meta-edc 0.3.37__py3-none-any.whl → 0.3.39__py3-none-any.whl

meta_pharmacy/utils/update_initial_pharmacy_data.py

@@ -0,0 +1,146 @@
+from django.contrib.sites.models import Site
+from django.core.exceptions import ObjectDoesNotExist
+from django_pylabels.models import LabelSpecification
+from edc_pharmacy.models import (
+    Assignment,
+    Container,
+    ContainerType,
+    ContainerUnits,
+    Formulation,
+    Location,
+    Product,
+    Supplier,
+)
+from edc_pylabels.models import LabelConfiguration
+from edc_pylabels.site_label_configs import site_label_configs
+
+
+def update_initial_pharmacy_data():
+    update_assignment()
+    update_container()
+    update_location()
+    update_product()
+    update_supplier()
+    update_labels()
+
+
+def update_assignment():
+    """For a trial with just active and placebo.
+
+    Better to get these labels from edc_randomizer.
+    """
+    for assignment in ["placebo", "active"]:
+        try:
+            Assignment.objects.get(name=assignment)
+        except ObjectDoesNotExist:
+            Assignment.objects.create(name=assignment, display_name=assignment.title())
+
+
+def update_container():
+    """Here we order a number of tablets. The manufacturer sends
+    the order in large containers, barrels of about 30K tablets
+    per barrel. We repack/decant into bottles of 128 tablets
+    """
+    tablet_type = ContainerType.objects.get(name="tablet")
+    bottle_type = ContainerType.objects.get(name="bottle")
+    units = ContainerUnits.objects.get(name="tablet")
+    opts = {
+        "tablet": dict(
+            name="tablet",
+            display_name="Tablet",
+            container_type=tablet_type,
+            units=units,
+            qty=1,
+            may_order_as=True,
+            max_per_subject=0,
+        ),
+        "bottle30k": dict(
+            name="bottle30k",
+            display_name="Barrel 30K",
+            container_type=bottle_type,
+            units=units,
+            qty=30000,
+            may_receive_as=True,
+            max_per_subject=0,
+        ),
+        "bottle128": dict(
+            name="bottle128",
+            display_name="Bottle 128",
+            container_type=bottle_type,
+            units=units,
+            qty=128,
+            max_per_subject=3,
+            may_repack_as=True,
+            may_request_as=True,
+            may_dispense_as=True,
+        ),
+    }
+    for name, data in opts.items():
+        try:
+            Container.objects.get(name=name)
+        except ObjectDoesNotExist:
+            Container.objects.create(**data)
+
+
+def update_location():
+    """Base the locations on the sites in the trial plus
+    a "central" pharmacy"""
+    for obj in Location.objects.exclude(name="central"):
+        obj.site_id = Site.objects.get(name=obj.name).id
+        obj.save(update_fields=["site_id"])
+
+
+def update_product():
+    """Define the product, in this case just two; active and placebo.
+
+    Formulation is defined before running this script.
+
+    In this case the formulation is just the study drug/IMP.
+    """
+    formulation = Formulation.objects.get()
+    active = Assignment.objects.get(name="active")
+    placebo = Assignment.objects.get(name="placebo")
+    try:
+        Product.objects.get(formulation=formulation, assignment=active)
+    except ObjectDoesNotExist:
+        Product(assignment=active, formulation=formulation).save()
+    try:
+        Product.objects.get(formulation=formulation, assignment=placebo)
+    except ObjectDoesNotExist:
+        Product(assignment=placebo, formulation=formulation).save()
+
+
+def update_supplier():
+    """In this case MERCK"""
+    try:
+        Supplier.objects.get(name="merck")
+    except ObjectDoesNotExist:
+        Supplier(name="merck").save()
+
+
+def update_labels():
+    """The default label spec is a 2 x 6 label sheet
+
+    Add "label congigs" as registered in the "site_label_configs"
+    global. In this case there are three labels:
+    * a bulk label for the barrels
+    * a generic vertical label for decanted stock (bottles of 128)
+    * a patient label for allocated stock (bottles of 128)
+
+    The patient label will be placed over the generic vertical label
+    once the stock item is allocated to a subject.
+    """
+    try:
+        default = LabelSpecification.objects.get(name="default")
+    except ObjectDoesNotExist:
+        LabelSpecification().save()
+        default = LabelSpecification.objects.get(name="default")
+
+    for name, label_config in site_label_configs.registry.items():
+        LabelConfiguration.objects.create(name=name, label_specification=default)
+    for label_configuration in LabelConfiguration.objects.filter(name__contains="patient"):
+        label_configuration.requires_allocation = True
+        label_configuration.save()
+
+
+__all__ = ["update_initial_pharmacy_data"]

