Remove unreachable else block in get_mod function

[Copilot]

User description

Addresses review feedback on #59 about unreachable code in get_mod. The else block was dead code since diann_mod_accession is guaranteed non-None when reached (function exits earlier if modification not found).

Changes

• Removed redundant elif diann_mod_accession is not None check
• Removed unreachable else block with duplicate error handling
• Added *.parquet to .gitignore to prevent test artifacts from being committed

Before

if "TMT" in diann_mod_name or ...:
    logging.error(...)
    exit(1)
elif diann_mod_accession is not None:  # Always true here
    site = ...
    return diann_mod_accession, site
else:  # Unreachable
    logging.error(...)
    exit(1)

After

if "TMT" in diann_mod_name or ...:
    logging.error(...)
    exit(1)

site = ...
return diann_mod_accession, site

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PR Type

Bug fix

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Description

• Removed unreachable else block in get_mod function

• Simplified control flow by eliminating redundant conditional checks

• Code is guaranteed to reach site processing after initial validation

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Diagram Walkthrough

flowchart LR
  A["Check unsupported modifications"] -->|Found| B["Log error and exit"]
  A -->|Not found| C["Extract and process sites"]
  C -->|No sites| D["Log error and exit"]
  C -->|Sites found| E["Normalize site notation"]
  E --> F["Return modification accession and site"]

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File Walkthrough

	Relevant files
Bug fix	dianncfg.py Remove unreachable else block in get_mod                                  quantmsutils/diann/dianncfg.py Removed unreachable elif diann_mod_accession is not None condition Removed dead else block with duplicate error handling Simplified control flow by making site processing unconditional after validation Preserved all functional logic while improving code clarity +22/-28

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[qodo-code-review]

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
🟢	No security concerns identified No security vulnerabilities detected by AI analysis. Human verification advised for critical code.
Ticket Compliance
⚪	🎫 No ticket provided Create ticket/issue
Codebase Duplication Compliance
⚪	Codebase context is not defined Follow the guide to enable codebase context checks.
Custom Compliance
🟢	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
⚪	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: Process termination: The new code still uses exit(1) on errors without clear audit context (e.g., user/action identifiers), which may limit comprehensive audit trails depending on surrounding logging. Referred Code logging.error( "quantms DIA-NN workflow only supports LFQ now! Unsupported modifications: " + mod ) exit(1) sites = re.findall(pattern, " ".join(mod.split(" ")[1:])) if not sites: logging.error( f"No site specification found in modification string: {mod}" ) exit(1) site = sites[0] Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Hard exits used: The function logs and calls exit(1) instead of raising exceptions or returning errors, which may hinder graceful degradation and upstream handling. Referred Code logging.error( "quantms DIA-NN workflow only supports LFQ now! Unsupported modifications: " + mod ) exit(1) sites = re.findall(pattern, " ".join(mod.split(" ")[1:])) if not sites: logging.error( f"No site specification found in modification string: {mod}" ) exit(1) site = sites[0] Learn more about managing compliance generic rules or creating your own custom rules

Compliance status legend

🟢 - Fully Compliant
🟡 - Partial Compliant
🔴 - Not Compliant
⚪ - Requires Further Human Verification
🏷️ - Compliance label

[qodo-code-review]

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