🧪 Add mocked 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 +1,136 @@
+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

.gitignore

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

tests/test_pathwaycommons.py

@@ -0,0 +1,136 @@
+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

.gitignore

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

tests/test_pathwaycommons.py

@@ -0,0 +1,136 @@
+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

.gitignore

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

tests/test_pathwaycommons.py

@@ -0,0 +1,136 @@
+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

.gitignore

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

tests/test_pathwaycommons.py

@@ -0,0 +1,136 @@
+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

.gitignore

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

tests/test_pathwaycommons.py

@@ -0,0 +1,136 @@
+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

.gitignore

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

tests/test_pathwaycommons.py

@@ -0,0 +1,136 @@
+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

.gitignore

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

tests/test_pathwaycommons.py

@@ -0,0 +1,136 @@
+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