clinicedc 2.0.11__py3-none-any.whl → 2.0.13__py3-none-any.whl

edc_action_item/migrations/0041_alter_actionitem_revision_alter_actiontype_revision_and_more.py

@@ -0,0 +1,86 @@
+# Generated by Django 5.2.6 on 2025-09-24 04:56
+
+import django_revision.revision_field
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_action_item", "0040_alter_actionitem_report_datetime_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="actionitem",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="actiontype",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalactionitem",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalreference",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reference",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+    ]

edc_adverse_event/migrations/0001_initial.py

@@ -4,7 +4,7 @@ import _socket
 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.utils.timezone
 import django_revision.revision_field
 from django.db import migrations, models
 import django.utils.timezone

edc_adverse_event/migrations/0002_auto_20190802_0059.py

@@ -4,7 +4,7 @@ import _socket
 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.utils.timezone
 import django_revision.revision_field
 from django.db import migrations, models
 import django.utils.timezone

edc_adverse_event/migrations/0008_auto_20220825_0451.py

@@ -4,7 +4,7 @@ import _socket
 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.utils.timezone
 import django_revision.revision_field
 from django.db import migrations, models
 import django.utils.timezone

edc_adverse_event/migrations/0009_auto_20220907_0157.py

@@ -4,7 +4,7 @@ import _socket
 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.utils.timezone
 import django_revision.revision_field
 from django.db import migrations, models
 import django.utils.timezone

edc_adverse_event/migrations/0017_alter_aeactionclassification_revision_and_more.py

@@ -0,0 +1,77 @@
+# Generated by Django 5.2.6 on 2025-09-24 04:56
+
+import django_revision.revision_field
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "edc_adverse_event",
+            "0016_alter_aeactionclassification_device_created_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="aeactionclassification",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="aeclassification",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="causeofdeath",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edcpermissions",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="saereason",
+            name="revision",
+            field=django_revision.revision_field.RevisionField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="System field. From git repository (tag:branch:commit), project metadata, project toml, project VERSION, or settings.",
+                max_length=75,
+                verbose_name="Revision",
+            ),
+        ),
+    ]

edc_adverse_event/model_mixins/hospitaization/hospitalization_model_mixin.py

@@ -54,9 +54,7 @@ class HospitalizationModelMixin(NonUniqueSubjectIdentifierFieldMixin, models.Mod
     )
 
     narrative = models.TextField(
-        verbose_name="Narrative",
-        max_length=500,
-        blank=True,
+        verbose_name="Narrative", max_length=500, blank=True, default=""
     )
 
     class Meta(NonUniqueSubjectIdentifierFieldMixin.Meta):

edc_analytics/__init__.py

@@ -0,0 +1,3 @@
+from .row import RowDefinition, RowStatistics, RowStatisticsWithGender
+from .styler import Styler
+from .table import Table

edc_analytics/apps.py

@@ -0,0 +1,8 @@
+from django.apps import AppConfig as DjangoAppConfig
+
+
+class AppConfig(DjangoAppConfig):
+    name = "edc_analytics"
+    verbose_name = "Edc Analytics"
+    has_exportable_data = False
+    include_in_administration_section = False

edc_analytics/constants.py

@@ -0,0 +1,26 @@
+MEAN_95CI = "mean_95ci"
+MEAN_RANGE = "mean_range"
+MEAN_SD = "mean_sd"
+MEDIAN_IQR = "median_iqr"
+MEDIAN_RANGE = "median_range"
+N_MEAN = "n_mean"
+N_ONLY = "n_only"
+N_RANGE = "n_range"
+N_WITH_COL_PROP = "n_with_col_prop"
+N_WITH_ROW_PROP: str = "n_with_row_prop"
+
+COUNT_COLUMN = "count"
+TITLE_COLUMN = "title"
+
+STATISTICS = [
+    MEAN_95CI,
+    MEAN_RANGE,
+    MEAN_SD,
+    MEDIAN_IQR,
+    MEDIAN_RANGE,
+    N_MEAN,
+    N_ONLY,
+    N_RANGE,
+    N_WITH_COL_PROP,
+    N_WITH_ROW_PROP,
+]

edc_analytics/custom_tables/__init__.py

@@ -0,0 +1,11 @@
+from .age import AgeTable
+from .art import ArtTable
+from .bmi import BmiTable
+from .bp import BpTable
+from .fasting import FastingTable
+from .fbg import FbgTable
+from .fbg_ogtt import FbgOgttTable
+from .gender import GenderTable
+from .hba1c import HbA1cTable
+from .ogtt import OgttTable
+from .waist import WaistCircumferenceTable

