meta-edc 0.3.7__py3-none-any.whl → 0.3.50__py3-none-any.whl

meta_pharmacy/migrations/0008_remove_lotnumber_medication_and_more.py

@@ -0,0 +1,390 @@
+# Generated by Django 5.1.2 on 2024-11-14 20:53
+
+import _socket
+import django.db.models.deletion
+import django_audit_fields.fields.hostname_modification_field
+import django_audit_fields.fields.userfield
+import django_audit_fields.fields.uuid_auto_field
+import django_audit_fields.models.audit_model_mixin
+import django_revision.revision_field
+import edc_sites.managers
+import simple_history.models
+import uuid
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_registration", "0031_alter_historicalregisteredsubject_site_and_more"),
+        ("meta_pharmacy", "0007_lotnumber_medication"),
+        ("sites", "0002_alter_domain_unique"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="lotnumber",
+            name="medication",
+        ),
+        migrations.AlterField(
+            model_name="historicalrx",
+            name="registered_subject",
+            field=models.ForeignKey(
+                blank=True,
+                db_constraint=False,
+                null=True,
+                on_delete=django.db.models.deletion.DO_NOTHING,
+                related_name="+",
+                to="edc_registration.registeredsubject",
+                verbose_name="Subject Identifier",
+            ),
+        ),
+        migrations.CreateModel(
+            name="HistoricalLabelData",
+            fields=[
+                (
+                    "revision",
+                    django_revision.revision_field.RevisionField(
+                        blank=True,
+                        editable=False,
+                        help_text="System field. Git repository tag:branch:commit.",
+                        max_length=75,
+                        null=True,
+                        verbose_name="Revision",
+                    ),
+                ),
+                (
+                    "created",
+                    models.DateTimeField(
+                        blank=True,
+                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                    ),
+                ),
+                (
+                    "modified",
+                    models.DateTimeField(
+                        blank=True,
+                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                    ),
+                ),
+                (
+                    "user_created",
+                    django_audit_fields.fields.userfield.UserField(
+                        blank=True,
+                        help_text="Updated by admin.save_model",
+                        max_length=50,
+                        verbose_name="user created",
+                    ),
+                ),
+                (
+                    "user_modified",
+                    django_audit_fields.fields.userfield.UserField(
+                        blank=True,
+                        help_text="Updated by admin.save_model",
+                        max_length=50,
+                        verbose_name="user modified",
+                    ),
+                ),
+                (
+                    "hostname_created",
+                    models.CharField(
+                        blank=True,
+                        default=_socket.gethostname,
+                        help_text="System field. (modified on create only)",
+                        max_length=60,
+                        verbose_name="Hostname created",
+                    ),
+                ),
+                (
+                    "hostname_modified",
+                    django_audit_fields.fields.hostname_modification_field.HostnameModificationField(
+                        blank=True,
+                        help_text="System field. (modified on every save)",
+                        max_length=50,
+                        verbose_name="Hostname modified",
+                    ),
+                ),
+                (
+                    "device_created",
+                    models.CharField(blank=True, max_length=10, verbose_name="Device created"),
+                ),
+                (
+                    "device_modified",
+                    models.CharField(
+                        blank=True, max_length=10, verbose_name="Device modified"
+                    ),
+                ),
+                (
+                    "locale_created",
+                    models.CharField(
+                        blank=True,
+                        help_text="Auto-updated by Modeladmin",
+                        max_length=10,
+                        null=True,
+                        verbose_name="Locale created",
+                    ),
+                ),
+                (
+                    "locale_modified",
+                    models.CharField(
+                        blank=True,
+                        help_text="Auto-updated by Modeladmin",
+                        max_length=10,
+                        null=True,
+                        verbose_name="Locale modified",
+                    ),
+                ),
+                (
+                    "id",
+                    django_audit_fields.fields.uuid_auto_field.UUIDAutoField(
+                        blank=True,
+                        db_index=True,
+                        editable=False,
+                        help_text="System auto field. UUID primary key.",
+                    ),
+                ),
+                ("subject_identifier", models.CharField(max_length=15, null=True)),
+                ("sid", models.IntegerField(help_text="Pharmacy reference", null=True)),
+                (
+                    "reference",
+                    models.CharField(
+                        db_index=True,
+                        help_text="Bottle reference",
+                        max_length=10,
+                        null=True,
+                    ),
+                ),
+                ("site_name", models.CharField(max_length=15, null=True)),
+                ("gender", models.CharField(max_length=5, null=True)),
+                ("pills_per_bottle", models.IntegerField(default=128, null=True)),
+                ("printed_datetime", models.DateTimeField(null=True)),
+                ("printed", models.BooleanField(default=False)),
+                ("scanned", models.BooleanField(default=False)),
+                ("scanned_datetime", models.DateTimeField(null=True)),
+                ("received_datetime", models.DateTimeField(null=True)),
+                (
+                    "received",
+                    models.BooleanField(default=False, help_text="Received at site"),
+                ),
+                (
+                    "dispensed",
+                    models.BooleanField(default=False, help_text="Dispensed to clinic"),
+                ),
+                ("dispensed_datetime", models.DateTimeField(null=True)),
+                (
+                    "crf",
+                    models.BooleanField(default=False, help_text="Entered into subject's CRF"),
+                ),
+                ("crf_datetime", models.DateTimeField(null=True)),
+                (
+                    "history_id",
+                    models.UUIDField(
+                        default=uuid.uuid4,
+                        editable=False,
+                        primary_key=True,
+                        serialize=False,
+                    ),
+                ),
+                ("history_date", models.DateTimeField(db_index=True)),
+                ("history_change_reason", models.CharField(max_length=100, null=True)),
