Fix handling of DOIs

[koppor]

User description

Closes https://github.com/JabRef/jabref-issue-melting-pot/issues/1160

Steps to test

Use DOI cleanup for entries

Mandatory checks

• I own the copyright of the code submitted and I license it under the MIT license
• [/] I manually tested my changes in running JabRef (always required)
• I added JUnit tests for changes (if applicable)
• [/] I added screenshots in the PR description (if change is visible to the user)
• I described the change in CHANGELOG.md in a way that is understandable for the average user (if change is visible to the user)
• [/] I checked the user documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request updating file(s) in https://github.com/JabRef/user-documentation/tree/main/en.

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PR Type

Bug fix

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Description

• Refactored DOI cleanup logic to handle malformed percent-encoded characters gracefully

• Added error handling for URLDecoder to prevent crashes on invalid encoding

• Simplified field list initialization using List.of() instead of Arrays.asList()

• Improved code structure with functional programming patterns and AtomicBoolean tracking

• Added test cases for wrongly encoded DOI characters in various fields

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Diagram Walkthrough

flowchart LR
  A["DOI Field Processing"] --> B["URL Decode with Error Handling"]
  B --> C["Parse and Validate DOI"]
  C --> D["Clean Other Fields"]
  E["Other Fields Processing"] --> F["Extract DOI if Present"]
  F --> G["Set DOI Field if Empty"]
  G --> H["Remove DOI from Source Field"]
  I["ArXiv Processing"] --> J["Infer DOI from ArXiv ID"]
  J --> K["Set DOI if Not Exists"]
  B --> L["Graceful Fallback on Decode Error"]

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File Walkthrough

	Relevant files
Bug fix	DoiCleanup.java Refactor DOI cleanup with error handling                                  jablib/src/main/java/org/jabref/logic/cleanup/DoiCleanup.java Replaced Arrays.asList() with List.of() for FIELDS initialization Added try-catch block around URLDecoder to handle IllegalArgumentException gracefully Refactored DOI field processing using functional programming with ifPresent() and map() Introduced AtomicBoolean to track if valid DOI exists in DOI field Restructured logic to separate DOI field cleanup from other field processing Simplified ArXiv DOI inference to only execute when DOI field is empty Removed unused imports and improved code readability with better variable naming +58/-50
Tests	DoiCleanupTest.java Add tests for malformed percent-encoded DOIs                          jablib/src/test/java/org/jabref/logic/cleanup/DoiCleanupTest.java Changed @MethodSource annotation to use implicit method name matching instead of explicit string reference Renamed test data provider method from provideDoiForAllLowers() to changeDoi() to match test method name Added three new test cases for malformed percent-encoded characters Added test for invalid percent encoding in NOTE field that should remain unchanged Added test for valid percent-encoded DOI in NOTE field that should be moved to DOI field Added test for invalid percent encoding in DOI field that should remain unchanged +21/-3
Documentation	CHANGELOG.md Document DOI encoding fix in changelog                                      CHANGELOG.md Added entry documenting the fix for wrongly encoded DOI cleaning issue Entry references issue Remove %s in formatter descriptions #1160 (marked as TODO in the PR) +1/-0

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[qodo-free-for-open-source-projects]

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: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	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: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Silent error handling: The catch block at line 41-43 silently falls back to the original value without logging the IllegalArgumentException, making debugging difficult. Referred Code } catch (IllegalArgumentException e) { // If decoding fails, we keep the original value decodedDoiFieldValue = currentlyStoredDoi; Learn more about managing compliance generic rules or creating your own custom rules

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⚪ - Requires Further Human Verification
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[qodo-free-for-open-source-projects]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	Prevent data loss from redundant cleanup Wrap the DOI search loop in an if block to prevent redundant cleanup and potential data loss. This ensures the loop only runs if no valid DOI was found in the main DOI field. jablib/src/main/java/org/jabref/logic/cleanup/DoiCleanup.java [68-78] -for (Field field : FIELDS) { - entry.getField(field) - .flatMap(DOI::parse) // covers a full DOI only - .ifPresent(doi -> { - if (!validDoiExistsInDoiField.get()) { - Optional<FieldChange> change = entry.setField(StandardField.DOI, doi.asString()); - change.ifPresent(changes::add); - } - removeFieldValue(entry, field, changes); - }); +if (!validDoiExistsInDoiField.get()) { + for (Field field : FIELDS) { + entry.getField(field) + .flatMap(DOI::parse) // covers a full DOI only + .ifPresent(doi -> { + if (!validDoiExistsInDoiField.get()) { + Optional<FieldChange> change = entry.setField(StandardField.DOI, doi.asString()); + change.ifPresent(changes::add); + validDoiExistsInDoiField.set(true); + } + removeFieldValue(entry, field, changes); + }); + } } Apply / Chat Suggestion importance[1-10]: 8 __ Why: The suggestion correctly identifies a logic flaw where a redundant loop can cause unintended side effects and proposes a sound fix that makes the code more robust and correct by preventing multiple DOIs from being moved from different fields.	Medium
	Correct test case for malformed DOIs Correct a test case by changing the field from StandardField.NOTE to StandardField.DOI. This ensures the test accurately verifies the cleanup behavior for malformed percent-encoded characters in the DOI field. jablib/src/test/java/org/jabref/logic/cleanup/DoiCleanupTest.java [83-87] // cleanup of wrong percent encoded chars in DOI field Arguments.of(new BibEntry() - .withField(StandardField.NOTE, "10.18726/2018%7B%%5Ctextunderscore%7D3"), + .withField(StandardField.DOI, "10.18726/2018%7B%%5Ctextunderscore%7D3"), new BibEntry() - .withField(StandardField.NOTE, "10.18726/2018%7B%%5Ctextunderscore%7D3")); + .withField(StandardField.DOI, "10.18726/2018%7B%%5Ctextunderscore%7D3")); Apply / Chat Suggestion importance[1-10]: 7 __ Why: The suggestion correctly identifies a mismatch between the test case's description and its implementation, proposing a change that aligns the test with its intended purpose and improves test coverage for the DOI field.	Medium
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