clinicedc 2.0.0__py3-none-any.whl → 2.0.2__py3-none-any.whl

edc_reportable/migrations/0006_alter_gradingdata_revision_and_more.py

@@ -0,0 +1,370 @@
+# Generated by Django 5.2.4 on 2025-09-10 03:24
+
+import uuid
+
+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.utils
+import django_revision.revision_field
+import simple_history.models
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_reportable", "0005_historicalnormaldata_auto_created_and_more"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="gradingdata",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="gradingexception",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalgradingdata",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalnormaldata",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="normaldata",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="referencerangecollection",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.CreateModel(
+            name="HistoricalMolecularWeight",
+            fields=[
+                (
+                    "revision",
+                    django_revision.revision_field.RevisionField(
+                        blank=True,
+                        editable=False,
+                        help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                        max_length=75,
+                        null=True,
+                        verbose_name="Revision",
+                    ),
+                ),
+                (
+                    "created",
+                    models.DateTimeField(blank=True, default=django_audit_fields.utils.utcnow),
+                ),
+                (
+                    "modified",
+                    models.DateTimeField(blank=True, default=django_audit_fields.utils.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.",
+                    ),
+                ),
+                ("label", models.CharField(db_index=True, max_length=25)),
+                (
+                    "mw",
+                    models.FloatField(
+                        default=0, help_text="in g/mol", verbose_name="Molecular weight"
+                    ),
+                ),
+                (
+                    "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,
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "historical Molecular weight",
+                "verbose_name_plural": "historical Molecular weights",
+                "ordering": ("-history_date", "-history_id"),
+                "get_latest_by": ("history_date", "history_id"),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+        migrations.CreateModel(
+            name="MolecularWeight",
+            fields=[
+                (
+                    "revision",
+                    django_revision.revision_field.RevisionField(
+                        blank=True,
+                        editable=False,
+                        help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                        max_length=75,
+                        null=True,
+                        verbose_name="Revision",
+                    ),
+                ),
+                (
+                    "created",
+                    models.DateTimeField(blank=True, default=django_audit_fields.utils.utcnow),
+                ),
+                (
+                    "modified",
+                    models.DateTimeField(blank=True, default=django_audit_fields.utils.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,
+                    ),
+                ),
+                ("label", models.CharField(max_length=25, unique=True)),
+                (
+                    "mw",
+                    models.FloatField(
+                        default=0, help_text="in g/mol", verbose_name="Molecular weight"
+                    ),
+                ),
+            ],
+            options={
+                "verbose_name": "Molecular weight",
+                "verbose_name_plural": "Molecular weights",
+                "abstract": False,
+                "default_permissions": (
+                    "add",
+                    "change",
+                    "delete",
+                    "view",
+                    "export",
+                    "import",
+                ),
+                "default_manager_name": "objects",
+                "indexes": [
+                    models.Index(
+                        fields=["modified", "created"],
+                        name="edc_reporta_modifie_7e6235_idx",
+                    ),
+                    models.Index(
+                        fields=["user_modified", "user_created"],
+                        name="edc_reporta_user_mo_e8f92b_idx",
+                    ),
+                ],
+            },
+        ),
+    ]

edc_reportable/models/mw.py

@@ -7,9 +7,7 @@ class MolecularWeight(BaseUuidModel):
 
     label = models.CharField(max_length=25, unique=True)
 
-    mw = models.FloatField(
-        verbose_name="Molecular weight", default=0, help_text="in g/mol"
-    )
+    mw = models.FloatField(verbose_name="Molecular weight", default=0, help_text="in g/mol")
 
     history = HistoricalRecords()
 

edc_reportable/models/reference_model_mixins.py

@@ -55,9 +55,7 @@ class ReferenceModelMixin(models.Model):
         help_text="calculated by the formula instance",
     )
 
-    age_phrase = models.CharField(
-        max_length=25, null=True, help_text="calculated in save()"
-    )
+    age_phrase = models.CharField(max_length=25, null=True, help_text="calculated in save()")
 
     grade = models.IntegerField(
         null=True, validators=[MinValueValidator(1), MaxValueValidator(5)]

edc_reportable/models/reference_range_collection.py

@@ -47,9 +47,7 @@ class ReferenceRangeCollection(BaseUuidModel):
 
