Mode aware consistency check by dcarpentiero · Pull Request #13584 · JabRef/jabref

dcarpentiero · 2025-07-24T11:57:29Z

This draft PR refactors BibliographyConsistencyCheck to take a full BibDatabaseContext instead of just a list of entries.
The goal is to prepare the logic for BibTeX/BibLaTeX-aware consistency checking, as discussed in the issue.
So far, logic separation for mode (BibDatabaseMode) and extraction of EntryType has been implemented.

Steps to test

This is a work-in-progress. No final test procedure yet.
Initial behavior should be unchanged (functional refactoring).
Can be tested with a .bib file containing @online entries with and without date.

Mandatory checks

I own the copyright of the code submitted and I license 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 (if change is visible to the user)
[/] 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.

dcarpentiero · 2025-07-24T11:58:33Z

@subhramit hi that's me. I deleted the old branch with the old rebase problem and i've started clean.

…67-clean' into mode-aware-consistency-check-13467-clean

dcarpentiero · 2025-07-24T13:42:02Z

Hello all, I'd like to get some help regarding a failing test in jablib which seems unrelated to my modifications. Since this seems to fall outside the scope of the issue I'm addressing, how would you like me to proceed?
Thanks for the replies!

subhramit · 2025-07-24T15:12:24Z

@subhramit hi that's me. I deleted the old branch with the old rebase problem and i've started clean.

It's fine this time - but for future, we generally don't recommend closing and opening - one can update the existing branch so that the PR is also updated.

subhramit · 2025-07-24T15:15:41Z

Hello all, I'd like to get some help regarding a failing test in jablib which seems unrelated to my modifications. Since this seems to fall outside the scope of the issue I'm addressing, how would you like me to proceed?
Thanks for the replies!

Open the failing check by clicking on it, compare the expected and actual values in the log.
Then trace back how your changes caused this.

As far as I can see:

org.jabref.logic.quality.consistency.BibliographyConsistencyCheckResultCsvWriterTest

 Test checkComplexLibrary(Path) FAILED

  org.opentest4j.AssertionFailedError: expected: <entry type,citation key,Location,Pages,Publisher
  Article,first,-,o,-
  Article,second,-,-,?
  InProceedings,fourth,-,-,o
  InProceedings,third,?,o,-
  > but was: <entry type,citation key,Pages,Publisher
  Article,first,o,-
  Article,second,-,?
  >

Some things seem to be missing from the actual.
Similarly:

org.jabref.logic.quality.consistency.BibliographyConsistencyCheckTest

  Test unsetFieldsReported() FAILED

  org.opentest4j.AssertionFailedError: expected: <[@online{withDate,
    date = {date},
    urldate = {urldate},
    _jabref_shared = {sharedId: -1, version: 1}
  }, @online{withoutDate,
    urldate = {urldate},
    _jabref_shared = {sharedId: -1, version: 1}
  }]> but was: <[@online{withDate,
    date = {date},
    urldate = {urldate},
    _jabref_shared = {sharedId: -1, version: 1}
  }]>

subhramit · 2025-07-24T15:17:32Z

Mandatory checks

I own the copyright ...

[/] Change in CHANGELOG.md ...

Tests created ...

[/] Manually tested ...

[/] Screenshots added ...

[/] Checked developer's documentation ...

[/] Checked documentation ...

Why are the mandatory checks trimmed with "..." by the way?

dcarpentiero · 2025-07-24T15:24:29Z

@subhramit I don't know I think I found it like this if I remember correctly. BTW i removed the "..."
tomorrow I will resolve the test issues, thanks for helping out

subhramit · 2025-07-24T15:25:57Z

@subhramit I don't know I think I found it like this if I remember correctly. BTW i removed the "..."

Check the other PRs to see the unmodified version

dcarpentiero · 2025-07-24T15:29:41Z

@subhramit I don't know I think I found it like this if I remember correctly. BTW i removed the "..."

Check the other PRs to see the unmodified version

Ohh thanks I see... I corrected it!

koppor · 2025-08-27T14:49:49Z


-            resultMap.put(entryType, new EntryTypeResult(uniqueFields, differingEntries));
+            Set<BibEntry> entries = entryTypeToEntriesMap.get(entryType);
+            if (entries == null || entries.size() <= 1 || differingFields.isEmpty()) {


I think, the check is OK. However, I think, this case never happens. Therefore, I added an assert stgatement.

koppor · 2025-08-27T15:28:36Z

We use this PR to fix #13765

calixtus

Looks fine to me. Lets get this merged.

subhramit · 2025-08-27T18:15:01Z

+                }
+
+                entryTypeToEntriesMap
+                        .computeIfAbsent(entryType, _ -> new java.util.LinkedHashSet<>())


I think we could use a hash set here?
Also, should use import

Oh, yes. Follow-up? ^^

…n-c23b1a88-5c29-46a2-a007-701edd344b9b' into jetbrains-junie-issue-13623-run-c23b1a88-5c29-46a2-a007-701edd344b9b * upstream/jetbrains-junie-issue-13623-run-c23b1a88-5c29-46a2-a007-701edd344b9b: Streamline code for getTabTitle() (#13781) Add missing variables Reformat BibTex in Show BibTex Source (#13761) Auto publish before JBang tests (#13779) Hotfix: calling of publish.yml Support BibLaTeX datamodel validations (#13693) Auto add and remove of "status: changes-required" label (#13778) New Crowdin updates (#13777) Restore local-only Git behavior for SLR to fix repository initialization error (#13775) Use vanilla hashset (#13771) Fix Springer Fetcher names (#13770) Fix condition Publish SNAPSHOT on jablib change (#13774) Adapt as per new set of checks (#13772) Bump jablib/src/main/resources/csl-styles from `1194364` to `17cfa60` (#13750) Fix path (#13769) Mode aware consistency check (#13584) Refine JBang check (#13765) Add Language Server to the UI and add the integrity/consistency check (#13697) Fix/remove comment code (#13763)

