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

meta_pharmacy/admin/lot_number_admin.py

@@ -1,43 +0,0 @@
-from django.contrib import admin
-from django_audit_fields import audit_fieldset_tuple
-from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
-
-from ..admin_site import meta_pharmacy_admin
-from ..models import LotNumber
-
-
-@admin.register(LotNumber, site=meta_pharmacy_admin)
-class LotNumberAdmin(ModelAdminSubjectDashboardMixin, admin.ModelAdmin):
-    """Admin class for proxy model of edc_pharmacy.Rx"""
-
-    show_object_tools = True
-
-    # form = LotNumberForm
-
-    fieldsets = (
-        (
-            None,
-            {
-                "fields": (
-                    "lot_no",
-                    "expiration_date",
-                    "allocation",
-                    "qty",
-                )
-            },
-        ),
-        audit_fieldset_tuple,
-    )
-
-    list_display = (
-        "lot_no",
-        "expiration_date",
-    )
-
-    radio_fields = {"allocation": admin.VERTICAL}
-
-    list_filter = ("allocation",)
-
-    search_fields = [
-        "lot_no",
-    ]

meta_pharmacy/labels/get_label_data.py

@@ -1,30 +0,0 @@
-from django.core.exceptions import ObjectDoesNotExist
-from tqdm import tqdm
-
-from meta_consent.models import SubjectConsent
-from meta_rando.models import RandomizationList
-
-from ..models import Label, LotNumber, Rx
-
-
-class InvalidLotNumber(Exception):
-    pass
-
-
-def get_label_data(lot_no, max_labels: int | None = None) -> list[Label]:
-    try:
-        lot_no = LotNumber.objects.get(lot_no=lot_no)
-    except ObjectDoesNotExist:
-        raise ObjectDoesNotExist("The lot number given is invalid")
-    else:
-        labels = []
-        qs = SubjectConsent.objects.values("subject_identifier", "site_id", "gender").all()
-        for obj in tqdm(qs, total=qs.count()):
-            if max_labels and len(labels) >= max_labels:
-                break
-            rando = RandomizationList.objects.get(subject_identifier=obj["subject_identifier"])
-            if rando.assignment != lot_no.allocation:
-                continue
-            rx = Rx.objects.get(subject_identifier=obj["subject_identifier"])
-            labels.append(Label.objects.create(rx=rx, lot_no=lot_no))
-    return labels

meta_pharmacy/models/lot_number.py

@@ -1,25 +0,0 @@
-from django.db import models
-from edc_model.models import BaseUuidModel
-from edc_pharmacy.models import Medication
-from edc_randomization.constants import ACTIVE, PLACEBO
-
-
-class LotNumber(BaseUuidModel):
-
-    lot_no = models.CharField(max_length=25, unique=True)
-
-    medication = models.ForeignKey(
-        Medication, on_delete=models.PROTECT, null=True, blank=False
-    )
-
-    allocation = models.CharField(
-        max_length=25, choices=((ACTIVE, "Active"), (PLACEBO, "Placebo"))
-    )
-
-    expiration_date = models.DateField()
-
-    qty = models.IntegerField(null=True)
-
-    class Meta(BaseUuidModel.Meta):
-        verbose_name = "Lot Number"
-        verbose_name_plural = "Lot Numbers"

meta_reports/models/unmanaged/README

@@ -1,14 +0,0 @@
-The models in this folder represent VIEWS in the DB. Since the VIEWS
- are created separately, the model classes are "unmanaged". Unmanaged
- models do not trigger migrations that change the schema. However,
- a change to any of these model classes will trigger a migration, but
- the migration does to change the schema.
-
- Each model class has a corresponding SQL file. A migration has been
- created to run the ``CREATE VIEW`` commands using the
- ``migrations.RunSQL`` method.
-
- If you change the ``CREATE VIEW`` command, you have to generate a
- new empty migration which calls ``migrations.RunSQL`` to re-run the
- modified ``CREATE VIEW`` SQL command.
- (remember to ``DROP VIEW`` first.)

