Increase test coverage

.github/workflows/backend_ci.yml

@@ -52,7 +52,7 @@ jobs:
 
       - name: Run tests and build coverage file
         run: |
-          export PYTHONPATH=. pytest 
+          export PYTHONPATH=backend pytest 
           pytest --cache-clear --cov=. --cov-report term-missing backend/tests/
 
       - name: Format with black

backend/main/views.py

@@ -116,7 +116,7 @@ def add_run(request):
         converted_run_name, additional_message = sanitize_name(run_name)
 
         try:
-            Run(converted_run_name, workflow_name, df_mode_name,)
+            Run(converted_run_name, workflow_name, df_mode_name)
             message = f"Created run {converted_run_name}. \n{additional_message}" if len(additional_message) > 0 else f"Created run {converted_run_name}."
             return JsonResponse({"success": True, "message": message, "data": {"run_name": converted_run_name}})
         except Exception as e:

backend/protzilla/run.py

@@ -15,6 +15,7 @@
 from backend.protzilla.form import Form
 from backend.protzilla.steps import Messages, Output, Plots, Step, StepManager
 from backend.protzilla.utilities import format_trace
+from backend.protzilla.workflow import get_available_workflow_names
 
 
 def get_available_run_names() -> list[str]:
@@ -64,7 +65,7 @@ def get_available_run_info() -> str | tuple[
             metadata = {}
         tags = metadata.get("tags", set())
 
-        run_name = {
+        run = {
             "run_name": run_name,
             "creation_date": metadata.get("creation_date", "date not available"),
             "modification_date": metadata.get("modification_date", "date not available"),
@@ -74,10 +75,10 @@ def get_available_run_info() -> str | tuple[
             "run_tags": list(tags)
         }
 
-        if run_name["favourite_status"]:
-            runs_favourited.append(run_name)
+        if run["favourite_status"]:
+            runs_favourited.append(run)
         else:
-            runs.append(run_name)
+            runs.append(run)
 
         for tag in tags:
             all_tags.add(tag)
@@ -176,12 +177,13 @@ def __init__(
 
         if run_name in get_available_run_names():
             self._run_read()
-        elif workflow_name:
+        elif workflow_name and workflow_name in get_available_workflow_names():
             self.df_mode = df_mode
             self._workflow_read()
         else:
-            raise ValueError(
-                f"No run named {run_name} has been found and no workflow has been provided. Please reference an existing run or provide a workflow to create a new one."
+            self.__class__._instances.pop(run_name)
+            raise FileNotFoundError(
+                f"No run named {run_name} or workflow named {workflow_name} has been found. Please reference an existing run or workflow to create a new one."
             )
 
         self._initialized = True
@@ -212,12 +214,16 @@ def run_path(self) -> str:
     @auto_save
     def update_run_name(self, new_run_name: str) -> None:
         if self.run_name != new_run_name:
+            old_name = self.run_name
             self.disk_operator.update_run_name(new_run_name)
             self.update_modification_date()
             self._instances.pop(self.run_name, None)
             self._instances[new_run_name] = self
             self.run_name = new_run_name
 
+            self.__class__._instances[new_run_name] = self
+            self.__class__._instances.pop(old_name, None)
+
     @error_handling
     def metadata_read(self) -> dict:
         return self.disk_operator.read_metadata()

backend/protzilla/runner.py

@@ -53,7 +53,7 @@ def __init__(
             if run_name is not None and run_name.strip() is not None
             else f"runner_{random_string()}"
         )
-
+        print("PATH: ", RUNS_PATH, self.run_name)
         if os.path.exists(Path(f"{RUNS_PATH}/{self.run_name}")):
             self._overwrite_run_prompt()
             print("\n\n")

backend/tests/conftest.py

@@ -3,6 +3,7 @@
 import logging
 import time
 import uuid
+import tempfile
 from pathlib import Path
 from shutil import rmtree
 
@@ -11,11 +12,14 @@
 import pytest
 from PIL import Image
 
+from django.conf import settings
+from unittest.mock import patch
+
 from backend.protzilla.methods.importing import MaxQuantImport
 from backend.protzilla.run import Run
 
 from backend.protzilla.constants.paths import RUNS_PATH
-from backend.tests.paths import TEST_METADATA_PATH, TEST_MSDATA_PATH
+from backend.tests.paths import TEST_METADATA_PATH, TEST_MSDATA_PATH, TEST_TEMPLATE_PATH, TEST_RUNS_PATH, TEST_WORKFLOWS_PATH
 from backend.protzilla.utilities import random_string
 
