clinicedc 2.0.1__py3-none-any.whl → 2.0.3__py3-none-any.whl

edc_egfr/model_mixins/egfr_model_mixin.py

@@ -0,0 +1,120 @@
+from __future__ import annotations
+
+from decimal import Decimal
+
+from django.core.exceptions import ObjectDoesNotExist
+from django.db import models, transaction
+
+from edc_lab_results.model_mixin_factories import reportable_result_model_mixin_factory
+from edc_registration.models import RegisteredSubject
+from edc_reportable.units import EGFR_UNITS, PERCENT
+from edc_reportable.utils import get_reference_range_collection
+
+from ..calculators import EgfrCalculatorError
+from ..egfr import Egfr
+
+
+class EgfrModelMixin(
+    reportable_result_model_mixin_factory(
+        utest_id="egfr",
+        verbose_name="eGFR",
+        decimal_places=4,
+        default_units=EGFR_UNITS,
+        max_digits=8,
+        units_choices=((EGFR_UNITS, EGFR_UNITS),),
+    ),
+    reportable_result_model_mixin_factory(
+        utest_id="egfr_drop",
+        verbose_name="eGFR Drop",
+        decimal_places=4,
+        default_units=PERCENT,
+        max_digits=10,
+        units_choices=((PERCENT, PERCENT),),
+    ),
+    models.Model,
+):
+    """Declared with a bloodresult RFT CRF model.
+
+    As a lab result CRF, expects subject_visit, requisition
+    and report_datetime.
+
+    See edc_lab_result, edc_crf.
+    """
+
+    percent_drop_threshold: float = 20.0
+    baseline_timepoint: int = 0
+    egfr_formula_name: str = None
+    egfr_cls = Egfr
+
+    def save(self, *args, **kwargs):
+        if self.creatinine_value:
+            self.set_egfr_value_or_raise()
+        super().save(*args, **kwargs)
+
+    def set_egfr_value_or_raise(self) -> None:
+        egfr = self.egfr_cls(**self.egfr_options)
+        try:
+            self.egfr_value = egfr.egfr_value
+        except EgfrCalculatorError:
+            if self.creatinine_value:
+                raise
+            self.egfr_value = None
+            self.egfr_units = None
+            self.egfr_grade = None
+            self.egfr_drop_value = None
+            self.egfr_drop_units = None
+            self.egfr_drop_grade = None
+        else:
+            self.egfr_units = egfr.egfr_units
+            self.egfr_grade = egfr.egfr_grade
+            self.egfr_drop_value = egfr.egfr_drop_value
+            self.egfr_drop_units = egfr.egfr_drop_units
+            self.egfr_drop_grade = egfr.egfr_drop_grade
+
+    @property
+    def egfr_options(self) -> dict:
+        rs = RegisteredSubject.objects.get(
+            subject_identifier=self.related_visit.subject_identifier
+        )
+        return dict(
+            calling_crf=self,
+            dob=rs.dob,
+            gender=rs.gender,
+            ethnicity=rs.ethnicity,
+            weight_in_kgs=self.get_weight_in_kgs_for_egfr(),
+            percent_drop_threshold=self.percent_drop_threshold,
+            value_threshold=45.0000,
+            report_datetime=self.report_datetime,
+            baseline_egfr_value=self.get_baseline_egfr_value(),
+            formula_name=self.egfr_formula_name,
+            reference_range_collection=get_reference_range_collection(self),
+        )
+
+    def get_baseline_egfr_value(self) -> float | None:
+        """Returns a baseline or reference eGFR value.
+
+        Expects a longitudinal / CRF model with attrs `subject_visit`.
+        """
+        egfr_value = None
+        with transaction.atomic():
+            baseline_visit = self.related_visit.__class__.objects.get(
+                appointment__subject_identifier=self.related_visit.subject_identifier,
+                appointment__visit_schedule_name=self.related_visit.visit_schedule_name,
+                appointment__schedule_name=self.related_visit.schedule_name,
+                appointment__timepoint=self.baseline_timepoint,
+                visit_code_sequence=0,
+            )
+        with transaction.atomic():
+            try:
+                egfr_value = self.__class__.objects.get(
+                    subject_visit=baseline_visit
+                ).egfr_value
+            except ObjectDoesNotExist:
+                pass
+        return egfr_value
+
+    def get_weight_in_kgs_for_egfr(self) -> Decimal | None:
+        return None
+
+    class Meta:
+        abstract = True