meta_prn/admin/pregnancy_notification_admin.py

@@ -57,11 +57,15 @@ class PregnancyNotificationAdmin(
             "subject_identifier",
             "dashboard",
             "edd",
-            "may_contact",
+            "contact_agreed",
         )
         return custom_fields + tuple(f for f in list_display if f not in custom_fields)
 
     def get_list_filter(self, request) -> Tuple[str, ...]:
-        list_filter = super().get_list_display(request)
+        list_filter = super().get_list_filter(request)
         custom_fields = ("edd", "may_contact")
         return custom_fields + tuple(f for f in list_filter if f not in custom_fields)
+
+    @admin.display(description="May contact?", ordering="may_contact")
+    def contact_agreed(self, obj):
+        return obj.may_contact

meta_reports/admin/__init__.py

@@ -12,3 +12,4 @@ from .dbviews import (
 )
 from .endpoints_admin import EndpointsAdmin
 from .endpoints_all_admin import EndpointsAllAdmin
+from .last_imp_refill_admin import LastImpRefillAdmin

meta_reports/admin/dbviews/glucose_summary_admin.py

@@ -62,7 +62,7 @@ class GlucoseSummaryAdmin(
         except ObjectDoesNotExist:
             value = None
         else:
-            if endpoint_obj.offstudy_datetime:
+            if endpoint_obj.offstudy_date:
                 url = reverse("meta_reports_admin:meta_reports_endpointsproxy_changelist")
                 title = f"Go to {EndpointsProxy._meta.verbose_name}"
             else:

meta_reports/admin/endpoints_admin.py

@@ -8,7 +8,7 @@ from .modeladmin_mixins import EndpointsModelAdminMixin
 
 @admin.register(Endpoints, site=meta_reports_admin)
 class EndpointsAdmin(EndpointsModelAdminMixin, admin.ModelAdmin):
-    queryset_filter = dict(offstudy_datetime__isnull=True)
+    queryset_filter = dict(offstudy_date__isnull=True)
 
     def rendered_change_list_note(self):
         return render_to_string("meta_reports/endpoints_change_list_note.html")

