Merge pull request #145 from FAIRDataPipeline/adding_field_to_qc

Add additional object to QualityControlled representing the quality control document

data_management/models.py

@@ -667,16 +667,19 @@ class QualityControlled(BaseModel):
     ### Writable Fields:
     `object`: API URL of the associated `Object`
 
+    `document`: API URL of the `Object` representing the quality control document
+
     ### Read-only Fields:
     `url`: Reference to the instance of the `QualityControlled`, final integer is the `QualityControlled` id
 
     `last_updated`: Datetime that this record was last updated
 
     `updated_by`: Reference to the user that updated this record
     """
-    ADMIN_LIST_FIELDS = ('object',)
+    ADMIN_LIST_FIELDS = ('object', 'document')
 
     object = models.OneToOneField(Object, on_delete=models.PROTECT, related_name='quality_control')
+    document = models.ForeignKey(Object, on_delete=models.PROTECT, related_name='quality_control_document')
 
 
 class Keyword(BaseModel):

data_management/tests/initdb.py

@@ -55,6 +55,11 @@ def init_db(test=True):
         root='https://raw.githubusercontent.com/ScottishCovidResponse/temporary_data/master/',
     )
 
+    scl_repo = StorageRoot.objects.create(
+        updated_by=user,
+        root='https://raw.githubusercontent.com/ScottishCovidResponse/modelling-software-checklist',
+    )
+
     sl_repo_prob = StorageLocation.objects.create(
         updated_by=user,
         path='master/SCRC/human/infection/SARS-CoV-2/symptom-probability/0.1.0.toml',
@@ -104,6 +109,13 @@ def init_db(test=True):
         storage_root=sr_boydorr,
     )
 
+    scl_repo_checklist = StorageLocation.objects.create(
+        updated_by=user,
+        path='main/software-checklist.md',
+        hash='f250b8dff4783cb59ee537d375a9420e3fbe66c2',
+        storage_root=scl_repo,
+    )
+
     StorageLocation.objects.create(
         updated_by=user,
         path='PREFIX qb: <http://purl.org/linked-data/cube#>PREFIX data: <http://statistics.gov.scot/data/>PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>PREFIX mp: <http://statistics.gov.scot/def/measure-properties/>PREFIX dim: <http://purl.org/linked-data/sdmx/2009/dimension#>PREFIX sdim: <http://statistics.gov.scot/def/dimension/>PREFIX stat: <http://statistics.data.gov.uk/def/statistical-entity#>SELECT ?featurecode ?featurename ?date ?measure ?variable ?countWHERE {  ?indicator qb:dataSet data:coronavirus-covid-19-management-information;              dim:refArea ?featurecode;              dim:refPeriod ?period;              sdim:variable ?varname;              qb:measureType ?type.{?indicator mp:count ?count.} UNION {?indicator mp:ratio ?count.}  ?featurecode <http://publishmydata.com/def/ontology/foi/displayName> ?featurename.  ?period rdfs:label ?date.  ?varname rdfs:label ?variable.  ?type rdfs:label ?measure.}',
@@ -423,9 +435,13 @@ def init_db(test=True):
     cr.inputs.set([oc_prob, oc_infect, oc_latent])
     cr.outputs.set([oc_prob, oc_infect, oc_latent])
 
-    QualityControlled.objects.create(updated_by=user, object=o_code)
-    QualityControlled.objects.create(updated_by=user, object=o_boy_cases_h5)
-    QualityControlled.objects.create(updated_by=user, object=o_boy_mort_h5)
+    o_scl_1 = Object.objects.create(updated_by=user, storage_location=scl_repo_checklist)
+    o_scl_2 = Object.objects.create(updated_by=user, storage_location=scl_repo_checklist)
+    o_scl_3 = Object.objects.create(updated_by=user, storage_location=scl_repo_checklist)
+
+    QualityControlled.objects.create(updated_by=user, object=o_code, document=o_scl_1)
+    QualityControlled.objects.create(updated_by=user, object=o_boy_cases_h5, document=o_scl_2)
+    QualityControlled.objects.create(updated_by=user, object=o_boy_mort_h5, document=o_scl_3)
 
