Refactor _extract_class_hierarchy Method in ChEBIOverXPartial for Data preprocessing
We can refactor of the _extract_class_hierarchy method in the subclass to leverage the existing functionality from the superclass. This change will improve code reuse and maintainability.
Current Implementation
The current implementation in the subclass duplicates the logic for extracting the class hierarchy from the ChEBI ontology and then filters the graph to include only the subclasses of the top class ID.
We can simplify the subclass method by calling the superclass method to extract the full class hierarchy and then filter the graph to include only the descendants of self.top_class_id. Since the graph is already transitively closed, we can use g.successors directly instead of nx.descendants, which simplifies the filtering process. This approach ensures that we reuse the existing extraction logic and focus only on the specific filtering needed for the subclass.
Updated Method
Here's the proposed updated method for the subclass:
def _extract_class_hierarchy(self, chebi_path: str) -> nx.DiGraph:
"""
Extracts a subset of ChEBI based on subclasses of the top class ID.
This method calls the superclass method to extract the full class hierarchy,
then extracts the subgraph containing only the descendants of the top class ID.
Args:
chebi_path (str): The file path to the ChEBI ontology file.
Returns:
nx.DiGraph: The extracted class hierarchy as a directed graph, limited to the
descendants of the top class ID.
"""
g = super()._extract_class_hierarchy(chebi_path)
g = g.subgraph(list(g.successors(self.top_class_id)) + [self.top_class_id])
return g
Please review the proposed change and let me know if you have any feedback or concerns.
Refactor
_extract_class_hierarchyMethod inChEBIOverXPartialfor Data preprocessingWe can refactor of the
_extract_class_hierarchymethod in the subclass to leverage the existing functionality from the superclass. This change will improve code reuse and maintainability.Current Implementation
The current implementation in the subclass duplicates the logic for extracting the class hierarchy from the ChEBI ontology and then filters the graph to include only the subclasses of the top class ID.
Method Implementation in
_ChEBIDataExtractorMethod Implementation in
ChEBIOverXPartialProposed Change
We can simplify the subclass method by calling the superclass method to extract the full class hierarchy and then filter the graph to include only the descendants of
self.top_class_id. Since the graph is already transitively closed, we can useg.successorsdirectly instead ofnx.descendants, which simplifies the filtering process. This approach ensures that we reuse the existing extraction logic and focus only on the specific filtering needed for the subclass.Updated Method
Here's the proposed updated method for the subclass:
Please review the proposed change and let me know if you have any feedback or concerns.