meta_reports/admin/last_imp_refill_admin.py

@@ -0,0 +1,181 @@
+from django.contrib import admin, messages
+from django.core.exceptions import FieldDoesNotExist
+from django.db import models
+from django.db.models import QuerySet
+from django.utils.html import format_html
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+from edc_model_admin.list_filters import PastDateListFilter
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_pdutils.actions import export_to_csv
+from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
+from edc_sites.admin.list_filters import SiteListFilter
+from edc_utils import get_utcnow
+
+from meta_analytics.dataframes import get_last_imp_visits_df
+
+from ..admin_site import meta_reports_admin
+from ..models import LastImpRefill
+
+
+class ImpVisitDateListFilter(PastDateListFilter):
+    title = "IMP visit date"
+
+    parameter_name = "imp_visit_date"
+    field_name = "imp_visit_date"
+
+
+class NextApptDateListFilter(PastDateListFilter):
+    title = "Next appt date"
+
+    parameter_name = "next_appt_date"
+    field_name = "next_appt_date"
+
+
+def update_report(modeladmin, request, queryset):
+    now = get_utcnow()
+    modeladmin.model.objects.all().delete()
+    df = get_last_imp_visits_df()
+    if not df.empty:
+        data = [
+            modeladmin.model(
+                subject_identifier=row["subject_identifier"],
+                site_id=row["site_id"],
+                imp_visit_date=row["imp_visit_date"],
+                imp_visit_code=row["imp_visit_code"],
+                next_appt_date=row["next_appt_datetime"],
+                next_visit_code=row["next_visit_code"],
+                days_since=row["days_since"].days,
+                days_until=row["days_until"].days,
+                visit_code=str(int(row["imp_visit_code"])),
+                visit_code_sequence=row["imp_visit_code"] % 1,
+                report_model=modeladmin.model._meta.label_lower,
+                created=now,
+            )
+            for _, row in df.iterrows()
+        ]
+        created = len(modeladmin.model.objects.bulk_create(data))
+        messages.success(request, "{} records were successfully created.".format(created))
+
+
+@admin.register(LastImpRefill, site=meta_reports_admin)
+class LastImpRefillAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    include_note_column = False
+
+    change_list_title = "List of most recent IMP refills per subject"
+
+    change_list_note = format_html(
+        """
+        This report fetches the most recent Study Medication report where IMP was
+        refilled and adds the subject's next visit. Subjects taken "Off Schedule"
+        are not included in this report. To update ALL rows in this report, tick
+        at least one row and select 'Update report' action below.
+        <BR><BR>
+        This report has additional search features for numeric columns:
+        <code>days_since</code>, <code>days_until</code>, <code>imp_visit_code</code>
+        and <code>next_visit_code</code>.
+        <BR><BR>For example, type <code>days_until>=25</code> in the search below
+        to show rows for subjects who have an appointment 25 or more days from the
+        date this report was created. You might also try typing
+        <code>days_since>365</code> or <code>days_until<0</code>.
+        <BR><BR>
+        This also works: <code>next_visit_code>=1060</code>.
+        """
+    )
+
+    actions = [update_report, export_to_csv]
+
+    list_display = [
+        "dashboard",
+        "subject_identifier",
+        "imp_visit_code",
+        "imp_visit_date",
+        "days_since",
+        "next_visit_code",
+        "next_appt_date",
+        "days_until",
+        "created",
+    ]
+
+    list_filter = [
+        ImpVisitDateListFilter,
+        NextApptDateListFilter,
+        "imp_visit_code",
+        "next_visit_code",
+        SiteListFilter,
+    ]
+
+    search_fields = ["subject_identifier"]
+
+    def get_queryset(self, request) -> QuerySet:
+        qs = super().get_queryset(request)
+        if qs.count() == 0:
+            update_report(self, request, None)
+            qs = super().get_queryset(request)
+        return qs
+
+    def dataframe_to_model(self):
+        now = get_utcnow()
+        self.model.objects.all().delete()
+        created = 0
+        df = get_last_imp_visits_df()
+        if not df.empty:
+            data = [
+                self.model(
+                    subject_identifier=row["subject_identifier"],
+                    site_id=row["site_id"],
+                    imp_visit_date=row["imp_visit_date"],
+                    imp_visit_code=row["imp_visit_code"],
+                    next_appt_date=row["next_appt_datetime"],
+                    next_visit_code=row["next_visit_code"],
+                    days_since=row["days_since"],
+                    days_until=row["days_until"],
+                    visit_code=str(int(row["imp_visit_code"])),
+                    visit_code_sequence=row["imp_visit_code"] % 1,
+                    report_model=self.model._meta.label_lower,
+                    created=now,
+                )
+                for _, row in df.iterrows()
+            ]
+            created = len(self.model.objects.bulk_create(data))
+        return created
+
+    def get_search_results(self, request, queryset, search_term):
+        value = None
+        fldname = None
+        search_term = search_term.replace(" ", "")
+        operators = {">=": "gte", "<=": "lte", "<": "lt", ">": "gt"}
+        if op := [op for op in operators if op in search_term]:
+            op = op[0]
+            fldname, value = search_term.split(op)
+            try:
+                fldcls = self.model._meta.get_field(fldname)
+            except FieldDoesNotExist:
+                fldname = None
+            else:
+                if isinstance(fldcls, (models.IntegerField,)):
+                    try:
+                        value = int(value)
+                    except ValueError:
+                        value = None
+                elif isinstance(fldcls, (models.FloatField,)):
+                    try:
+                        value = float(value)
+                    except ValueError:
+                        value = None
+        if (
+            value is not None
+            and fldname
+            and fldname in ["days_until", "days_since", "imp_visit_code", "next_visit_code"]
+        ):
+            queryset, use_distinct = super().get_search_results(request, queryset, None)
+            queryset = queryset.filter(**{f"{fldname}__{operators[op]}": value})
+        else:
+            queryset, use_distinct = super().get_search_results(request, queryset, search_term)
+        return queryset, use_distinct

