Enhance JSON Comparison and Logging in BokehSnapshotExtension.py
#61
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…ging - Improved error handling for JSON extraction and comparison in matches method. - Enhanced logging with more informative messages for easier debugging. - Adjusted list comparison logic for better efficiency and clarity. - Added warnings for missing keys and unequal values during JSON comparison. - Ensured consistent logging levels (warning for mismatched data, error for critical issues).
WalkthroughThe pull request enhances the Changes
Sequence Diagram(s)sequenceDiagram
participant U as User
participant B as BokehSnapshotExtension
participant L as Logger
U->>B: matches(serialized_data, snapshot_data)
Note over B: Begin matching process
B->>B: extract_bokeh_json(serialized_data)
alt JSON extraction successful
B->>B: Compare extracted JSON with snapshot_data
B->>U: Return comparison result (bool)
else Extraction fails (Exception)
B->>L: Log error message
B->>U: Return False
end
sequenceDiagram
participant B as BokehSnapshotExtension
participant L as Logger
B->>B: extract_bokeh_json(html)
alt Valid JSON parsed
B->>B: Return Dict
else Parsing error occurs
B->>L: Log error message
B->>B: Raise JSONDecodeError
end
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Actionable comments posted: 0
🧹 Nitpick comments (5)
pyopenms_viz/testing/BokehSnapshotExtension.py (5)
6-6: Remove unused importListThe
Listtype is imported fromtypingbut never used in the code. Remove this unused import to keep the imports clean.-from typing import Any, Dict, List +from typing import Any, Dict🧰 Tools
🪛 Ruff (0.8.2)
6-6:
typing.Listimported but unusedRemove unused import:
typing.List(F401)
73-88: Good improvement in error handling for extract_bokeh_jsonThe addition of proper error handling when
bokehJsonis None improves the robustness of the code. One suggestion would be to add more specific information in the error message to help with debugging.- logger.error("Bokeh JSON extraction failed.") - raise json.JSONDecodeError("Bokeh JSON extraction failed.", html, 0) + logger.error("Bokeh JSON extraction failed, bokehJson is None.") + raise json.JSONDecodeError("Bokeh JSON extraction failed: parser could not find a script tag with JSON content.", html, 0)
91-136: Improved compare_json method with better logging and list comparisonThe enhanced logic for list comparison and addition of warning logs for mismatches is excellent. However, there's a small optimization that can be made based on the static analysis hint:
- if isinstance(json1, dict) and isinstance(json2, dict): - for key in json1.keys(): + if isinstance(json1, dict) and isinstance(json2, dict): + for key in json1:Also, note that the list comparison could become inefficient for large lists due to the nested loops. Consider adding a comment about the time complexity or optimizing the algorithm if performance becomes an issue with large datasets.
🧰 Tools
🪛 Ruff (0.8.2)
103-103: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
137-156: Good documentation and error handling for read operationAdding proper docstring, return type, and error handling for the file read operation is a great improvement. One small issue: the docstring says the return can be None, but the type annotation says it's just
str. You might want to update the type annotation to includeNoneas a possible return type:- ) -> str: + ) -> str | None:
159-177: Good documentation and error handling for write operationAdding proper docstring and error handling for file writing operations is an excellent improvement for robustness. However, I notice there's no return value or re-raising of the exception when the file write fails. Consider whether you should propagate the error or at least return a boolean indicating success/failure.
except OSError as e: logger.error(f"Failed to write snapshot file: {e}") + return False + return True
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pyopenms_viz/testing/BokehSnapshotExtension.py(2 hunks)
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🪛 Ruff (0.8.2)
pyopenms_viz/testing/BokehSnapshotExtension.py
6-6: typing.List imported but unused
Remove unused import: typing.List
(F401)
103-103: Use key in dict instead of key in dict.keys()
Remove .keys()
(SIM118)
🔇 Additional comments (4)
pyopenms_viz/testing/BokehSnapshotExtension.py (4)
16-18: Good addition of logging configurationAdding structured logging is a good improvement for better observability and debugging. Consider setting the logging level from an environment variable to make it configurable without code changes.
23-24: Good documentation improvementAdding clear comments to explain class attributes makes the code more maintainable and easier to understand.
48-72: Excellent error handling and type annotations improvementsThe addition of type annotations, proper error handling with try-except, and structured logging greatly improves the robustness of the
matchesmethod. This will make debugging easier when JSON extraction fails.