 
@@ -27,21 +31,39 @@ def pytest_addoption(parser):
         help="If 'True', tests will open figures using the default renderer",
     )
 
+@pytest.fixture(scope="session",autouse=True)
+def setup_paths_and_cleanup():
+
+    TEST_RUNS_PATH.mkdir(parents=True, exist_ok=True)
+
+    with (
+        patch("backend.protzilla.constants.paths.RUNS_PATH", TEST_RUNS_PATH),
+        patch("backend.protzilla.runner.RUNS_PATH", TEST_RUNS_PATH),
+        patch("backend.protzilla.data_analysis.protein_graphs.RUNS_PATH", TEST_RUNS_PATH),
+        patch("backend.protzilla.constants.paths.WORKFLOWS_PATH", TEST_WORKFLOWS_PATH)
+    ):
+        yield
+
+    # After the test or fixture that uses this fixture is done, remove the directory
+    while TEST_RUNS_PATH.exists():
+        time.sleep(1)
+        rmtree(TEST_RUNS_PATH)
+
+
 
 @pytest.fixture(scope="function")
-def run_name_and_cleanup():
+def run_name():
     # Generate a unique run name
     run_name = f"test_run_{uuid.uuid4()}"
-    run_path = Path(RUNS_PATH) / run_name
 
     # Yield the run name to the test or fixture that uses this fixture
     yield run_name
 
-    # After the test or fixture that uses this fixture is done, remove the directory
-    while run_path.exists():
-        time.sleep(1)
-        rmtree(run_path)
-
+@pytest.fixture(scope="session")
+def static_run_name():
+    #provide a static run_name to use in multiple tests
+    static_run_name = "static_run_name"
+    yield static_run_name
 
 @pytest.fixture
 def maxquant_data_file():
@@ -53,20 +75,20 @@ def metadata_file():
 
 
 @pytest.fixture(scope="function")
-def run_standard(run_name_and_cleanup):
-    run_name = run_name_and_cleanup
+def run_standard(run_name):
+    run_name = run_name
     yield Run(run_name=run_name, workflow_name="standard", df_mode="memory")
 
 
 @pytest.fixture(scope="function")
-def run_empty(run_name_and_cleanup):
-    run_name = run_name_and_cleanup
+def run_empty(run_name):
+    run_name = run_name
     yield Run(run_name=run_name, workflow_name="test-run-empty", df_mode="memory")
 
 
 @pytest.fixture(scope="function")
-def run_imported(run_name_and_cleanup, maxquant_data_file):
-    run_name = run_name_and_cleanup
+def run_imported(run_name, maxquant_data_file):
+    run_name = run_name
     run = Run(run_name=run_name, workflow_name="test-run-empty", df_mode="memory")
     run.step_add(MaxQuantImport())
     run.current_form(
@@ -90,9 +112,6 @@ def show_figures(request):
 def tests_folder_name():
     name = f"tests_{random_string()}"
     yield name
-    while Path(f"{RUNS_PATH}/{name}").exists():
-        time.sleep(1)
-        rmtree(Path(f"{RUNS_PATH}/{name}"))
 
 
 @pytest.fixture
@@ -265,3 +284,11 @@ def open_graph_from_base64(encoded_string):
 @pytest.fixture
 def helpers():
     return Helpers
+
+@pytest.fixture(scope="session", autouse=True)
+def test_template_dir():
+    """
+    Adds the backend/tests/templates directory to Django's template DIRS during tests,
+    so that test-only templates like dummy index.html can be used.
+    """
+    settings.TEMPLATES[0]['DIRS'].insert(0, TEST_TEMPLATE_PATH)

backend/tests/main/test_url.py

@@ -0,0 +1,12 @@
+from django.test import TestCase
+from django.urls import reverse
+
+class FrontendRoutingTest(TestCase):
+
+    def test_get_csrf_token_url(self):
+        response = self.client.get(reverse('get_csrf_token'))
+        self.assertEqual(response.status_code, 200)
+
+    def test_random_route(self):
+        response = self.client.get('/some-random-route/')
+        self.assertTemplateUsed(response, 'index.html')