✨ Add pagination to resources

dataservice/api/demographic/resources.py

@@ -3,6 +3,7 @@
 from marshmallow import ValidationError
 
 from dataservice.extensions import db
+from dataservice.api.common.pagination import paginated, Pagination
 from dataservice.api.demographic.models import Demographic
 from dataservice.api.demographic.schemas import DemographicSchema
 from dataservice.api.common.views import CRUDView
@@ -16,7 +17,8 @@ class DemographicListAPI(CRUDView):
     rule = '/demographics'
     schemas = {'Demographic': DemographicSchema}
 
-    def get(self):
+    @paginated
+    def get(self, after, limit):
         """
         Get all demographics
         ---
@@ -27,8 +29,9 @@ def get(self):
             resource:
               Demographic
         """
-        d = Demographic.query.all()
-        return DemographicSchema(many=True).jsonify(d)
+        q = Demographic.query
+        return (DemographicSchema(many=True)
+                .jsonify(Pagination(q, after, limit)))
 
     def post(self):
         """

dataservice/api/demographic/schemas.py

@@ -14,6 +14,7 @@ class DemographicSchema(BaseSchema):
                                load_only=True)
 
     class Meta(BaseSchema.Meta):
+        resource_url = 'api.demographics_list'
         model = Demographic
 
     _links = ma.Hyperlinks({

dataservice/api/diagnosis/resources.py

@@ -3,6 +3,7 @@
 from marshmallow import ValidationError
 
 from dataservice.extensions import db
+from dataservice.api.common.pagination import paginated, Pagination
 from dataservice.api.diagnosis.models import Diagnosis
 from dataservice.api.diagnosis.schemas import DiagnosisSchema
 from dataservice.api.common.views import CRUDView
@@ -16,7 +17,8 @@ class DiagnosisListAPI(CRUDView):
     rule = '/diagnoses'
     schemas = {'Diagnosis': DiagnosisSchema}
 
-    def get(self):
+    @paginated
+    def get(self, after, limit):
         """
         Get all diagnoses
         ---
@@ -28,8 +30,10 @@ def get(self):
             resource:
               Diagnosis
         """
-        d = Diagnosis.query.all()
-        return DiagnosisSchema(many=True).jsonify(d)
+        q = Diagnosis.query
+
+        return (DiagnosisSchema(many=True)
+                .jsonify(Pagination(q, after, limit)))
 
     def post(self):
         """

dataservice/api/diagnosis/schemas.py

@@ -20,6 +20,7 @@ class DiagnosisSchema(BaseSchema):
 
     class Meta(BaseSchema.Meta):
         model = Diagnosis
+        resource_url = 'api.diagnoses_list'
 
     _links = ma.Hyperlinks({
         'self': ma.URLFor('api.diagnoses', kf_id='<kf_id>'),

dataservice/api/sample/resources.py

@@ -3,6 +3,7 @@
 from marshmallow import ValidationError
 
 from dataservice.extensions import db
+from dataservice.api.common.pagination import paginated, Pagination
 from dataservice.api.sample.models import Sample
 from dataservice.api.sample.schemas import SampleSchema
 from dataservice.api.common.views import CRUDView
@@ -16,7 +17,8 @@ class SampleListAPI(CRUDView):
     rule = '/samples'
     schemas = {'Sample': SampleSchema}
 
-    def get(self):
+    @paginated
+    def get(self, after, limit):
         """
         Get all samples
         ---
@@ -28,8 +30,10 @@ def get(self):
             resource:
               Sample
         """
-        s = Sample.query.all()
-        return SampleSchema(many=True).jsonify(s)
+        q = Sample.query
+
+        return (SampleSchema(many=True)
+                .jsonify(Pagination(q, after, limit)))
 
     def post(self):
         """

dataservice/api/sample/schemas.py

@@ -19,6 +19,7 @@ class SampleSchema(BaseSchema):
 
     class Meta(BaseSchema.Meta):
         model = Sample
+        resource_url = 'api.samples_list'
 
     _links = ma.Hyperlinks({
         'self': ma.URLFor('api.samples', kf_id='<kf_id>'),

tests/test_pagination.py

@@ -4,6 +4,9 @@
 
 from dataservice.extensions import db
 from dataservice.api.participant.models import Participant
+from dataservice.api.demographic.models import Demographic
+from dataservice.api.sample.models import Sample
+from dataservice.api.diagnosis.models import Diagnosis
 from dataservice.api.study.models import Study
 
 
@@ -21,11 +24,20 @@ def participants(client):
             p = Participant(external_id="test",
                             study_id=s.kf_id,
                             is_proband=True)
+            d = Demographic(race='cat')
+            p.demographic = d
+            samp = Sample()
+            p.samples = [samp]
+            diag = Diagnosis()
+            p.diagnoses = [diag]
             db.session.add(p)
         db.session.commit()
 
     @pytest.mark.parametrize('endpoint', [
         ('/participants'),
+        ('/demographics'),
+        ('/samples'),
+        ('/diagnoses'),
     ])
     def test_pagination(self, client, participants, endpoint):
         """ Test pagination of resource """
@@ -51,10 +63,12 @@ def test_pagination(self, client, participants, endpoint):
         ids_seen.extend([r['kf_id'] for r in resp['results']])
 
         assert len(ids_seen) == resp['total']
-        assert set(ids_seen) == {p.kf_id for p in Participant.query.all()}
 
     @pytest.mark.parametrize('endpoint', [
         ('/participants'),
+        ('/demographics'),
+        ('/samples'),
+        ('/diagnoses'),
     ])
     def test_limit(self, client, participants, endpoint):
         # Check that limit param operates correctly
@@ -75,6 +89,9 @@ def test_limit(self, client, participants, endpoint):
 
     @pytest.mark.parametrize('endpoint', [
         ('/participants'),
+        ('/demographics'),
+        ('/samples'),
+        ('/diagnoses'),
     ])
     def test_after(self, client, participants, endpoint):
         """ Test `after` offeset paramater """
@@ -100,6 +117,9 @@ def test_after(self, client, participants, endpoint):
 
     @pytest.mark.parametrize('endpoint', [
         ('/participants'),
+        ('/demographics'),
+        ('/samples'),
+        ('/diagnoses'),
     ])
     def test_self(self, client, participants, endpoint):
         """ Test that the self link gives the same page """