Add initial testing

.github/workflows/ci.yaml

@@ -0,0 +1,66 @@
+name: ci
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+  schedule:
+    # Nightly tests run on main by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
+  workflow_dispatch:
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Install docker-compose
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y docker-compose
+
+      - name: Copy example env file
+        run: |
+          cp devtools/deployment/.env.example .env
+
+      - name: Make OpenEye directory
+        run: |
+          mkdir -p ~/.OpenEye
+
+      - name: Copy OpenEye license file
+        env:
+          OE_LICENSE: ${{ secrets.OE_LICENSE }}
+        run: |
+          echo "$OE_LICENSE" > ~/.OpenEye/oe_license.txt
+
+      - name: Build containers
+        run: |
+          docker-compose -f docker-compose-dev.yml  build  --build-arg USER_ID=$(id -u) --build-arg GROUP_ID=$(id -g)        
+          docker container ls
+          docker-compose -f docker-compose-dev.yml  up -d
+
+      - name: Chown volume
+        run: |
+          ls -alsh
+          ls -alsh argos
+          sudo chown -R $(id -u):$(id -g) argos/pdb_data
+
+      - name: Run tests
+        run: |
+          docker-compose -f docker-compose-dev.yml exec -T web bash -c "cd argos && /opt/conda/bin/python manage.py test --no-input"

Dockerfile

@@ -1,6 +1,17 @@
 # Use the conda-forge base image with Python
 FROM mambaorg/micromamba:jammy
 
+
+ARG USER_ID
+ARG GROUP_ID
+
+USER root
+
+RUN addgroup --gid $GROUP_ID user
+RUN adduser --disabled-password --gecos '' --uid $USER_ID --gid $GROUP_ID user
+USER user
+
+
 # set environment variables
 ENV PYTHONUNBUFFERED 1
 
@@ -13,15 +24,17 @@ COPY . /argos
 RUN micromamba config append channels conda-forge 
 RUN  micromamba config append channels openeye
 
-COPY --chown=$MAMBA_USER:$MAMBA_USER devtools/conda-envs/argos-ubuntu-latest.yml /tmp/env.yaml
+COPY --chown=user:user devtools/conda-envs/argos-ubuntu-latest.yml /tmp/env.yaml
 
 RUN micromamba install -y -n base git -f /tmp/env.yaml && \
     micromamba clean --all --yes
 
 USER root
 RUN mkdir /openeye
+RUN chown -R user:user /openeye
 RUN mkdir /argos/pdb_data
-USER $MAMBA_USER
+RUN chown -R user:user /argos/pdb_data
+USER user
 ENV OE_LICENSE=/openeye/oe_license.txt
 
 

argos/argos/settings.py

@@ -48,6 +48,7 @@
     'django.contrib.sessions',
     'django.contrib.messages',
     'django.contrib.staticfiles',
+    'django_cleanup.apps.CleanupConfig',
     'argos_viewer.apps.ArgosViewerConfig',
 
 ]
@@ -89,6 +90,7 @@
 
 DATABASES = {
     'default': env.db(),
+
 }
 
 
@@ -146,3 +148,18 @@
 
 # Redirect to home URL after login (Default redirects to /accounts/profile/)
 LOGIN_REDIRECT_URL = '/'
+
+
+LOGGING = {
+    "version": 1,
+    "disable_existing_loggers": False,
+    "handlers": {
+        "console": {"class": "logging.StreamHandler"},
+    },
+    "loggers": {
+        "django": {
+            "handlers": ["console"],
+            "level": "INFO",
+        },
+    }
+}

argos/argos_viewer/models.py

@@ -1,12 +1,26 @@
+from typing import Any
 from django.db import models
 from django.core.validators import FileExtensionValidator
-
+import os
 
 class PDBFile(models.Model):
     file = models.FileField(validators=[FileExtensionValidator(['pdb'])], upload_to="pdb_data")
 
