+    # investigations
+    investigations_performed = models.CharField(
+        verbose_name="Were any further investigations conducted at this visit?",
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        max_length=25,
+    )
+
+    investigations = models.ManyToManyField(
+        Investigations,
+        verbose_name="If 'Yes', please indicate what investigations were conducted.",
+        blank=True,
+    )
+
+    other_investigations = OtherCharField(
+        verbose_name="If other 'investigations', please specify ...",
+        null=True,
+        blank=True,
+    )
+
+    complications_checks_performed = models.CharField(
+        verbose_name=(
+            "Was the patient checked for diabetes related complications at this visit?"
+        ),
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        max_length=25,
+    )
+    complications_checks = models.ManyToManyField(
+        Complications,
+        verbose_name="If 'Yes, which diabetes related complications were checked for?",
+        blank=True,
+    )
+
+    other_complications_checks = OtherCharField(
+        verbose_name=(
+            "If other 'diabetes related complications checked for ', please specify ..."
+        ),
+        null=True,
+        blank=True,
+    )
+
+    # dm treatment
+
+    treatment_prescribed = models.CharField(
+        verbose_name="Was any treatment prescribed at this visit?",
+        choices=YES_NO_NA,
+        max_length=25,
+        default=NOT_APPLICABLE,
+    )
+    dm_treatments = models.ManyToManyField(
+        DmTreatments,
+        verbose_name="What treatment was prescribed?",
+        blank=True,
+    )
+
+    on_dm_medications = models.CharField(
+        verbose_name="Are you currently taking any drug therapy for diabetes?",
+        choices=YES_NO_NA,
+        max_length=25,
+    )
+
+    dm_medications_init_date = models.DateField(
+        verbose_name="If 'Yes', please give the date when drug treatment was started.",
+        null=True,
+        blank=True,
+    )
+
+    dm_medications = models.ManyToManyField(
+        DmMedications,
+        verbose_name=(
+            "If 'Yes', please indicate which diabetes drug "
+            "treatments you are currently taking."
+        ),
+        blank=True,
+    )
+
+    other_dm_medications = OtherCharField(
+        verbose_name="If other 'drug treatments', please specify ...",
+        null=True,
+        blank=True,
+    )
+
+    # Diabetes Medication Adherence
+
+    medications_adherent = models.CharField(
+        verbose_name="Are you taking the diabetes drug treatments regularly, i.e. every day?",
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+        max_length=25,
+    )
+
+    visual_score_slider = models.CharField(
+        verbose_name="Visual score",
+        max_length=3,
+        help_text="%",
+        default="",
+        blank=True,
+    )
+
+    visual_score_confirmed = models.IntegerField(
+        verbose_name=mark_safe(
+            "<B><font color='orange'>Interviewer</font></B>: "
+            "please transcribe the score indicated from above."
+        ),  # nosec B308
+        validators=[MinValueValidator(0), MaxValueValidator(100)],
+        help_text="%",
+        null=True,
+        blank=True,
+    )
+
+    last_missed_pill = models.CharField(
+        verbose_name="When was the last time you missed your study pill?",
+        max_length=25,
+        choices=MISSED_PILLS,
+        default="",
+        blank=True,
+    )
+
+    def save(self, *args, **kwargs):
+        self.action_item = ActionItem.objects.get(
+            subject_identifier=self.subject_identifier, action_type__name=self.action_name
+        )
+        self.action_identifier = self.action_item.action_identifier
+        super().save(*args, **kwargs)
+
+    class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Diabetes follow-up after referral"
+        verbose_name_plural = "Diabetes follow-up after referral"

meta_subject/models/diet_and_lifestyle.py

@@ -1,18 +1,18 @@
 from django.db import models
 from edc_constants.choices import YES_NO
-from edc_model import models as edc_models
+from edc_model.models import BaseUuidModel
 
 from ..model_mixins import CrfModelMixin
 
 
-class DietAndLifestyle(CrfModelMixin, edc_models.BaseUuidModel):
+class DietAndLifestyle(CrfModelMixin, BaseUuidModel):
     diet_and_lifestyle = models.CharField(
         verbose_name=(
-            "Has the participant received the META3 " "approved diet and lifetsyle counseling?"
+            "Has the participant received the META3 approved diet and lifetsyle counseling?"
         ),
         max_length=15,
         choices=YES_NO,
-        null=True,
+        default="",
         blank=False,
         help_text="This response is not criteria for eligibility",
     )
@@ -27,6 +27,6 @@ class DietAndLifestyle(CrfModelMixin, edc_models.BaseUuidModel):
         help_text="Report in minutes. This response is not criteria for eligibility",
     )
 
-    class Meta(CrfModelMixin.Meta, edc_models.BaseUuidModel.Meta):
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
         verbose_name = "Clinic follow up: Examination"
         verbose_name_plural = "Clinic follow up: Examination"

meta_subject/models/egfr_drop_notification.py

@@ -10,7 +10,6 @@ class EgfrDropNotification(
     CrfWithActionModelMixin,
     BaseUuidModel,
 ):
-
     action_name = EGFR_DROP_NOTIFICATION_ACTION
 
     class Meta(CrfWithActionModelMixin.Meta, BaseUuidModel.Meta):

meta_subject/models/followup_examination.py

@@ -1,8 +1,8 @@
+from clinicedc_constants import NOT_APPLICABLE
 from django.db import models
 from django.db.models import PROTECT
 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_constants.choices import YES_NO, YES_NO_NA, YES_NO_NOT_EVALUATED
 from edc_model.models import BaseUuidModel
 from edc_model_fields.fields import OtherCharField
 
