clinicedc 2.0.1__py3-none-any.whl → 2.0.2__py3-none-any.whl

edc_glucose/model_mixin_factories/fasting_model_mixin_factory.py

@@ -0,0 +1,63 @@
+from django.db import models
+
+from edc_constants.choices import YES_NO_NA
+from edc_constants.constants import NOT_APPLICABLE
+from edc_model.utils import duration_hm_to_timedelta
+from edc_model.validators import hm_validator
+
+
+def fasting_model_mixin_factory(
+    prefix: str = None, verbose_names: dict | None = None, **kwargs
+):
+    prefix = "" if prefix is None else f"{prefix}_"
+    verbose_names = verbose_names or {}
+
+    class AbstractModel(models.Model):
+        def save(self, *args, **kwargs):
+            if duration_str := getattr(self, f"{prefix}fasting_duration_str", None):
+                tdelta = duration_hm_to_timedelta(duration_str)
+                setattr(self, f"{prefix}fasting_duration_delta", tdelta)
+            super().save(*args, **kwargs)
+
+        class Meta:
+            abstract = True
+
+    opts = {
+        f"{prefix}fasting": models.CharField(
+            verbose_name=verbose_names.get(
+                f"{prefix}fasting",
+                "Has the participant fasted?",
+            ),
+            max_length=15,
+            choices=YES_NO_NA,
+            default=NOT_APPLICABLE,
+            blank=False,
+            help_text="As reported by patient",
+        ),
+        f"{prefix}fasting_duration_str": models.CharField(
+            verbose_name=verbose_names.get(
+                f"{prefix}fasting_duration_str",
+                "How long have they fasted in hours and/or minutes?",
+            ),
+            max_length=8,
+            validators=[hm_validator],
+            null=True,
+            blank=True,
+            help_text=(
+                "As reported by patient. Duration of fast. Format is `HHhMMm`. "
+                "For example 1h23m, 12h7m, etc"
+            ),
+        ),
+        f"{prefix}fasting_duration_delta": models.DurationField(
+            null=True,
+            blank=True,
+            help_text="system calculated to microseconds. (hours=microseconds/3.6e+9)",
+        ),
+    }
+
+    opts.update(**kwargs)
+
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_glucose/model_mixin_factories/fbg_model_mixin_factory.py

@@ -0,0 +1,48 @@
+from django.db import models
+
+from edc_constants.constants import NOT_APPLICABLE
+from edc_lab.choices import GLUCOSE_UNITS_NA, RESULT_QUANTIFIER
+from edc_lab.constants import EQ
+
+from ..constants import GLUCOSE_HIGH_READING
+
+
+def fbg_model_mixin_factory(utest_id: str, **kwargs):
+    class AbstractModel(models.Model):
+        class Meta:
+            abstract = True
+
+    opts = {
+        f"{utest_id}_value": models.DecimalField(
+            verbose_name="FBG level",
+            max_digits=8,
+            decimal_places=2,
+            null=True,
+            blank=True,
+            help_text=f"A `HIGH` reading may be entered as {GLUCOSE_HIGH_READING}",
+        ),
+        f"{utest_id}_quantifier": models.CharField(
+            verbose_name="FBG quantifier",
+            max_length=10,
+            choices=RESULT_QUANTIFIER,
+            default=EQ,
+        ),
+        f"{utest_id}_units": models.CharField(
+            verbose_name="FBG units",
+            max_length=15,
+            choices=GLUCOSE_UNITS_NA,
+            default=NOT_APPLICABLE,
+        ),
+        f"{utest_id}_datetime": models.DateTimeField(
+            verbose_name="FBG date/time measured",
+            null=True,
+            blank=True,
+        ),
+    }
+
+    opts.update(**kwargs)
+
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_glucose/model_mixin_factories/glucose_model_mixin_factory.py