     def reportable_grades(self, label: str) -> list[int]:
         if not label:
-            raise ValueError(
-                "Unable to determine reportable grades. Label may not be None"
-            )
+            raise ValueError("Unable to determine reportable grades. Label may not be None")
         try:
             grading_exception = GradingException.objects.get(
                 reference_range_collection=self, label=label
@@ -73,9 +71,7 @@ class ReferenceRangeCollection(BaseUuidModel):
         site: Site | None = None,
     ) -> tuple[GradingData | None, str | None]:
         if subject_identifier:
-            rs_obj = RegisteredSubject.objects.get(
-                subject_identifier=subject_identifier
-            )
+            rs_obj = RegisteredSubject.objects.get(subject_identifier=subject_identifier)
             dob = rs_obj.dob
             gender = rs_obj.gender
         grading_data, eval_phrase = get_grade_for_value(
@@ -104,9 +100,7 @@ class ReferenceRangeCollection(BaseUuidModel):
         site: Site | None = None,
     ) -> tuple[bool, NormalData]:
         if subject_identifier:
-            rs_obj = RegisteredSubject.objects.get(
-                subject_identifier=subject_identifier
-            )
+            rs_obj = RegisteredSubject.objects.get(subject_identifier=subject_identifier)
             dob = rs_obj.dob
             gender = rs_obj.gender
         normal_data = get_normal_data_or_raise(

edc_reportable/post_migrate_signals.py

@@ -14,9 +14,7 @@ style = color_style()
 
 
 def load_mw():
-    model_cls: MolecularWeight = django_apps.get_model(
-        "edc_reportable", "MolecularWeight"
-    )
+    model_cls: MolecularWeight = django_apps.get_model("edc_reportable", "MolecularWeight")
     for label, mw in molecular_weights.items():
         model_cls.objects.get_or_create(label=label, mw=mw)
 

edc_reportable/reference_range_evaluator.py

@@ -176,8 +176,7 @@ class ReferenceRangeEvaluator:
         if (
             grading_data
             and grading_data.grade
-            and str(user_form_response.reportable)
-            in [str(g) for g in self.grades(utest_id)]
+            and str(user_form_response.reportable) in [str(g) for g in self.grades(utest_id)]
             and str(grading_data.grade) != str(user_form_response.reportable)
         ):
             raise forms.ValidationError(
@@ -196,9 +195,7 @@ class ReferenceRangeEvaluator:
             NOT_APPLICABLE,
         ]:
             raise forms.ValidationError(
-                {
-                    f"{utest_id}_reportable": "Invalid. Expected 'No' or 'Not applicable'."
-                }
+                {f"{utest_id}_reportable": "Invalid. Expected 'No' or 'Not applicable'."}
             )
         self._check_normal_range(
             utest_id, value, field, grading_data, user_form_response, opts
@@ -290,9 +287,7 @@ class ReferenceRangeEvaluator:
         )
         answers = [str(v) for v in answers if v is not None]
         if len(answers) == 0:
-            raise forms.ValidationError(
-                {"results_abnormal": "No results have been entered."}
-            )
+            raise forms.ValidationError({"results_abnormal": "No results have been entered."})
         answers_as_bool = [True for v in answers if v in responses]
         if self.cleaned_data.get(field) == NO:
             if any(answers_as_bool):
@@ -302,6 +297,4 @@ class ReferenceRangeEvaluator:
                 )
         elif self.cleaned_data.get(field) == YES:
             if not any(answers_as_bool):
-                raise forms.ValidationError(
-                    {field: f"None of the above results are {word}"}
-                )
+                raise forms.ValidationError({field: f"None of the above results are {word}"})

edc_reportable/utils/convert_units.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 from django.core.exceptions import ObjectDoesNotExist
 
 from edc_utils.round_up import round_half_away_from_zero
-from .molecular_weight_model_cls import molecular_weight_model_cls
+
 from ..exceptions import ConversionNotHandled
 from ..units import (
     GRAMS_PER_LITER,
@@ -12,6 +12,7 @@ from ..units import (
     MILLIGRAMS_PER_LITER,
     MILLIMOLES_PER_LITER,
 )
+from .molecular_weight_model_cls import molecular_weight_model_cls
 