edc_analytics/custom_tables/age.py

@@ -0,0 +1,72 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import MEDIAN_RANGE, N_ONLY, N_WITH_COL_PROP, N_WITH_ROW_PROP
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class AgeTable(Table):
+
+    col_a = FEMALE
+    col_b = MALE
+    column_name = "gender"
+
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(colname="age_in_years", main_df=main_df, title="Age (years)")
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp[self.column_name].notna()),
+            columns={
+                self.col_a: (N_ONLY, 2),
+                self.col_b: (N_ONLY, 2),
+                "All": (N_ONLY, 2),
+            },
+            drop=False,
+        )
+        row_defs.add(row0)
+        columns = {
+            self.col_a: (N_WITH_COL_PROP, 2),
+            self.col_b: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+        bin1 = (df_tmp[self.colname] >= 18) & (df_tmp[self.colname] < 35)
+        bin2 = (df_tmp[self.colname] >= 35) & (df_tmp[self.colname] < 50)
+        bin3 = (df_tmp[self.colname] >= 50) & (df_tmp[self.colname] < 65)
+        bin4 = df_tmp[self.colname] >= 65
+        row_defs.add(RowDefinition(label="18-34", condition=bin1, columns=columns, drop=False))
+        row_defs.add(RowDefinition(label="35-49", condition=bin2, columns=columns, drop=False))
+        row_defs.add(RowDefinition(label="50-64", condition=bin3, columns=columns, drop=False))
+        row_defs.add(
+            RowDefinition(label="65 and older", condition=bin4, columns=columns, drop=False)
+        )
+        if len(df_tmp[df_tmp[self.colname].isna()]) > 0:
+            row_defs.add(
+                RowDefinition(
+                    colname="age_in_years",
+                    label="not recorded",
+                    condition=(df_tmp[self.colname].isna()),
+                    columns=columns,
+                    drop=False,
+                )
+            )
+        columns = {
+            self.col_a: (MEDIAN_RANGE, 2),
+            self.col_b: (MEDIAN_RANGE, 2),
+            "All": (MEDIAN_RANGE, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname="age_in_years",
+                label="Median (range)",
+                condition=(self.main_df[self.colname].notna()),
+                columns=columns,
+            )
+        )
+        return row_defs

edc_analytics/custom_tables/art.py

@@ -0,0 +1,88 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import N_ONLY, N_WITH_COL_PROP, N_WITH_ROW_PROP
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class ArtTable(Table):
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(colname=None, main_df=main_df, title="HIV Care")
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp["gender"].notna()),
+            columns={FEMALE: (N_ONLY, 2), MALE: (N_ONLY, 2), "All": (N_ONLY, 2)},
+            drop=False,
+        )
+        row_defs.add(row0)
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+
+        cond_art_stable = (
+            (df_tmp["on_rx_stable"] == "Yes")
+            & (df_tmp["vl_undetectable"] == "Yes")
+            & (df_tmp["art_six_months"] == "Yes")
+        )
+        row_defs.add(
+            RowDefinition(
+                label="Stable on ART (6m)",
+                condition=cond_art_stable,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        # look for anyone that is not stable by these three values
+        condition_partially_stable = (
+            (df_tmp["on_rx_stable"] == "Yes")
+            | (df_tmp["vl_undetectable"] == "Yes")
+            | (df_tmp["art_six_months"] == "Yes")
+        )
+        row_defs.add(
+            RowDefinition(
+                label="Other stable (`VL` or `on ART` or `stable 6m`)",
+                condition=condition_partially_stable,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition_other = (
+            (df_tmp["on_rx_stable"] == "No")
+            | (df_tmp["vl_undetectable"] == "No")
+            | (df_tmp["art_six_months"] == "No")
+        )
+
+        row_defs.add(
+            RowDefinition(
+                label="Other",
+                condition=condition_other,
+                columns=columns,
+                drop=True,
+            )
+        )
+
+        condition_not_recorded = (
+            (df_tmp["on_rx_stable"].isna())
+            & (df_tmp["vl_undetectable"].isna())
+            & (df_tmp["art_six_months"].isna())
+        )
+        row_defs.add(
+            RowDefinition(
+                label="Not recorded",
+                condition=condition_not_recorded,
+                columns=columns,
+                drop=True,
+            )
+        )
+        return row_defs