edc_export/archive_exporter.py

@@ -64,9 +64,7 @@ class ArchiveExporter:
             )
             self.exported.append(csv_exporter.to_csv())
         if not self.exported:
-            raise ArchiveExporterNothingExported(
-                f"Nothing exported. Got models={models}."
-            )
+            raise ArchiveExporterNothingExported(f"Nothing exported. Got models={models}.")
         else:
             if archive:
                 archiver = self.files_archiver_cls(
@@ -92,6 +90,4 @@ class ArchiveExporter:
                 else:
                     self.emailed_to = user.email
                     self.emailed_datetime = get_utcnow()
-                    self.exported_datetime = (
-                        self.exported_datetime or self.emailed_datetime
-                    )
+                    self.exported_datetime = self.exported_datetime or self.emailed_datetime

edc_export/exportables.py

@@ -69,9 +69,7 @@ class Exportable(OrderedDict):
             for site in sites.all_sites:
                 for model_cls, admin_site in site._registry.items():
                     for inline_cls in admin_site.inlines:
-                        model_opts = ModelOptions(
-                            model=inline_cls.model._meta.label_lower
-                        )
+                        model_opts = ModelOptions(model=inline_cls.model._meta.label_lower)
                         try:
                             self._inlines[model_cls._meta.app_label].append(model_opts)
                         except KeyError:
@@ -105,9 +103,7 @@ class Exportables(OrderedDict):
         try:
             user.groups.get(name=self.export_group_name)
         except ObjectDoesNotExist:
-            messages.error(
-                request, "You do not have sufficient permissions to export data."
-            )
+            messages.error(request, "You do not have sufficient permissions to export data.")
         else:
             for app_config in app_configs:
                 self.update({app_config.name: Exportable(app_config=app_config)})

edc_export/files_emailer.py

@@ -70,9 +70,7 @@ class FilesEmailer:
         try:
             email_message.send()
         except socket.gaierror:
-            raise FilesEmailerError(
-                "Unable to connect to email server.", code="gaierror"
-            )
+            raise FilesEmailerError("Unable to connect to email server.", code="gaierror")
 
     def email_files(self) -> None:
         email_message = self.get_email_message()

edc_export/management/commands/import_receipts.py

@@ -72,9 +72,7 @@ class Command(BaseCommand):
         try:
             app_label1, app_label2 = self.app_labe1.split("_")
             error_filename = (
-                "_".join(
-                    ["error", app_label1, app_label2, self.object_name, self.timestamp]
-                )
+                "_".join(["error", app_label1, app_label2, self.object_name, self.timestamp])
                 + "."
                 + self.extension
             )

edc_export/managers.py

@@ -20,17 +20,11 @@ class ExportHistoryManager(models.Manager):
 
         .. note:: If change_type == 'D', entire tx is still sent."""
         try:
-            ready_to_export_transaction = (
-                force_export or instance.ready_to_export_transaction
-            )
+            ready_to_export_transaction = force_export or instance.ready_to_export_transaction
         except AttributeError as attribute_error:
-            if str(attribute_error).endswith(
-                "has no attribute 'ready_to_export_transaction'"
-            ):
+            if str(attribute_error).endswith("has no attribute 'ready_to_export_transaction'"):
                 ready_to_export_transaction = True
             else:
                 raise
         if ready_to_export_transaction:
-            self.obj_creator.create(
-                model_obj=instance, change_type=change_type, using=using
-            )
+            self.obj_creator.create(model_obj=instance, change_type=change_type, using=using)

edc_export/migrations/0001_initial.py

@@ -7,13 +7,14 @@ import django.db.models.deletion
 import django_audit_fields.fields.uuid_auto_field
 import django_crypto_fields.fields.encrypted_text_field
 import django_revision.revision_field
-import edc_model_fields.fields.hostname_modification_field
-import edc_model_fields.fields.userfield
-import edc_utils
 import simple_history.models
 from django.conf import settings
 from django.db import migrations, models
 