 __all__ = ["convert_units"]
 
@@ -40,9 +41,7 @@ def micromoles_per_liter_to(
     elif units_to == MILLIGRAMS_PER_DECILITER:
         return {MILLIGRAMS_PER_DECILITER: (float(value) * get_mw(label)) / 10000.00}
     else:
-        raise ConversionNotHandled(
-            f"Conversion not found. Tried umol/L to {units_to}. "
-        )
+        raise ConversionNotHandled(f"Conversion not found. Tried umol/L to {units_to}. ")
 
 
 def milligrams_per_deciliter_to(

edc_reportable/utils/get_grade_for_value.py

@@ -142,6 +142,8 @@ def get_grading_data_instances(
         if qs.count() == 0:
             msg = f"No matching grading data found for {label} {units} {gender}"
         else:
-            msg = f"No matching grading data found for {label} {units} {gender} given age bounds"
+            msg = (
+                f"No matching grading data found for {label} {units} {gender} given age bounds"
+            )
         raise NotEvaluated(f"Value not graded. {msg}")
     return grading_data_objs

edc_reportable/utils/get_reference_range_collection.py

@@ -22,8 +22,8 @@ def get_reference_range_collection(obj) -> ReferenceRangeCollection:
         except AttributeError:
             name = obj.panel_object.reference_range_collection_name
         try:
-            reference_range_collection = (
-                reference_range_colllection_model_cls().objects.get(name=name)
+            reference_range_collection = reference_range_colllection_model_cls().objects.get(
+                name=name
             )
         except ObjectDoesNotExist:
             pass

edc_reportable/utils/load_data.py

@@ -72,9 +72,7 @@ def load_reference_ranges(
     (
         reference_range_collection,
         _,
-    ) = reference_range_colllection_model_cls().objects.get_or_create(
-        name=collection_name
-    )
+    ) = reference_range_colllection_model_cls().objects.get_or_create(name=collection_name)
     reportable_grades = reportable_grades or get_default_reportable_grades()
     for grade in reportable_grades:
         setattr(reference_range_collection, f"grade{grade}", True)

edc_reportable/utils/molecular_weight_model_cls.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Type, TYPE_CHECKING
+from typing import TYPE_CHECKING, Type
 
 from django.apps import apps as django_apps
 

edc_reportable/utils/update_grading_data.py

@@ -35,12 +35,8 @@ def update_grading_data(
         ).delete()
     for label, formulas in grading_data.items():
         for formula in formulas:
-            if get_reportable_grades(
-                reference_range_collection, label, reportable_grades
-            ):
-                formula_opts = {
-                    k: v for k, v in formula.__dict__.items() if k != "gender"
-                }
+            if get_reportable_grades(reference_range_collection, label, reportable_grades):
+                formula_opts = {k: v for k, v in formula.__dict__.items() if k != "gender"}
                 age_opts = {k: v for k, v in formula_opts.items() if "age" in k}
                 for gender in formula.__dict__.get("gender"):
                     grading_data_model_cls().objects.create(

edc_review_dashboard/migrations/0001_initial.py

@@ -1,12 +1,12 @@
 # Generated by Django 3.2.13 on 2022-08-23 23:42
 
 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_review_dashboard/migrations/0003_alter_edcpermissions_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="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",

edc_review_dashboard/migrations/0005_alter_edcpermissions_revision.py

@@ -0,0 +1,26 @@
+# Generated by Django 5.2.4 on 2025-09-10 03:24
+
+import django_revision.revision_field
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_review_dashboard", "0004_edcpermissions_locale_created_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                null=True,
+                verbose_name="Revision",
+            ),
+        ),
+    ]

edc_review_dashboard/views/subject_review_listboard_view.py

@@ -46,9 +46,7 @@ class SubjectReviewListboardView(
     listboard_url = "subject_review_listboard_url"
     listboard_panel_style = "default"
     listboard_panel_title = "Subject Review"
-    listboard_view_permission_codename = (
-        "edc_review_dashboard.view_subject_review_listboard"
-    )
+    listboard_view_permission_codename = "edc_review_dashboard.view_subject_review_listboard"
 
     navbar_selected_item = "subject_review"
     ordering = ["subject_identifier", "visit_code", "visit_code_sequence"]

edc_screening/eligibility.py

@@ -57,9 +57,7 @@ class Eligibility:
                     elif k not in ["age", "gender"]:
                         self.reasons_ineligible.update({k: k})
             if not self.age_evaluator.eligible(age):
-                self.reasons_ineligible.update(
-                    age=self.age_evaluator.reasons_ineligible
-                )
+                self.reasons_ineligible.update(age=self.age_evaluator.reasons_ineligible)
             if not self.gender_evaluator.eligible:
                 self.reasons_ineligible.update(
                     gender=f"{' and '.join(self.gender_evaluator.reasons_ineligible)}."

edc_screening/fc.py

@@ -26,6 +26,4 @@ class FC:
         self.missing_value = missing_value
 
     def __repr__(self):
-        return (
-            f"{self.__class__.__name__}({self.value, self.msg, self.ignore_if_missing})"
-        )
+        return f"{self.__class__.__name__}({self.value, self.msg, self.ignore_if_missing})"