@@ -0,0 +1,49 @@
+from __future__ import annotations
+
+from django.db import models
+
+from edc_constants.constants import NOT_APPLICABLE
+from edc_lab.choices import GLUCOSE_UNITS_NA, RESULT_QUANTIFIER_NA
+
+from ..constants import GLUCOSE_HIGH_READING
+
+
+def glucose_model_mixin_factory(utest_id: str, **kwargs):
+    class AbstractModel(models.Model):
+        class Meta:
+            abstract = True
+
+    opts = {
+        f"{utest_id}_value": models.DecimalField(
+            verbose_name="Glucose level",
+            max_digits=8,
+            decimal_places=2,
+            null=True,
+            blank=True,
+            help_text=f"A `HIGH` reading may be entered as {GLUCOSE_HIGH_READING}",
+        ),
+        f"{utest_id}_quantifier": models.CharField(
+            verbose_name="Glucose quantifier",
+            max_length=10,
+            choices=RESULT_QUANTIFIER_NA,
+            default=NOT_APPLICABLE,
+        ),
+        f"{utest_id}_units": models.CharField(
+            verbose_name="Glucose units",
+            max_length=15,
+            choices=GLUCOSE_UNITS_NA,
+            default=NOT_APPLICABLE,
+        ),
+        f"{utest_id}_date": models.DateField(
+            verbose_name="Glucose date measured",
+            null=True,
+            blank=True,
+        ),
+    }
+
+    opts.update(**kwargs)
+
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_glucose/model_mixin_factories/ogtt_model_mixin_factory.py

@@ -0,0 +1,71 @@
+from django.db import models
+from django.utils.html import format_html
+from django.utils.safestring import mark_safe
+
+from edc_constants.constants import NOT_APPLICABLE
+from edc_lab.choices import GLUCOSE_UNITS_NA, RESULT_QUANTIFIER
+from edc_lab.constants import EQ
+from edc_model.validators import datetime_not_future
+
+from ..constants import GLUCOSE_HIGH_READING
+
+
+def ogtt_model_mixin_factory(utest_id: str, **kwargs):
+    class AbstractModel(models.Model):
+        class Meta:
+            abstract = True
+
+    opts = {
+        f"{utest_id}_base_datetime": models.DateTimeField(
+            verbose_name="Date/time oral glucose solution given",
+            validators=[datetime_not_future],
+            null=True,
+            blank=True,
+            help_text="(glucose solution given)",
+        ),
+        f"{utest_id}_value": models.DecimalField(
+            verbose_name=format_html(
+                "{html}",
+                html=mark_safe(
+                    "Blood glucose measure 2hrs <u>after</u> oral glucose solution given"
+                ),  # nosec B703, B308
+            ),
+            max_digits=8,
+            decimal_places=2,
+            null=True,
+            blank=True,
+            help_text=f"A `HIGH` reading may be entered as {GLUCOSE_HIGH_READING}",
+        ),
+        f"{utest_id}_quantifier": models.CharField(
+            max_length=10,
+            choices=RESULT_QUANTIFIER,
+            default=EQ,
+        ),
+        f"{utest_id}_units": models.CharField(
+            verbose_name="Units (Blood glucose 2hrs after...)",
+            max_length=15,
+            default=NOT_APPLICABLE,
+            choices=GLUCOSE_UNITS_NA,
+            blank=False,
+        ),
+        f"{utest_id}_datetime": models.DateTimeField(
+            verbose_name=format_html(
+                "{html}",
+                html=mark_safe(
+                    "Date/time blood glucose measured 2hrs <u>after</u> "
+                    "oral glucose solution given"
+                ),  # nosec B703, B308
+            ),
+            validators=[datetime_not_future],
+            blank=True,
+            null=True,
+            help_text="(2 hours after glucose solution given)",
+        ),
+    }
+
+    opts.update(**kwargs)
+
+    for name, fld_cls in opts.items():
+        AbstractModel.add_to_class(name, fld_cls)
+
+    return AbstractModel

edc_glucose/model_mixins/__init__.py

@@ -0,0 +1,5 @@
+from .fasting_model_mixin import FastingModelMixin
+from .fbg_model_mixin import FbgModelMixin
+from .glucose_model_mixin import GlucoseModelMixin
+from .hba1c_model_mixin import Hba1cModelMixin
+from .ogtt_model_mixin import OgttModelMixin

edc_glucose/model_mixins/fasting_model_mixin.py

@@ -0,0 +1,15 @@
+from __future__ import annotations
+
+from django.db import models
+
+from ..model_mixin_factory import fasting_model_mixin_factory
+
+
+class FastingModelMixin(fasting_model_mixin_factory(), models.Model):
+    """A model mixin of fields about fasting.
+
+    Used together with mixins for glucose measurements.
+    """
+
+    class Meta:
+        abstract = True

edc_glucose/model_mixins/fbg_model_mixin.py

@@ -0,0 +1,10 @@
+from django.db import models
+
+from ..model_mixin_factories import fbg_model_mixin_factory
+
+
+class FbgModelMixin(fbg_model_mixin_factory("fbg"), models.Model):
+    """A model mixin of fields for the FBG"""
+
+    class Meta:
+        abstract = True

