Adjusted devcontainer; added a test case for a variant query; included pytest-django plugin in the dev requirements

Author: dameyerdave

.devcontainer/devcontainer.json

@@ -17,13 +17,13 @@
 
 	// The optional 'workspaceFolder' property is the path VS Code should open by default when
 	// connected. This is typically a file mount in .devcontainer/docker-compose.yml
-	"workspaceFolder": "/workspace",
+	"workspaceFolder": "/app",
 
 	// Set *default* container specific settings.json values on container create.
 	"settings": {
-		"python.analysis.extraPaths": [
-    	"${workspaceFolder}/svip_api"
-  	],
+		// "python.analysis.extraPaths": [
+    // 	"${workspaceFolder}/svip_api"
+  	// ],
 		// "python.testing.unittestArgs": [
 		// 	"-v",
 		// 	"-s",
@@ -33,12 +33,11 @@
 		// ],
 		"python.testing.unittestEnabled": false,
 		"python.testing.pytestArgs": [
-			"./svip_api/api/tests/",
+			"./api/tests/",
 			"--exitfirst",
 			"--verbose"
-		]	,
+		],
 		"python.testing.pytestEnabled": true
-		
 	},
 
 	// Add the IDs of extensions you want installed when the container is created.
@@ -64,7 +63,7 @@
 
 	// Uncomment the next line to run commands after the container is created - for example installing curl.
 	// "postCreateCommand": "apt-get update && apt-get install -y curl",
-	"postCreateCommand": "pip install -r ./svip_api/requirements.dev.txt"
+	"postCreateCommand": "pip install -r ./requirements.dev.txt"
 
 	// Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root.
 	// "remoteUser": "vscode"

.devcontainer/docker-compose.yml

@@ -22,10 +22,10 @@ services:
 
     volumes:
       # Update this to wherever you want VS Code to mount the folder of your project
-      - .:/workspace:cached
+      # - .:/workspace:cached
 
       # Uncomment the next line to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker-compose for details.
-      # - /var/run/docker.sock:/var/run/docker.sock 
+      - /var/run/docker.sock:/var/run/docker.sock 
 
     # Uncomment the next four lines if you will use a ptrace-based debugger like C++, Go, and Rust.
     # cap_add:

svip_api/.env.TEMPLATE

@@ -0,0 +1,62 @@
+# Generated by Django 2.2.28 on 2022-08-12 13:39
+
+from django.db import migrations, models
+import django_db_cascade.deletions
+import django_db_cascade.fields
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('api', '0161_merge_20220203_0937'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='curationevidence',
+            name='association',
+        ),
+        migrations.RemoveField(
+            model_name='curationentry',
+            name='curation_evidences',
+        ),
+        migrations.RemoveField(
+            model_name='curationreview',
+            name='curation_evidence',
+        ),
+        migrations.RemoveField(
+            model_name='revisedreview',
+            name='curation_evidence',
+        ),
+        migrations.AddField(
+            model_name='revisedreview',
+            name='curation_entry',
+            field=django_db_cascade.fields.ForeignKey(null=True, on_delete=django_db_cascade.deletions.DB_CASCADE, related_name='revised_reviews', to='api.CurationEntry'),
+        ),
+        migrations.AlterField(
+            model_name='curationentry',
+            name='variant',
+            field=models.ForeignKey(on_delete=django_db_cascade.deletions.DB_CASCADE, related_name='curation_entries', to='api.Variant'),
+        ),
+        migrations.AlterField(
+            model_name='curationreview',
+            name='curation_entry',
+            field=django_db_cascade.fields.ForeignKey(null=True, on_delete=django_db_cascade.deletions.DB_CASCADE, related_name='curation_reviews', to='api.CurationEntry'),
+        ),
+        migrations.AlterField(
+            model_name='sibannotation1',
+            name='evidence',
+            field=models.OneToOneField(on_delete=django_db_cascade.deletions.DB_CASCADE, related_name='annotation1', to='api.CurationEntry'),
+        ),
+        migrations.AlterField(
+            model_name='sibannotation2',
+            name='evidence',
+            field=models.OneToOneField(on_delete=django_db_cascade.deletions.DB_CASCADE, related_name='annotation2', to='api.CurationEntry'),
+        ),
+        migrations.DeleteModel(
+            name='CurationAssociation',
+        ),
+        migrations.DeleteModel(
+            name='CurationEvidence',
+        ),
+    ]

svip_api/api/migrations/0162_auto_20220812_1339.py

@@ -1,3 +1,3 @@
 [pytest]
-DJANGO_SETTINGS_MODULE = svip_server.settings.development
-python_files = test_*.py
+DJANGO_SETTINGS_MODULE=svip_server.settings.development
+python_files=test_*.py

svip_api/api/pytest.ini

@@ -1,8 +1,8 @@
 from django.test import TestCase
 
 class ModelTests(TestCase):
-    def test_model_coice_class(self):
-      """ Testing the Model Choice Class"""
+    def test_model_choice_class(self):
+      """ Testing the Model Choice Class """
       from api.utils import ModelChoice
       class MyModelChoice(ModelChoice):
         prop1='Prop1'
@@ -13,3 +13,5 @@ class MyModelChoice(ModelChoice):
         ('prop1', 'Prop1'),
         ('prop2', 'Prop2')
       ])
+
+

svip_api/api/tests/test_models.py

@@ -1,2 +1,29 @@
-from django.test import TestCase
+from rest_framework.test import APITestCase
+from rest_framework import status
+from django.urls import reverse
+from api.models.genomic import Variant, Gene
 
+class ViewTests(APITestCase):
+  def setUp(self):
+    gene = Gene.objects.create(
+      entrez_id=673,
+      ensembl_gene_id='ENSG00000157764',
+      symbol='BRAF'
+    )
+    variant = Variant.objects.create(
+      gene=gene,
+      name='V600E',
+      description='BRAF V600E'
+    )
+
+  def test_variant_list(self):
+    """ Test the variant list """
+    url = reverse('variant-list')
+    response = self.client.get(url, format='json')
+    self.assertEqual(response.status_code, status.HTTP_200_OK)
+
+    data = response.json()
+    self.assertEqual(data['count'], 1, "We expect 1 result")
+    self.assertEqual(data['results'][0]['name'], 'V600E', "We expenct the variant name to be 'V600E")
+
+    

svip_api/api/tests/test_views.py

@@ -3,3 +3,4 @@
 # git+https://github.com/falquaddoomi/nplusone.git@24632de42d8c309d7181c02f1a93684ffc96567e#egg=nplusone-TrialSpark
 # structlog==20.1.0
 pytest==7.1.2
+pytest-django==4.5.2