Merge pull request #96 from c3g/dataset-table-ownership

Serialize dataset table ownership

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                      #
@@ -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_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}")

requirements.txt

@@ -3,13 +3,13 @@ attrs==19.3.0
 Babel==2.8.0
 certifi==2019.11.28
 chardet==3.0.4
-chord-lib==0.5.0
+chord-lib==0.6.0
 codecov==2.0.16
 colorama==0.4.3
 coreapi==2.3.3
 coreschema==0.0.4
 coverage==5.0.3
-Django==2.2.10
+Django==2.2.11
 django-filter==2.2.0
 django-nose==1.4.6
 django-rest-swagger==2.2.0
@@ -30,9 +30,9 @@ MarkupSafe==1.1.1
 more-itertools==8.2.0
 nose==1.3.7
 openapi-codec==1.3.2
-packaging==20.1
+packaging==20.3
 psycopg2-binary==2.8.4
-Pygments==2.5.2
+Pygments==2.6.1
 pyparsing==2.4.6
 pyrsistent==0.15.7
 python-dateutil==2.8.1
@@ -45,7 +45,7 @@ requests==2.23.0
 simplejson==3.17.0
 six==1.14.0
 snowballstemmer==2.0.0
-Sphinx==2.4.3
+Sphinx==2.4.4
 sphinx-rtd-theme==0.4.3
 sphinxcontrib-applehelp==1.0.2
 sphinxcontrib-devhelp==1.0.2

setup.py

@@ -16,12 +16,13 @@
 
     python_requires=">=3.6",
     install_requires=[
-        "chord_lib[django]==0.5.0",
+        "chord_lib[django]==0.6.0",
         "Django>=2.2,<3.0",
         "django-filter>=2.2,<3.0",
         "django-nose>=1.4,<2.0",
         "djangorestframework>=3.10,<3.11",
         "djangorestframework-camel-case>=1.1,<2.0",
+        "django-rest-swagger==2.2.0",
         "elasticsearch==7.1.0",
         "fhirclient>=3.2,<4.0",
         "jsonschema>=3.2,<4.0",
@@ -32,7 +33,6 @@
         "rdflib-jsonld==0.4.0",
         "requests>=2.23,<3.0",
         "uritemplate>=3.0,<4.0",
-        "django-rest-swagger==2.2.0",
     ],
 
     author=config["package"]["authors"],