TaskExtractorConfig accepts optional predicates_path to split predica… #82
Conversation
…tes from main config_path (#42)
WalkthroughThe recent changes enhance the functionality of the codebase, particularly by improving the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant TaskExtractorConfig
participant YAMLLoader
User->>TaskExtractorConfig: load(config_path, predicates_path)
TaskExtractorConfig->>YAMLLoader: validate(predicates_path)
alt If predicates_path is valid
YAMLLoader-->>TaskExtractorConfig: load predicates from predicates_path
TaskExtractorConfig->>User: return TaskExtractorConfig with new predicates
else If predicates_path is invalid
TaskExtractorConfig->>User: raise error
end
TaskExtractorConfig->>YAMLLoader: load config from config_path
TaskExtractorConfig->>User: return TaskExtractorConfig
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Files selected for processing (1)
- src/aces/config.py (2 hunks)
Additional comments not posted (7)
src/aces/config.py (7)
811-811: Method signature update.The method signature has been updated to accept an additional optional parameter
predicates_path. This change enhances the method's flexibility by allowing the user to specify a separate path for predicates.
835-836: Check ifpredicates_pathis provided.The code correctly checks if
predicates_pathis provided before proceeding with further logic.
836-837: Convertpredicates_pathtoPathobject.The code correctly converts
predicates_pathto aPathobject if it is a string.
839-842: Check ifpredicates_pathexists and is a file.The code correctly checks if
predicates_pathexists and is a file. If not, it raises aFileNotFoundError.
844-850: Load predicates file and check file extension.The code correctly loads the predicates file if it has a
.yamlextension. If the extension is not.yaml, it raises aValueError.
852-860: Extract and validate predicates from the loaded file.The code extracts the
predicatesfrom the loaded file and removes thedescriptionkey if it exists. It also raises aValueErrorif there are unrecognized keys in the configuration file.
862-863: Default to extracting predicates from the main config file.If
predicates_pathis not provided, the code defaults to extractingpredicatesfrom the main configuration file.
* Make windows struct optional when loading config * Update spacing
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Actionable comments posted: 2
Outside diff range, codebase verification and nitpick comments (2)
src/aces/config.py (2)
868-870: Default handling of predicates whenpredicates_pathis not providedThe current tests in
tests/test_e2e.pydo not explicitly cover the scenario wherepredicates_pathis not provided. To ensure robust testing, please add a test case that verifies the default handling of predicates whenpredicates_pathis not set.
- Add a test case where
predicates_pathis not provided and verify the behavior.Analysis chain
Default handling of predicates when
predicates_pathis not providedThe default handling of predicates when
predicates_pathis not provided is consistent with the previous logic. Ensure that this path is also covered by tests.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify if the default handling of predicates when `predicates_path` is not provided is covered by tests. # Test: Search for test cases that cover the default logic. Expect: Test cases covering the default logic. rg --type python -A 5 'load\(.*config_path'Length of output: 76
Script:
#!/bin/bash # Description: Verify if the default handling of predicates when `predicates_path` is not provided is covered by tests. # Find all Python test files and search for test cases that cover the default logic. fd --extension py --glob '*test*' | xargs rg 'load\(.*config_path'Length of output: 68
Script:
#!/bin/bash # Description: Broaden the search to verify if the default handling of predicates when `predicates_path` is not provided is covered by tests. # Find all Python test files and search for references to `predicates` and `predicates_path`. fd --extension py --glob '*test*' | xargs rg 'predicates|predicates_path'Length of output: 399
Script:
#!/bin/bash # Description: Extract relevant portions of `tests/test_e2e.py` to analyze the test cases involving `predicates`. # Display lines around the references to `predicates` in `tests/test_e2e.py`. rg 'predicates|predicates_path' -A 10 -B 10 tests/test_e2e.pyLength of output: 2196
840-867: Tests missing forpredicates_pathhandlingThe new logic for handling the
predicates_pathparameter is not covered by tests. Please add test cases to ensure this functionality is properly validated.