@@ -14,11 +14,8 @@ from ..model_mixins import CrfWithActionModelMixin
 
 
 class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
-
     action_name = FOLLOWUP_EXAMINATION_ACTION
 
-    tracking_identifier_prefix = "FU"
-
     # 4a
     symptoms = models.ManyToManyField(
         Symptoms,
@@ -43,12 +40,12 @@ class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
         related_name="symptoms_g3",
         verbose_name="For these symptoms, were any grade 3 events",
         help_text=(
-            "Refer to DAIDS toxicity table. " "Please complete Serious Adverse Event form"
+            "Refer to DAIDS toxicity table. Please complete Serious Adverse Event form"
         ),
     )
     symptoms_g3_detail = models.TextField(
         verbose_name="Please provide details on any of the Grade 3 symptoms above.",
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -58,54 +55,51 @@ class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
         related_name="symptoms_g4",
         verbose_name="For these symptoms, were any grade 4 events",
         help_text=(
-            "Refer to DAIDS toxicity table. " "Please complete Serious Adverse Event form"
+            "Refer to DAIDS toxicity table. Please complete Serious Adverse Event form"
         ),
     )
     symptoms_g4_detail = models.TextField(
         verbose_name="Please provide details on any of the Grade 4 symptoms above.",
-        null=True,
+        default="",
         blank=True,
     )
 
     # 4c
     symptoms_detail = models.TextField(
         verbose_name="Please provide details on any of the symptoms above.",
-        null=True,
+        default="",
         blank=True,
     )
 
-    # 5a
     attended_clinic = models.CharField(
         verbose_name=(
-            "Since the participant's last visit did they attend any other clinic or hospital "
-            "for care for any reason"
+            "Since the participant's last study visit did they attend any clinic or hospital "
+            "for care for ANY reason"
         ),
         max_length=25,
         choices=YES_NO,
         help_text="Includes other routine appointments, e.g. BP check or family planning",
     )
 
-    # 5b
-    admitted_hospital = models.CharField(
-        verbose_name="If YES, were they admitted to hospital?",
-        max_length=25,
-        choices=YES_NO_NA,
-        default=NOT_APPLICABLE,
-    )
-
-    # 5c
     attended_clinic_detail = models.TextField(
         verbose_name=(
-            "If YES, attend other clinic or hospital, " "please provide details of this event"
+            "If YES, attend clinic or hospital, please provide details of this event"
         ),
         help_text=(
             "If the participant was given a referral letter or "
             "discharge summary record details here"
         ),
-        null=True,
+        default="",
         blank=True,
     )
 
+    admitted_hospital = models.CharField(
+        verbose_name="If YES, were they admitted to hospital?",
+        max_length=25,
+        choices=YES_NO_NA,
+        default=NOT_APPLICABLE,
+    )
+
     attended_clinic_sae = models.CharField(
         verbose_name=mark_safe(  # nosec B308
             "Does the event constitute a <u>Serious Adverse Event</u>"
@@ -130,9 +124,9 @@ class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
     # 5d
     prescribed_medication_detail = models.TextField(
         verbose_name=(
-            "If YES, prescribed any other medication, " "please provide details of this visit"
+            "If YES, prescribed any other medication, please provide details of this visit"
         ),
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -151,7 +145,7 @@ class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
     # 6a
     any_other_problems_detail = models.TextField(
         verbose_name="If YES, please provide details of the event",
-        null=True,
+        default="",
         blank=True,
     )
 
@@ -182,7 +176,7 @@ class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
 
     # 7b
     art_change_reason = models.TextField(
-        verbose_name="If YES, please provide reason for change", null=True, blank=True
+        verbose_name="If YES, please provide reason for change", default="", blank=True
     )
 
     # 7c
@@ -198,14 +192,16 @@ class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
     art_new_regimen_other = OtherCharField()
 
     abdominal_tenderness = models.CharField(
-        verbose_name="Abdominal tenderness", max_length=25, choices=YES_NO
+        verbose_name="Abdominal tenderness", max_length=25, choices=YES_NO_NOT_EVALUATED
     )
 
     enlarged_liver = models.CharField(
-        verbose_name="Enlarged liver", max_length=25, choices=YES_NO
+        verbose_name="Enlarged liver", max_length=25, choices=YES_NO_NOT_EVALUATED
     )
 
-    jaundice = models.CharField(verbose_name="Jaundice", max_length=25, choices=YES_NO)
+    jaundice = models.CharField(
+        verbose_name="Jaundice", max_length=25, choices=YES_NO_NOT_EVALUATED
+    )
 
     comment = models.TextField(
         verbose_name=(
@@ -245,7 +241,7 @@ class FollowupExamination(CrfWithActionModelMixin, BaseUuidModel):
 
     referral_reason = models.TextField(
         verbose_name="If YES, where are they being referred to",
-        null=True,
+        default="",
         blank=True,
         help_text=(
             "Note: remind participant that admission or discharge information "