* upstream/main: (32 commits) Fix path (#13769) Mode aware consistency check (#13584) Refine JBang check (#13765) Add Language Server to the UI and add the integrity/consistency check (#13697) Fix/remove comment code (#13763) New Crowdin updates (#13760) Bump org.openrewrite.rewrite from 7.14.0 to 7.14.1 (#13757) Bump com.autonomousapps:dependency-analysis-gradle-plugin (#13756) Bump dev.langchain4j:langchain4j-bom from 1.2.0 to 1.3.0 in /versions (#13755) Bump jablib/src/main/resources/csl-locales from `fa56de1` to `e29c453` (#13754) Bump com.autonomousapps:dependency-analysis-gradle-plugin (#13753) Bump org.mockito:mockito-core from 5.18.0 to 5.19.0 in /versions (#13752) Bump actions/upload-pages-artifact from 3 to 4 (#13751) Migrate fetchers to Search.g4 ANTLR parser. (#13691) [Junie]: fix: resolve IllegalArgumentException for non-absolute URIs (#13669) Add auto-renaming of linked files on entry data change (#13295) Walkthrough additions (#13745) Switch from zulu to corretto (#13749) New Crowdin updates (#13747) Fix copy to (#13741) ...

dcarpentiero added 14 commits July 24, 2025 13:50

feat: consistency check draft

da1a87f

Feat: mode comparison draft

fa9892a

fix: removed comment

faaabd6

Feat: mode diversification operations

b8a7714

fix: removed @test for testing purposes

ff5b30a

fix: hashset constructor refactor

2d87046

Update BibliographyConsistencyCheckTest.java

c7fef21

fix: passing whole dbContext instead of entries into execute() method

b997c22

fix: passing whole database context instead of list of entries

3bf5d85

fix: code refactor

00bcbde

fix: typo

dee0214

fix: typo

5afdeab

feat: tests now are passed whole database instead of a list of entries

e72ed61

fix: typo

f24bd58

trag-bot Bot reviewed Jul 24, 2025

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Comment thread jablib/src/main/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheck.java Outdated

trag-bot Bot reviewed Jul 24, 2025

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Comment thread jablib/src/test/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheckTest.java Outdated

dcarpentiero and others added 3 commits July 24, 2025 14:03

Merge branch 'main' into mode-aware-consistency-check-13467-clean

a8319a5

fix: consistent variable naming, bibEntryList -> bibEntriesList

1ac9add

Merge remote-tracking branch 'origin/mode-aware-consistency-check-134…

0646bfe

…67-clean' into mode-aware-consistency-check-13467-clean

dcarpentiero marked this pull request as ready for review July 24, 2025 13:42

subhramit changed the title ~~Mode aware consistency check #13467 clean~~ Mode aware consistency check Jul 24, 2025

Merge branch 'main' into mode-aware-consistency-check-13467-clean

6167daa

dcarpentiero and others added 7 commits August 27, 2025 14:19

Merge branch 'main' into mode-aware-consistency-check-13467-clean

484f529

Use weaker HashMap type

34d4265

Refine data structure

3c752c3

Avoid elvis

29a8499

Add small assert

5ce4a00

Fix assert

8ceafb0

Tweak algorithm

395a05c

koppor approved these changes Aug 27, 2025

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trag-bot Bot reviewed Aug 27, 2025

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Comment thread jablib/src/main/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheck.java

trag-bot Bot reviewed Aug 27, 2025

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Comment thread jablib/src/test/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheckTest.java

trag-bot Bot reviewed Aug 27, 2025

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Comment thread jablib/src/test/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheckTest.java

subhramit added the status: awaiting-second-review For non-trivial changes label Aug 27, 2025

calixtus approved these changes Aug 27, 2025

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calixtus added this pull request to the merge queue Aug 27, 2025

Merged via the queue into JabRef:main with commit 9b2772b Aug 27, 2025
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github-actions Bot mentioned this pull request Aug 27, 2025

Mode-aware consistency check #13467

Closed

koppor mentioned this pull request Aug 27, 2025

Fix path #13769

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subhramit reviewed Aug 27, 2025

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Comment thread jablib/src/main/java/org/jabref/logic/quality/consistency/BibliographyConsistencyCheck.java

subhramit mentioned this pull request Aug 27, 2025

Minor refinements on Consistency Check #13771

Merged

1 task

koppor mentioned this pull request Aug 27, 2025

Publish SNAPSHOT on jablib change #13774

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dcarpentiero deleted the mode-aware-consistency-check-13467-clean branch August 28, 2025 07:15

dcarpentiero restored the mode-aware-consistency-check-13467-clean branch August 28, 2025 07:15

dcarpentiero deleted the mode-aware-consistency-check-13467-clean branch August 28, 2025 07:39

This was referenced Aug 31, 2025

Support customized entry types in BibliographyConsistencyCheck #13794

Closed

Improve ConsistencyCheck code (and one minor other code place) #13795

Merged

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Steps to test

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dcarpentiero commented Jul 24, 2025

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