- No references to
predicates_pathwere found in any test files.Analysis chain
Handling of
predicates_pathparameterThe handling of the
predicates_pathparameter includes checking if the path is valid and loading the predicates from the specified file. The error handling is appropriate, raising exceptions for missing files or incorrect file types. Ensure that this new logic is covered by tests.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify if the new logic for handling `predicates_path` is covered by tests. # Test: Search for test cases that cover the new logic. Expect: Test cases covering the new logic. rg --type python -A 5 'load\(.*predicates_path'Length of output: 80
Script:
#!/bin/bash # Description: Verify if the new logic for handling `predicates_path` is covered by tests. # Test: Search for test cases that cover the new logic. Expect: Test cases covering the new logic. rg --type-add 'py:*.py' -t py -A 5 'predicates_path'Length of output: 1690
Script:
#!/bin/bash # Description: Verify if the new logic for handling `predicates_path` is covered by tests. # Search for references to `predicates_path` within typical test directories. rg --type-add 'py:*.py' -t py -A 5 'predicates_path' tests testLength of output: 108
Script:
#!/bin/bash # Description: Verify if the new logic for handling `predicates_path` is covered by tests. # Locate all Python test files and search for references to `predicates_path`. fd --type f --extension py | xargs rg 'predicates_path'Length of output: 831
Tools
GitHub Check: codecov/patch
[warning] 841-842: src/aces/config.py#L841-L842
Added lines #L841 - L842 were not covered by tests
[warning] 844-845: src/aces/config.py#L844-L845
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[warning] 849-851: src/aces/config.py#L849-L851
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[warning] 857-858: src/aces/config.py#L857-L858
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[warning] 861-861: src/aces/config.py#L861
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[warning] 863-864: src/aces/config.py#L863-L864
Added lines #L863 - L864 were not covered by tests
Review details
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Files ignored due to path filters (1)
sample_data/sample_data.csvis excluded by!**/*.csv
Files selected for processing (6)
- sample_configs/inhospital_mortality.yaml (1 hunks)
- src/aces/config.py (8 hunks)
- src/aces/constraints.py (1 hunks)
- src/aces/predicates.py (17 hunks)
- src/aces/query.py (2 hunks)
- tests/test_e2e.py (8 hunks)
Additional context used
GitHub Check: codecov/patch
src/aces/query.py
[warning] 65-66: src/aces/query.py#L65-L66
Added lines #L65 - L66 were not covered by testssrc/aces/constraints.py
[warning] 152-152: src/aces/constraints.py#L152
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[warning] 501-501: src/aces/predicates.py#L501
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[warning] 514-514: src/aces/predicates.py#L514
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[warning] 841-842: src/aces/config.py#L841-L842
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[warning] 844-845: src/aces/config.py#L844-L845
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[warning] 853-853: src/aces/config.py#L853
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[warning] 857-858: src/aces/config.py#L857-L858
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[warning] 861-861: src/aces/config.py#L861
Added line #L861 was not covered by tests
[warning] 863-864: src/aces/config.py#L863-L864
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[warning] 898-899: src/aces/config.py#L898-L899
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Additional comments not posted (21)
sample_configs/inhospital_mortality.yaml (1)
12-14: LGTM!The addition of
patient_demographicswith themaledemographic is correct and logically integrates within thepredicatessection.src/aces/query.py (2)
12-12: LGTM!The import
check_static_variablesfrom theconstraintsmodule is necessary for the new logic introduced in thequeryfunction.
60-66: LGTM!The new logic for static variable filtering in the
queryfunction is correct and logically integrates within the existing structure.Tools
GitHub Check: codecov/patch
[warning] 65-66: src/aces/query.py#L65-L66
Added lines #L65 - L66 were not covered by testssrc/aces/constraints.py (1)
103-167: LGTM!The new function
check_static_variablescorrectly filters a DataFrame based on static patient demographics and logically integrates within the existing structure.Tools
GitHub Check: codecov/patch
[warning] 152-152: src/aces/constraints.py#L152
Added line #L152 was not covered by teststests/test_e2e.py (6)
19-19: LGTM!The constant
EVENT_INDEX_TYPEis correctly set topl.UInt64.
21-21: LGTM!The constant
LAST_EVENT_INDEX_COLUMNis correctly set to"_LAST_EVENT_INDEX".
26-74: LGTM!The input data format changes, including the
maleandfemalecolumns, are consistent with the enhanced data schema to better capture patient demographics.
97-100: LGTM!The addition of the
patient_demographicsfield and themalepredicate enhances the task configuration to handle demographic data.
133-135: LGTM!The expected output changes are consistent with the updated input data and task configuration.
299-303: LGTM!The changes in the data type casting logic to accommodate the new
EVENT_INDEX_TYPEensure that the event indices are handled correctly.src/aces/predicates.py (8)
38-50: LGTM!The function
direct_load_plain_predicateshas been correctly updated to include additional columns:is_male,is_female, andbrown_eyes.