meta_reports/admin/modeladmin_mixins.py

@@ -79,9 +79,9 @@ class EndpointsModelAdminMixin(
     def visit(self, obj=None):
         return obj.visit_code
 
-    @admin.display(description="FBG DATE", ordering="fbg_date")
-    def fbg_date(self, obj=None):
-        return obj.fbg_datetime.date() if obj.fbg_datetime else None
+    # @admin.display(description="FBG DATE", ordering="fbg_date")
+    # def fbg_date(self, obj=None):
+    #     return obj.fbg_datetime.date() if obj.fbg_datetime else None
 
     @admin.display(description="FAST", ordering="fasting")
     def fast(self, obj=None):

meta_reports/migrations/0052_lastimpvisit.py

@@ -0,0 +1,57 @@
+# Generated by Django 5.1.2 on 2024-10-16 00:53
+
+import django.db.models.deletion
+import edc_utils.date
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0051_remove_endpoints_baseline_datetime_and_more"),
+        ("sites", "0002_alter_domain_unique"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="LastImpVisit",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("report_model", models.CharField(max_length=50)),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("created", models.DateTimeField(default=edc_utils.date.get_utcnow)),
+                ("reference_date", models.DateField(null=True)),
+                ("imp_visit_code", models.FloatField(null=True)),
+                ("imp_visit_date", models.DateField(null=True)),
+                ("next_visit_code", models.FloatField(null=True)),
+                ("next_appt_date", models.DateField(null=True)),
+                ("visit_code", models.CharField(max_length=15, null=True)),
+                ("visit_code_sequence", models.IntegerField(null=True)),
+                ("days_since", models.IntegerField(null=True)),
+                ("days_until", models.IntegerField(null=True)),
+                (
+                    "site",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.DO_NOTHING, to="sites.site"
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "Last IMP Visit",
+                "verbose_name_plural": "Last IMP Visits",
+                "abstract": False,
+                "default_permissions": ("view", "export", "viewallsites"),
+                "indexes": [
+                    models.Index(
+                        fields=["subject_identifier", "site"],
+                        name="meta_report_subject_4a9e15_idx",
+                    )
+                ],
+            },
+        ),
+    ]

meta_reports/migrations/0053_rename_lastimpvisit_lastimprefill_and_more.py

@@ -0,0 +1,31 @@
+# Generated by Django 5.1.2 on 2024-10-16 01:39
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0052_lastimpvisit"),
+        ("sites", "0002_alter_domain_unique"),
+    ]
+
+    operations = [
+        migrations.RenameModel(
+            old_name="LastImpVisit",
+            new_name="LastImpRefill",
+        ),
+        migrations.AlterModelOptions(
+            name="lastimprefill",
+            options={
+                "default_permissions": ("view", "export", "viewallsites"),
+                "verbose_name": "Last IMP Refill",
+                "verbose_name_plural": "Last IMP Refills",
+            },
+        ),
+        migrations.RenameIndex(
+            model_name="lastimprefill",
+            new_name="meta_report_subject_bc8268_idx",
+            old_name="meta_report_subject_4a9e15_idx",
+        ),
+    ]

