feat: add rfam_searcher #177
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Summary of ChangesHello @ChenZiHong-Gavin, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed! This pull request introduces a new Highlights
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Code Review
This pull request introduces a new RfamSearcher class to interact with the Rfam and RNAcentral APIs. The implementation is well-structured, featuring retry logic, helper methods, and a unified search interface. My review focuses on improving code clarity, addressing a potential performance issue, suggesting a more robust resource management pattern, and removing unused code. Overall, this is a solid addition.
| # RNA molecule type mapping | ||
| RNA_TYPES = { | ||
| "Gene": "gene", | ||
| "snRNA": "snrna", | ||
| "snoRNA": "snorna", | ||
| "rRNA": "rrna", | ||
| "tRNA": "trna", | ||
| "miRNA": "mirna", | ||
| "ribozyme": "ribozyme", | ||
| "riboswitch": "riboswitch", | ||
| } |
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The RNA_TYPES dictionary is defined but appears to be unused within the class. To improve code clarity and remove dead code, it's recommended to remove it.
| rna_type = ( | ||
| types[-1] | ||
| if types[-1] != "CD-box" | ||
| else types[-2] | ||
| if len(types) > 1 | ||
| else types[0] | ||
| ) |
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The nested ternary expression for determining rna_type is difficult to read and maintain. Refactoring this into a more explicit if/elif/else block would improve readability.
| rna_type = ( | |
| types[-1] | |
| if types[-1] != "CD-box" | |
| else types[-2] | |
| if len(types) > 1 | |
| else types[0] | |
| ) | |
| if types[-1] != "CD-box": | |
| rna_type = types[-1] | |
| elif len(types) > 1: | |
| rna_type = types[-2] | |
| else: | |
| # Fallback to the first type if it's the only one (even if 'CD-box') | |
| rna_type = types[0] | |
| for entry in result["entries"]: | ||
| accession = entry.get("fields", {}).get("accession", [None])[0] | ||
| if accession: | ||
| family = self.get_by_accession(accession) | ||
| if family: | ||
| families.append(family) |
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This loop makes a separate API call to get_by_accession for each search result. If the search returns many items (e.g., limit=10), this will result in 11 API calls (1 search + 10 get_by_accession), which can be slow and may lead to hitting API rate limits. This is a form of the N+1 query problem.
Consider returning a summarized version of the families using only the information from the initial EBI search to improve performance. If full details are necessary, this behavior should be documented in the method's docstring to make users aware of the performance implications.
| def __del__(self): | ||
| """Cleanup session.""" | ||
| if hasattr(self, "session"): | ||
| self.session.close() |
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Using __del__ for resource cleanup (like closing a requests.Session) is not reliable in Python, as its execution is not guaranteed. A more robust and idiomatic approach is to implement the class as a context manager. This ensures that resources are cleaned up properly when the object is used within a with statement.
You can achieve this by adding __enter__ and __exit__ methods and removing __del__.
Example:
def __enter__(self):
return self
def __exit__(self, exc_type, exc_val, exc_tb):
self.session.close()This would allow for usage like with RfamSearcher() as searcher: ....
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