+                (
+                    "history_type",
+                    models.CharField(
+                        choices=[("+", "Created"), ("~", "Changed"), ("-", "Deleted")],
+                        max_length=1,
+                    ),
+                ),
+                (
+                    "history_user",
+                    models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.SET_NULL,
+                        related_name="+",
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+                (
+                    "site",
+                    models.ForeignKey(
+                        blank=True,
+                        db_constraint=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.DO_NOTHING,
+                        related_name="+",
+                        to="sites.site",
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "historical Label Data",
+                "verbose_name_plural": "historical Label Data",
+                "ordering": ("-history_date", "-history_id"),
+                "get_latest_by": ("history_date", "history_id"),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+        migrations.CreateModel(
+            name="LabelData",
+            fields=[
+                (
+                    "revision",
+                    django_revision.revision_field.RevisionField(
+                        blank=True,
+                        editable=False,
+                        help_text="System field. Git repository tag:branch:commit.",
+                        max_length=75,
+                        null=True,
+                        verbose_name="Revision",
+                    ),
+                ),
+                (
+                    "created",
+                    models.DateTimeField(
+                        blank=True,
+                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                    ),
+                ),
+                (
+                    "modified",
+                    models.DateTimeField(
+                        blank=True,
+                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                    ),
+                ),
+                (
+                    "user_created",
+                    django_audit_fields.fields.userfield.UserField(
+                        blank=True,
+                        help_text="Updated by admin.save_model",
+                        max_length=50,
+                        verbose_name="user created",
+                    ),
+                ),
+                (
+                    "user_modified",
+                    django_audit_fields.fields.userfield.UserField(
+                        blank=True,
+                        help_text="Updated by admin.save_model",
+                        max_length=50,
+                        verbose_name="user modified",
+                    ),
+                ),
+                (
+                    "hostname_created",
+                    models.CharField(
+                        blank=True,
+                        default=_socket.gethostname,
+                        help_text="System field. (modified on create only)",
+                        max_length=60,
+                        verbose_name="Hostname created",
+                    ),
+                ),
+                (
+                    "hostname_modified",
+                    django_audit_fields.fields.hostname_modification_field.HostnameModificationField(
+                        blank=True,
+                        help_text="System field. (modified on every save)",
+                        max_length=50,
+                        verbose_name="Hostname modified",
+                    ),
+                ),
+                (
+                    "device_created",
+                    models.CharField(blank=True, max_length=10, verbose_name="Device created"),
+                ),
+                (
+                    "device_modified",
+                    models.CharField(
+                        blank=True, max_length=10, verbose_name="Device modified"
+                    ),
+                ),
+                (
+                    "locale_created",
+                    models.CharField(
+                        blank=True,
+                        help_text="Auto-updated by Modeladmin",
+                        max_length=10,
+                        null=True,
+                        verbose_name="Locale created",
+                    ),
+                ),
+                (
+                    "locale_modified",
+                    models.CharField(
+                        blank=True,
+                        help_text="Auto-updated by Modeladmin",
+                        max_length=10,
+                        null=True,
+                        verbose_name="Locale modified",
+                    ),
+                ),
+                (
+                    "id",
+                    django_audit_fields.fields.uuid_auto_field.UUIDAutoField(
+                        blank=True,
+                        editable=False,
+                        help_text="System auto field. UUID primary key.",
+                        primary_key=True,
+                        serialize=False,
+                    ),
+                ),
+                ("subject_identifier", models.CharField(max_length=15, null=True)),
+                ("sid", models.IntegerField(help_text="Pharmacy reference", null=True)),
+                (
+                    "reference",
+                    models.CharField(
+                        help_text="Bottle reference",
+                        max_length=10,
+                        null=True,
+                        unique=True,
+                    ),
+                ),
+                ("site_name", models.CharField(max_length=15, null=True)),
+                ("gender", models.CharField(max_length=5, null=True)),
+                ("pills_per_bottle", models.IntegerField(default=128, null=True)),
+                ("printed_datetime", models.DateTimeField(null=True)),
+                ("printed", models.BooleanField(default=False)),
+                ("scanned", models.BooleanField(default=False)),
+                ("scanned_datetime", models.DateTimeField(null=True)),
+                ("received_datetime", models.DateTimeField(null=True)),
+                (
+                    "received",
+                    models.BooleanField(default=False, help_text="Received at site"),
+                ),
+                (
+                    "dispensed",
+                    models.BooleanField(default=False, help_text="Dispensed to clinic"),
+                ),
+                ("dispensed_datetime", models.DateTimeField(null=True)),
+                (
+                    "crf",
+                    models.BooleanField(default=False, help_text="Entered into subject's CRF"),
+                ),
+                ("crf_datetime", models.DateTimeField(null=True)),
+                (
+                    "site",
+                    models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.PROTECT,
+                        related_name="+",
+                        to="sites.site",
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "Label Data",
+                "verbose_name_plural": "Label Data",
+            },
+            managers=[
+                ("on_site", edc_sites.managers.CurrentSiteManager()),
+            ],
+        ),
+        migrations.DeleteModel(
+            name="Label",
+        ),
+        migrations.DeleteModel(
+            name="LotNumber",
+        ),
+    ]

