LO/OO: Refresh citations before syncing bibliography by subhramit · Pull Request #15352 · JabRef/jabref

subhramit · 2026-03-16T22:25:59Z

Closes #14387
Make CSL citations inserted using JabRef LO Converter extension recognizable by "Make/Sync bibliography" out of the box.

Convert using JabRef_LibreOffice_Extension to CSL

Open JabRef, refresh bibliography

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

Signed-off-by: subhramit <subhramit.bb@live.in>

qodo-free-for-open-source-projects · 2026-03-16T22:26:22Z

Review Summary by Qodo

Refresh citations before syncing bibliography in LibreOffice

✨ Enhancement 🐞 Bug fix

Walkthroughs

Description

• Refresh citations before syncing bibliography in OO/LO panel
• Simplify exception handling by catching generic Exception
• Add test case for LibreOffice extension citation format
• Update changelog with CSL support improvements

Diagram

flowchart LR
  A["Make/Sync Bibliography"] --> B["Refresh Citations"]
  B --> C["Update Citation Styles"]
  C --> D["Mark Manager Updates"]
  D --> E["Generate Bibliography"]

File Changes

1. jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java Error handling +2/-8

Simplify exception handling in OO bibliography update
• Removed unused import UnknownPropertyException
• Simplified exception handling by catching generic com.sun.star.uno.Exception instead of multiple
 specific exceptions
• Removed WrappedTargetException from catch block
jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java

2. jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java ✨ Enhancement +5/-2

Refresh citations before inserting bibliography
• Added citation refresh logic before bibliography generation
• Call updateAllCitationsWithNewStyle() to refresh citations
• Set real-time number update requirement and read existing marks
• Changed exception signature from WrappedTargetException to generic Exception
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java

3. jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java Error handling +3/-5

Simplify exception handling in bibliography rebuild
• Removed unused imports for PropertyVetoException, UnknownPropertyException,
 NoSuchElementException
• Added import for generic com.sun.star.uno.Exception
• Simplified exception signatures in method declarations to use generic Exception
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java

View more (2)

4. jablib/src/test/java/org/jabref/logic/openoffice/ReferenceMarkTest.java 🧪 Tests +4/-0

Add test for LibreOffice extension citation format
• Added new test case for LibreOffice extension citation format
• Test validates parsing of citation mark with format "JABREF_Keen_2011 CID_100 cite"
jablib/src/test/java/org/jabref/logic/openoffice/ReferenceMarkTest.java

5. CHANGELOG.md 📝 Documentation +2/-0

Document citation refresh and CSL improvements

• Added entry documenting citation refresh feature in OO/LO panel
• Added entry about improved CSL support with LibreOffice converter extension
• Both entries reference issue #14387

CHANGELOG.md

qodo-free-for-open-source-projects · 2026-03-16T22:26:23Z

Code Review by Qodo

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

1. OOBibBase rethrows RuntimeException ☑ 📘 Rule violation ⛯ Reliability

Description

The new catch block wraps UNO/document exceptions into an unchecked RuntimeException, which can
crash the update flow and violates the project’s exception-handling standards. It also broadens
exception handling by catching the generic com.sun.star.uno.Exception.

Code

jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java[R930-931]

+                } catch (NoDocumentException | com.sun.star.uno.Exception e) {
              throw new RuntimeException(e);

Evidence
PR Compliance requires avoiding unchecked throws and overly broad exception handling. The updated
code now catches a broad UNO exception type and rethrows it as RuntimeException.
AGENTS.md
AGENTS.md
jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java[929-932]

Agent prompt

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

## Issue description
`OOBibBase.guiActionUpdateDocument` catches a broad `com.sun.star.uno.Exception` and rethrows it as an unchecked `RuntimeException`, which violates the exception-handling compliance rules and risks crashing the UI update flow.
## Issue Context
The PR broadened exception handling in the CSL bibliography update path.
## Fix Focus Areas
- jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java[929-939]

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

2. CSLUpdateBibliography throws UNO Exception 📘 Rule violation ⛯ Reliability

Description

CSLUpdateBibliography now declares throws com.sun.star.uno.Exception instead of specific UNO
exceptions, reducing precision and making error handling less robust. This conflicts with the
requirement to avoid broad exception types.