edc_glucose/model_mixins/glucose_model_mixin.py

@@ -0,0 +1,17 @@
+from __future__ import annotations
+
+from django.db import models
+
+from ..model_mixin_factory import glucose_model_mixin_factory
+from .fasting_model_mixin import fasting_model_mixin_factory
+
+
+class GlucoseModelMixin(
+    glucose_model_mixin_factory("glucose"),
+    fasting_model_mixin_factory("glucose"),
+    models.Model,
+):
+    """A model mixin of fields for the Glucose, fasting or random"""
+
+    class Meta:
+        abstract = True

edc_glucose/model_mixins/hba1c_model_mixin.py

@@ -0,0 +1,42 @@
+from django.db import models
+
+from edc_lab.constants import EQ
+from edc_reportable import PERCENT
+
+from ..constants import GLUCOSE_HIGH_READING
+
+
+class Hba1cModelMixin(models.Model):
+    """A model mixin of fields for the HbA1c"""
+
+    hba1c_value = models.DecimalField(
+        verbose_name="HbA1c value",
+        max_digits=8,
+        decimal_places=2,
+        null=True,
+        blank=True,
+        help_text=f"In percent. A `HIGH` reading may be entered as {GLUCOSE_HIGH_READING}",
+    )
+
+    hba1c_quantifier = models.CharField(
+        verbose_name="HbA1c quantifier",
+        max_length=10,
+        default=EQ,
+        editable=False,
+    )
+
+    hba1c_units = models.CharField(
+        verbose_name="HbA1c units",
+        max_length=15,
+        default=PERCENT,
+        editable=False,
+    )
+
+    hba1c_datetime = models.DateTimeField(
+        verbose_name="Date/time HbA1c measured",
+        null=True,
+        blank=True,
+    )
+
+    class Meta:
+        abstract = True

edc_glucose/model_mixins/ogtt_model_mixin.py

@@ -0,0 +1,10 @@
+from django.db import models
+
+from ..model_mixin_factory import ogtt_model_mixin_factory
+
+
+class OgttModelMixin(ogtt_model_mixin_factory("ogtt"), models.Model):
+    """A model mixin of fields for the OGTT"""
+
+    class Meta:
+        abstract = True

edc_glucose/utils.py

@@ -0,0 +1,42 @@
+from decimal import Decimal
+
+from django import forms
+
+from edc_reportable import MILLIMOLES_PER_LITER, ConversionNotHandled
+from edc_reportable.utils import convert_units
+from edc_utils.round_up import round_half_away_from_zero
+
+from .constants import GLUCOSE_HIGH_READING
+
+
+def validate_glucose_as_millimoles_per_liter(
+    prefix: str = None, cleaned_data: dict = None
+) -> None | Decimal:
+    converted_value = None
+    min_val = Decimal("0.00")
+    max_val = Decimal("30.00")
+    high_value = Decimal(f"{GLUCOSE_HIGH_READING}")
+    value = cleaned_data.get(f"{prefix}_value")
+    units = cleaned_data.get(f"{prefix}_units")
+    if value and units:
+        try:
+            converted_value = convert_units(
+                label=prefix,
+                value=value,
+                units_from=units,
+                units_to=MILLIMOLES_PER_LITER,
+            )
+        except ConversionNotHandled as e:
+            raise forms.ValidationError({f"{prefix}_units": str(e)})
+        if (
+            not (min_val <= round_half_away_from_zero(converted_value, 2) <= max_val)
+            and round_half_away_from_zero(converted_value, 2) != high_value
+        ):
+            raise forms.ValidationError(
+                {
+                    f"{prefix}_value": (
+                        f"This value is out-of-range. Got {converted_value} mmol/L"
+                    )
+                }
+            )
+    return converted_value

edc_identifier/admin_site.py

@@ -2,6 +2,4 @@ from edc_model_admin.admin_site import EdcAdminSite
 
 from .apps import AppConfig
 
-edc_identifier_admin = EdcAdminSite(
-    name="edc_identifier_admin", app_label=AppConfig.name
-)
+edc_identifier_admin = EdcAdminSite(name="edc_identifier_admin", app_label=AppConfig.name)

edc_identifier/identifier.py

@@ -18,9 +18,7 @@ class Identifier:
     seed: str = "0"
     separator: str | None = None
 