meta_reports/models/__init__.py

@@ -13,3 +13,4 @@ from .dbviews import (
 )
 from .endpoints import Endpoints
 from .endpoints_proxy import EndpointsProxy
+from .last_imp_refill import LastImpRefill

meta_reports/models/last_imp_refill.py

@@ -0,0 +1,34 @@
+from django.db import models
+from django_pandas.managers import DataFrameManager
+from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
+
+
+class LastImpRefill(QaReportModelMixin, models.Model):
+
+    reference_date = models.DateField(null=True)
+
+    imp_visit_code = models.FloatField(null=True)
+
+    imp_visit_date = models.DateField(null=True)
+
+    next_visit_code = models.FloatField(null=True)
+
+    next_appt_date = models.DateField(null=True)
+
+    visit_code = models.CharField(max_length=15, null=True)
+
+    visit_code_sequence = models.IntegerField(null=True)
+
+    days_since = models.IntegerField(null=True)
+
+    days_until = models.IntegerField(null=True)
+
+    objects = DataFrameManager()
+
+    def recreate_db_view(self, **kwargs):
+        raise NotImplementedError()
+
+    class Meta(QaReportModelMixin.Meta):
+        verbose_name = "Last IMP Refill"
+        verbose_name_plural = "Last IMP Refills"
+        default_permissions = qa_reports_permissions

meta_subject/admin/study_medication_admin.py

@@ -64,6 +64,16 @@ class StudyMedicationAdmin(CrfModelAdminMixin, SimpleHistoryAdmin):
                 ),
             },
         ),
+        (
+            "Dispensed medication",
+            {
+                "description": (
+                    "Type in the stock code on the medication "
+                    "bottle or bottles. Separate by comma."
+                ),
+                "fields": ("stock_codes",),
+            },
+        ),
         crf_status_fieldset,
         audit_fieldset_tuple,
     )

meta_subject/forms/study_medication_form.py

@@ -1,9 +1,12 @@
+import re
+
 from django import forms
 from edc_crf.modelform_mixins import CrfModelFormMixin
 from edc_form_validators import INVALID_ERROR
 from edc_pharmacy.form_validators import (
     StudyMedicationFormValidator as BaseStudyMedicationFormValidator,
 )
+from edc_pharmacy.models import Stock
 from edc_visit_schedule.constants import DAY1
 
 from ..models import StudyMedication
@@ -13,6 +16,7 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
     def clean(self):
         super().clean()
         self.validate_half_dose_at_baseline()
+        self.validate_stock_codes_are_dispensed()
 
     def validate_half_dose_at_baseline(self):
         """Require 1000mg dose at baseline"""
@@ -32,6 +36,37 @@ class StudyMedicationFormValidator(BaseStudyMedicationFormValidator):
                         {"dosage_guideline": "Invalid. Expected 1000mg/day at baseline"}
                     )
 
+    def validate_stock_codes_are_dispensed(self):
+        if self.cleaned_data.get("stock_codes"):
+            pattern = re.compile("^([A-Z0-9]{6})(,[A-Z0-9]{6})*$")
+            if not pattern.match(self.cleaned_data.get("stock_codes")):
+                raise forms.ValidationError(
+                    {
+                        "stock_codes": (
+                            "Invalid format. Enter one or more valid codes separated by comma"
+                        )
+                    }
+                )
+            for stock_code in self.cleaned_data.get("stock_codes").split(","):
+                try:
+                    Stock.objects.get(
+                        code=stock_code,
+                        dispensed=True,
+                        allocation__registered_subject__subject_identifier=(
+                            self.subject_identifier
+                        ),
+                    )
+                except Stock.DoesNotExist:
+                    raise forms.ValidationError(
+                        {
+                            "stock_codes": (
+                                f"Invalid. Got {stock_code}. "
+                                "Either not allocated to this subject or not dispensed. "
+                                "Please check the bottle or check with your pharmacist."
+                            )
+                        }
+                    )
+
 
 class StudyMedicationForm(CrfModelFormMixin, forms.ModelForm):
     form_validator_cls = StudyMedicationFormValidator