Fix/citation refresh button by Syimyk43 · Pull Request #15363 · JabRef/jabref

Syimyk43 · 2026-03-18T08:21:46Z

Related issues and pull requests

PR Description

Improved the refresh button behavior in the Citation Relations tab.
Before, clicking refresh always refetched from the remote unconditionally.
Now it checks the cache state first:
if there was an error it retries immediately,
if the data was fetched recently it asks the user for confirmation,
if the data is old enough it refetches normally.

Steps to test

Open JabRef and load a library with an entry that has a DOI
Click the "Citations" tab in the entry editor
Wait for citations to load
Immediately click the refresh button -> a confirmation dialog should appear
Click "No" -> nothing happens
Click refresh again and click "Yes" -> citations are refetched

Checklist

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 added a screenshot in the PR description showing a library with a single entry with me as author and as title the issue number

I described the change in CHANGELOG.md in a way that can be understood by the average user (if change is visible to the user)
[/] I checked the user documentation for up to dateness and submitted a pull request to our user documentation repository

qodo-free-for-open-source-projects · 2026-03-18T08:22:21Z

Review Summary by Qodo

Improve citation refresh button and fix DOI case sensitivity

✨ Enhancement 🐞 Bug fix

Walkthroughs

Description

• Improved citation refresh button with smart caching logic
  - Retries immediately on error state
  - Requests confirmation if data fetched recently
  - Refetches normally if data is old enough
• Fixed case-insensitive DOI comparison in duplicate detection
• Added public methods to expose cache state checking
• Enhanced test coverage with new duplicate detection scenarios

Diagram

flowchart LR
  A["Refresh Button Clicked"] --> B{"Check Cache State"}
  B -->|Error Found| C["Retry Immediately"]
  B -->|Recently Fetched| D["Ask User Confirmation"]
  D -->|User Confirms| E["Refetch Data"]
  D -->|User Declines| F["Cancel"]
  B -->|Data Old| E
  C --> E
  E --> G["Update Citations"]
  G["Update Citations"] --> H["Display Results"]
  
  I["DOI Comparison"] --> J{"Case Insensitive?"}
  J -->|Yes| K["Match Found"]
  J -->|No| L["No Match"]

File Changes

1. jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java ✨ Enhancement +31/-2

Implement smart refresh button with cache awareness

• Replaced direct searchForRelations calls with new handleRefresh method
• Added handleRefresh method implementing smart cache-aware refresh logic
• Checks for error state and retries immediately if found
• Checks if data is updatable and prompts user confirmation if recently fetched
• Proceeds with normal refetch if data is old enough

jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java

2. jablib/src/main/java/org/jabref/logic/citation/SearchCitationsRelationsService.java ✨ Enhancement +8/-0

Expose cache state checking methods
• Added isReferencesUpdatable public method to check if references need updating
• Added isCitationsUpdatable public method to check if citations need updating
• Both methods delegate to relationsRepository for cache state checking
jablib/src/main/java/org/jabref/logic/citation/SearchCitationsRelationsService.java

3. jablib/src/main/java/org/jabref/logic/database/DuplicateCheck.java 🐞 Bug fix +9/-1

Fix case-insensitive DOI duplicate detection

• Modified haveSameIdentifier method to perform case-insensitive DOI comparison
• Added special handling for StandardField.DOI using equalsIgnoreCase
• Other identifier fields continue to use case-sensitive comparison
• Fixes issue where DOIs differing only in letter casing were not recognized as duplicates

jablib/src/main/java/org/jabref/logic/database/DuplicateCheck.java

View more (2)

4. jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java 🧪 Tests +249/-232

Add case-insensitive DOI duplicate detection tests

• Reformatted existing test code with consistent indentation
• Added twoEntriesWithSameDoiButDifferentCasingAreDuplicates test
• Added twoEntriesWithSameDoiButDifferentCasingAndDifferentTypesAreDuplicates test
• New tests verify case-insensitive DOI matching works correctly

jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java

5. CHANGELOG.md 📝 Documentation +2/-0

Document citation refresh and DOI comparison improvements

• Added entry describing improved refresh button behavior in Citation Relations tab
• Added entry documenting fix for case-insensitive DOI comparison in duplicate detection
• Both entries reference their respective GitHub issues

CHANGELOG.md

qodo-free-for-open-source-projects · 2026-03-18T08:22:22Z

Code Review by Qodo

🐞 Bugs (1) 📘 Rule violations (3) 📎 Requirement gaps (0)

1. setField() used in DOI tests 📘 Rule violation ✓ Correctness

Description

New tests mutate BibEntry using setField, contrary to the preferred withField style. This
reduces consistency with JabRef’s functional/withers pattern.

