meta-edc 0.3.47__py3-none-any.whl → 0.3.48__py3-none-any.whl

meta_ae/tests/holidays.csv

@@ -12,4 +12,4 @@
 2019-12-01,Mawlid Day,tanzania
 2019-12-09,Independence Day,tanzania
 2019-12-25,Christmas Day,tanzania
-2019-12-26,Boxing Day,tanzania
+2019-12-26,Boxing Day,tanzania

meta_analytics/dataframes/screening/get_screening_df.py

@@ -149,6 +149,7 @@ def get_screening_df(df: pd.DataFrame | None = None) -> pd.DataFrame:
         on="subject_identifier",
         how="left",
     )
+    df.reset_index(drop=True, inplace=True)
     # set waist_circumference=waist_circumference_baseline
     # if `waist_circumference` is none and `waist_circumference_baseline` is not
     df.loc[

meta_analytics/tables/enrolled/glucose.py

@@ -17,10 +17,12 @@ class GlucoseTable(Table):
         super().__init__(colname="", main_df=main_df, title="Glucose (enrolled)")
 
     def build_table_df(self) -> None:
+        super().build_table_df()
         df = self.main_df
         s = df.groupby("subject_identifier")[["age_in_years", "gender"]].value_counts()
         df_tmp = s.to_frame()
         df_tmp = df_tmp.reset_index()
         gender_tbl = GenderTable(main_df=df_tmp).table_df
         age_tbl = AgeTable(main_df=df_tmp).table_df
-        return pd.concat([gender_tbl, age_tbl])
+        self.table_df = pd.concat([self.table_df, gender_tbl, age_tbl])
+        self.table_df.reset_index(drop=True, inplace=True)

meta_consent/action_items.py

@@ -1,7 +1,7 @@
 from edc_action_item import Action, site_action_items
 from edc_constants.constants import HIGH_PRIORITY
 
-from .constants import RECONSENT_ACTION
+from .constants import CONSENT_V1_EXTENSION_ACTION, RECONSENT_ACTION
 
 
 class ReconsentAction(Action):
@@ -23,4 +23,21 @@ class ReconsentAction(Action):
         return False
 
 
+class ConsentV1ExtensionAction(Action):
+    name = CONSENT_V1_EXTENSION_ACTION
+    display_name = "Ask to extend followup (required)"
+    reference_model = "meta_consent.subjectconsentv1ext"
+    priority = HIGH_PRIORITY
+    show_on_dashboard = True
+    show_link_to_changelist = True
+    admin_site_name = "meta_consent_admin"
+    create_by_user = False
+    singleton = True
+    instructions = "Participant must complete as soon as able. "
+
+    def reopen_action_item_on_change(self):
+        return False
+
+
 site_action_items.register(ReconsentAction)
+site_action_items.register(ConsentV1ExtensionAction)

meta_consent/admin/__init__.py

@@ -1,2 +1,3 @@
 from .subject_consent_admin import SubjectConsentAdmin
 from .subject_consent_v1_admin import SubjectConsentV1Admin
+from .subject_consent_v1_ext_admin import SubjectConsentV1ExtAdmin

meta_consent/admin/subject_consent_v1_ext_admin.py

@@ -0,0 +1,45 @@
+from django.contrib import admin
+from django_audit_fields import audit_fieldset_tuple
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+
+from ..admin_site import meta_consent_admin
+from ..forms import SubjectConsentV1ExtForm
+from ..models import SubjectConsentV1Ext
+
+
+@admin.register(SubjectConsentV1Ext, site=meta_consent_admin)
+class SubjectConsentV1ExtAdmin(
+    ModelAdminSubjectDashboardMixin,
+    SimpleHistoryAdmin,
+):
+    form = SubjectConsentV1ExtForm
+
+    fieldsets = (
+        (
+            None,
+            {
+                "fields": (
+                    "subject_consent",
+                    "report_datetime",
+                    "agrees_to_extension",
+                )
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    radio_fields = {"agrees_to_extension": admin.VERTICAL}
+
+    def get_readonly_fields(self, request, obj=None) -> tuple[str, ...]:
+        if obj:
+            return ("subject_consent",)
+        return ()
+
+    def formfield_for_foreignkey(self, db_field, request, **kwargs):
+        if db_field.name == "subject_consent":
+            subject_identifier = request.GET.get("subject_identifier")
+            kwargs["queryset"] = db_field.related_model.objects.filter(
+                subject_identifier=subject_identifier
+            )
+        return super().formfield_for_foreignkey(db_field, request, **kwargs)

meta_consent/baker_recipes.py

@@ -35,6 +35,7 @@ opts = dict(
 )
 subjectconsent = Recipe(SubjectConsent, **opts)
 subjectconsentv1 = Recipe(SubjectConsentV1, **opts)
+# subjectconsentv1ext = Recipe(SubjectConsentV1Ext, **opts)
 
 subjectreconsent = Recipe(
     SubjectReconsent,

meta_consent/consents.py

@@ -1,4 +1,8 @@
+from datetime import datetime
+from zoneinfo import ZoneInfo
+
 from edc_consent.consent_definition import ConsentDefinition
+from edc_consent.consent_definition_extension import ConsentDefinitionExtension
 from edc_consent.site_consents import site_consents
 from edc_constants.constants import FEMALE, MALE
 from edc_protocol.research_protocol_config import ResearchProtocolConfig
@@ -18,6 +22,15 @@ consent_v1 = ConsentDefinition(
         "meta_screening.screeningparttwo",
         "meta_screening.screeningpartthree",
     ],
+    timepoints=list(range(1, 14 + 1)),
+)
+
+consent_v1_ext = ConsentDefinitionExtension(
+    "meta_consent.subjectconsentv1ext",
+    version="1.1",
+    start=datetime(2024, 12, 16, tzinfo=ZoneInfo("UTC")),
+    extends=consent_v1,
+    timepoints=[15, 16, 17, 18],
 )
 
-site_consents.register(consent_v1)
+site_consents.register(consent_v1, extended_by=consent_v1_ext)

meta_consent/constants.py

@@ -1 +1,2 @@
 RECONSENT_ACTION = "reconsent"
+CONSENT_V1_EXTENSION_ACTION = "consent_v1_ext"

meta_consent/forms/__init__.py

@@ -1,3 +1,4 @@
 from .subject_consent_form import SubjectConsentForm
+from .subject_consent_v1_ext_form import SubjectConsentV1ExtForm
 from .subject_consent_v1_form import SubjectConsentV1Form
 from .subject_reconsent_form import SubjectReconsentForm

meta_consent/forms/subject_consent_v1_ext_form.py

@@ -0,0 +1,16 @@
+from django import forms
+from edc_form_validators import FormValidatorMixin
+from edc_sites.forms import SiteModelFormMixin
+
+from ..models import SubjectConsentV1Ext
+
+
+class SubjectConsentV1ExtForm(SiteModelFormMixin, FormValidatorMixin, forms.ModelForm):
+
+    widgets = {
+        "subject_identifier": forms.TextInput(attrs={"readonly": "readonly"}),
+    }
+
+    class Meta:
+        model = SubjectConsentV1Ext
+        fields = "__all__"