+    def delete(self, *args, **kwargs):
+        # Delete the file when the instance is deleted
+        if self.file:
+            if os.path.isfile(self.file.path):
+                os.remove(self.file.path)
+        super(PDBFile, self).delete(*args, **kwargs)
 
 class TargetPDBFile(models.Model):
     pdb_file = models.ForeignKey(PDBFile, on_delete=models.CASCADE)
     target = models.CharField(max_length=200)
     upload_date = models.DateTimeField(auto_now_add=True)
+
+
+    def delete(self, *args, **kwargs):
+        # Delete the associated PDBFile instance, which should trigger its delete method
+        if self.pdb_file:
+            self.pdb_file.delete()
+        super(TargetPDBFile, self).delete(*args, **kwargs)

argos/argos_viewer/tests/test_models.py

@@ -0,0 +1,43 @@
+from django.test import TestCase
+from argos_viewer.models import PDBFile, TargetPDBFile
+from django.core.files.uploadedfile import SimpleUploadedFile
+from django.utils import timezone
+import os
+
+class PDBFileModelTest(TestCase):
+    def setUp(self):
+        self.file = SimpleUploadedFile("test.pdb", b"pdb file content")
+        self.pdb_file = PDBFile.objects.create(file=self.file)
+
+
+    def test_pdb_file_created(self):
+        self.assertTrue(os.path.exists(self.pdb_file.file.path))
+
+    def test_file_extension(self):
+        self.assertEqual(self.pdb_file.file.name.split(".")[-1], "pdb")
+
+class TargetPDBFileModelTest(TestCase):
+    def setUp(self):
+        self.file = SimpleUploadedFile("test.pdb", b"pdb file content")
+        self.pdb_file = PDBFile.objects.create(file=self.file)
+        self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="test_target", upload_date=timezone.now())
+
+    def tearDown(self):
+        if os.path.exists(self.target_pdb_file.pdb_file.file.path):
+            os.remove(self.target_pdb_file.pdb_file.file.path)
+
+    def test_target_pdb_file_created(self):
+        self.assertTrue(TargetPDBFile.objects.exists())
+
+    def test_target(self):
+        self.assertEqual(self.target_pdb_file.target, "test_target")
+
+    def test_upload_date(self):
+        self.assertIsNotNone(self.target_pdb_file.upload_date)
+
+    def test_pdb_file_deletion_on_target_pdb_file_deletion(self):
+        self.target_pdb_file.delete()
+        self.assertFalse(os.path.exists(self.pdb_file.file.path))
+
+
+

argos/argos_viewer/tests/test_oe_license.py

@@ -0,0 +1,6 @@
+from django.test import TestCase
+
+class OELicenseTests(TestCase):
+    def test_oechem_is_licensed(self):
+        from asapdiscovery.data.openeye import oechem
+        self.assertTrue(oechem.OEChemIsLicensed())

argos/argos_viewer/tests/test_urls.py

@@ -0,0 +1,28 @@
+from django.test import SimpleTestCase
+from django.urls import reverse, resolve
+from argos_viewer.views import home, upload_sucessful, TargetPDBListView, target_pdb_detail_view, failed, no_fitness_data
+
+class TestUrls(SimpleTestCase):
+    def test_home_url_resolves(self):
+        url = reverse('home')
+        self.assertEqual(resolve(url).func, home)
+
+    def test_upload_sucessful_url_resolves(self):
+        url = reverse('upload_sucessful')
+        self.assertEqual(resolve(url).func, upload_sucessful)
+
+    def test_pdb_files_url_resolves(self):
+        url = reverse('pdb_files')
+        self.assertEqual(resolve(url).func.view_class, TargetPDBListView)
+
+    def test_detail_url_resolves(self):
+        url = reverse('detail', args=[1])  # assuming pk=1
+        self.assertEqual(resolve(url).func, target_pdb_detail_view)
+
+    def test_failed_url_resolves(self):
+        url = reverse('failed')
+        self.assertEqual(resolve(url).func, failed)
+
+    def test_no_fitness_data_url_resolves(self):
+        url = reverse('no_fitness_data', args=['target_name'])
+        self.assertEqual(resolve(url).func, no_fitness_data)