+import edc_model_fields.fields.hostname_modification_field
+import edc_model_fields.fields.userfield
+import edc_utils
+
 
 class Migration(migrations.Migration):
     initial = True
@@ -95,9 +96,7 @@ class Migration(migrations.Migration):
                 ("decrypt", models.BooleanField(default=False)),
                 (
                     "export_format",
-                    models.CharField(
-                        choices=[("CSV", "CSV")], default="CSV", max_length=25
-                    ),
+                    models.CharField(choices=[("CSV", "CSV")], default="CSV", max_length=25),
                 ),
                 (
                     "models",
@@ -389,9 +388,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "filename",
-                    models.CharField(
-                        help_text="original filename on export", max_length=250
-                    ),
+                    models.CharField(help_text="original filename on export", max_length=250),
                 ),
                 (
                     "file_contents",
@@ -422,9 +419,7 @@ class Migration(migrations.Migration):
                 ("received_datetime", models.DateTimeField(null=True)),
                 (
                     "closed",
-                    models.BooleanField(
-                        default=False, help_text="exported, sent, received"
-                    ),
+                    models.BooleanField(default=False, help_text="exported, sent, received"),
                 ),
                 ("closed_datetime", models.DateTimeField(null=True)),
             ],
@@ -503,9 +498,7 @@ class Migration(migrations.Migration):
                 ("decrypt", models.BooleanField(default=False)),
                 (
                     "export_format",
-                    models.CharField(
-                        choices=[("CSV", "CSV")], default="CSV", max_length=25
-                    ),
+                    models.CharField(choices=[("CSV", "CSV")], default="CSV", max_length=25),
                 ),
                 (
                     "models",
@@ -766,9 +759,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "filename",
-                    models.CharField(
-                        help_text="original filename on export", max_length=250
-                    ),
+                    models.CharField(help_text="original filename on export", max_length=250),
                 ),
                 (
                     "file_contents",
@@ -799,9 +790,7 @@ class Migration(migrations.Migration):
                 ("received_datetime", models.DateTimeField(null=True)),
                 (
                     "closed",
-                    models.BooleanField(
-                        default=False, help_text="exported, sent, received"
-                    ),
+                    models.BooleanField(default=False, help_text="exported, sent, received"),
                 ),
                 ("closed_datetime", models.DateTimeField(null=True)),
                 ("history_change_reason", models.CharField(max_length=100, null=True)),
@@ -959,9 +948,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "received",
-                    models.BooleanField(
-                        default=False, help_text="True if ACK received"
-                    ),
+                    models.BooleanField(default=False, help_text="True if ACK received"),
                 ),
                 (
                     "received_datetime",
@@ -1106,9 +1093,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "encrypt",
-                    models.BooleanField(
-                        default=True, verbose_name="Mask encrypted values"
-                    ),
+                    models.BooleanField(default=True, verbose_name="Mask encrypted values"),
                 ),
                 ("history_change_reason", models.CharField(max_length=100, null=True)),
                 ("history_date", models.DateTimeField()),
@@ -1266,9 +1251,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "received",
-                    models.BooleanField(
-                        default=False, help_text="True if ACK received"
-                    ),
+                    models.BooleanField(default=False, help_text="True if ACK received"),
                 ),
                 (
                     "received_datetime",
@@ -1385,9 +1368,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "encrypt",
-                    models.BooleanField(
-                        default=True, verbose_name="Mask encrypted values"
-                    ),
+                    models.BooleanField(default=True, verbose_name="Mask encrypted values"),
                 ),
             ],
             options={
@@ -1471,9 +1452,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "file_name",
-                    models.CharField(
-                        editable=False, max_length=50, null=True, unique=True
-                    ),
+                    models.CharField(editable=False, max_length=50, null=True, unique=True),
                 ),
                 ("app_label", models.CharField(max_length=50)),
                 ("model_name", models.CharField(max_length=50)),

