diff --git a/.gitignore b/.gitignore
index 39aa9026..f9bf9c80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/
diff --git a/tests/test_pathwaycommons.py b/tests/test_pathwaycommons.py
new file mode 100644
index 00000000..cba3d26a
--- /dev/null
+++ b/tests/test_pathwaycommons.py
@@ -0,0 +1,136 @@
+import pytest
+from unittest.mock import patch, MagicMock
+import urllib.error
+import sys
+import os
+import importlib.util
+
+
+class DummyUtil:
+    @staticmethod
+    def logMess(*args, **kwargs):
+        pass
+
+
+# We use a pytest fixture to safely inject mock modules into sys.modules
+# only for the duration of this test module.
+@pytest.fixture(scope="module", autouse=True)
+def mock_dependencies():
+    with patch.dict("sys.modules", {"bionetgen.atomizer.utils.util": DummyUtil()}):
+        spec = importlib.util.spec_from_file_location(
+            "bionetgen.atomizer.utils.pathwaycommons",
+            os.path.abspath("bionetgen/atomizer/utils/pathwaycommons.py"),
+        )
+        pathwaycommons = importlib.util.module_from_spec(spec)
+
+        with patch.dict(
+            "sys.modules", {"bionetgen.atomizer.utils.pathwaycommons": pathwaycommons}
+        ):
+            spec.loader.exec_module(pathwaycommons)
+
+            # Make it accessible to the module via a global or by yielding it
+            yield pathwaycommons
+
+
+# Because of memoization, we need to bypass it or clear cache between tests.
+@pytest.fixture(autouse=True)
+def clear_memoize_cache(mock_dependencies):
+    if hasattr(mock_dependencies.name2uniprot, "cache"):
+        mock_dependencies.name2uniprot.cache.clear()
+    yield
+
+
+def test_name2uniprot_with_organism(mock_dependencies):
+    with patch("urllib.request.urlopen") as mock_urlopen:
+        mock_response = MagicMock()
+        mock_response.read.return_value = (
+            "Entry name\tEntry\nEGFR_HUMAN\tP00533\nOther_HUMAN\tQ12345"
+        )
+        mock_urlopen.return_value = mock_response
+
+        # Call with organism
+        result = mock_dependencies.name2uniprot("EGFR", organism=["NCBI:9606"])
+
+        assert result == ["P00533"]
+
+        mock_urlopen.assert_called_once()
+        args, kwargs = mock_urlopen.call_args
+        assert "organism%3ANCBI%3A9606" in kwargs["data"].decode("utf-8")
+
+
+def test_name2uniprot_without_organism(mock_dependencies):
+    with patch("urllib.request.urlopen") as mock_urlopen:
+        mock_response = MagicMock()
+        mock_response.read.return_value = "Entry name\tEntry\nEGFR_MOUSE\tQ01279\n"
+        mock_urlopen.return_value = mock_response
+
+        # Call without organism
+        result = mock_dependencies.name2uniprot("EGFR", organism=None)
+
+        assert result == ["Q01279"]
+
+        mock_urlopen.assert_called_once()
+        args, kwargs = mock_urlopen.call_args
+        assert "organism:" not in kwargs["data"].decode("utf-8")
+
+
+def test_name2uniprot_fallback(mock_dependencies):
+    with patch("urllib.request.urlopen") as mock_urlopen:
+        mock_response_empty = MagicMock()
+        mock_response_empty.read.return_value = ""
+
+        mock_response_valid = MagicMock()
+        mock_response_valid.read.return_value = "Entry name\tEntry\nEGFR_RAT\tO00111\n"
+
+        mock_urlopen.side_effect = [mock_response_empty, mock_response_valid]
+
+        result = mock_dependencies.name2uniprot("EGFR", organism=["NCBI:9606"])
+
+        assert result == ["O00111"]
+        assert mock_urlopen.call_count == 2
+
+        args1, kwargs1 = mock_urlopen.call_args_list[0]
+        assert "organism%3ANCBI%3A9606" in kwargs1["data"].decode("utf-8")
+
+        args2, kwargs2 = mock_urlopen.call_args_list[1]
+        assert "organism:" not in kwargs2["data"].decode("utf-8")
+
+
+def test_name2uniprot_http_error_first_call(mock_dependencies):
+    with patch("urllib.request.urlopen") as mock_urlopen:
+        mock_urlopen.side_effect = urllib.error.HTTPError(
+            url="http://www.uniprot.org/uniprot/?",
+            code=500,
+            msg="Internal Server Error",
+            hdrs={},
+            fp=None,
+        )
+
+        with patch.object(mock_dependencies, "logMess") as mock_log:
+            result = mock_dependencies.name2uniprot("EGFR", organism=["NCBI:9606"])
+
+            assert result is None
+            mock_log.assert_called_once_with(
+                "ERROR:MSC03", "A connection could not be established to uniprot"
+            )
+
+
+def test_name2uniprot_http_error_second_call(mock_dependencies):
+    with patch("urllib.request.urlopen") as mock_urlopen:
+        mock_response_empty = MagicMock()
+        mock_response_empty.read.return_value = ""
+
+        mock_urlopen.side_effect = [
+            mock_response_empty,
+            urllib.error.HTTPError(
+                url="http://www.uniprot.org/uniprot/?",
+                code=500,
+                msg="Internal Server Error",
+                hdrs={},
+                fp=None,
+            ),
+        ]
+
+        result = mock_dependencies.name2uniprot("EGFR", organism=["NCBI:9606"])
+
+        assert result is None