[Fix] Frontend Testing Fixtures (#249)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Reviewed-on: enviPath/enviPy#249

epdb/management/commands/localize_urls.py

@@ -24,7 +24,6 @@ class Command(BaseCommand):
 
     def handle(self, *args, **options):
         Package = s.GET_PACKAGE_MODEL()
-        print("Localizing urls for Package")
         Package.objects.update(url=Replace(F("url"), Value(options["old"]), Value(options["new"])))
 
         MODELS = [
@@ -50,7 +49,6 @@ class Command(BaseCommand):
         ]
         for model in MODELS:
             obj_cls = apps.get_model("epdb", model)
-            print(f"Localizing urls for {model}")
             obj_cls.objects.update(
                 url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
             )

tests/frontend/frontend_base.py

@@ -0,0 +1,69 @@
+import os
+
+from django.conf import settings as s
+from django.contrib.staticfiles.testing import StaticLiveServerTestCase
+from django.core.management import call_command
+from django.test import override_settings
+from playwright.sync_api import sync_playwright
+
+
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
+class EnviPyStaticLiveServerTestCase(StaticLiveServerTestCase):
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
+
+    @staticmethod
+    def repair_polymorphic_ctypes():
+        from django.contrib.contenttypes.models import ContentType
+
+        from epdb.models import EPModel
+
+        for obj in EPModel.objects.filter(polymorphic_ctype__isnull=True):
+            obj.polymorphic_ctype = ContentType.objects.get_for_model(obj.__class__)
+            obj.save(update_fields=["polymorphic_ctype"])
+
+    @classmethod
+    def setUpClass(cls):
+        os.environ["DJANGO_ALLOW_ASYNC_UNSAFE"] = "true"
+        super().setUpClass()
+
+        cls.playwright = sync_playwright().start()
+        cls.browser = cls.playwright.chromium.launch()
+        cls.username = "user0"
+        cls.password = "SuperSafe"
+
+    def setUp(self):
+        # DB gets flushed after each test and rolled back to initial fixture state.
+        # Hence, we have to localize the urls per test.
+        # The fixtures have "http://localhost:8000/" in all of the URLs
+        # Use the custom mgmt command to adjust it to the current live_server_url
+        call_command("localize_urls", old="http://localhost:8000/", new=f"{self.live_server_url}/")
+
+        # Fix broken polymorphic ctypes
+        EnviPyStaticLiveServerTestCase.repair_polymorphic_ctypes()
+
+        s.SERVER_URL = self.live_server_url
+        self.context = self.browser.new_context()
+        self.page = self.context.new_page()
+
+    def tearDown(self):
+        self.page.wait_for_load_state("networkidle")
+        self.page.close()
+
+    @classmethod
+    def tearDownClass(cls):
+        cls.browser.close()
+        cls.playwright.stop()
+        super().tearDownClass()
+
+    def login(self):
+        """Sign in with the test user, 'user0'"""
+        self.page.goto(self.live_server_url + "/login")
+        self.page.get_by_role("textbox", name="Username").click()
+        self.page.get_by_role("textbox", name="Username").fill(self.username)
+        self.page.get_by_role("textbox", name="Password").click()
+        self.page.get_by_role("textbox", name="Password").fill(self.password)
+
+        with self.page.expect_navigation():
+            self.page.get_by_role("button", name="Sign In").click()
+
+        return self.page

tests/frontend/test_homepage.py

@@ -1,108 +1,38 @@
-import os
-
-from django.conf import settings as s
-from django.contrib.staticfiles.testing import StaticLiveServerTestCase
 from django.test import tag
-from playwright.sync_api import expect, sync_playwright
+from playwright.sync_api import expect
 
-from epdb.logic import UserManager
+from .frontend_base import EnviPyStaticLiveServerTestCase
-from epdb.models import User, ExternalDatabase
 
