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

edc_analytics/table.py

@@ -0,0 +1,108 @@
+import pandas as pd
+from edc_constants.constants import FEMALE, MALE
+
+from .constants import COUNT_COLUMN, N_ONLY, N_WITH_ROW_PROP, TITLE_COLUMN
+from .row import RowDefinition, RowDefinitions, RowStatisticsWithGender
+
+
+class Table:
+
+    title_column = "Characteristics"
+    label_column = "Statistic"
+    default_sublabel = "n"
+    gender_column = "gender"
+    row_statistics_cls: RowStatisticsWithGender = RowStatisticsWithGender
+
+    def __init__(
+        self,
+        colname: str | None = None,
+        main_df: pd.DataFrame = None,
+        title: str | None = None,
+        include_zero_counts: bool | None = None,
+    ):
+
+        self.colname = colname
+        self.main_df = main_df
+        self.title = title
+        self.include_zero_counts = include_zero_counts
+        self.table_df: pd.DataFrame = pd.DataFrame()
+
+        self.build_table_df()
+        if self.title:
+            # add a redundant column to hold title name for each
+            # row in this table.
+            self.table_df[TITLE_COLUMN] = self.title
+
+    @property
+    def row_definitions(self) -> RowDefinitions:
+        """Override with your RowDefs
+
+        The default adds a first row with gender breakdown.
+        """
+        row_defs = RowDefinitions(
+            colname=self.colname, row_statistics_cls=self.row_statistics_cls
+        )
+        row_defs.add(
+            RowDefinition(
+                title=self.title,
+                label=self.default_sublabel,
+                colname=None,
+                condition=(self.main_df[self.gender_column].notna()),
+                columns={
+                    FEMALE: (N_WITH_ROW_PROP, 2),
+                    MALE: (N_WITH_ROW_PROP, 2),
+                    "All": (N_ONLY, 2),
+                },
+                drop=False,
+            )
+        )
+        return row_defs
+
+    def reorder_df(self):
+        """Override to reorder the rows in `table_df`."""
+        pass
+
+    def build_table_df(self) -> None:
+        """Build the table_df using the row definitions."""
+        df_denominator = self.main_df.copy()
+        rows = []
+        for index, rd in enumerate(self.row_definitions.definitions):
+            if not rd.condition.empty:
+                df_numerator = df_denominator.loc[rd.condition]
+            else:
+                # default to first col non-null values
+                df_numerator = df_denominator.loc[
+                    df_denominator[df_denominator.columns[0]].notna()
+                ]
+            row_stats = self.row_statistics_cls(
+                colname=rd.colname,
+                df_numerator=df_numerator,
+                df_denominator=df_denominator,
+                df_all=self.main_df,
+                columns=rd.columns,
+            )
+            if index == 0:
+                columns = (
+                    [self.title_column, self.label_column]
+                    + row_stats.labels()
+                    + [TITLE_COLUMN]
+                )
+                # reset table_df
+                self.table_df = pd.DataFrame(columns=columns)
+            rows.append([rd.title, rd.label] + row_stats.values_list() + [self.title])
+            if rd.drop and not df_numerator.empty:
+                df_denominator.drop(df_numerator.index, inplace=True)
+        if self.row_definitions.reverse_rows:
+            rows.reverse()
+        for index, values_list in enumerate(rows):
+            self.table_df.loc[index] = values_list
+        if not self.include_zero_counts:
+            self.table_df.drop(
+                self.table_df[self.table_df[COUNT_COLUMN] == 0].index, inplace=True
+            )
+        self.reorder_df()
+
+    @property
+    def formatted_df(self) -> pd.DataFrame:
+        """Return DF with first 5 columns"""
+        return self.table_df.iloc[:, :5]

edc_analytics/urls.py

@@ -0,0 +1,6 @@
+from django.contrib import admin
+from django.urls import path
+
+urlpatterns = [
+    path("admin/", admin.site.urls),
+]

edc_appointment/migrations/0018_auto_20190305_0123.py

@@ -2,7 +2,7 @@
 
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 from django.db import migrations, models
 import django.utils.timezone
 

edc_appointment/migrations/0051_alter_appointment_revision_and_more.py

@@ -0,0 +1,38 @@
+# 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_appointment", "0050_alter_appointment_appt_type_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="appointment",
+            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="historicalappointment",
+            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_auth/migrations/0001_squashed_0033_alter_userprofile_is_multisite_viewer.py

@@ -6,7 +6,7 @@ import django.db.models.deletion
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 import django_revision.revision_field
 from django.conf import settings
 from django.db import migrations, models

edc_auth/migrations/0012_auto_20191026_0034.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_auth/migrations/0013_auto_20191026_0055.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_auth/migrations/0025_permissions.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_auth/migrations/0037_alter_edcpermissions_revision_alter_role_revision.py

@@ -0,0 +1,38 @@
+# 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_auth", "0036_alter_userprofile_alternate_email_and_more"),
+    ]
+
+    operations = [
+        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="role",
+            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_consent/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_consent/migrations/0007_alter_edcpermissions_revision.py

@@ -0,0 +1,26 @@
+# 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_consent", "0006_alter_edcpermissions_device_created_and_more"),
+    ]
+
+    operations = [
+        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",
+            ),
+        ),
+    ]

edc_crf/migrations/0010_alter_crfstatus_revision.py

@@ -0,0 +1,26 @@
+# 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_crf", "0009_alter_crfstatus_device_created_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="crfstatus",
+            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_dashboard/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_dashboard/migrations/0007_alter_edcpermissions_revision.py

@@ -0,0 +1,26 @@
+# 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_dashboard", "0006_alter_edcpermissions_device_created_and_more"),
+    ]
+
+    operations = [
+        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",
+            ),
+        ),
+    ]

edc_data_manager/migrations/0001_initial.py

@@ -10,7 +10,7 @@ import django.db.models.manager
 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
 import simple_history.models
 from django.conf import settings

edc_data_manager/migrations/0025_edcpermissions.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_data_manager/migrations/0042_alter_datadictionary_revision_and_more.py

@@ -0,0 +1,98 @@
+# 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_data_manager", "0041_alter_dataquery_dm_user_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="datadictionary",
+            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="dataquery",
+            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="historicaldatadictionary",
+            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="historicaldataquery",
+            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="historicalqueryrule",
+            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="queryrule",
+            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_dx/__init__.py

@@ -0,0 +1,6 @@
+from .diagnoses import Diagnoses
+from .utils import (
+    get_diagnosis_labels,
+    get_diagnosis_labels_prefixes,
+    raise_on_unknown_diagnosis_labels,
+)

edc_dx/apps.py

@@ -0,0 +1,5 @@
+from django.apps import AppConfig as DjangoAppConfig
+
+
+class AppConfig(DjangoAppConfig):
+    name = "edc_dx"