Merge pull request #21 from cmu-delphi/main

Update development branch

Author: dmytrotsko

src/datasources/migrations/0002_alter_datasource_display_name.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.0.7 on 2024-10-15 12:31
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('datasources', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='datasource',
+            name='display_name',
+            field=models.CharField(blank=True, max_length=128, verbose_name='Display Name'),
+        ),
+    ]

src/datasources/models.py

@@ -16,6 +16,7 @@ class DataSource(TimeStampedModel):
     display_name: models.CharField = models.CharField(
         verbose_name=_('Display Name'),
         max_length=128,
+        blank=True
     )
     description: models.TextField = models.TextField(
         verbose_name=_('Description'),

src/signal_documentation/settings.py

@@ -104,6 +104,7 @@
     'base',
     'datasources',
     'signals',
+    'signal_sets',
 ]
 
 INSTALLED_APPS: list[str] = DEFAULT_APPS + EXTERNAL_APPS + LOCAL_APPS

src/signal_documentation/urls.py

@@ -20,8 +20,12 @@
 from django.contrib import admin
 from django.urls import include, path
 
-from base.views import (BadRequestErrorView, ForbiddenErrorView,
-                        InternalServerErrorView, NotFoundErrorView)
+from base.views import (
+    BadRequestErrorView,
+    ForbiddenErrorView,
+    InternalServerErrorView,
+    NotFoundErrorView,
+)
 
 handler400 = BadRequestErrorView.as_view()
 handler403 = ForbiddenErrorView.as_view()
@@ -31,13 +35,19 @@
 
 urlpatterns = [
     path(f'{settings.MAIN_PAGE}/admin/' if settings.MAIN_PAGE else 'admin/', admin.site.urls),
+    # signal_sets
+    path(
+        f"{settings.MAIN_PAGE}/" if settings.MAIN_PAGE else "",
+        include("signal_sets.urls"),
+    ),
     # signals
     path(
-        f"{settings.MAIN_PAGE}/" if settings.MAIN_PAGE else "", include("signals.urls")
+        f"{settings.MAIN_PAGE}/signals/" if settings.MAIN_PAGE else "signals/",
+        include("signals.urls"),
     ),
     # datasources
     path(
-        f"{settings.MAIN_PAGE}/datasources" if settings.MAIN_PAGE else "datasources",
+        f"{settings.MAIN_PAGE}/datasources/" if settings.MAIN_PAGE else "datasources",
         include("datasources.urls"),
     ),
     path("__debug__/", include("debug_toolbar.urls")),

src/signal_sets/__init__.py

@@ -0,0 +1,12 @@
+from django.contrib import admin
+from import_export.admin import ImportExportModelAdmin
+
+from signal_sets.resources import SignalSetResource
+from signal_sets.models import SignalSet
+
+
+@admin.register(SignalSet)
+class SignalSetAdmin(ImportExportModelAdmin):
+    list_display = ('name', 'data_description', 'maintainer_name', 'maintainer_email', 'organization')
+    search_fields = ('name', 'maintainer_name', 'maintainer_email', 'organization')
+    resource_class = SignalSetResource

src/signal_sets/admin.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class SignalSetsConfig(AppConfig):
+    default_auto_field = 'django.db.models.BigAutoField'
+    name = 'signal_sets'