     Licence.objects.create(updated_by=user, object=o_code, licence_info='''
     Copyright 2020 SCRC

data_management/tests/test_api.py

@@ -13,6 +13,12 @@ def setUp(self):
         self.user = get_user_model().objects.create(username='Test User')
         init_db()
 
+    def test_full_name(self):
+        self.assertEqual(self.user.full_name(), 'User Not Found')
+
+    def test_user_orgs(self):
+        self.assertEqual(self.user.orgs(), [])
+
     # def _get_token(self):
     #     request = self.factory.get(reverse('get_token'))
     #     request.user = self.user
@@ -98,7 +104,7 @@ def test_get_list(self):
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response['Content-Type'], 'application/json')
         results = response.json()['results']
-        self.assertEqual(len(results), 7)
+        self.assertEqual(len(results), 8)
 
     def test_get_detail(self):
         client = APIClient()
@@ -137,7 +143,7 @@ def test_get_list(self):
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response['Content-Type'], 'application/json')
         results = response.json()['results']
-        self.assertEqual(len(results), 18)
+        self.assertEqual(len(results), 19)
 
     def test_get_detail(self):
         client = APIClient()
@@ -173,6 +179,28 @@ def test_filter_by_hash(self):
         self.assertEqual(len(results), 1)
         self.assertEqual(results[0]['path'], 'human/infection/SARS-CoV-2/scotland/cases_and_management/v0.1.0.h5')
 
+class StorageAPITests(TestCase):
+
+    def setUp(self):
+        self.user = get_user_model().objects.create(username='Test User')
+        init_db()
+
+    def test_get_data(self):
+        client = APIClient()
+        client.force_authenticate(user=self.user)
+        url = reverse("get_data_product", kwargs={"data_product_name": "human/infection/SARS-CoV-2/symptom-probability", "namespace": "FAIR", "version": "0.1.0"})
+        response = client.get(url)
+
+        self.assertEqual(response.status_code, 302)
+        self.assertEqual(response.url, 'https://raw.githubusercontent.com/ScottishCovidResponse/DataRepository/master/SCRC/human/infection/SARS-CoV-2/symptom-probability/0.1.0.toml')
+
+    def test_get_external_object(self):
+        client = APIClient()
+        client.force_authenticate(user=self.user)
+        url = reverse("get_external_object", kwargs={"alternate_identifier": "scottish deaths-involving-coronavirus-covid-19", "title": "scottish deaths-involving-coronavirus-covid-19", "version": "0.1.0"})
+        response = client.get(url)
+
+        self.assertEqual(response.status_code, 302)
 
 class ObjectAPITests(TestCase):
 
@@ -189,29 +217,29 @@ def test_get_list(self):
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response['Content-Type'], 'application/json')
         results = response.json()['results']
-        self.assertEqual(len(results), 16)
+        self.assertEqual(len(results), 19)
 
     def test_get_detail(self):
         client = APIClient()
         client.force_authenticate(user=self.user)
         url = reverse('object-detail', kwargs={'pk': 3})
-        response = client.get(url, format='json')
+        response = client.get(url, format='json', HTTP_HOST='localhost')
 
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response['Content-Type'], 'application/json')
-        self.assertEqual(response.json()['storage_location'], 'http://testserver/api/storage_location/2/')
+        self.assertEqual(response.json()['storage_location'], 'http://localhost/api/storage_location/2/')
 
     def test_filter_by_storage_location(self):
         client = APIClient()
         client.force_authenticate(user=self.user)
         url = reverse('object-list')
-        response = client.get(url, data={'storage_location': '3'}, format='json')
+        response = client.get(url, data={'storage_location': '3'}, format='json', HTTP_HOST='localhost')
 