 
-class TestHomepage(StaticLiveServerTestCase):
+class TestHomepage(EnviPyStaticLiveServerTestCase):
-    @classmethod
+    @tag("frontend")
-    def setUpClass(cls):
+    def test_predict(self):
-        os.environ["DJANGO_ALLOW_ASYNC_UNSAFE"] = "true"
+        page = self.login()
-        super().setUpClass()
+        page.get_by_role("textbox", name="canonical SMILES string").click()
-        cls.playwright = sync_playwright().start()
+        page.get_by_role("textbox", name="canonical SMILES string").fill("CCCN")
-        cls.browser = cls.playwright.chromium.launch()
+        page.get_by_role("button", name="Predict!").click()
-
+        # Check that the pathway box is visible
-    def setUp(self):
+        expect(page.locator("rect")).to_be_visible(timeout=10000)
-        # Create test data
-        s.SERVER_URL = self.live_server_url
-        self.anonymous = UserManager.create_user(
-            "anonymous",
-            "anon@envipath.com",
-            "SuperSafe",
-            is_active=True,
-            add_to_group=False,
-            set_setting=False,
-        )
-        databases = [
-            {
-                "name": "PubChem Compound",
-                "full_name": "PubChem Compound Database",
-                "description": "Chemical database of small organic molecules",
-                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
-                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/compound/{id}",
-            },
-            {
-                "name": "PubChem Substance",
-                "full_name": "PubChem Substance Database",
-                "description": "Database of chemical substances",
-                "base_url": "https://pubchem.ncbi.nlm.nih.gov",
-                "url_pattern": "https://pubchem.ncbi.nlm.nih.gov/substance/{id}",
-            },
-            {
-                "name": "ChEBI",
-                "full_name": "Chemical Entities of Biological Interest",
-                "description": "Dictionary of molecular entities",
-                "base_url": "https://www.ebi.ac.uk/chebi",
-                "url_pattern": "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{id}",
-            },
-            {
-                "name": "RHEA",
-                "full_name": "RHEA Reaction Database",
-                "description": "Comprehensive resource of biochemical reactions",
-                "base_url": "https://www.rhea-db.org",
-                "url_pattern": "https://www.rhea-db.org/rhea/{id}",
-            },
-            {
-                "name": "KEGG Reaction",
-                "full_name": "KEGG Reaction Database",
-                "description": "Database of biochemical reactions",
-                "base_url": "https://www.genome.jp",
-                "url_pattern": "https://www.genome.jp/entry/{id}",
-            },
-            {
-                "name": "UniProt",
-                "full_name": "MetaCyc Metabolic Pathway Database",
-                "description": "UniProt is a freely accessible database of protein sequence and functional information",
-                "base_url": "https://www.uniprot.org",
-                "url_pattern": 'https://www.uniprot.org/uniprotkb?query="{id}"',
-            },
-        ]
-
-        for db_info in databases:
-            ExternalDatabase.objects.get_or_create(name=db_info["name"], defaults=db_info)
-        self.username = "testuser"
-        self.password = "password123"
-        self.user = User.objects.create_user(username=self.username, password=self.password)
-
-    @classmethod
-    def tearDownClass(cls):
-        super().tearDownClass()
-        cls.browser.close()
-        cls.playwright.stop()
 
     @tag("frontend")
-    def test_login(self):
+    def test_advanced_predict(self):
         page = self.login()
-        expect(page.locator("#loggedInButton")).to_be_visible()
+        page.get_by_role("link", name="Advanced").click()
-        page.close()
+        # Check predict page opens correctly
+        expect(page.get_by_role("heading", name="Predict a Pathway in")).to_be_visible()
+        page.get_by_role("textbox", name="Name").click()
+        page.get_by_role("textbox", name="Name").fill("Test Pathway")
+        page.get_by_role("textbox", name="Description").click()
+        page.get_by_role("textbox", name="Description").fill("Test Description")
+        page.get_by_role("textbox", name="SMILES").click()
+        page.get_by_role("textbox", name="SMILES").fill("OCCCN")
+        page.locator("#predict-submit-button").click()
+        # Check that the pathway box is visible
+        expect(page.locator("rect")).to_be_visible(timeout=10000)
 
     @tag("frontend")
     def test_go_home(self) -> None:
         page = self.login()
         page.get_by_role("link").first.click()
+        # Check the homepage predict box is visible
         expect(page.get_by_text("SMILES Draw Predict! Caffeine")).to_be_visible()
-
-    def login(self):
-        page = self.browser.new_page()
-        page.goto(self.live_server_url + "/login/")
-        page.get_by_role("textbox", name="Username").click()
-        page.get_by_role("textbox", name="Username").fill(self.username)
-        page.get_by_role("textbox", name="Password").click()
-        page.get_by_role("textbox", name="Password").fill(self.password)
-        page.get_by_role("button", name="Sign In").click()
-        return page