src/signal_sets/apps.py

@@ -0,0 +1,64 @@
+import logging
+
+import django_filters
+from django_filters.widgets import QueryArrayWidget
+
+from signals.models import Pathogen, GeographicScope, Geography, SeverityPyramidRung
+from signal_sets.models import SignalSet
+from datasources.models import DataSource
+
+logger = logging.getLogger(__name__)
+
+
+class SignalSetFilter(django_filters.FilterSet):
+
+    pathogens = django_filters.ModelMultipleChoiceFilter(
+        field_name="pathogens",
+        queryset=Pathogen.objects.all(),
+        widget=QueryArrayWidget,
+    )
+
+    geographic_scope = django_filters.ModelMultipleChoiceFilter(
+        field_name="geographic_scope",
+        queryset=GeographicScope.objects.all(),
+        widget=QueryArrayWidget,
+    )
+
+    available_geographies = django_filters.ModelMultipleChoiceFilter(
+        field_name="available_geographies",
+        queryset=Geography.objects.all().order_by("display_order_number"),
+        widget=QueryArrayWidget,
+    )
+
+    severity_pyramid_rungs = django_filters.ModelMultipleChoiceFilter(
+        field_name="severity_pyramid_rungs",
+        queryset=SeverityPyramidRung.objects.all(),
+        widget=QueryArrayWidget,
+    )
+
+    data_source = django_filters.ModelMultipleChoiceFilter(
+        field_name="data_source",
+        queryset=DataSource.objects.all(),
+        widget=QueryArrayWidget,
+    )
+
+    temporal_granularity = django_filters.MultipleChoiceFilter(
+        field_name="temporal_granularity",
+        choices=[
+            ("Daily", "Daily"),
+            ("Weekly", "Weekly"),
+            ("Hourly", "Hourly"),
+        ],
+        lookup_expr="icontains",
+    )
+
+    class Meta:
+        model = SignalSet
+        fields: list[str] = [
+            "pathogens",
+            "geographic_scope",
+            "available_geographies",
+            "severity_pyramid_rungs",
+            "data_source",
+            "temporal_granularity"
+        ]

src/signal_sets/filters.py

@@ -0,0 +1,63 @@
+from django import forms
+
+from signals.models import Pathogen, GeographicScope, Geography, SeverityPyramidRung
+from signal_sets.models import SignalSet
+from datasources.models import DataSource
+
+
+class SignalSetFilterForm(forms.ModelForm):
+
+    pathogens = forms.ModelChoiceField(
+        queryset=Pathogen.objects.all(), widget=forms.CheckboxSelectMultiple()
+    )
+
+    geographic_scope = forms.ModelChoiceField(
+        queryset=GeographicScope.objects.all(), widget=forms.CheckboxSelectMultiple()
+    )
+
+    available_geographies = forms.ModelChoiceField(
+        queryset=Geography.objects.all().order_by("display_order_number"),
+        widget=forms.CheckboxSelectMultiple(),
+    )
+
+    severity_pyramid_rungs = forms.ModelChoiceField(
+        queryset=SeverityPyramidRung.objects.all(),
+        widget=forms.CheckboxSelectMultiple(),
+    )
+
+    data_source = forms.ModelChoiceField(
+        queryset=DataSource.objects.all(),
+        widget=forms.CheckboxSelectMultiple(),
+    )
+
+    temporal_granularity = forms.ChoiceField(
+        choices=[
+            ("Daily", "Daily"),
+            ("Weekly", "Weekly"),
+            ("Hourly", "Hourly"),
+        ],
+        widget=forms.CheckboxSelectMultiple(),
+    )
+
+    class Meta:
+        model = SignalSet
+        fields: list[str] = [
+            "pathogens",
+            "geographic_scope",
+            "available_geographies",
+            "severity_pyramid_rungs",
+            "data_source",
+            "temporal_granularity"
+        ]
+
+    def __init__(self, *args, **kwargs) -> None:
+        """
+        Initialize the form.
+        """
+        super().__init__(*args, **kwargs)
+
+        # Set required attribute to False and disable helptext for all fields
+        for field_name, field in self.fields.items():
+            field.required = False
+            field.help_text = ""
+            field.label = ""

