From 1dd1205a8fc52fa2d99e504be5d512a662653e82 Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Thu, 9 Apr 2026 18:03:23 +0000
Subject: [PATCH 1/3] Add test for name2uniprot HTTPError handling

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 tests/test_pathwaycommons.py | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 tests/test_pathwaycommons.py

diff --git a/tests/test_pathwaycommons.py b/tests/test_pathwaycommons.py
new file mode 100644
index 00000000..6501fb93
--- /dev/null
+++ b/tests/test_pathwaycommons.py
@@ -0,0 +1,22 @@
+import urllib.request
+import urllib.error
+from unittest.mock import patch
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+def test_name2uniprot_organism_httperror():
+    with patch('urllib.request.urlopen') as mock_urlopen:
+        # Create an HTTPError instance
+        # HTTPError requires url, code, msg, hdrs, fp
+        mock_urlopen.side_effect = urllib.error.HTTPError(
+            url="http://www.uniprot.org/uniprot/?",
+            code=500,
+            msg="Internal Server Error",
+            hdrs={},
+            fp=None
+        )
+
+        # Call the function with an organism to hit the target try/except block
+        result = name2uniprot("TestGene", ["http://identifiers.org/taxonomy/9606"])
+
+        # The function should catch the HTTPError and return None
+        assert result is None

From ba5f06f442659161fbda07c52e0312606a74554b Mon Sep 17 00:00:00 2001
From: "google-labs-jules[bot]"
 <161369871+google-labs-jules[bot]@users.noreply.github.com>
Date: Thu, 9 Apr 2026 21:15:44 +0000
Subject: [PATCH 2/3] Add test for name2uniprot HTTPError handling

Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
---
 tests/test_pathwaycommons.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/test_pathwaycommons.py b/tests/test_pathwaycommons.py
index 6501fb93..ae7d3bfd 100644
--- a/tests/test_pathwaycommons.py
+++ b/tests/test_pathwaycommons.py
@@ -3,8 +3,9 @@
 from unittest.mock import patch
 from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
 
+
 def test_name2uniprot_organism_httperror():
-    with patch('urllib.request.urlopen') as mock_urlopen:
+    with patch("urllib.request.urlopen") as mock_urlopen:
         # Create an HTTPError instance
         # HTTPError requires url, code, msg, hdrs, fp
         mock_urlopen.side_effect = urllib.error.HTTPError(
@@ -12,7 +13,7 @@ def test_name2uniprot_organism_httperror():
             code=500,
             msg="Internal Server Error",
             hdrs={},
-            fp=None
+            fp=None,
         )
 
         # Call the function with an organism to hit the target try/except block

From 1d9296427b7e4886dbd895e32777e02e4e6a919c Mon Sep 17 00:00:00 2001
From: akutuva21 <akutuva22@gmail.com>
Date: Mon, 13 Apr 2026 10:16:25 -0400
Subject: [PATCH 3/3] chore: PR #60 remove forbidden artifacts and run black

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

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__/