Code

jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[R405-416]

+        simpleArticle.setField(StandardField.DOI, "10.1016/j.is.2004.02.002");
+        unrelatedArticle.setField(StandardField.DOI, "10.1016/J.IS.2004.02.002");
+
+        assertTrue(duplicateChecker.isDuplicate(simpleArticle, unrelatedArticle, BibDatabaseMode.BIBTEX));
+    }
+
+    @Test
+    void twoEntriesWithSameDoiButDifferentCasingAndDifferentTypesAreDuplicates() {
+        simpleArticle.setField(StandardField.DOI, "10.1016/j.is.2004.02.002");
+        unrelatedArticle.setField(StandardField.DOI, "10.1016/J.IS.2004.02.002");
+        unrelatedArticle.setType(StandardEntryType.Misc);
+

Evidence
PR Compliance ID 19 requires using withField instead of setField when creating/modifying
BibEntry instances; the newly added tests set DOIs via setField.
AGENTS.md
jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[405-416]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
New tests use `setField` to modify `BibEntry` instances, but JabRef prefers `withField`.

## Issue Context
The project encourages immutable/functional patterns and consistent test/code style.

## Fix Focus Areas
- jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[405-418]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

2. Localized error retry broken 🐞 Bug ✓ Correctness

Description

CitationRelationsTab.handleRefresh detects an error state by checking whether the placeholder label
text starts with the localized token "Error", but the actual localized error sentences may not start
with that token (e.g., zh_CN), so errors are not recognized and refresh won’t reliably retry
immediately after a failure. Additionally, the DOI lookup failure path sets placeholders with
hardcoded "Error ", which will never match non-English Localization.lang("Error") prefixes.

Code

jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[R999-1005]

+        boolean hasError = citationComponents.listView().getPlaceholder() instanceof Label label
+                && label.getText().startsWith(Localization.lang("Error"));
+
+        if (hasError) {
+            searchForRelations(citationComponents, otherCitationComponents, true);
+            return;
+        }

Evidence
The refresh handler uses a string-prefix heuristic based on Localization.lang("Error"). However, the
fetch failure placeholder is a fully localized sentence ("Error while fetching …"), and in zh_CN
that sentence does not begin with the translation of "Error" ("错误"), so the prefix check returns
false and the code does not take the immediate-retry path. Separately, the DOI lookup failure path
uses a hardcoded English "Error " prefix, which also won’t match Localization.lang("Error") in
non-English locales.
jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[995-1005]
jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[847-858]
jablib/src/main/resources/l10n/JabRef_zh_CN.properties[240-243]
jablib/src/main/resources/l10n/JabRef_zh_CN.properties[1698-1701]
jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[787-811]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
`CitationRelationsTab.handleRefresh` decides whether to “retry immediately on error” by checking if the list placeholder is a `Label` whose text starts with `Localization.lang(&quot;Error&quot;)`. This is not reliable across locales (some translations of the full error sentence don’t start with the localized “Error” token) and also fails for the DOI lookup failure path, which sets placeholders to a hardcoded English prefix (`&quot;Error &quot; + ex.getMessage()`).

## Issue Context
The UI already sets error placeholders in `executeSearch(...).onFailure(...)` using fully localized sentences. The refresh logic should not depend on the *rendered* (localized) text to detect error state.

## Fix approach (one of these)
1) **Explicit state**: add a boolean/enum fetch state to `CitationComponents` or maintain a `Map&lt;CitationComponents, FetchState&gt;` in the tab; set it to ERROR on failures and OK on success. `handleRefresh` should consult that state.