-    def __init__(
-        self, last_identifier: str | None = None, prefix: str | None = None
-    ) -> None:
+    def __init__(self, last_identifier: str | None = None, prefix: str | None = None) -> None:
         self.identifier_as_list: list = []
         self.prefix: str = prefix or self.prefix or ""
         edc_device_app_config = django_apps.get_app_config("edc_device")

edc_identifier/migrations/0001_initial.py

@@ -6,9 +6,10 @@ import django.utils.timezone
 import django_audit_fields.fields.uuid_auto_field
 import django_extensions.db.fields
 import django_revision.revision_field
+from django.db import migrations, models
+
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -253,9 +254,7 @@ class Migration(migrations.Migration):
                 ("is_derived", models.BooleanField(default=False)),
                 (
                     "sequence_app_label",
-                    models.CharField(
-                        default="identifier", editable=False, max_length=50
-                    ),
+                    models.CharField(default="identifier", editable=False, max_length=50),
                 ),
                 (
                     "sequence_model_name",

edc_identifier/migrations/0001_squashed_0018_auto_20180128_1054.py

@@ -6,11 +6,12 @@ import django.db.models.deletion
 import django.db.models.manager
 import django_audit_fields.fields.uuid_auto_field
 import django_revision.revision_field
+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
-from django.conf import settings
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_identifier/migrations/0005_alter_identifiermodel_managers.py

@@ -1,7 +1,8 @@
 # Generated by Django 3.2.13 on 2022-09-29 14:42
 
-from django.db import migrations
 import django.db.models.manager
+from django.db import migrations
+
 import edc_sites.models
 
 

edc_identifier/migrations/0005_historicalidentifierhistory_historicalidentifiertracker_historicalsubjectidentifier.py

@@ -7,11 +7,12 @@ import django.utils.timezone
 import django_audit_fields.fields.uuid_auto_field
 import django_extensions.db.fields
 import django_revision.revision_field
-import edc_model_fields.fields.hostname_modification_field
-import edc_model_fields.fields.userfield
 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
+
 
 class Migration(migrations.Migration):
     dependencies = [
@@ -235,9 +236,7 @@ class Migration(migrations.Migration):
                 ("is_derived", models.BooleanField(default=False)),
                 (
                     "sequence_app_label",
-                    models.CharField(
-                        default="identifier", editable=False, max_length=50
-                    ),
+                    models.CharField(default="identifier", editable=False, max_length=50),
                 ),
                 (
                     "sequence_model_name",

edc_identifier/migrations/0006_auto_20161127_2226.py

@@ -4,10 +4,11 @@ from __future__ import unicode_literals
 
 import django_audit_fields.fields.uuid_auto_field
 import django_revision.revision_field
+from django.db import migrations, models
+
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
 import edc_utils
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -22,9 +23,7 @@ class Migration(migrations.Migration):
         migrations.AddField(
             model_name="historicalidentifierhistory",
             name="created",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AddField(
             model_name="historicalidentifierhistory",
@@ -49,9 +48,7 @@ class Migration(migrations.Migration):
         migrations.AddField(
             model_name="historicalidentifierhistory",
             name="modified",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AddField(
             model_name="historicalidentifierhistory",
@@ -82,9 +79,7 @@ class Migration(migrations.Migration):
         migrations.AddField(
             model_name="identifierhistory",
             name="created",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AddField(
             model_name="identifierhistory",
@@ -109,9 +104,7 @@ class Migration(migrations.Migration):
         migrations.AddField(
             model_name="identifierhistory",
             name="modified",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AddField(
             model_name="identifierhistory",
@@ -159,30 +152,22 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalidentifiertracker",
             name="created",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="historicalidentifiertracker",
             name="modified",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="historicalsubjectidentifier",
             name="created",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="historicalsubjectidentifier",
             name="modified",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="identifierhistory",
@@ -198,43 +183,31 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="identifiertracker",
             name="created",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="identifiertracker",
             name="modified",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="sequence",
             name="created",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="sequence",
             name="modified",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="subjectidentifier",
             name="created",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
         migrations.AlterField(
             model_name="subjectidentifier",
             name="modified",
-            field=models.DateTimeField(
-                default=edc_utils.date.get_utcnow, editable=False
-            ),
+            field=models.DateTimeField(default=edc_utils.date.get_utcnow, editable=False),
         ),
     ]

edc_identifier/migrations/0007_alter_identifiermodel_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="identifiermodel",
             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="identifiermodel",
             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="identifiermodel",