178-187: Clearer docstring for serialize methodThe updated docstring for the
serializemethod is clearer about what the method does - it returns an HTML string representation of the Bokeh plot.
|
@jcharkow Please review and let me know if any modifications are required. |
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Great job so far, changes make everything much easier to read! However, it seems that the tests are now failing. I think that it might be because you are modifying the logic of the code but I am not sure so please investigate. Also just a few minor comments above.
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Actionable comments posted: 0
🧹 Nitpick comments (2)
pyopenms_viz/testing/BokehSnapshotExtension.py (2)
6-6: Remove unused import:ListThe
Listimport is not being used in the code. Consider removing it to keep the imports clean.-from typing import Any, Dict, List +from typing import Any, Dict🧰 Tools
🪛 Ruff (0.8.2)
6-6:
typing.Listimported but unusedRemove unused import:
typing.List(F401)
91-111: Usekey in dictinstead ofkey in dict.keys()For better performance and readability, consider changing line 103 to use
key in json2instead ofkey in json2.keys().- for key in json1.keys(): - if key not in json2: + for key in json1: + if key not in json2:🧰 Tools
🪛 Ruff (0.8.2)
103-103: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
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Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
pyopenms_viz/testing/BokehSnapshotExtension.py(2 hunks)
🧰 Additional context used
🪛 Ruff (0.8.2)
pyopenms_viz/testing/BokehSnapshotExtension.py
6-6: typing.List imported but unused
Remove unused import: typing.List
(F401)
103-103: Use key in dict instead of key in dict.keys()
Remove .keys()
(SIM118)
🔇 Additional comments (10)
pyopenms_viz/testing/BokehSnapshotExtension.py (10)
16-18: Good addition of structured loggingAdding structured logging is a great improvement. It provides better visibility into the application's behavior and will make debugging easier.
48-58: Type annotations improve code clarityThe addition of type hints for parameters and return values enhances code clarity and makes it easier for IDEs to provide assistance during development.
59-71: Good addition of structured error handlingAdding a try-except block to catch specific exceptions (
JSONDecodeError,IndexError,KeyError) and logging the errors is a great improvement for robustness. This will help identify issues more quickly during testing.
73-88: Improved error handling for JSON extractionThe enhanced error handling for when
bokehJsonisNoneis a valuable addition. Logging the error and raising a specific exception with a clear message will make debugging much easier.
115-130: Improved list comparison algorithm with better loggingThe refactored list comparison algorithm is more structured and provides better diagnostics through logging. Using a set to track matched elements is an effective approach.
132-136: Enhanced value comparison with better loggingAdding specific warning logs for value mismatches will make it easier to identify exactly what's different between snapshots.
140-157: Keep this line as reference for how to edit this functionThe function now has a comprehensive docstring and proper error handling with logging, which are excellent improvements. Note that there was a previous comment to "Keep this line as reference for how to edit this function" at line 142, so please ensure these changes align with the intended reference.
163-177: Well-documented error handling for file operationsAdding the docstring and try-except block for handling file operation errors is a good practice. This will make the code more robust and easier to maintain.
181-188: Improved docstring clarityThe updated docstring provides a clearer explanation of what the method does and what it returns.
107-108:❓ Verification inconclusive
Verify if 'root_ids' should always be ignored
The code now ignores both "id" and "root_ids" keys during comparison. Please verify that ignoring "root_ids" is intentional and doesn't affect the test results. If this is a new addition, it might be modifying the comparison logic.
🏁 Script executed:
#!/bin/bash # Check if tests that rely on JSON comparison might be affected by ignoring 'root_ids' echo "Searching for tests using BokehSnapshotExtension..." grep -r "BokehSnapshotExtension" --include="*test*.py" .Length of output: 297
Attention: Verify "root_ids" Ignoring Behavior
After checking the tests (see usage in
./test/conftest.py), there’s no immediate evidence that ignoring"root_ids"in the snapshot comparison is causing test failures. However, please confirm that excluding"root_ids"—along with"id"—is intentional and aligns with the desired snapshot logic. If this behavior is by design to mitigate dynamic key changes, consider adding a comment in the code to explain its purpose.
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Hi @jcharkow , i have done the required changes, please check and update me if any changes permits. |
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Seems that some of the changes requested were dismissed without being addressed. Please add the lines back that were deleted or explain why it is necessary to delete these lines. Waiting for tests to see if they pass.
