🧪 Tests for name2uniprot in pathwaycommons

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

tests/test_pathwaycommons.py

@@ -0,0 +1,88 @@
+import pytest
+from unittest.mock import patch, MagicMock
+from urllib.error import HTTPError
+import urllib.request
+from bionetgen.atomizer.utils.pathwaycommons import name2uniprot
+
+
+def test_name2uniprot_with_organism():
+ """Test name2uniprot when organism is provided and response is successful."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF_HUMAN\tP01133\nEGF_MOUSE\tP01132\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ # Use an organism that ends in '9606' to trigger organism query building
+ result = name2uniprot("EGF", ["taxonomy/9606"])
+
+ # It should parse matching symbols based on `nameStr` ignoring case.
+ # Since 'EGF' is in 'EGF_HUMAN' and 'EGF_MOUSE', both should be returned.
+ assert result == ["P01133", "P01132"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_fallback_no_organism():
+ """Test name2uniprot fallback when initial organism query returns no results."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response_1 = MagicMock()
+ # Empty string response or missing to trigger fallback
+ mock_response_1.read.return_value = b"".decode("utf-8")
+
+ mock_response_2 = MagicMock()
+ # Mocking the fallback response
+ mock_response_2.read.return_value = (
+ b"entry name\tid\nEGF2_HUMAN\tP01133\n".decode("utf-8")
+ )
+
+ # urlopen will return mock_response_1 then mock_response_2 on successive calls
+ mock_urlopen.side_effect = [mock_response_1, mock_response_2]
+
+ result = name2uniprot("EGF2", ["taxonomy/9606"])
+
+ assert result == ["P01133"]
+ assert mock_urlopen.call_count == 2
+
+
+def test_name2uniprot_no_organism():
+ """Test name2uniprot when no organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_response = MagicMock()
+ mock_response.read.return_value = (
+ b"entry name\tid\nEGF3_HUMAN\tP01133\n".decode("utf-8")
+ )
+ mock_urlopen.return_value = mock_response
+
+ result = name2uniprot("EGF3", None)
+
+ assert result == ["P01133"]
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_with_organism():
+ """Test name2uniprot handling of HTTPError when organism is provided."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF4", ["taxonomy/9606"])
+
+ # It should catch the error, log it, and return None
+ assert result is None
+ mock_urlopen.assert_called_once()
+
+
+def test_name2uniprot_http_error_no_organism():
+ """Test name2uniprot handling of HTTPError when no organism is provided (fallback)."""
+ with patch("urllib.request.urlopen") as mock_urlopen:
+ # Side effect raises error for the query
+ mock_urlopen.side_effect = HTTPError(
+ url="", code=500, msg="Internal Server Error", hdrs={}, fp=None
+ )
+
+ result = name2uniprot("EGF5", None)
+
+ assert result is None
+ mock_urlopen.assert_called_once()