edc_export/migrations/0005_exportdata_importdata.py

@@ -23,9 +23,7 @@ class Migration(migrations.Migration):
                 ),
             ],
             options={
-                "permissions": (
-                    ("display_export_admin_action", "Display export action"),
-                ),
+                "permissions": (("display_export_admin_action", "Display export action"),),
             },
         ),
         migrations.CreateModel(

edc_export/migrations/0006_auto_20200512_0208.py

@@ -11,15 +11,11 @@ class Migration(migrations.Migration):
     operations = [
         migrations.AlterModelOptions(
             name="exportdata",
-            options={
-                "permissions": [("show_export_admin_action", "Show export action")]
-            },
+            options={"permissions": [("show_export_admin_action", "Show export action")]},
         ),
         migrations.AlterModelOptions(
             name="importdata",
-            options={
-                "permissions": [("show_import_admin_action", "Show import action")]
-            },
+            options={"permissions": [("show_import_admin_action", "Show import action")]},
         ),
         migrations.AlterModelOptions(
             name="plan",

edc_export/migrations/0010_auto_20210910_1636.py

@@ -12,17 +12,13 @@ class Migration(migrations.Migration):
         migrations.AlterModelOptions(
             name="exportdata",
             options={
-                "permissions": [
-                    ("display_export_admin_action", "Display export action")
-                ]
+                "permissions": [("display_export_admin_action", "Display export action")]
             },
         ),
         migrations.AlterModelOptions(
             name="importdata",
             options={
-                "permissions": [
-                    ("display_import_admin_action", "Display import action")
-                ]
+                "permissions": [("display_import_admin_action", "Display import action")]
             },
         ),
     ]

edc_export/migrations/0013_edcpermissions.py

@@ -1,12 +1,12 @@
 # Generated by Django 3.2.13 on 2022-08-25 01:51
 
 import _socket
-from django.db import migrations, models
 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
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_export/migrations/0015_alter_datarequest_managers_and_more.py

@@ -1,9 +1,10 @@
 # Generated by Django 4.2.3 on 2023-07-18 17:27
 
 import django.db.models.deletion
-import edc_sites.models
 from django.db import migrations, models
 
+import edc_sites.models
+
 
 class Migration(migrations.Migration):
     dependencies = [

edc_export/migrations/0016_alter_datarequest_device_created_and_more.py

@@ -1,8 +1,8 @@
 # Generated by Django 4.2.4 on 2023-08-23 01:13
 
 import _socket
-from django.db import migrations, models
 import django_audit_fields.fields.hostname_modification_field
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -14,16 +14,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="datarequest",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="datarequest",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="datarequest",
@@ -49,16 +45,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="datarequesthistory",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="datarequesthistory",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="datarequesthistory",
@@ -84,16 +76,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",
@@ -119,16 +107,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="exportreceipt",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="exportreceipt",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="exportreceipt",
@@ -154,16 +138,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="filehistory",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="filehistory",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="filehistory",
@@ -189,16 +169,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicaldatarequest",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicaldatarequest",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicaldatarequest",
@@ -224,16 +200,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalexportreceipt",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicalexportreceipt",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicalexportreceipt",
@@ -259,16 +231,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalfilehistory",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicalfilehistory",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicalfilehistory",
@@ -294,16 +262,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalobjecthistory",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicalobjecthistory",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicalobjecthistory",
@@ -329,16 +293,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalplan",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicalplan",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicalplan",
@@ -364,16 +324,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="objecthistory",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="objecthistory",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="objecthistory",
@@ -399,16 +355,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="plan",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="plan",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="plan",
@@ -434,16 +386,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="uploadexportreceiptfile",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="uploadexportreceiptfile",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="uploadexportreceiptfile",