tests/frontend/test_loginpage.py

@@ -0,0 +1,51 @@
+from django.test import tag
+from playwright.sync_api import expect
+from django.conf import settings as s
+from .frontend_base import EnviPyStaticLiveServerTestCase
+
+
+class TestLoginPage(EnviPyStaticLiveServerTestCase):
+    @tag("frontend")
+    def test_register(self):
+        page = self.page
+        page.goto(self.live_server_url + "/login")
+        page.get_by_text("Register", exact=True).click()
+        page.get_by_role("textbox", name="Username").click()
+        page.get_by_role("textbox", name="Username").fill("newuser")
+        page.get_by_role("textbox", name="Email").click()
+        page.get_by_role("textbox", name="Email").fill("newuser@new.com")
+        page.get_by_role("textbox", name="Password", exact=True).click()
+        page.get_by_role("textbox", name="Password", exact=True).fill("NewUser_1")
+        page.get_by_role("textbox", name="Repeat Password").click()
+        page.get_by_role("textbox", name="Repeat Password").fill("NewUser_1")
+        page.get_by_role("button", name="Sign Up").click()
+
+        if s.ADMIN_APPROVAL_REQUIRED:
+            expected_text = "Your account has been created! An admin will activate it soon!"
+        else:
+            expected_text = (
+                "Account has been created! You'll receive a mail to activate your account shortly."
+            )
+        # Check for success text after Sign Up is clicked
+        expect(page.get_by_text(expected_text)).to_be_visible(timeout=10000)
+
+        if s.ADMIN_APPROVAL_REQUIRED:
+            from django.contrib.auth import get_user_model
+
+            u = get_user_model().objects.get(username="newuser")
+            u.is_active = True
+            u.save()
+
+        page.get_by_role("textbox", name="Username").click()
+        page.get_by_role("textbox", name="Username").fill("newuser")
+        page.get_by_role("textbox", name="Password").click()
+        page.get_by_role("textbox", name="Password").fill("NewUser_1")
+        page.get_by_role("button", name="Sign In").click()
+        # Check that the logged in button is visible indicating the user is logged in
+        expect(page.locator("#loggedInButton")).to_be_visible(timeout=100000000)
+
+    @tag("frontend")
+    def test_login(self):
+        page = self.login()
+        # Check that the logged in button is visible indicating the user is logged in
+        expect(page.locator("#loggedInButton")).to_be_visible()

tests/frontend/test_packagepage.py

@@ -0,0 +1,69 @@
+import re
+from django.test import tag
+from playwright.sync_api import expect
+
+from .frontend_base import EnviPyStaticLiveServerTestCase
+
+
+class TestPackagePage(EnviPyStaticLiveServerTestCase):
+    @tag("frontend")
+    def test_create_package(self):
+        page = self.login()
+        page = self.create_package(page)
+        # Check the package name is correct
+        expect(page.locator("h2")).to_contain_text("test package")
+
+    @tag("frontend")
+    def test_package_permissions(self):
+        page = self.login()
+        page = self.create_package(page)
+        page.get_by_role("button", name="Actions").click()
+        page.get_by_role("button", name="Edit Permissions").click()
+        # Add read and write permission to enviPath Users group
+        page.locator("#select_grantee").select_option(label="enviPath Users")
+        page.locator("#read_new").check()
+        page.locator("#write_new").check()
+        page.get_by_role("button", name="+", exact=True).click()
+        page.get_by_role("button", name="Actions").click()
+        page.get_by_role("button", name="Edit Permissions").click()
+        # Check the permissions saved when re-opening the permissions box
+        expect(page.get_by_text("enviPath Users")).to_be_visible()
+
+    @tag("frontend")
+    def test_predict_in_package(self):
+        page = self.login()
+        page = self.create_package(page)
+        pathway_button = page.get_by_role("link", name="Pathways")
+        # Find number of current pathways by extracting it from pathway button
+        num_pathways = int(re.search(r"Pathways \((\d+)\)", pathway_button.inner_text()).group(1))
+        pathway_button.click()
+        page.get_by_role("button", name="Actions").click()
+        page.get_by_role("link", name="New Pathway").click()
+        # Check that the predict page 'in [package_name]' text shows the current package
+        expect(page.get_by_role("strong").get_by_text("test package")).to_be_visible()
+        page.get_by_role("textbox", name="Name").click()
+        page.get_by_role("textbox", name="Name").fill("Test Pathway")
+        page.get_by_role("textbox", name="Description").click()
+        page.get_by_role("textbox", name="Description").fill("Test description")
+        page.get_by_role("textbox", name="SMILES").click()
+        page.get_by_role("textbox", name="SMILES").fill("OCCCN")
+        page.locator("#predict-submit-button").click()
+        # Check a pathway is visible
+        expect(page.locator("rect")).to_be_visible()
+        page.get_by_role("link", name="test package").click()
+        # Check that the package now has one more pathway than initially
+        expect(page.locator("#docContent")).to_contain_text(f"Pathways ({num_pathways + 1})")
+
+    @staticmethod
+    def create_package(page):
+        """Make a new empty package with name 'test package'"""
+        page.get_by_role("button", name="Browse").click()
+        page.get_by_role("link", name="Package", exact=True).click()
+        page.get_by_role("button", name="Actions").click()
+        page.get_by_role("button", name="New Package").click()
+        page.get_by_role("textbox", name="Name").click()
+        page.get_by_role("textbox", name="Name").fill("test package")
+        page.get_by_role("textbox", name="Description").click()
+        page.get_by_role("textbox", name="Description").fill("test description")
+        page.get_by_role("button", name="Submit").click()
+        return page