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response['Content-Type'], 'application/json')
         results = response.json()['results']
         self.assertEqual(len(results), 1)
-        self.assertEqual(results[0]['storage_location'], 'http://testserver/api/storage_location/3/')
+        self.assertEqual(results[0]['storage_location'], 'http://localhost/api/storage_location/3/')
 
 
 class ObjectComponentAPITests(TestCase):
@@ -229,7 +257,7 @@ def test_get_list(self):
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response['Content-Type'], 'application/json')
         results = response.json()['results']
-        self.assertEqual(len(results), 48)
+        self.assertEqual(len(results), 51)
 
     def test_get_detail_whole_object(self):
         client = APIClient()
@@ -427,11 +455,12 @@ def test_get_detail(self):
         client = APIClient()
         client.force_authenticate(user=self.user)
         url = reverse('qualitycontrolled-detail', kwargs={'pk': 1})
-        response = client.get(url, format='json')
+        response = client.get(url, format='json', HTTP_HOST='localhost')
 
         self.assertEqual(response.status_code, 200)
         self.assertEqual(response['Content-Type'], 'application/json')
-        self.assertEqual(response.json()['object'], 'http://testserver/api/object/15/')
+        self.assertEqual(response.json()['object'], 'http://localhost/api/object/15/')
+        self.assertEqual(response.json()['document'], 'http://localhost/api/object/17/')
 
 
 class KeywordAPITests(TestCase):
@@ -1063,7 +1092,7 @@ def test_get_provn(self):
         client.force_authenticate(user=self.user)
         url = reverse("prov_report", kwargs={"pk": 1})
         response = client.get(
-            url, format="provn", HTTP_ACCEPT="text/provenance-notation"
+            url, format="provn", HTTP_ACCEPT="text/provenance-notation", HTTP_HOST='localhost'
         )
         self.assertEqual(response.status_code, 200)
         self.assertEqual(
@@ -1074,7 +1103,7 @@ def test_get_provn(self):
         result_end = result_bits[1].split("xsd:dateTime, ", 1)[1]
         result = result_bits[0] + result_end
         expected_result = """document
-  default <http://testserver/>
+  default <http://localhost/>
   
   entity(api/data_product/1, [prov:type="file", storage="https://data.scrc.uk/api/text_file/input/1", description="input 1 object", namespace="prov", name="this/is/cr/test/input/1", version="0.2.0"])
   agent(api/author/1, [prov:type="prov:Person", name="Ivana Valenti"])

data_management/urls.py

@@ -33,8 +33,8 @@
     path('tables/dataproducts', cache_page(cache_duration)(tables.data_product_table_data)),
     path('tables/externalobjects', cache_page(cache_duration)(tables.external_objects_table_data)),
     path('tables/codereporeleases', cache_page(cache_duration)(tables.code_repo_release_table_data)),
-    path('data_product/<str:namespace>:<path:data_product_name>@<str:version>', views.data_product),
-    path('external_object/<path:alternate_identifier>:<path:title>@<str:version>', views.external_object),
+    path('data_product/<str:namespace>:<path:data_product_name>@<str:version>', views.data_product, name='get_data_product'),
+    path('external_object/<path:alternate_identifier>:<path:title>@<str:version>', views.external_object, name='get_external_object'),
     path('data/<str:name>', views.get_data),
     path('api/data/<str:checksum>', api_views.ObjectStorageView.as_view()),
     path('api/data', api_views.ObjectStorageView.as_view())

data_management/views.py

@@ -251,10 +251,10 @@ def external_object(request, alternate_identifier, title, version):
         return HttpResponseNotFound()
 
     # Use storage location if it exists and user has not requested the original_store
-    if external_object.object.storage_location and 'original' not in request.GET:
+    if external_object.data_product.object.storage_location and 'original' not in request.GET:
         if 'root' in request.GET:
-            return HttpResponse(external_object.object.storage_location.storage_root.root)
-        return redirect(external_object.object.storage_location.full_uri())
+            return HttpResponse(external_object.data_product.object.storage_location.storage_root.root)
+        return redirect(external_object.data_product.object.storage_location.full_uri())
 
     # Use original_store if it exists
     if external_object.original_store: