Fix: Ignore "Math superscript (^) and subscript (_) characters are not allowed in text mode" error for citation key (#11948) #12391

Satyamkumarnavneet · 2025-01-16T14:04:20Z

This pull request addresses the issue #11948 of false positive integrity check errors for citation keys containing superscript (^) and subscript (_) characters in text mode. Specifically:

Updated LatexIntegrityChecker#check to:
- Ignore the validation error TTEM03 for InternalField.KEY_FIELD.
Added test cases to ensure:
- Citation key fields containing ^ or _ are ignored during validation.
- Other fields (e.g., TITLE, AUTHOR, JOURNAL, BOOKTITLE, NOTE) are still checked for invalid LaTeX syntax.

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I own the copyright of the code submitted and I licence it under the MIT license
Change in CHANGELOG.md described in a way that is understandable for the average user (if change is visible to the user)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (for UI changes)
[/] Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
[/] Checked 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 to the documentation repository.

… key (JabRef#11948)

…ssue (JabRef#11948)

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We use Checkstyle to identify issues.
Please carefully follow the setup guide for the codestyle.
Afterwards, please run checkstyle locally and fix the issues.

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koppor · 2025-01-16T15:08:27Z

src/main/java/org/jabref/logic/integrity/LatexIntegrityChecker.java

+                    // Ignore checks for the citation key field
+                    .filter(field -> !(field.getKey().equals(InternalField.KEY_FIELD) && field.getValue().matches(".*[\\^_].*")))


No. Please take "nore error TTEM03" of the task description serious.

Hi @koppor, Thanks for the feedback! Could you share any suggestions on how to better address the TTEM03 handling?

koppor · 2025-01-16T15:09:00Z

src/test/java/org/jabref/logic/integrity/LatexIntegrityCheckerTest.java

+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.TITLE, "Title with ^ and _ characters"),
+                // Ensure invalid LaTeX syntax with special characters in other fields is detected
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.AUTHOR, "Author_Name"),
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.JOURNAL, "Journal_Name"),
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.BOOKTITLE, "Book^Title"),
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.NOTE, "Note_with_subscript_and_superscript^_")


OK, but you did not test for org.jabref.model.entry.field.InternalField#KEY_FIELD, where you changed the behavior.

Thanks for pointing that out! I've added a new test case for InternalField.KEY_FIELD, but it's currently failing.

I assume, it is not failing now?

src/test/java/org/jabref/logic/integrity/LatexIntegrityCheckerTest.java

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Your code currently does not meet JabRef's code guidelines.
We use OpenRewrite to ensure "modern" Java coding practices.
The issues found can be automatically fixed.
Please execute the gradle task rewriteRun, check the results, commit, and push.

You can check the detailed error output by navigating to your pull request, selecting the tab "Checks", section "Tests" (on the left), subsection "OpenRewrite".

Satyamkumarnavneet · 2025-01-17T12:15:37Z

Hi @koppor, I have addressed all feedback and made the necessary changes. Could you please review the updates at your convenience? Thank you!

koppor · 2025-02-03T13:19:14Z

src/main/java/org/jabref/logic/integrity/LatexIntegrityChecker.java

@@ -66,6 +65,9 @@ public List<IntegrityMessage> check(BibEntry entry) {
                    .flatMap(LatexIntegrityChecker::getUnescapedAmpersandsWithCount)
                    // Exclude all DOM building errors as this functionality is not used.
                    .filter(pair -> !pair.getValue().getErrorCode().getErrorGroup().equals(CoreErrorGroup.TDE))
+                    // Exclude TTEM03 error for citation key field
+                    .filter(pair -> !(pair.getValue().getErrorCode().equals(CoreErrorCode.TTEM03) && pair.getKey().equals(InternalField.KEY_FIELD)))
+                    // Exclude errors present in EXCLUDED_ERRORS set


Why this comment? This is really what is in the next line - normally one adds the why on top - or summarizes the next line. Please just remove line 70

Got it! Thanks for pointing that out! I’ll remove line 70.

koppor · 2025-02-03T13:19:44Z

src/test/java/org/jabref/logic/integrity/LatexIntegrityCheckerTest.java

+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.TITLE, "Title with ^ and _ characters"),
+                // Ensure invalid LaTeX syntax with special characters in other fields is detected
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.AUTHOR, "Author_Name"),
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.JOURNAL, "Journal_Name"),
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.BOOKTITLE, "Book^Title"),
+                Arguments.of(LatexIntegrityChecker.errorMessageFormatHelper(CoreErrorCode.TTEM03), StandardField.NOTE, "Note_with_subscript_and_superscript^_")


I assume, it is not failing now?

koppor · 2025-02-03T13:20:37Z

src/test/java/org/jabref/logic/integrity/LatexIntegrityCheckerTest.java

+    @MethodSource("provideCitationKeyInputs")
+    void citationKeyField(String expectedMessage, Field field, String value) {
+        entry.setField(field, value);
+        // Ensure TTEM03 error is not raised for citation key field


This comment has to move above Arguments.of("", InternalField.KEY_FIELD, "Corti_2009"), to explain the _ in the inputs. -- In this place, it does not make sense.

Yes, it's not failing now. It's working for all pre-existing tests as well as the newly added ones.

…atyamkumarnavneet/jabref into ignore-citation-key-validation

Satyamkumarnavneet · 2025-02-03T15:26:08Z

Hi @koppor, I've made the requested changes: removed the comment in LatexIntegrityChecker.java, moved the test comment, and confirmed TTEM03 no longer triggers for citation keys. All tests are passing. Let me know if everything looks good to you and we can proceed with the merge. Thanks!

Satyam Kumar Navneet added 2 commits January 16, 2025 19:16

Fix: Ignore superscript (^) and subscript (_) validation for citation…

55916ca

… key (JabRef#11948)

Changelog: Update with fix for superscript and subscript validation i…

1319e8a

…ssue (JabRef#11948)

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Ignore error "Math superscript (^) and subscript (_) characters are not allowed in text mode" #11948

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Satyamkumarnavneet marked this pull request as draft January 16, 2025 18:22

Fix: Address feedback for TTEM03 citation key validation

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Satyamkumarnavneet marked this pull request as ready for review January 17, 2025 12:15

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Merge branch 'main' into ignore-citation-key-validation

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Address feedback for TTEM03 citation key validation

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…atyamkumarnavneet/jabref into ignore-citation-key-validation

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Fix: Ignore "Math superscript (^) and subscript (_) characters are not allowed in text mode" error for citation key (#11948) #12391

Fix: Ignore "Math superscript (^) and subscript (_) characters are not allowed in text mode" error for citation key (#11948) #12391

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		// Ignore checks for the citation key field
		.filter(field -> !(field.getKey().equals(InternalField.KEY_FIELD) && field.getValue().matches(".[\\^_].")))

Fix: Ignore "Math superscript (^) and subscript (_) characters are not allowed in text mode" error for citation key (#11948) #12391

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Fix: Ignore "Math superscript (^) and subscript (_) characters are not allowed in text mode" error for citation key (#11948) #12391

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