argos/argos_viewer/tests/test_views.py

@@ -0,0 +1,55 @@
+from django.test import TestCase, Client, RequestFactory
+from django.urls import reverse
+from argos_viewer.models import PDBFile, TargetPDBFile
+from django.core.files.uploadedfile import SimpleUploadedFile
+from django.utils import timezone
+from django.contrib.auth.models import User
+from asapdiscovery.data.testing.test_resources import fetch_test_file
+
+
+class ViewTests(TestCase):
+    def setUp(self):
+        self._test_file = fetch_test_file("Mpro-P2660_0A_bound.pdb")
+        with open(self._test_file, "r") as f:
+            self._file_contents = f.read()
+        # Create a user
+        self.user = User.objects.create_user(username='testuser', password='12345')
+        self.file = SimpleUploadedFile("test.pdb", self._file_contents.encode())
+        self.pdb_file = PDBFile.objects.create(file=self.file)
+        self.target_pdb_file = TargetPDBFile.objects.create(pdb_file=self.pdb_file, target="SARS-CoV-2-Mpro", upload_date=timezone.now())
+
+    def test_index_view(self):
+        response = self.client.get(reverse('index'))
+        self.assertEqual(response.status_code, 302)  # Redirects to home
+
+    def test_home_view_GET(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('home'))
+        self.assertEqual(response.status_code, 200)
+        self.assertTemplateUsed(response, 'argos_viewer/home.html')
+
+    def test_upload_successful_view(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('upload_sucessful'))
+        self.assertEqual(response.status_code, 200)
+        self.assertContains(response, 'upload worked!')
+
+
+    def test_target_pdb_detail_view_GET(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('detail', args=[self.target_pdb_file.pk]), follow=True)
+        self.assertEqual(response.status_code, 200)
+
+    def test_failed_view_GET(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('failed'))
+        self.assertEqual(response.status_code, 200)
+        self.assertTemplateUsed(response, 'argos_viewer/failed.html')
+
+    def test_no_fitness_data_view_GET(self):
+        self.client.force_login(self.user)
+        response = self.client.get(reverse('no_fitness_data', args=['target_name']))
+        self.assertEqual(response.status_code, 200)
+        self.assertTemplateUsed(response, 'argos_viewer/no_fitness_data.html')
+
+    # Add tests for POST requests as well if necessary

argos/argos_viewer/views.py

@@ -15,6 +15,10 @@
 from asapdiscovery.data.fitness import target_has_fitness_data
 import tempfile
 
+import logging
+
+logger = logging.getLogger('django')
+
 def index(request):
     context = {}
     return redirect("home")
@@ -74,14 +78,13 @@ def target_pdb_detail_view(request, pk):
             target_kwargs={"target_name": "unknown"},
         )
 
-        tf = tempfile.NamedTemporaryFile()  
+        tf = tempfile.NamedTemporaryFile()
         html_viz = HTMLVisualizer(
-            [c.ligand.to_oemol()], [tf], obj.target, c.target.to_oemol(), color_method="fitness", align=False 
-        )
-        # align=True is broken, see https://github.com/choderalab/asapdiscovery/issues/709
+            [c.ligand.to_oemol()], [tf], obj.target, c.target.to_oemol(), color_method="fitness", align=True)
         html = html_viz.make_poses_html()[0]
+        logger.debug("Made pose html")
     except Exception as e:
-        print(f"rendering failed with exception {e}")
+        logger.error(f"rendering failed with exception {e}")
         return redirect("failed")
 
     return HttpResponse(html)

devtools/conda-envs/argos-ubuntu-latest.yml

@@ -6,20 +6,27 @@ dependencies:
 
   # Base depends
   - pip
-  - python =3.10
-  - git
+  - python >=3.10,<3.11
+
 
   # argos deps
   - django
   - gunicorn
+  - django-cleanup
+
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - pooch
+
   # asapdiscovery deps
 
   # Others
   - appdirs
-  - openeye-toolkits
+  - openeye-toolkits <2023.2.3
   - pydantic >=1.10.8,<2.0.0a0
 
-
   # data
   - requests
   - boto3

devtools/deployment/.env.example

@@ -5,4 +5,4 @@ DATABASE_URL=postgresql://django_traefik:django_traefik@db:5432/django_traefik
 HOST_DOMAIN=localhost
 POSTGRES_USER=django_traefik
 POSTGRES_PASSWORD=django_traefik
-POSTGRES_DB=django_traefik
+POSTGRES_DB=django_traefik