meta_pharmacy/migrations/0009_remove_historicalrx_slug.py

@@ -0,0 +1,17 @@
+# Generated by Django 5.1.2 on 2024-11-19 11:42
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_pharmacy", "0008_remove_lotnumber_medication_and_more"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="historicalrx",
+            name="slug",
+        ),
+    ]

meta_pharmacy/models/__init__.py

@@ -0,0 +1,3 @@
+from .label_data import LabelData
+from .rx import Rx
+from .substitutions import MyManager, Substitutions

meta_pharmacy/models/label_data.py

@@ -0,0 +1,38 @@
+import random
+
+import edc_model.models
+from django.db import models
+from edc_model.models import BaseUuidModel
+from edc_sites.model_mixins import SiteModelMixin
+
+random.seed(237548)
+
+
+class LabelData(SiteModelMixin, BaseUuidModel):
+
+    subject_identifier = models.CharField(max_length=15, null=True)
+    sid = models.IntegerField(null=True, help_text="Pharmacy reference")
+    reference = models.CharField(
+        max_length=10, null=True, unique=True, help_text="Bottle reference"
+    )
+    site_name = models.CharField(max_length=15, null=True)
+    gender = models.CharField(max_length=5, null=True)
+    pills_per_bottle = models.IntegerField(null=True, default=128)
+
+    printed_datetime = models.DateTimeField(null=True)
+    printed = models.BooleanField(default=False)
+    scanned = models.BooleanField(default=False)
+    scanned_datetime = models.DateTimeField(null=True)
+
+    received_datetime = models.DateTimeField(null=True)
+    received = models.BooleanField(default=False, help_text="Received at site")
+    dispensed = models.BooleanField(default=False, help_text="Dispensed to clinic")
+    dispensed_datetime = models.DateTimeField(null=True)
+    crf = models.BooleanField(default=False, help_text="Entered into subject's CRF")
+    crf_datetime = models.DateTimeField(null=True)
+
+    history = edc_model.models.HistoricalRecords()
+
+    class Meta:
+        verbose_name = "Label Data"
+        verbose_name_plural = "Label Data"

meta_pharmacy/models/rx.py

@@ -0,0 +1,18 @@
+from edc_pharmacy.models import Rx as BaseRx
+
+
+class Rx(BaseRx):
+    """A proxy model of edc_pharmacy.Rx.
+
+    A model for the prescription.
+
+    For autocomplete only.
+    """
+
+    def save(self, *args, **kwargs):
+        raise NotImplementedError(
+            "This proxy model may not be saved. Permissions should be view only"
+        )
+
+    class Meta:
+        proxy = True

