fix tests

lib/DirectoryWatcher.py

@@ -20,8 +20,6 @@ def on_created(self, event):
         asyncio.run(self.async_callback(event.src_path))
 
     def start_watching(self):
-        if not os.path.exists(self.directory):
-            os.mkdir(self.directory)
         # Define a thread target function
         def run_observer():
             self.observer.schedule(

main.py

@@ -44,7 +44,11 @@ async def newFileCreated(file_path: str):
 
 @app.on_event("startup")
 async def startEvent():
-    dirWatcher.start_watching()
+    if not os.path.exists(DIRECTORY_TO_WATCH):
+        os.mkdir(DIRECTORY_TO_WATCH)
+
+    if os.path.exists(DIRECTORY_TO_WATCH):
+        dirWatcher.start_watching()
 
 
 @app.on_event("shutdown")

tests/unit/test_DirectoryWatcher.py

@@ -12,10 +12,10 @@ async def test_on_created():
     # Mock asyncio.run to avoid the RuntimeError
     with patch('asyncio.run'):
         # Simulate an on_created event
-        event_mock = MagicMock(is_directory=False, src_path='/path/to/file.txt')
+        event_mock = MagicMock(is_directory=False, src_path='/path/to/watch/file.txt')
         watcher.on_created(event_mock)
     # Ensure that async_callback is called with the correct parameters
-    async_callback_mock.assert_called_once_with('/path/to/file.txt')
+    async_callback_mock.assert_called_once_with('/path/to/watch/file.txt')
 
 @pytest.mark.asyncio
 async def test_start_and_stop_watching():

tests/unit/test_EntityLinker.py

@@ -32,7 +32,7 @@ async def mock_insert(db_path, table, entity_name):
             ]
 
             # Call the entitylinkerFunc
-            entLinks = await entitylinkerFunc(entMentions)
+            entLinks = await entitylinkerFunc(entMentions, db_path="DB_PATH")
             # Check the results
             assert len(entLinks) == 2
 
@@ -66,7 +66,7 @@ async def mock_insert(db_path, table, entity_name):
             ]
 
             # Call the entitylinkerFunc
-            entLinks = await entitylinkerFunc(entMentions)
+            entLinks = await entitylinkerFunc(entMentions, db_path="DB_PATH")
             # Check the results
             assert len(entLinks) == 1
 
@@ -99,7 +99,7 @@ async def mock_insert(db_path, table, entity_name):
             ]
 
             # Call the entitylinkerFunc
-            entLinks = await entitylinkerFunc(entMentions)
+            entLinks = await entitylinkerFunc(entMentions, db_path="DB_PATH")
             # Check the results
             assert len(entLinks) == 1
 
@@ -167,7 +167,7 @@ async def mock_insert(db_path, table, queryInformation):
             }
 
             # Call the entitylinkerFunc
-            entLinks = await entitylinkerFunc(TestingDataset["test"])
+            entLinks = await entitylinkerFunc(TestingDataset["test"], db_path="DB_PATH")
             for index, link in enumerate(entLinks):
                 assert link.name == TestingDataset["GoldStandardNames"][index]
                 assert link.iri == TestingDataset["GoldStandardIRIs"][index]

tests/unit/test_GetSpacyData.py

@@ -15,7 +15,7 @@ def test_GetText_fileExists():
         testFile.write("This is a testfile")
 
     testText = GetSpacyData.GetText("test_article_file.txt")
-    assert testText == "This is a testfile"
+    assert testText == "This is a testfile. "
 
 
 # Test that GetText returns an error if the file does not exist