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Actionable comments posted: 0
🧹 Nitpick comments (2)
pyopenms_viz/testing/BokehSnapshotExtension.py (2)
6-6: Unused import:Listis imported but never used.The
Listtype is imported but not used anywhere in the code. It's good practice to remove unused imports to keep the codebase clean.-from typing import Any, Dict, List +from typing import Any, Dict🧰 Tools
🪛 Ruff (0.8.2)
6-6:
typing.Listimported but unusedRemove unused import:
typing.List(F401)
103-103: Style improvement suggestion for dict key checking.Consider simplifying the key presence check.
- for key in json1.keys(): - if key not in json2: + for key in json1: + if key not in json2:🧰 Tools
🪛 Ruff (0.8.2)
103-103: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
pyopenms_viz/testing/BokehSnapshotExtension.py(2 hunks)
🧰 Additional context used
🪛 Ruff (0.8.2)
pyopenms_viz/testing/BokehSnapshotExtension.py
6-6: typing.List imported but unused
Remove unused import: typing.List
(F401)
103-103: Use key in dict instead of key in dict.keys()
Remove .keys()
(SIM118)
🔇 Additional comments (17)
pyopenms_viz/testing/BokehSnapshotExtension.py (17)
9-9: Good addition of structured logging.Adding logging is a great improvement as it helps with debugging and traceability. Setting up a module-level logger with the
__name__pattern follows best practices.Also applies to: 16-18
23-24: Improved property documentation.Enhancing the documentation of class properties adds clarity to the code. The code now clearly indicates the purpose of
recordingandbokehJsonproperties.
43-43: Improved class docstring.The updated docstring provides better context on the functionality of
BokehSnapshotExtension.
48-48: Enhanced method signature with type annotations and return documentation.Adding proper type annotations and documenting the return value improves the code's readability and helps with static type checking.
Also applies to: 56-58
59-71: Good error handling implementation.The try-except block added to the
matchesmethod effectively handles potential exceptions (JSONDecodeError, IndexError, KeyError) during JSON extraction and comparison. Logging the error provides useful debugging information.
73-73: Improved method signature and docstring.The return type annotation was updated from
jsontoDictwhich is more accurate. The docstring now clearly indicates the parameters and return types.Also applies to: 78-82
85-87: Enhanced error handling for JSON extraction.Adding explicit error handling and logging when
bokehJsonis None improves robustness and debuggability of the code.
91-101: Improved method signature and documentation.The
compare_jsonmethod now has proper type annotations and a more detailed docstring that explains its recursive behavior.
105-111: Enhanced error reporting with logging.Replacing print statements with proper logging improves the system's observability. The warning level is appropriate for non-critical issues like mismatched keys.
116-117: Improved error reporting.Adding logging for list length mismatches enhances debuggability.
119-130: Optimized JSON list comparison.The new implementation of list comparison using a set to track matched elements is more efficient. This prevents the possibility of matching the same element multiple times.
134-136: Enhanced value comparison with logging.Adding logging for mismatched values provides better visibility into comparison failures.
142-152: Added docstring to inherited method.Adding a docstring to the inherited
_read_snapshot_data_from_locationmethod improves code documentation. This has been correctly implemented based on the previous review comments.
155-158: Improved error handling for file operations.Adding proper error handling and logging for file read operations improves robustness and helps with debugging.
165-170: Added docstring to inherited method.Adding a docstring to the inherited
_write_snapshot_collectionmethod improves code documentation.
171-179: Enhanced error handling for file write operations.Adding a try-except block with proper error logging for file write operations improves robustness.
183-183: Improved method documentation.The updated docstring for the
serializemethod now clearly indicates that it returns an HTML string representation of the Bokeh plot.Also applies to: 189-190
2 participants
This PR includes several improvements and fixes for the
BokehSnapshotExtensionclass. The following changes have been made:Improved Error Handling:
bokehJsonisNone).matchesmethod to catchJSONDecodeError,IndexError, andKeyErrorexceptions, providing a more robust error handling mechanism.Enhanced Logging:
logger.errorandlogger.warningto provide better visibility during the snapshot matching process.logger.warningfor mismatched keys/values andlogger.errorfor failures like JSON extraction issues.Optimized JSON Comparison:
compare_jsonmethod to ensure better performance and readability.Code Clarity and Readability:
Additional Fixes:
_read_snapshot_data_from_locationand_write_snapshot_collectionmethods to handle potential I/O errors more gracefully.Related Issue:
BokehSnapshotExtension.py#59Summary by CodeRabbit
Refactor
Documentation