Merge pull request #48 from EBI-G2P/dglemos-run-test

Set up tests to run automatically
EBI-G2P · Oct 16, 2024 · df85b5d · df85b5d
2 parents 128611e + bfbdd87
commit df85b5d
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Showing 4 changed files with 86 additions and 5 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,59 @@
+name: G2P API tests
+
+on: [pull_request]
+
+permissions:
+  contents: read
+  actions: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      mysql:
+        image: mysql:8.0
+        env:
+          MYSQL_ROOT_PASSWORD: root
+          MYSQL_DATABASE: test_db
+        ports:
+          - 3306:3306
+        options: >-
+          --health-cmd="mysqladmin ping -h localhost" --health-interval=10s
+          --health-timeout=5s --health-retries=3
+    
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Change to the root directory
+        run: cd /home/runner/work
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          
+      - name: Create project config file
+        run: |
+          echo "# config.ini" > /home/runner/work/config.ini
+          echo "[database]" >> /home/runner/work/config.ini
+          echo "name=test_db" >> /home/runner/work/config.ini
+          echo "user=root" >> /home/runner/work/config.ini
+          echo "password=root" >> /home/runner/work/config.ini
+          echo "host=127.0.0.1" >> /home/runner/work/config.ini
+          echo "port=3306" >> /home/runner/work/config.ini
+        
+      - name: Run tests
+        run: |
+          python manage.py makemigrations
+          python manage.py migrate
+          python manage.py test gene2phenotype_app.tests
+        env:
+          SECRET_KEY: ${{ secrets.SECRET_KEY }}
+          PROJECT_CONFIG_PATH: /home/runner/work/config.ini
+        working-directory: gene2phenotype_project
diff --git a/gene2phenotype_project/gene2phenotype_app/fixtures/locus_genotype_disease.json b/gene2phenotype_project/gene2phenotype_app/fixtures/locus_genotype_disease.json
@@ -6,6 +6,7 @@
 			"locus": 1,
 			"genotype": 9,
 			"disease": 2,
+			"molecular_mechanism": 1,
 			"confidence": 1,
 			"confidence_support": null,
 			"date_review": "2017-04-24T16:33:40Z",

diff --git a/gene2phenotype_project/gene2phenotype_app/fixtures/molecular_mechanism.json b/gene2phenotype_project/gene2phenotype_app/fixtures/molecular_mechanism.json
@@ -0,0 +1,14 @@
+[
+    {
+        "model": "gene2phenotype_app.molecularmechanism",
+        "pk": 1,
+        "fields": {
+            "mechanism": 1,
+            "mechanism_support": 16,
+            "synopsis": null,
+            "synopsis_support": null,
+            "mechanism_description": null,
+            "is_deleted": 0
+        }
+    }
+]
diff --git a/gene2phenotype_project/gene2phenotype_app/tests/views/test_panel.py b/gene2phenotype_project/gene2phenotype_app/tests/views/test_panel.py
@@ -1,6 +1,7 @@
 from django.test import TestCase
 from django.urls import reverse
-
+from knox.models import AuthToken
+from gene2phenotype_app.models import User
 
 class PanelListEndpointTests(TestCase):
     """
@@ -25,11 +26,15 @@ def test_login_get_panel_list(self):
             Test for autenticated users.
             All panels are included in the response.
         """
-        login = self.client.login(username="[email protected]", password="user5pass")
-        self.assertTrue(login)
+        user = User.objects.get(email="[email protected]")
+        # Create token for the user
+        token_id = AuthToken.objects.create(user)[1]
+        # Authenticate using the token
+        self.client.defaults['HTTP_AUTHORIZATION'] = 'Token ' + token_id
 
         response = self.client.get(self.url_panels)
         self.assertEqual(response.status_code, 200)
+
         self.assertEqual(response.data.get("count"), 3)
 
 class PanelDetailsEndpointTests(TestCase):
@@ -40,7 +45,8 @@ class PanelDetailsEndpointTests(TestCase):
                 "gene2phenotype_app/fixtures/g2p_stable_id.json", "gene2phenotype_app/fixtures/locus.json",
                 "gene2phenotype_app/fixtures/sequence.json", "gene2phenotype_app/fixtures/disease.json",
                 "gene2phenotype_app/fixtures/ontology_term.json", "gene2phenotype_app/fixtures/source.json",
-                "gene2phenotype_app/fixtures/locus_genotype_disease.json", "gene2phenotype_app/fixtures/lgd_panel.json"]
+                "gene2phenotype_app/fixtures/locus_genotype_disease.json", "gene2phenotype_app/fixtures/lgd_panel.json",
+                "gene2phenotype_app/fixtures/molecular_mechanism.json", "gene2phenotype_app/fixtures/cv_molecular_mechanism.json"]
 
     def setUp(self):
         self.url_panels = reverse('panel_details', kwargs={'name': 'DD'})
@@ -61,7 +67,8 @@ class PanelSummaryEndpointTests(TestCase):
                 "gene2phenotype_app/fixtures/g2p_stable_id.json", "gene2phenotype_app/fixtures/locus.json",
                 "gene2phenotype_app/fixtures/sequence.json", "gene2phenotype_app/fixtures/disease.json",
                 "gene2phenotype_app/fixtures/ontology_term.json", "gene2phenotype_app/fixtures/source.json",
-                "gene2phenotype_app/fixtures/locus_genotype_disease.json", "gene2phenotype_app/fixtures/lgd_panel.json"]
+                "gene2phenotype_app/fixtures/locus_genotype_disease.json", "gene2phenotype_app/fixtures/lgd_panel.json",
+                "gene2phenotype_app/fixtures/molecular_mechanism.json", "gene2phenotype_app/fixtures/cv_molecular_mechanism.json"]
 
     def setUp(self):
         self.url_panels = reverse('panel_summary', kwargs={'name': 'DD'})