meta_pharmacy/models/rx_label.py

@@ -0,0 +1,39 @@
+from django.db import models
+from edc_identifier.simple_identifier import SimpleUniqueIdentifier
+from edc_model.models import BaseUuidModel
+from edc_pharmacy.models import Lot
+
+from .rx import Rx
+
+
+class LabelIdentifier(SimpleUniqueIdentifier):
+    random_string_length = 6
+    identifier_type = "rx_label_reference"
+    template = "{random_string}"
+
+
+class RxLabel(BaseUuidModel):
+
+    identifier_cls = LabelIdentifier
+
+    rx = models.ForeignKey(Rx, on_delete=models.PROTECT)
+    lot = models.ForeignKey(Lot, on_delete=models.PROTECT)
+    label_identifier = models.CharField(max_length=15, unique=True)
+
+    printed_datetime = models.DateTimeField(null=True)
+    printed = models.BooleanField(default=False)
+    scanned = models.BooleanField(default=False)
+    scanned_datetime = models.DateTimeField(null=True)
+
+    def __str__(self):
+        return self.label_identifier
+
+    def save(self, *args, **kwargs):
+        """Label reference is always allocated."""
+        if not self.id:
+            self.label_identifier = self.identifier_cls().identifier
+        super().save(*args, **kwargs)
+
+    class Meta(BaseUuidModel.Meta):
+        verbose_name = "Label"
+        verbose_name_plural = "Labels"

meta_pharmacy/models/substitutions.py

@@ -0,0 +1,88 @@
+from django.core.exceptions import ObjectDoesNotExist
+from django.db import models
+from django.db.models import Index
+from edc_constants.choices import YES_NO_NOT_EVALUATED
+from edc_constants.constants import NO, NOT_EVALUATED, YES
+from edc_identifier.model_mixins import NonUniqueSubjectIdentifierFieldMixin
+from edc_model.models import BaseUuidModel, HistoricalRecords
+from edc_sites.managers import CurrentSiteManager
+from edc_sites.model_mixins import SiteModelMixin
+
+from meta_pharmacy.constants import MISSING_SUBJECT_IDENTIFIER
+from meta_rando.models import RandomizationList
+
+from .rx import Rx
+
+
+class MyManager(models.Manager):
+    use_in_migrations = True
+
+
+class Substitutions(NonUniqueSubjectIdentifierFieldMixin, SiteModelMixin, BaseUuidModel):
+    """A model to capture a CSV file that lists IMP substitutions
+    made where a bottle of `sid` is substituted with a bottle of
+    `dispensed_sid`.
+
+    The IMP substitutions were not done by any approved procedure. SID
+    values are sequential and not designed for human transcription.
+    """
+
+    report_datetime = models.DateTimeField(null=True, blank=False)
+
+    row_index = models.IntegerField(null=True)
+
+    rx = models.ForeignKey(Rx, on_delete=models.PROTECT, null=True, blank=True)
+
+    sid = models.IntegerField(verbose_name="SID")
+
+    visit_no = models.IntegerField("Visit Number", null=True, blank=True)
+
+    dispensed_sid = models.IntegerField(verbose_name="Dispensed SID")
+
+    updated_visit_no = models.IntegerField("Visit Number", null=True, blank=True)
+
+    updated_subject_identifier = models.CharField(
+        max_length=50, verbose_name="Taken from subject", null=True, blank=True
+    )
+
+    arm_match = models.CharField(
+        max_length=15, choices=YES_NO_NOT_EVALUATED, default=NOT_EVALUATED
+    )
+
+    notes = models.TextField(verbose_name="Notes")
+
+    objects = MyManager()
+    on_site = CurrentSiteManager()
+    history = HistoricalRecords(inherit=True)
+
+    def __str__(self):
+        if self.rx:
+            return self.rx.subject_identifier
+        return str(self.sid)
+
+    def save(self, *args, **kwargs):
+        if not self.rx:
+            try:
+                self.rx = Rx.objects.get(rando_sid=self.sid)
+            except ObjectDoesNotExist:
+                self.status = MISSING_SUBJECT_IDENTIFIER
+            else:
+                self.subject_identifier = self.rx.subject_identifier
+        else:
+            self.subject_identifier = self.rx.subject_identifier
+        rando_a = RandomizationList.objects.get(sid=self.sid)
+        rando_b = RandomizationList.objects.get(sid=self.dispensed_sid)
+        if rando_a.assignment != rando_b.assignment:
+            self.arm_match = NO
+        else:
+            self.arm_match = YES
+
+        super().save(*args, **kwargs)
+
+    class Meta(SiteModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name_plural = "IMP Substitutions"
+        verbose_name = "IMP Substitution"
+        indexes = [
+            Index(fields=["sid", "dispensed_sid", "subject_identifier"]),
+            Index(fields=["row_index"]),
+        ]

meta_pharmacy/urls.py

@@ -0,0 +1,8 @@
+from django.urls.conf import path
+from django.views.generic import RedirectView
+
+app_name = "meta_pharmacy"
+
+urlpatterns = [
+    path("", RedirectView.as_view(url=f"/{app_name}/admin/"), name="home_url"),
+]

meta_pharmacy/utils/__init__.py

@@ -0,0 +1 @@
+from .update_initial_pharmacy_data import update_initial_pharmacy_data