Merge pull request #42 from cmu-delphi/API-endpoints-#41

Api endpoints #41

Author: BrainIsDead

Pipfile

@@ -27,8 +27,11 @@ django-extensions-models = "*"
 mypy = "*"
 django-stubs = "*"
 tzdata = "*"
+djangorestframework = "*"
 pyparsing = "*"
 pydot = "*"
+markdown = "*"
+drf-spectacular = "*"
 django-docs = "*"
 sphinxcontrib-django = "*"
 sphinx-rtd-theme = "*"

Pipfile.lock

@@ -0,0 +1,12 @@
+from rest_framework.serializers import ModelSerializer
+
+from base.models import Link
+
+
+class LinkSerializer(ModelSerializer):
+    """
+    Serializer for the Link model.
+    """
+    class Meta:
+        model = Link
+        fields = ['link_type', 'url']

git

@@ -81,6 +81,8 @@
     'debug_toolbar',
     'django_extensions',
     'models_extensions',
+    'rest_framework',
+    'drf_spectacular',
     'django_filters',
     'health_check',
     'health_check.db',
@@ -151,6 +153,53 @@
     }
 }
 
+
+PAGE_SIZE = os.environ.get('PAGE_SIZE', 10)
+
+
+# Django REST framework
+# https://www.django-rest-framework.org/
+REST_FRAMEWORK = {
+    "DEFAULT_PAGINATION_CLASS": "rest_framework.pagination.LimitOffsetPagination",
+    "PAGE_SIZE": os.environ.get('PAGE_SIZE', PAGE_SIZE),
+    'DEFAULT_RENDERER_CLASSES': [
+        'rest_framework.renderers.JSONRenderer',
+        'rest_framework.renderers.BrowsableAPIRenderer',
+    ],
+    'DEFAULT_PARSER_CLASSES': [
+        'rest_framework.parsers.JSONParser',
+        'rest_framework.parsers.MultiPartParser',
+    ],
+    'DEFAULT_AUTHENTICATION_CLASSES': [
+        'rest_framework.authentication.BasicAuthentication',
+        'rest_framework.authentication.SessionAuthentication',
+    ],
+    'DEFAULT_SCHEMA_CLASS': 'drf_spectacular.openapi.AutoSchema',
+    'DEFAULT_FILTER_BACKENDS': (
+        'django_filters.rest_framework.DjangoFilterBackend',
+    ),
+}
+
+
+# DRF Spectacular settings
+# https://drf-spectacular.readthedocs.io/en/latest/settings.html
+SPECTACULAR_SETTINGS = {
+    'TITLE': 'Signal Documentation',
+    'DESCRIPTION': 'Signal Documentation API',
+    'VERSION': '1.0.0',
+    "COMPONENT_SPLIT_PATCH": True,
+    "COMPONENT_SPLIT_REQUEST": True,
+    'SERVE_PUBLIC': True,
+    'SCHEMA_PATH_PREFIX': '/api/v[0-9]',
+    'SWAGGER_UI_SETTINGS': {
+        'docExpansion': 'list',
+        'filter': True,
+        'tagsSorter': 'alpha',
+    },
+    'SERVE_INCLUDE_SCHEMA': False,
+}
+
+
 # Django chache
 # https://docs.djangoproject.com/en/4.2/topics/cache/#redis
 

src/base/serializers.py

@@ -6,6 +6,11 @@
     include,
     path,
 )
+from drf_spectacular.views import (
+    SpectacularAPIView,
+    SpectacularRedocView,
+    SpectacularSwaggerView,
+)
 
 from base.views import (
     BadRequestErrorView,
@@ -23,7 +28,23 @@
     path(f'{settings.MAIN_PAGE}/admin/' if settings.MAIN_PAGE else 'admin/', admin.site.urls),
     path('__debug__/', include('debug_toolbar.urls')),
     path(f'{settings.MAIN_PAGE}/' if settings.MAIN_PAGE else '', include('signals.urls')),
+
+    # sphinx docs
     path(f'{settings.MAIN_PAGE}/docs/' if settings.MAIN_PAGE else 'docs/', include('docs.urls')),
+
+    # drf-spectacular
+    path(
+        f'{settings.MAIN_PAGE}/api/docs/schema/' if settings.MAIN_PAGE else 'api/docs/schema/',
+        SpectacularAPIView.as_view(), name="spectacular-schema"
+    ),
+    path(
+        f'{settings.MAIN_PAGE}/api/docs/swagger/' if settings.MAIN_PAGE else 'api/docs/swagger/',
+        SpectacularSwaggerView.as_view(url_name="spectacular-schema"), name="swagger"
+    ),
+    path(
+        f'{settings.MAIN_PAGE}/api/docs/redoc/' if settings.MAIN_PAGE else 'api/docs/redoc/',
+        SpectacularRedocView.as_view(url_name="spectacular-schema"), name="redoc"
+    ),
 ]
 
