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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 significantly expands the data retrieval capabilities of the 'graphgen' project by introducing a dedicated InterPro searcher. This new component allows for comprehensive querying of protein domain architectures, Gene Ontology (GO) terms, and pathway annotations. By supporting both sequence-based analysis and direct UniProt ID lookups, it provides a flexible and powerful tool for integrating rich biological context into the system's graph generation processes. Highlights
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Code Review
This pull request introduces a new searcher for the InterPro database. A critical security vulnerability, Server-Side Request Forgery (SSRF) / Path Traversal, was identified in the search_by_uniprot_id method due to unvalidated input in URL construction. Additionally, the InterProSearch class could benefit from improved flexibility and robustness, specifically by making polling parameters configurable and enhancing the resilience of search methods to network issues.
| url = f"https://www.ebi.ac.uk/interpro/api/entry/protein/uniprot/{accession}/" | ||
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| response = requests.get(url, timeout=self.api_timeout) |
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The search_by_uniprot_id method is vulnerable to Server-Side Request Forgery (SSRF) / Path Traversal because it constructs a URL using the accession parameter without proper sanitization or validation. An attacker could manipulate the request sent to the EBI InterPro API. Additionally, this method lacks proper error handling and retry mechanisms, making it less resilient to transient network failures.
# Ensure accession is safe for URL construction
import urllib.parse
safe_accession = urllib.parse.quote(accession.strip().upper(), safe='')
# Query InterPro REST API for UniProt entry
url = f"https://www.ebi.ac.uk/interpro/api/entry/protein/uniprot/{safe_accession}/"| def __init__( | ||
| self, | ||
| email: str = "graphgen@example.com", | ||
| api_timeout: int = 30, | ||
| ): | ||
| """ | ||
| Initialize the InterPro Search client. | ||
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| Args: | ||
| email (str): Email address for EBI API requests. | ||
| api_timeout (int): Request timeout in seconds. | ||
| """ | ||
| self.base_url = "https://www.ebi.ac.uk/Tools/services/rest/iprscan5" | ||
| self.email = email | ||
| self.api_timeout = api_timeout | ||
| self.poll_interval = 5 # Fixed interval between status checks | ||
| self.max_polls = 120 # Maximum polling attempts (10 minutes with 5s interval) |
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The __init__ method can be improved in a couple of ways for better flexibility and adherence to external API policies:
- Configurable Polling: The polling interval and maximum number of polls are currently hardcoded. Making these configurable would allow users to adjust them for sequences that might require longer analysis times.
- Default Email: EBI services recommend providing a valid email address. Using a default placeholder is not ideal. It's good practice to warn the user if the default email is being used to encourage compliance with the service's usage policy.
I've suggested an updated __init__ method that addresses both points.
def __init__(
self,
email: str = "graphgen@example.com",
api_timeout: int = 30,
poll_interval: int = 5,
max_polls: int = 120,
):
"""
Initialize the InterPro Search client.
Args:
email (str): Email address for EBI API requests.
api_timeout (int): Request timeout in seconds.
poll_interval (int): Interval in seconds between status checks.
max_polls (int): Maximum number of polling attempts.
"""
self.base_url = "https://www.ebi.ac.uk/Tools/services/rest/iprscan5"
self.email = email
if self.email == "graphgen@example.com":
logger.warning(
"Using default email for InterProSearch. It is recommended to provide a valid email address for EBI services."
)
self.api_timeout = api_timeout
self.poll_interval = poll_interval
self.max_polls = max_polls1 participant
No description provided.