2) **Stable marker on placeholder node**: when creating the error placeholder `Label`, set a stable marker such as `placeholder.setId(&quot;citation-relations-error&quot;)` or a style class. Then `handleRefresh` checks for that marker instead of string prefixes.

Also ensure the DOI lookup failure uses `Localization.lang(...)` and the same error marker.

## Fix Focus Areas
- jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[787-811]
- jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[847-858]
- jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[995-1005]

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3. Formatting-only changes in DuplicateCheckTest 📘 Rule violation ✓ Correctness

Description

Large portions of DuplicateCheckTest were reindented without any behavioral change, increasing
diff noise and review effort. This violates the requirement to avoid unrelated reformatting.

Code

jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[R30-34]

    private static BibEntry getSimpleArticle() {
        return new BibEntry(StandardEntryType.Article)
-                .withField(StandardField.AUTHOR, "Single Author")
-                .withField(StandardField.TITLE, "A serious paper about something")
-                .withField(StandardField.YEAR, "2017");
+            .withField(StandardField.AUTHOR, "Single Author")
+            .withField(StandardField.TITLE, "A serious paper about something")
+            .withField(StandardField.YEAR, "2017");

Evidence
PR Compliance ID 2 forbids unrelated/formatting-only churn; the shown hunk changes only
indentation/alignment for the same chained calls.
AGENTS.md
jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[30-34]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
`DuplicateCheckTest` includes broad indentation-only changes that are unrelated to the behavioral changes in this PR, creating review noise.

## Issue Context
The compliance checklist requires minimal diffs and avoiding unrelated reformatting.

## Fix Focus Areas
- jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[30-34]
- jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[103-344]
- jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[423-452]
- jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[457-552]
- jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[559-629]

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4. handleRefresh() behavior untested 📘 Rule violation ⛯ Reliability

Description

The refresh-button behavior in CitationRelationsTab was changed (error retry, confirmation on
recent fetch, refetch otherwise) without accompanying automated test coverage. This risks
regressions in the new decision logic.

Code

jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[R995-1022]

+    private void handleRefresh(CitationComponents citationComponents, CitationComponents otherCitationComponents) {
+        BibEntry entry = citationComponents.entry();
+        boolean isCites = citationComponents.searchType() == CitationFetcher.SearchType.CITES;
+
+        boolean hasError = citationComponents.listView().getPlaceholder() instanceof Label label
+                && label.getText().startsWith(Localization.lang("Error"));
+
+        if (hasError) {
+            searchForRelations(citationComponents, otherCitationComponents, true);
+            return;
+        }
+
+        boolean isUpdatable = isCites
+                              ? searchCitationsRelationsService.isReferencesUpdatable(entry)
+                              : searchCitationsRelationsService.isCitationsUpdatable(entry);
+
+        if (!isUpdatable) {
+            boolean confirmed = dialogService.showConfirmationDialogAndWait(
+                    Localization.lang("Refetch citations"),
+                    Localization.lang("The citations were fetched recently. Are you sure you want to refetch?")
+            );
+            if (!confirmed) {
+                return;
+            }
+        }
+
+        searchForRelations(citationComponents, otherCitationComponents, true);
+    }

Evidence
PR Compliance ID 15 requires updating/adding tests for behavior changes, and PR Compliance ID 16
requires test updates when org.jabref.logic changes; this PR adds new refresh decision logic and
new logic-service methods without any visible corresponding tests.
AGENTS.md
AGENTS.md
jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[995-1022]
jablib/src/main/java/org/jabref/logic/citation/SearchCitationsRelationsService.java[150-156]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
Refresh-button behavior was changed, but there are no accompanying automated tests verifying the new branches (retry on error, confirmation on recent fetch, normal refetch otherwise).

## Issue Context
This PR adds new decision logic in the GUI layer and introduces new logic-service methods; compliance requires updating tests for behavior changes.

