Merge pull request #110 from c3g/develop

Version 0.6.0

.travis.yml

@@ -1,7 +1,8 @@
 dist: bionic
 language: python
 python:
-  - "3.7"
+  - "3.6"
+  - "3.8"
 addons:
   postgresql: "11"
   apt:

chord_metadata_service/chord/api_views.py

@@ -1,11 +1,12 @@
 from rest_framework import viewsets
 from rest_framework.permissions import BasePermission, SAFE_METHODS
+from rest_framework.settings import api_settings
+
+from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer, JSONLDDatasetRenderer, RDFDatasetRenderer
 from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
 from .models import *
 from .permissions import OverrideOrSuperUserOnly
 from .serializers import *
-from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer, JSONLDDatasetRenderer, RDFDatasetRenderer
-from rest_framework.settings import api_settings
 
 
 __all__ = ["ProjectViewSet", "DatasetViewSet", "TableOwnershipViewSet"]

chord_metadata_service/chord/migrations/0010_auto_20200309_1945.py

@@ -0,0 +1,19 @@
+# Generated by Django 2.2.11 on 2020-03-09 19:45
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('chord', '0009_auto_20200218_1615'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='tableownership',
+            name='dataset',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='table_ownership', to='chord.Dataset'),
+        ),
+    ]

chord_metadata_service/chord/models.py

@@ -11,6 +11,7 @@
 def version_default():
     return f"version_{timezone.now()}"
 
+
 #############################################################
 #                                                           #
 #                   Project Management                      #
@@ -121,7 +122,7 @@ def n_of_tables(self):
     keywords = ArrayField(JSONField(null=True, blank=True), blank=True, null=True,
                           help_text="Tags associated with the dataset, which will help in its discovery.")
     version = models.CharField(max_length=200, blank=True, default=version_default,
-                                  help_text="A release point for the dataset when applicable.")
+                               help_text="A release point for the dataset when applicable.")
     extra_properties = JSONField(blank=True, null=True,
                                  help_text="Extra properties that do not fit in the previous specified attributes.")
 
@@ -146,7 +147,7 @@ class TableOwnership(models.Model):
     data_type = models.CharField(max_length=200)  # TODO: Is this needed?
 
     # Delete table ownership upon project/dataset deletion
-    dataset = models.ForeignKey(Dataset, on_delete=models.CASCADE, related_name='table_ownerships')
+    dataset = models.ForeignKey(Dataset, on_delete=models.CASCADE, related_name='table_ownership')
     # If not specified, compound table which may link to many samples TODO: ???
     sample = models.ForeignKey("phenopackets.Biosample", on_delete=models.CASCADE, blank=True, null=True)
 

chord_metadata_service/chord/serializers.py

@@ -19,13 +19,22 @@
 #############################################################
 
 
+class TableOwnershipSerializer(GenericSerializer):
+    class Meta:
+        model = TableOwnership
+        fields = '__all__'
+
+
 class DatasetSerializer(GenericSerializer):
     always_include = (
         "description",
         "contact_info",
         "linked_field_sets",
+        "table_ownership",
     )
 
+    table_ownership = TableOwnershipSerializer(read_only=True, many=True, exclude_when_nested=["dataset"])
+
     # noinspection PyMethodMayBeStatic
     def validate_title(self, value):
         if len(value.strip()) < 3:
@@ -140,9 +149,3 @@ def validate_title(self, value):
     class Meta:
         model = Project
         fields = '__all__'
-
-
-class TableOwnershipSerializer(GenericSerializer):
-    class Meta:
-        model = TableOwnership
-        fields = '__all__'

chord_metadata_service/chord/tests/test_api_search.py

@@ -1,5 +1,7 @@
 import json
-from unittest.mock import Mock, patch
+import uuid
+
+from unittest.mock import patch
 
 from django.test import override_settings
 from django.urls import reverse
@@ -83,6 +85,15 @@ def test_table_list(self):
         self.assertEqual(len(c), 1)
         self.assertEqual(c[0], self.dataset_rep(self.dataset, c[0]["metadata"]["created"], c[0]["metadata"]["updated"]))
 
+    def test_table_summary(self):
+        r = self.client.get(reverse("table-summary", kwargs={"table_id": str(uuid.uuid4())}))
+        self.assertEqual(r.status_code, 404)
+
+        r = self.client.get(reverse("table-summary", kwargs={"table_id": self.dataset["identifier"]}))
+        s = r.json()
+        self.assertEqual(s["count"], 0)  # No phenopackets
+        self.assertIn("data_type_specific", s)
+
 
 class SearchTest(APITestCase):
     def setUp(self) -> None:
@@ -182,25 +193,48 @@ def test_private_search(self):
 
     def test_private_table_search_1(self):
         # No body
-        r = self.client.post(reverse("table-search", args=[str(self.dataset.identifier)]))
+
+        r = self.client.post(reverse("public-table-search", args=[str(self.dataset.identifier)]))
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        r = self.client.post(reverse("private-table-search", args=[str(self.dataset.identifier)]))
         self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
 
     def test_private_table_search_2(self):
         # No query
-        r = self.client.post(reverse("table-search", args=[str(self.dataset.identifier)]), data=json.dumps({}),
+
+        r = self.client.post(reverse("public-table-search", args=[str(self.dataset.identifier)]), data=json.dumps({}),
+                             content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        r = self.client.post(reverse("private-table-search", args=[str(self.dataset.identifier)]), data=json.dumps({}),
                              content_type="application/json")
         self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
 
     def test_private_table_search_3(self):
         # Bad syntax for query
-        r = self.client.post(reverse("table-search", args=[str(self.dataset.identifier)]), data=json.dumps({
+
+        r = self.client.post(reverse("public-table-search", args=[str(self.dataset.identifier)]), data=json.dumps({
+            "query": ["hello", "world"]
+        }), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
+
+        r = self.client.post(reverse("private-table-search", args=[str(self.dataset.identifier)]), data=json.dumps({
             "query": ["hello", "world"]
         }), content_type="application/json")
         self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
 
     def test_private_table_search_4(self):
         # Valid query with one result
-        r = self.client.post(reverse("table-search", args=[str(self.dataset.identifier)]), data=json.dumps({
+
+        r = self.client.post(reverse("public-table-search", args=[str(self.dataset.identifier)]), data=json.dumps({
+            "query": TEST_SEARCH_QUERY_1
+        }), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_200_OK)
+        c = r.json()
+        self.assertEqual(c, True)
+
+        r = self.client.post(reverse("private-table-search", args=[str(self.dataset.identifier)]), data=json.dumps({
             "query": TEST_SEARCH_QUERY_1
         }), content_type="application/json")
         self.assertEqual(r.status_code, status.HTTP_200_OK)

chord_metadata_service/chord/tests/test_models.py

@@ -65,6 +65,6 @@ def test_table_ownership(self):
         self.assertEqual(t.data_type, "variant")
         self.assertEqual(t.dataset, d)
 
-        self.assertIn(t, d.table_ownerships.all())
+        self.assertIn(t, d.table_ownership.all())
 
         self.assertEqual(str(t), f"{str(d)} -> {t.table_id}")