 urlpatterns += static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)  # type: ignore

src/signal_documentation/settings.py

@@ -57,13 +57,13 @@ class SignalAdmin(ImportExportModelAdmin):
     list_display: tuple[Literal['name']] = ('name',)
     search_fields: tuple[Literal['name'], Literal['description'], Literal['short_description']]
     search_fields = ('name', 'description', 'short_description')
-    list_filter: tuple[Literal['pathogen'], Literal['available_geography'], Literal['signal_type'], Literal['format'],
+    list_filter: tuple[Literal['pathogen'], Literal['available_geography'], Literal['signal_type'], Literal['format_type'],
                        Literal['is_smoothed'], Literal['is_weighted'], Literal['is_cumulative'], Literal['has_stderr'], Literal['has_sample_size']]
     list_filter = (
         'pathogen',
         'available_geography',
         'signal_type',
-        'format',
+        'format_type',
         'is_smoothed',
         'is_weighted',
         'is_cumulative',

src/signal_documentation/urls.py

@@ -8,6 +8,10 @@
 
 
 class SignalFilter(django_filters.FilterSet):
+    """
+    FilterSet for the Signal model.
+    """
+
     search = CharFilter(method='filter_search')
 
     class Meta:
@@ -18,12 +22,24 @@ class Meta:
             'available_geography',
             'signal_type',
             'category',
-            'format',
+            'format_type',
             'source',
             'time_label',
         ]
 
     def filter_search(self, queryset, name, value) -> Any:
+        """
+        Custom filter method to perform a search on the Signal model.
+
+        Args:
+            queryset (QuerySet): The initial queryset.
+            name (str): The name of the filter field.
+            value (Any): The value to search for.
+
+        Returns:
+            QuerySet: The filtered queryset based on the search value.
+        """
+
         if not value:
             return queryset
 

src/signals/admin.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.6 on 2023-11-01 16:40
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('signals', '0003_alter_signal_options'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='signal',
+            old_name='format',
+            new_name='format_type',
+        ),
+    ]

src/signals/filters.py

@@ -177,7 +177,7 @@ class Signal(TimeStampedModel):
         null=True,
         blank=True
     )
-    format = models.CharField(
+    format_type = models.CharField(
         help_text=_('Format'),
         max_length=128,
         choices=FormatChoices.choices

src/signals/migrations/0004_rename_format_signal_format_type.py

@@ -17,6 +17,10 @@
 
 
 class SignalBaseResource(resources.ModelResource):
+    """
+    Resource class for importing Signals base.
+    """
+
     name = Field(attribute='name', column_name='Signal')
     display_name = Field(attribute='display_name', column_name='Name')
     base = Field(
@@ -49,7 +53,9 @@ def process_base(self, row) -> None:
 
 
 class SignalResource(resources.ModelResource):
-    """Resource class for importing and exporting Signal models."""
+    """
+    Resource class for importing and exporting Signal models
+    """
 
     name = Field(attribute='name', column_name='Signal')
     display_name = Field(attribute='display_name', column_name='Name')
@@ -122,19 +128,26 @@ class Meta:
         import_id_fields: list[str] = ['name', 'source', 'display_name']
 
     def before_import_row(self, row, **kwargs) -> None:
-        """Pre-processes each row before importing."""
+        """
+        Pre-processes each row before importing.
+        """
+
         self.fix_boolean_fields(row, ['Active', 'Is Smoothed', 'Is Weighted', 'Is Cumulative', 'Has StdErr', 'Has Sample Size'])
         self.process_links(row)
         self.process_pathogen(row)
 
     def is_url_in_domain(self, url, domain) -> Any:
-        """Checks if a URL belongs to a specific domain."""
+        """
+        Checks if a URL belongs to a specific domain.
+        """
 
         parsed_url: Any = urlparse(url)
         return parsed_url.netloc == domain
 
     def fix_boolean_fields(self, row, fields: list) -> Any:
-        """Fixes boolean fields."""
+        """
+        Fixes boolean fields.
+        """
 
         for k in fields:
             if row[k] == 'TRUE':
@@ -144,7 +157,9 @@ def fix_boolean_fields(self, row, fields: list) -> Any:
         return row
 
     def process_links(self, row) -> Any:
-        """Processes links."""
+        """
+        Processes links.
+        """
 
         row['Links'] = ''
         if row['Link']:
@@ -170,7 +185,9 @@ def process_links(self, row) -> Any:
         return row
 
     def process_pathogen(self, row) -> None:
-        """Processes pathogen."""
+        """
+        Processes pathogen.
+        """
 
         if row['Pathogen/ Disease Area']:
             pathogens: str = row['Pathogen/ Disease Area'].split(',')