meta_reports/models/unmanaged/patient_history_missing_baseline_cd4.py

@@ -1,26 +0,0 @@
-from django.db import models
-from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
-
-
-class PatientHistoryMissingBaselineCd4(QaReportModelMixin, models.Model):
-
-    visit_code = models.CharField(max_length=25)
-
-    visit_code_sequence = models.IntegerField()
-
-    cd4 = models.IntegerField(verbose_name="Last CD4")
-
-    cd4_date = models.DateField(verbose_name="Date of last CD4")
-
-    user_created = models.CharField(max_length=25)
-
-    user_modified = models.CharField(max_length=25)
-
-    modified = models.DateTimeField()
-
-    class Meta:
-        verbose_name = "Patient History: Missing Baseline Cd4"
-        verbose_name_plural = "Missing Baseline Cd4"
-        managed = False
-        db_table = "patient_history_missing_baseline_cd4_view"
-        default_permissions = qa_reports_permissions

meta_reports/models/unmanaged/patient_history_missing_baseline_cd4.sql

@@ -1,10 +0,0 @@
-create view patient_history_missing_baseline_cd4_view as
-    select *, uuid() as 'id', now() as created, 'meta_reports.patienthistorymissingbaselinecd4' as report_model from (
-        select subject_identifier, v.visit_code, v.visit_code_sequence,cd4,
-           cd4_date, crf.site_id, crf.user_created, crf.user_modified,
-           crf.modified
-        from meta_subject_patienthistory as crf
-            left join meta_subject_subjectvisit as v on crf.subject_visit_id=v.id
-        where cd4 is null or cd4_date is null
-    ) as A
-    order by subject_identifier;

meta_reports/models/unmanaged/unattended_three_in_row.py

@@ -1,24 +0,0 @@
-from django.db import models
-from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
-
-
-class UnattendedThreeInRow(QaReportModelMixin, models.Model):
-
-    appt_datetime = models.DateTimeField()
-
-    first = models.CharField(max_length=25)
-
-    second = models.CharField(max_length=25)
-
-    third = models.CharField(max_length=25)
-
-    interval_days = models.IntegerField()
-
-    from_now_days = models.IntegerField()
-
-    class Meta:
-        managed = False
-        db_table = "unattended_three_in_row_view"
-        verbose_name = "R100: Unattended appointments: Three in a row"
-        verbose_name_plural = "R100: Unattended appointments: Three in a row"
-        default_permissions = qa_reports_permissions

meta_reports/models/unmanaged/unattended_three_in_row.sql

@@ -1,19 +0,0 @@
-create view unattended_three_in_row_view as (
-    select *, uuid() as 'id', now() as created, 'meta_reports.unattendedthreeinrow' as report_model from (
-        select `subject_identifier`, `site_id`, `appt_datetime`, `first`, `second`, `third`,
-            datediff(`third_date`, `first_date`) as 'interval_days',
-            datediff(now(), `first_date`) as 'from_now_days'
-        from (
-            select `subject_identifier`,`site_id`,`appt_datetime`,
-            FIRST_VALUE(`visit_code`) OVER w as 'first',
-            NTH_VALUE(`visit_code`, 2) OVER w as 'second',
-            NTH_VALUE(`visit_code`, 3) OVER w as 'third',
-            FIRST_VALUE(`appt_datetime`) OVER w as 'first_date',
-            NTH_VALUE(`appt_datetime`, 3) OVER w as 'third_date'
-            from edc_appointment_appointment where `visit_code_sequence`=0 and `appt_status`='New'
-            and `appt_datetime` <= now()
-            WINDOW w as (PARTITION BY `subject_identifier` order by `appt_datetime` ROWS UNBOUNDED PRECEDING)
-        ) as A
-    where `second` is not null and `third` is not null
-    ) as B
-order by `site_id`, `from_now_days` desc);

meta_reports/models/unmanaged/unattended_three_in_row2.py

@@ -1,24 +0,0 @@
-from django.db import models
-from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
-
-
-class UnattendedThreeInRow2(QaReportModelMixin, models.Model):
-
-    first = models.CharField(max_length=25)
-
-    second = models.CharField(max_length=25)
-
-    third = models.CharField(max_length=25)
-
-    interval_days = models.IntegerField()
-
-    from_now_days = models.IntegerField()
-
-    missed_count = models.IntegerField()
-
-    class Meta:
-        managed = False
-        db_table = "unattended_three_in_row2_view"
-        verbose_name = "R110: Unattended appointments: Three in a row (with missed)"
-        verbose_name_plural = "R110: Unattended appointments: Three in a row (with missed)"
-        default_permissions = qa_reports_permissions