203-203: LGTM!The data selection logic in
direct_load_plain_predicatescorrectly includes the new columns.
295-305: LGTM!The function
generate_plain_predicates_from_medshas been correctly updated to accommodate a new column formalein the predicate configuration.
319-319: LGTM!The data loading logic in
generate_plain_predicates_from_medscorrectly handles the new columns.
341-341: LGTM!The function
process_esgpt_datahas been correctly updated to include a new parametersubjects_dfand enhance the data processing logic.
421-424: LGTM!The logic for handling static predicates in
process_esgpt_datacorrectly integrates the new parametersubjects_df.
536-554: LGTM!The method
get_predicates_dfhas been correctly updated to handle the newpredicates_pathparameter and enhance the data processing logic.
Line range hint
700-732:
LGTM!The logic for generating special predicate columns in
get_predicates_dfcorrectly integrates the new changes.src/aces/config.py (3)
36-36: Addition ofstaticattribute inPlainPredicateConfigThe addition of the
staticattribute to thePlainPredicateConfigclass is clear and consistent with the class's purpose. Ensure that this attribute is properly utilized in the rest of the codebase.
183-183: Addition ofstaticattribute inDerivedPredicateConfigThe addition of the
staticattribute to theDerivedPredicateConfigclass is clear and consistent with the class's purpose. Ensure that this attribute is properly utilized in the rest of the codebase.
816-816: Update method signature to includepredicates_pathThe method signature has been updated to include an optional
predicates_pathparameter. This change is clear and consistent with the PR objectives.
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Files selected for processing (2)
- src/aces/config.py (9 hunks)
- tests/test_check_static_variables.py (1 hunks)
Files skipped from review as they are similar to previous changes (1)
- src/aces/config.py
Additional comments not posted (4)
tests/test_check_static_variables.py (4)
1-7: Imports look good.The imports include necessary standard libraries, third-party libraries, and a local module.
9-29: Test data setup looks comprehensive.The sample DataFrame includes various columns and data types, covering different scenarios.
31-47: Test cases look well-designed.The test cases cover filtering based on a demographic column and checking for a ValueError when a column is missing.
Consider adding tests for additional edge cases, such as:
- Empty DataFrame.
- DataFrame with missing values in the demographic columns.
- Multiple demographic columns.
54-55: Main block is appropriate.The main block correctly runs the tests using
pytest.
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (1)
src/aces/config.py (1)
1021-1021: Update the docstring to reflect the new parameter.The docstring should include the
predicates_pathparameter to maintain clarity and completeness.""" + Args: + config_path: The path to which a configuration object will be read from in YAML form. + predicates_path: The path to an optional predicates configuration file in YAML form. + Raises:
Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (1)
- src/aces/config.py (14 hunks)
Additional context used
GitHub Check: codecov/patch
src/aces/config.py
[warning] 1104-1105: src/aces/config.py#L1104-L1105
Added lines #L1104 - L1105 were not covered by tests
Additional comments not posted (3)
src/aces/config.py (3)
36-36: LGTM!The addition of the
staticattribute is well-integrated.
210-210: LGTM!The addition of the
staticattribute is well-integrated.
1045-1075: LGTM! But verify the function usage in the codebase.The code changes are approved.
However, ensure that all function calls to
TaskExtractorConfig.loadmatch the new signature.Verification successful
Function usage matches the new signature
The function
TaskExtractorConfig.loadhas been verified to match the new signature with an optionalpredicates_pathparameter. The usage insrc/aces/__main__.pycorrectly calls this function without the optional parameter, which is acceptable.
src/aces/config.py: Verified function signature.src/aces/__main__.py: Verified function usage.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `TaskExtractorConfig.load` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type python -A 5 $'TaskExtractorConfig.load'Length of output: 79
Script:
#!/bin/bash # Description: Verify all function calls to `TaskExtractorConfig.load` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type py -A 5 $'TaskExtractorConfig.load'Length of output: 2928
Script:
#!/bin/bash # Verify the function signature in src/aces/config.py rg --type py -A 10 'def load' src/aces/config.py # Verify the usage in src/aces/__main__.py rg --type py -A 5 'TaskExtractorConfig.load' src/aces/__main__.pyLength of output: 860
…tes from main config_path (#42)
Summary by CodeRabbit
New Features
Bug Fixes