src/signals/models.py

@@ -0,0 +1,32 @@
+from rest_framework.serializers import ModelSerializer, SlugRelatedField
+
+from base.serializers import LinkSerializer
+from signals.models import Signal
+
+
+class SignalBaseSerializer(ModelSerializer):
+    """
+    Serializer for the base Signal model.
+    """
+
+    class Meta:
+        model = Signal
+        fields = ['id', 'name', 'display_name']
+
+
+class SignalSerializer(ModelSerializer):
+    """
+    Serializer for the Signal model.
+    """
+
+    links = LinkSerializer(many=True)
+    pathogen = SlugRelatedField(many=True, read_only=True, slug_field='name')
+    signal_type = SlugRelatedField(many=True, read_only=True, slug_field='name')
+    available_geography = SlugRelatedField(many=True, read_only=True, slug_field='name')
+    category = SlugRelatedField(read_only=True, slug_field='name')
+    source = SlugRelatedField(read_only=True, slug_field='name')
+    base = SignalBaseSerializer()
+
+    class Meta:
+        model = Signal
+        fields = '__all__'

src/signals/resources.py

@@ -71,7 +71,7 @@ class SignalFactory(DjangoModelFactory):
     active = fake.boolean()
     short_description = fake.text(max_nb_chars=500)
     description = fake.text(max_nb_chars=500)
-    format = fake.random_element(FormatChoices.values)
+    format_type = fake.random_element(FormatChoices.values)
     time_type = fake.random_element(TimeTypeChoices.values)
     time_label = fake.random_element(TimeLabelChoices.values)
     category = SubFactory(SignalCategoryFactory)

src/signals/serializers.py

@@ -0,0 +1,52 @@
+from django.urls import reverse
+from faker import Faker
+from rest_framework.test import APITestCase
+
+from signals.models import Signal
+from signals.tests.factories import SignalFactory
+
+fake = Faker()
+
+
+class SignalListApiViewTest(APITestCase):
+
+    def setUp(self):
+        for i in range(fake.random_int(min=1, max=100)):
+            SignalFactory()
+
+    def test_signal_list_api_view(self):
+        response = self.client.get(reverse('signals_api'))
+        self.assertEqual(response.status_code, 200)
+        self.assertEqual(response.data['count'], Signal.objects.count())
+
+    def test_signal_list_api_view_filters(self):
+        signal = Signal.objects.order_by("?").first()
+        signal.base = signal
+        signal.save()
+        response = self.client.get(reverse('signals_api'), {'name': signal.name})
+        for result in response.json()['results']:
+            self.assertEqual(signal.name, result['name'])
+        response = self.client.get(reverse('signals_api'), {'pathogen__name': signal.pathogen.first().name})
+        for result in response.json()['results']:
+            self.assertTrue(signal.pathogen.first().name in result['pathogen'])
+        response = self.client.get(reverse('signals_api'), {'available_geography__name': signal.available_geography.first().name})
+        for result in response.json()['results']:
+            self.assertTrue(signal.available_geography.first().name in result['available_geography'])
+        response = self.client.get(reverse('signals_api'), {'signal_type__name': signal.signal_type.first().name})
+        for result in response.json()['results']:
+            self.assertTrue(signal.signal_type.first().name in result['signal_type'])
+        response = self.client.get(reverse('signals_api'), {'category__name': signal.category.name})
+        for result in response.json()['results']:
+            self.assertTrue(signal.category.name in result['category'])
+        response = self.client.get(reverse('signals_api'), {'source__name': signal.source.name})
+        for result in response.json()['results']:
+            self.assertTrue(signal.source.name in result['source'])
+        response = self.client.get(reverse('signals_api'), {'time_label': signal.time_label})
+        for result in response.json()['results']:
+            self.assertEqual(signal.time_label, result['time_label'])
+        response = self.client.get(reverse('signals_api'), {'format_type': signal.format_type})
+        for result in response.json()['results']:
+            self.assertEqual(signal.format_type, result['format_type'])
+        response = self.client.get(reverse('signals_api'), {'base': signal.base.id})
+        for result in response.json()['results']:
+            self.assertEqual(signal.base.id, result['base']['id'])

src/signals/tests/factories.py

@@ -1,9 +1,17 @@
 from django.urls import path
 from django.urls.resolvers import URLPattern
 
-from signals.views import SignalsDetailView, SignalsListView
+from signals.views import (
+    SignalsDetailView,
+    SignalsListApiView,
+    SignalsListView,
+)
 
 urlpatterns: list[URLPattern] = [
     path('', SignalsListView.as_view(), name='signals'),
     path('signals/<pk>/', SignalsDetailView.as_view(), name='signal'),
+
+    # REST API
+    path('api/v1/signals/', SignalsListApiView.as_view(), name='signals_api'),
+
 ]