edc_analytics/custom_tables/bmi.py

@@ -0,0 +1,125 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import (
+    MEDIAN_IQR,
+    MEDIAN_RANGE,
+    N_ONLY,
+    N_WITH_COL_PROP,
+    N_WITH_ROW_PROP,
+)
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class BmiTable(Table):
+
+    colname = "calculated_bmi_value"
+
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(
+            colname="calculated_bmi_value",
+            main_df=main_df,
+            title="BMI categories (kg/m2)",
+        )
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=False)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp["gender"].notna()),
+            columns={FEMALE: (N_ONLY, 2), MALE: (N_ONLY, 2), "All": (N_ONLY, 2)},
+            drop=False,
+        )
+        row_defs.add(row0)
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                colname="calculated_bmi_value",
+                label="Less than 18.5",
+                condition=(df_tmp[self.colname] < 18.5),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname="calculated_bmi_value",
+                label="18.5-24.9",
+                condition=(df_tmp[self.colname] >= 18.5) & (df_tmp[self.colname] < 25.0),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname="calculated_bmi_value",
+                label="25.0-29.9",
+                condition=(df_tmp[self.colname] >= 25.0) & (df_tmp[self.colname] < 30.0),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname="calculated_bmi_value",
+                label="30.0-39.9",
+                condition=(df_tmp[self.colname] >= 30.0) & (df_tmp[self.colname] < 40.0),
+                columns=columns,
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname="calculated_bmi_value",
+                label="40 or above",
+                condition=(df_tmp[self.colname] >= 40.0),
+                columns=columns,
+                drop=False,
+            )
+        )
+        cond = df_tmp[self.colname].isna()
+        if len(df_tmp[cond]) > 0:
+            row_defs.add(
+                RowDefinition(
+                    colname="calculated_bmi_value",
+                    label="not measured",
+                    condition=cond,
+                    columns=columns,
+                    drop=False,
+                )
+            )
+        row_defs.add(
+            RowDefinition(
+                colname="calculated_bmi_value",
+                label="Median (IQR)",
+                condition=(df_tmp["gender"].notna()),
+                columns={
+                    FEMALE: (MEDIAN_IQR, 2),
+                    MALE: (MEDIAN_IQR, 2),
+                    "All": (MEDIAN_IQR, 2),
+                },
+                drop=False,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                colname="calculated_bmi_value",
+                label="Median (range)",
+                condition=(df_tmp["gender"].notna()),
+                columns={
+                    FEMALE: (MEDIAN_RANGE, 2),
+                    MALE: (MEDIAN_RANGE, 2),
+                    "All": (MEDIAN_RANGE, 2),
+                },
+                drop=False,
+            )
+        )
+        return row_defs

edc_analytics/custom_tables/bp.py

@@ -0,0 +1,103 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from ..constants import N_ONLY, N_WITH_COL_PROP, N_WITH_ROW_PROP
+from ..row import RowDefinition, RowDefinitions
+from ..table import Table
+
+
+class BpTable(Table):
+
+    sys_col_name = "sys_blood_pressure_avg"
+    dia_col_name = "dia_blood_pressure_avg"
+
+    def __init__(self, main_df: pd.DataFrame = None):
+        super().__init__(
+            colname="",
+            main_df=main_df,
+            title="Blood pressure at baseline (mmHg)",
+        )
+        self.table_df = self.table_df.reindex(index=self.table_df.index[::-1])
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        df_tmp = self.main_df.copy()
+        row_defs = RowDefinitions(reverse_rows=True)
+        row0 = RowDefinition(
+            title=self.title,
+            label=self.default_sublabel,
+            condition=(df_tmp["gender"].notna()),
+            columns={
+                FEMALE: (N_ONLY, 2),
+                MALE: (N_ONLY, 2),
+                "All": (N_ONLY, 2),
+            },
+            drop=False,
+        )
+        row_defs.add(row0)
+        columns = {
+            FEMALE: (N_WITH_COL_PROP, 2),
+            MALE: (N_WITH_COL_PROP, 2),
+            "All": (N_WITH_ROW_PROP, 2),
+        }
+        row_defs.add(
+            RowDefinition(
+                label="Severe hypertension (>=180/110)",
+                condition=(
+                    (df_tmp[self.sys_col_name] >= 180) | (df_tmp[self.dia_col_name] >= 110)
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                label="Hypertension (>=140/90)",
+                condition=(
+                    (df_tmp[self.sys_col_name] >= 140) | (df_tmp[self.dia_col_name] >= 90)
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                label="Pre-hypertension (<140/90)",
+                condition=(
+                    (df_tmp[self.sys_col_name] >= 120) | (df_tmp[self.dia_col_name] >= 80)
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                label="Normal (<120/80)",
+                condition=(
+                    (df_tmp[self.sys_col_name] >= 90) | (df_tmp[self.dia_col_name] >= 60)
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                label="Low (<90/60)",
+                condition=(
+                    (df_tmp[self.sys_col_name] >= 0) | (df_tmp[self.dia_col_name] >= 0)
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+        row_defs.add(
+            RowDefinition(
+                label="not measured",
+                condition=(
+                    (df_tmp[self.sys_col_name].isna()) & (df_tmp[self.dia_col_name].isna())
+                ),
+                columns=columns,
+                drop=True,
+            )
+        )
+        return row_defs