Code

jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java[R40-43]

                                 CitationStyle citationStyle,
                                 BibDatabaseContext bibDatabaseContext,
                                 BibEntryTypesManager bibEntryTypesManager)
-            throws WrappedTargetException, NoDocumentException, CreationException, NoSuchElementException, PropertyVetoException, UnknownPropertyException {
+            throws Exception, NoDocumentException, CreationException {

Evidence
The compliance checklist requires specific exception types; the updated method signature now throws
the generic UNO base exception type (com.sun.star.uno.Exception).
AGENTS.md
AGENTS.md
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java[36-44]

Agent prompt

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

## Issue description
`CSLUpdateBibliography` now declares `throws com.sun.star.uno.Exception`, which is overly broad and violates the project’s exception specificity rules.
## Issue Context
This PR replaced a list of specific UNO exceptions with the generic UNO base exception.
## Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java[36-58]
- jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java[83-103]

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

3. ~~Refresh marks too late~~ ☑ 🐞 Bug ✓ Correctness

Description

CSLCitationOOAdapter.insertBibliography calls updateAllCitationsWithNewStyle before
markManager.readAndUpdateExistingMarks, so the citation update runs against stale cached reference
marks and won’t refresh citations created/converted after the adapter was initialized.

Code

jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[R173-183]

public void insertBibliography(XTextCursor cursor, CitationStyle selectedStyle, List<BibEntry> entries, BibDatabaseContext bibDatabaseContext, BibEntryTypesManager bibEntryTypesManager)
-            throws WrappedTargetException, CreationException {
+            throws Exception, CreationException {
  if (!selectedStyle.hasBibliography()) {
      return;
  }
-
  boolean isNumericStyle = selectedStyle.isNumericStyle();
+        updateAllCitationsWithNewStyle(selectedStyle, false);
+        markManager.setRealTimeNumberUpdateRequired(isNumericStyle);
+        markManager.readAndUpdateExistingMarks();
+

Evidence
insertBibliography updates citations first, but updateAllCitationsWithNewStyle relies on
markManager.getMarksInOrder() and isCitedEntry(); both are based on CSLReferenceMarkManager’s
cached state (marksInOrder/citationKeyToNumber), which is only rebuilt by
readAndUpdateExistingMarks(). Therefore, without reading marks first, newly converted/inserted CSL
reference marks are not considered in the refresh pass.
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[171-215]
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[264-292]
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLReferenceMarkManager.java[126-170]
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLReferenceMarkManager.java[302-309]

Agent prompt

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

## Issue description
`insertBibliography` refreshes citation text before refreshing the reference-mark cache, so style refresh runs on stale data and misses citations converted/inserted externally.
### Issue Context
`updateAllCitationsWithNewStyle` uses `markManager.getMarksInOrder()` and `isCitedEntry` (cache-backed). The cache is rebuilt only by `readAndUpdateExistingMarks()`.
### Fix Focus Areas
- jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[171-215]
- jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[264-360]

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

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4. ~~Stale citedEntries filtering~~ ☑ 🐞 Bug ✓ Correctness

Description

OOBibBase.guiActionUpdateDocument builds citedEntries using cslCitationOOAdapter.isCitedEntry
before any mark refresh, so it can incorrectly return early with “No cited entries found” and never
call bibliography rebuild/refresh.

Code

jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java[1]
              doc.lockControllers();

Evidence
The cited-entry detection is cache-based (isCitedEntry → markManager.hasCitationForKey). If the
document’s marks were changed by external tooling (the exact PR use case), the adapter cache can be
stale until readAndUpdateExistingMarks() runs. Since OOBibBase checks for emptiness and returns
before invoking rebuildCSLBibliography, the new refresh logic in insertBibliography may never
execute.
jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java[899-920]
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[362-367]
jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLReferenceMarkManager.java[126-134]

Agent prompt

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

## Issue description
The UI code filters cited entries using a cache-backed predicate before any refresh, so it can return early and skip bibliography rebuild.
### Issue Context
`isCitedEntry` depends on `CSLReferenceMarkManager`’s cached `citationKeyToNumber`, rebuilt only by `readAndUpdateExistingMarks()`.
### Fix Focus Areas
- jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java[899-932]
- jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[54-67]
- jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java[362-367]

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

ⓘ The new review experience is currently in Beta. Learn more

Signed-off-by: subhramit <subhramit.bb@live.in>

calixtus · 2026-03-17T07:36:06Z

    /// The list is generated based on the existing citations, in-text citations and empty citations in the document.
    public void insertBibliography(XTextCursor cursor, CitationStyle selectedStyle, List<BibEntry> entries, BibDatabaseContext bibDatabaseContext, BibEntryTypesManager bibEntryTypesManager)
-            throws WrappedTargetException, CreationException {
+            throws Exception, CreationException {


Maybe use qualified name here like in OOBibBase

to avoid confusion with java.lang.Exception

also in CSLUpdateBibliography

Signed-off-by: subhramit <subhramit.bb@live.in>

testlens-app · 2026-03-17T20:49:15Z

✅ All tests passed ✅

🏷️ Commit: 8ae559d
▶️ Tests: 10187 executed
⚪️ Checks: 52/52 completed

Learn more about TestLens at testlens.app.