## Fix Focus Areas
- jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[470-474]
- jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[995-1022]
- jablib/src/main/java/org/jabref/logic/citation/SearchCitationsRelationsService.java[150-156]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

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qodo-free-for-open-source-projects · 2026-03-18T08:27:19Z

+        simpleArticle.setField(StandardField.DOI, "10.1016/j.is.2004.02.002");
+        unrelatedArticle.setField(StandardField.DOI, "10.1016/J.IS.2004.02.002");
+
+        assertTrue(duplicateChecker.isDuplicate(simpleArticle, unrelatedArticle, BibDatabaseMode.BIBTEX));
+    }
+
+    @Test
+    void twoEntriesWithSameDoiButDifferentCasingAndDifferentTypesAreDuplicates() {
+        simpleArticle.setField(StandardField.DOI, "10.1016/j.is.2004.02.002");
+        unrelatedArticle.setField(StandardField.DOI, "10.1016/J.IS.2004.02.002");
+        unrelatedArticle.setType(StandardEntryType.Misc);
+


1. setfield() used in doi tests 📘 Rule violation ✓ Correctness

New tests mutate BibEntry using setField, contrary to the preferred withField style. This reduces consistency with JabRef’s functional/withers pattern.

Agent Prompt

## Issue description New tests use `setField` to modify `BibEntry` instances, but JabRef prefers `withField`. ## Issue Context The project encourages immutable/functional patterns and consistent test/code style. ## Fix Focus Areas - jablib/src/test/java/org/jabref/logic/database/DuplicateCheckTest.java[405-418]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

qodo-free-for-open-source-projects · 2026-03-18T08:27:19Z

+        boolean hasError = citationComponents.listView().getPlaceholder() instanceof Label label
+                && label.getText().startsWith(Localization.lang("Error"));
+
+        if (hasError) {
+            searchForRelations(citationComponents, otherCitationComponents, true);
+            return;
+        }


2. Localized error retry broken 🐞 Bug ✓ Correctness

CitationRelationsTab.handleRefresh detects an error state by checking whether the placeholder label text starts with the localized token "Error", but the actual localized error sentences may not start with that token (e.g., zh_CN), so errors are not recognized and refresh won’t reliably retry immediately after a failure. Additionally, the DOI lookup failure path sets placeholders with hardcoded "Error ", which will never match non-English Localization.lang("Error") prefixes.

Agent Prompt

## Issue description `CitationRelationsTab.handleRefresh` decides whether to “retry immediately on error” by checking if the list placeholder is a `Label` whose text starts with `Localization.lang("Error")`. This is not reliable across locales (some translations of the full error sentence don’t start with the localized “Error” token) and also fails for the DOI lookup failure path, which sets placeholders to a hardcoded English prefix (`"Error " + ex.getMessage()`). ## Issue Context The UI already sets error placeholders in `executeSearch(...).onFailure(...)` using fully localized sentences. The refresh logic should not depend on the *rendered* (localized) text to detect error state. ## Fix approach (one of these) 1) **Explicit state**: add a boolean/enum fetch state to `CitationComponents` or maintain a `Map<CitationComponents, FetchState>` in the tab; set it to ERROR on failures and OK on success. `handleRefresh` should consult that state. 2) **Stable marker on placeholder node**: when creating the error placeholder `Label`, set a stable marker such as `placeholder.setId("citation-relations-error")` or a style class. Then `handleRefresh` checks for that marker instead of string prefixes. Also ensure the DOI lookup failure uses `Localization.lang(...)` and the same error marker. ## Fix Focus Areas - jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[787-811] - jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[847-858] - jabgui/src/main/java/org/jabref/gui/entryeditor/citationrelationtab/CitationRelationsTab.java[995-1005]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

- Ask user before refetching if data was fetched recently - Retry immediately if last fetch resulted in an error - Refetch normally if data is old enough (TTL expired) Fixes JabRef#12247

calixtus · 2026-03-19T06:39:57Z

 - We enabled drag and drop of Windows shortcut (`.lnk`) files to open libraries. [#15036](https://github.com/JabRef/jabref/issues/15036)
 - We refined the "Select files to import" page in "Search for unlinked local files" dialog to give the users the choice of linking the file to a related entry or import it to a new entry. [#13689](https://github.com/JabRef/jabref/issues/13689)
 - The "Make/Sync bibliography" button in OO/LO panel now refreshes citations before generating bibliographies. [#14387](https://github.com/JabRef/jabref/issues/14387)
+- Improved refresh button in Citation Relations tab: asks for confirmation if data was fetched recently, retries immediately on error, and refetches normally if data is old. [#12247](https://github.com/JabRef/jabref/issues/12247)


Too much information.