meta_reports/models/unmanaged/unattended_three_in_row2.sql

@@ -1,39 +0,0 @@
-create view unattended_three_in_row2_view as (
-    with appointments as (
-        select `subject_identifier`, `site_id`, `visit_code`, `visit_code_sequence`, `appt_datetime`,
-        case when `appt_timing`='missed' then 'New' else `appt_status` end as 'appt_status',
-        case when `appt_timing`='missed' then 1 else 0 end as 'missed'
-        from edc_appointment_appointment
-        where `visit_code_sequence`=0 and appt_datetime<=now()
-        order by subject_identifier, appt_datetime
-        )
-    select *, uuid() as 'id', now() as 'created', 'meta_reports.unattendedthreeinrow2' as report_model from (
-        select  distinct `subject_identifier`, `site_id`,  `first`, `second`, `third`,
-            datediff(`third_date`, `first_date`) as 'interval_days',
-            datediff(now(), `first_date`) as 'from_now_days',
-            `first_status`, `second_status`, `third_status`, sum(`missed`) as `missed_count`
-        from (
-            select `subject_identifier`,`site_id`,`appt_datetime`, `missed`,
-            FIRST_VALUE(`appt_status`) OVER w as 'third_status',
-            NTH_VALUE(`appt_status`, 2) OVER w as 'second_status',
-            NTH_VALUE(`appt_status`, 3) OVER w as 'first_status',
-            FIRST_VALUE(`visit_code`) OVER w as 'third',
-            NTH_VALUE(`visit_code`, 2) OVER w as 'second',
-            NTH_VALUE(`visit_code`, 3) OVER w as 'first',
-            FIRST_VALUE(`appt_datetime`) OVER w as 'third_date',
-            NTH_VALUE(`appt_datetime`, 2) OVER w as 'second_date',
-            NTH_VALUE(`appt_datetime`, 3) OVER w as 'first_date'
-            from appointments
-            WINDOW w as (PARTITION BY `subject_identifier` order by `appt_datetime` desc ROWS UNBOUNDED PRECEDING)
-        ) as A
-        where `second` is not null and `third` is not null
-          and `first_status`='New'
-          and `second_status`='New'
-          and `third_status`='New'
-        group by `subject_identifier`, `site_id`,  `first`, `second`, `third`,
-                 datediff(`third_date`, `first_date`),
-                 datediff(now(), `first_date`),
-                 `first_status`, `second_status`, `third_status`
-        order by `subject_identifier`, `site_id`
-    ) as B
-);

meta_reports/models/unmanaged/unattended_two_in_row.py

@@ -1,22 +0,0 @@
-from django.db import models
-from edc_qareports.model_mixins import QaReportModelMixin, qa_reports_permissions
-
-
-class UnattendedTwoInRow(QaReportModelMixin, models.Model):
-
-    appt_datetime = models.DateTimeField()
-
-    first = models.CharField(max_length=25)
-
-    second = models.CharField(max_length=25)
-
-    interval_days = models.IntegerField()
-
-    from_now_days = models.IntegerField()
-
-    class Meta:
-        managed = False
-        db_table = "unattended_two_in_row_view"
-        verbose_name = "R120: Unattended appointments: Two in a row"
-        verbose_name_plural = "R120: Unattended appointments: Two in a row"
-        default_permissions = qa_reports_permissions

meta_reports/models/unmanaged/unattended_two_in_row.sql

@@ -1,19 +0,0 @@
-create view unattended_two_in_row_view as (
-    select *, uuid() as 'id', now() as 'created', 'meta_reports.unattendedtwoinrow' as report_model from (
-        select `subject_identifier`, `site_id`, `appt_datetime`, `first`, `second`,
-            datediff(`second_date`, `first_date`) as 'interval_days',
-            datediff(now(), `first_date`) as 'from_now_days'
-            from (
-                select `subject_identifier`,`site_id`,`appt_datetime`,
-                FIRST_VALUE(`visit_code`) OVER w as 'first',
-                NTH_VALUE(`visit_code`, 2) OVER w as 'second',
-                NTH_VALUE(`visit_code`, 3) OVER w as 'third',
-                FIRST_VALUE(`appt_datetime`) OVER w as 'first_date',
-                NTH_VALUE(`appt_datetime`, 2) OVER w as 'second_date'
-                from edc_appointment_appointment where `visit_code_sequence`=0 and `appt_status`='New'
-                and `appt_datetime` <= now()
-                WINDOW w as (PARTITION BY `subject_identifier` order by `appt_datetime` ROWS UNBOUNDED PRECEDING)
-            ) as A1
-        where `second` is not null and `third` is null
-    ) as A2
-    order by `site_id`, `from_now_days` desc);