* Refresh citations before syncing bibliography Signed-off-by: subhramit <subhramit.bb@live.in> * Add test Signed-off-by: subhramit <subhramit.bb@live.in> * Add comment to testcase Signed-off-by: subhramit <subhramit.bb@live.in> * Changelog Signed-off-by: subhramit <subhramit.bb@live.in> * Restore gap Signed-off-by: subhramit <subhramit.bb@live.in> * Better exception handling Signed-off-by: subhramit <subhramit.bb@live.in> * Take qodo suggestion Signed-off-by: subhramit <subhramit.bb@live.in> * l10n Signed-off-by: subhramit <subhramit.bb@live.in> * Change order of real time number update Signed-off-by: subhramit <subhramit.bb@live.in> * Change order of real time number update Signed-off-by: subhramit <subhramit.bb@live.in> * Better exception handling, use qualified names Signed-off-by: subhramit <subhramit.bb@live.in> --------- Signed-off-by: subhramit <subhramit.bb@live.in>

* upstream/main: Chore(deps): Bump jablib/src/main/resources/csl-styles (#15365) Chore(deps): Bump styfle/cancel-workflow-action from 0.13.0 to 0.13.1 (#15364) Update dependency com.ibm.icu:icu4j to v78.3 (#15361) LO/OO: Refresh citations before syncing bibliography (#15352)

* Refresh citations before syncing bibliography Signed-off-by: subhramit <subhramit.bb@live.in> * Add test Signed-off-by: subhramit <subhramit.bb@live.in> * Add comment to testcase Signed-off-by: subhramit <subhramit.bb@live.in> * Changelog Signed-off-by: subhramit <subhramit.bb@live.in> * Restore gap Signed-off-by: subhramit <subhramit.bb@live.in> * Better exception handling Signed-off-by: subhramit <subhramit.bb@live.in> * Take qodo suggestion Signed-off-by: subhramit <subhramit.bb@live.in> * l10n Signed-off-by: subhramit <subhramit.bb@live.in> * Change order of real time number update Signed-off-by: subhramit <subhramit.bb@live.in> * Change order of real time number update Signed-off-by: subhramit <subhramit.bb@live.in> * Better exception handling, use qualified names Signed-off-by: subhramit <subhramit.bb@live.in> --------- Signed-off-by: subhramit <subhramit.bb@live.in>

subhramit added 4 commits March 17, 2026 02:46

Refresh citations before syncing bibliography

f2b6eac

Signed-off-by: subhramit <subhramit.bb@live.in>

Add test

327a709

Signed-off-by: subhramit <subhramit.bb@live.in>

Add comment to testcase

0529f63

Signed-off-by: subhramit <subhramit.bb@live.in>

Changelog

d3b188d

Signed-off-by: subhramit <subhramit.bb@live.in>

Restore gap

206d0cf

Signed-off-by: subhramit <subhramit.bb@live.in>

github-actions Bot mentioned this pull request Mar 16, 2026

Version 6.0 no longer works with JabRef_LibreOffice_Converter #14387

Closed

github-actions Bot added the status: no-bot-comments label Mar 16, 2026

Merge branch 'main' into oo-refresh

f1db451

qodo-free-for-open-source-projects Bot reviewed Mar 16, 2026

View reviewed changes

Comment thread jabgui/src/main/java/org/jabref/gui/openoffice/OOBibBase.java Outdated

Comment thread jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLUpdateBibliography.java Outdated

Comment thread jablib/src/main/java/org/jabref/logic/openoffice/oocsltext/CSLCitationOOAdapter.java

koppor added the component: libre-office label Mar 16, 2026

Better exception handling

28bded5

Signed-off-by: subhramit <subhramit.bb@live.in>

Siedlerchr previously approved these changes Mar 16, 2026

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subhramit changed the title ~~Refresh citations before syncing bibliography~~ LO/OO: Refresh citations before syncing bibliography Mar 16, 2026