Suggested change

- Improved refresh button in Citation Relations tab: asks for confirmation if data was fetched recently, retries immediately on error, and refetches normally if data is old. [#12247](https://github.com/JabRef/jabref/issues/12247)

- Improved responsiveness and user interface of refresh button in Citation Relations tab. [#12247](https://github.com/JabRef/jabref/issues/12247)

calixtus · 2026-03-19T06:46:05Z

+
+    private void handleRefresh(CitationComponents citationComponents, CitationComponents otherCitationComponents) {
+        BibEntry entry = citationComponents.entry();
+        boolean isCites = citationComponents.searchType() == CitationFetcher.SearchType.CITES;


Wouldnt it be easier to just put this into the arguments of the method?

eg.

refreshCitingButton.setOnMouseClicked(_ -> handleRefresh(citingComponents, citedByComponents, refreshCitedByButton.setOnMouseClicked(_ -> handleRefresh(citedByComponents, citingComponents, CitationFetcher.SearchType.CITED_BY));

Can you expand? The current code reads: if mouse is clicked on the left, a new handler is installed on the right?

Maybe, you mean putting CitationFetcher.SearchType.CITED_BY as parameter and keep the parameter order? However, this is not the style of this component ^^

Maybe i misread the code. Was a quick interpretation by looking at CitationFetcher.SearchTypes enum providing only two alternatives CITES and CITED_BY and the method being called by the mentioned event triggers.

testlens-app · 2026-03-25T22:28:04Z

✅ All tests passed ✅

🏷️ Commit: a0d40d3
▶️ Tests: 10203 executed
⚪️ Checks: 52/52 completed

Learn more about TestLens at testlens.app.

Syimyk43 · 2026-03-25T22:48:51Z

@calixtus @koppor I addressed the missing localization keys and shortened the CHANGELOG entry as suggested. All checks are passing. Ready for review.

Syimyk43 · 2026-03-27T20:30:13Z

@calixtus This is ready for review when you have a moment!

* Improve refresh button behavior in Citation Relations tab - Ask user before refetching if data was fetched recently - Retry immediately if last fetch resulted in an error - Refetch normally if data is old enough (TTL expired) Fixes JabRef#12247 * Update CHANGELOG for JabRef#12247 * Add missing localization keys and shorten CHANGELOG entry

github-actions Bot added status: changes-required Pull requests that are not yet complete good third issue component: fetcher labels Mar 18, 2026

qodo-free-for-open-source-projects Bot reviewed Mar 18, 2026

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Syimyk43 force-pushed the fix/citation-refresh-button branch from 6ec4b39 to be4c490 Compare March 18, 2026 08:45

Syimyk43 added 2 commits March 18, 2026 03:48

Improve refresh button behavior in Citation Relations tab

c5c626b

- Ask user before refetching if data was fetched recently - Retry immediately if last fetch resulted in an error - Refetch normally if data is old enough (TTL expired) Fixes JabRef#12247

Update CHANGELOG for JabRef#12247

df2834a

Syimyk43 force-pushed the fix/citation-refresh-button branch from be4c490 to df2834a Compare March 18, 2026 08:48

github-actions Bot mentioned this pull request Mar 18, 2026

Improve "Refresh button" of Citation Relations #12247

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Add missing localization keys and shorten CHANGELOG entry

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github-actions Bot added status: no-bot-comments and removed status: changes-required Pull requests that are not yet complete labels Mar 25, 2026

Siedlerchr approved these changes Mar 30, 2026

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Merged via the queue into JabRef:main with commit ef82976 Mar 30, 2026
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	- Improved refresh button in Citation Relations tab: asks for confirmation if data was fetched recently, retries immediately on error, and refetches normally if data is old. [#12247](https://github.com/JabRef/jabref/issues/12247)
	- Improved responsiveness and user interface of refresh button in Citation Relations tab. [#12247](https://github.com/JabRef/jabref/issues/12247)

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