src/signal_sets/forms.py

@@ -0,0 +1,76 @@
+# Generated by Django 5.0.7 on 2024-10-07 18:20
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('datasources', '0001_initial'),
+        ('signals', '0002_auto_20241002_2027'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='SignalSet',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=128, unique=True, verbose_name='255')),
+                ('data_description', models.TextField(blank=True, verbose_name='Data Description')),
+                ('maintainer_name', models.CharField(blank=True, max_length=128, verbose_name='Maintainer Name')),
+                ('maintainer_email', models.CharField(blank=True, max_length=128, verbose_name='Maintainer Email')),
+                ('organization', models.CharField(blank=True, max_length=128, verbose_name='Organization')),
+                ('language', models.CharField(blank=True, max_length=128, verbose_name='Language')),
+                ('version_number', models.CharField(blank=True, max_length=128, verbose_name='Version Number')),
+                ('origin_datasource', models.CharField(blank=True, max_length=128, verbose_name='Origin Data Source')),
+                ('data_type', models.CharField(blank=True, max_length=128, verbose_name='Data Type')),
+                ('preprocessing_description', models.CharField(blank=True, max_length=128, verbose_name='Preprocessing Description')),
+                ('temporal_scope_start', models.CharField(help_text='Temporal scope start of the signal set.', max_length=255, verbose_name='temporal scope start')),
+                ('temporal_scope_end', models.CharField(help_text='Temporal scope end of the signal set.', max_length=255, verbose_name='temporal scope end')),
+                ('temporal_granularity', models.CharField(help_text='Temporal granularity of the signal set.', max_length=255, verbose_name='temporal granularity')),
+                ('reporting_cadence', models.CharField(help_text='Reporting cadence of the signal set.', max_length=255, verbose_name='reporting cadence')),
+                ('reporting_lag', models.CharField(help_text='Typical reporting lag of the signal set.', max_length=255, verbose_name='typical reporting lag')),
+                ('revision_cadence', models.CharField(help_text='Revision cadence of the signal set.', max_length=255, verbose_name='revision cadence')),
+                ('demographic_scope', models.CharField(help_text='Demographic scope of the signal set.', max_length=255, verbose_name='demographic scope')),
+                ('demographic_granularity', models.CharField(help_text='Demographic granularity of the signal set.', max_length=255, verbose_name='demographic granularity')),
+                ('censoring', models.CharField(help_text='Data censoring of the signal set.', max_length=255, verbose_name='data censoring')),
+                ('missingness', models.CharField(help_text='Missingness of the signal set.', max_length=255, verbose_name='missingness')),
+                ('dua_required', models.BooleanField(help_text='Whether a data use agreement is required to access the signal set.', verbose_name='DUA Required')),
+                ('license', models.CharField(help_text='License of the signal set.', max_length=255, verbose_name='license')),
+                ('dataset_location', models.CharField(help_text='Location of the dataset.', max_length=255, verbose_name='dataset location')),
+                ('link_to_dictionary', models.CharField(help_text='Link to the dictionary.', max_length=255, verbose_name='link to dictionary')),
+                ('data_source', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='datasources.datasource', verbose_name='Data Source')),
+                ('geographic_scope', models.ForeignKey(on_delete=django.db.models.deletion.PROTECT, related_name='signal_sets', to='signals.geographicscope', verbose_name='Geographic Scope')),
+                ('pathogens', models.ManyToManyField(help_text='Pathogen(s) associated with the signal set.', related_name='signal_sets', to='signals.pathogen', verbose_name='Pathogen')),
+                ('severity_pyramid_rungs', models.ManyToManyField(blank=True, help_text='Severity pyramid rungs of the signal set.', null=True, related_name='signal_sets', to='signals.severitypyramidrung')),
+            ],
+            options={
+                'ordering': ['name'],
+            },
+        ),
+        migrations.CreateModel(
+            name='SignalSetGeography',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('aggregated_by_delphi', models.BooleanField(default=False)),
+                ('geography', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='geography_signal_sets', to='signals.geography')),
+                ('signal_set', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='geography_signal_sets', to='signal_sets.signalset')),
+            ],
+            options={
+                'verbose_name_plural': 'Signal Geographies',
+                'unique_together': {('geography', 'signal_set')},
+            },
+        ),
+        migrations.AddField(
+            model_name='signalset',
+            name='available_geography',
+            field=models.ManyToManyField(related_name='signal_sets', through='signal_sets.SignalSetGeography', to='signals.geography', verbose_name='Available Geography'),
+        ),
+        migrations.AlterUniqueTogether(
+            name='signalset',
+            unique_together={('name', 'data_source')},
+        ),
+    ]