Git Integration and UI Improvements #12252

khola22 · 2024-12-02T00:24:59Z

This PR introduces several key updates and improvements aimed at enhancing the backup management, change detection, and UI functionalities.

Backup Management with Git Integration:
A new BackupManagerGit class has been implemented to handle backups using Git. This allows .bib files to be automatically copied to a dedicated jabref/backups directory every 19 seconds, ensuring that a comprehensive commit history is maintained via Git. This approach provides a centralized and version-controlled backup mechanism, independent of the file location.

Change Detection Logic:
Change detection is now triggered when .bib files are overwritten during explicit user actions such as Save, Save All, or the save prompts when exiting the application. While listeners continue to track edits, their strict conditions occasionally limit their ability to dynamically detect changes. As a result, we face two challenges:
Lack of autosave functionality without user interaction.
Potential failure to record unsaved changes if the application closes unexpectedly.

UI Enhancements:
The UI has been updated to provide functionality for saving, committing, and discarding changes, along with accurate commit details retrieval. While most features are working as expected, challenges remain with the checkout functionality, especially when reverting commits using JGit. We welcome feedback on this part of the implementation.
Date of backup refers to the date of the commit.

Code Refactoring and Adaptation:
We’ve refactored various components to integrate with BackupManagerGit, replacing the older BackupManager logic. Existing classes like CoarseChangeFilter have been retained without modification, as our focus was on implementing the new Git-based backup mechanism.

PS 1: We have retained the BackupManager class for reference, allowing us to review its contents should further clarification of the backup logic be necessary. However, we have ensured that this class is no longer used outside of the specific tests previously dedicated to it, and we have confirmed that BackupManagerGit is the primary class in operation. Despite these precautions, we have encountered an issue with the legacy backup tracking method. Specifically, we have observed occasional, unexpected creation of .bak files within the backup directory. This anomaly has occurred only once during testing. While we suspect the issue may be linked to the UI components of the code, we have yet to pinpoint the precise cause.

PS 2: A potential issue arose concerning the handling of two .bib files with identical names. Copying such files into the repository would result in one file overwriting the other, which is problematic. We are currently investigating a solution to this before finalizing the PR for review.

PS 3 : We didn't implement squashing older backup commits.

Update 1: The issue identified in PS 2 has been addressed by implementing UUID-generated unique file names. However, when a .bib file is relocated, a new UUID is generated, which results in a new file being recorded in the Git repository. To resolve this, we propose the following solutions: 1/ Move the .uuid file along with the .bib file when the move is performed through JabRef. 2/ Utilize a file system watcher to track and handle file movements performed outside of JabRef.

Updates 2 : Restore button works.

We have not yet pursued further investigation into these solutions.

The title of the isuue : Enhanced backup restore dialog #2961
The link of the issue : #2961 (comment)

Mandatory checks

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.

Removed BackupManagerJGit to do UI changes

…nch-1

…into branch-1" This reverts commit df21a4d, reversing changes made to 62a8beb.

…into branch-1" This reverts commit 0f9fcb9.

khola22 · 2024-12-05T00:15:49Z

hello @subhramit , we were trying to resolve the conflicts with submodules as said in the link, the first approache didn't work, but for the second one, we have an issue :

(base) khaoula@Khaoulas-MacBook-Air JabRef % cd src/main/resources/csl-locales
(base) khaoula@Khaoulas-MacBook-Air csl-locales % git checkout 96d704d
error: pathspec '96d704d' did not match any file(s) known to git
(base) khaoula@Khaoulas-MacBook-Air csl-locales % git checkout 96d704d
error: pathspec '96d704d' did not match any file(s) known to git
(base) khaoula@Khaoulas-MacBook-Air csl-locales % git status
HEAD detached at 8bc2af1
nothing to commit, working tree clean

khola22 · 2024-12-05T10:57:48Z

Update : we fixed the conflicts relative to submodules.

subhramit

Initial suggestions.

@calixtus I'd want you to take a look at the usage of 1. preferences 2. mockito in this PR once. I remember using RETURN_DEEP_STUBS for some preference in the past, the use case seems similar here. However, I think we can reduce the usage of mockito for other cases by using concrete instantiations (entries, database context, database, entrytypesmanager in particular).

subhramit · 2024-12-05T11:27:45Z

CHANGELOG.md

@@ -11,6 +11,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv

 ### Added

+- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961](https://github.com/JabRef/jabref/issues/2961)


Changelog entries are primarily for users, so they are not supposed to be aware of internal implementations or class names ("BackupManagerGit"). Just mention git-based version control. Ideally make entries short and crisp as well. For example:

Suggested change

- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961](https://github.com/JabRef/jabref/issues/2961)

- Implemented version-control based backup management of .bib files using Git. [#2961](https://github.com/JabRef/jabref/issues/2961)

subhramit · 2024-12-05T11:28:34Z

CHANGELOG.md

@@ -11,6 +11,11 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv

 ### Added

+- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Added automatic copying of .bib files to a jabref/backups directory every 19 seconds with comprehensive commit history. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Added support for unique file naming using UUIDs to prevent overwriting files with identical names in the backup directory. [#2961](https://github.com/JabRef/jabref/issues/2961)


Part of internal implementation of the introduced feature and not a "change" from existing release. Remove this.

@khola22 Please do not mark review comments as resolved (except if it is trivially visible that it has been resolved). In this case, this was asked to be removed, and it is not (yet).
Once you push fresh commits on the code window, this will automatically be marked "Outdated". Then, one of the maintainers can take a look and mark them resolved.
This also allows for conversations in case you get stuck in a particular comment's context or amongst maintainers if there's any change of plans or someone suggests a better idea.

@subhramit okay ! sorry about that .

@subhramit okay ! sorry about that .

No issues, and no need to be sorry. It's on us to guide new contributors!

subhramit · 2024-12-05T11:29:23Z

CHANGELOG.md

+- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Added automatic copying of .bib files to a jabref/backups directory every 19 seconds with comprehensive commit history. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Added support for unique file naming using UUIDs to prevent overwriting files with identical names in the backup directory. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Introduced UI functionality (only during opening) for saving, restoring, reviewing and discarding changes with accurate commit details retrieval. [#2961](https://github.com/JabRef/jabref/issues/2961)


Part of the introduced feature (also pertains to the same issue). Remove this as well.

subhramit · 2024-12-05T11:29:50Z

CHANGELOG.md

+- Added automatic copying of .bib files to a jabref/backups directory every 19 seconds with comprehensive commit history. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Added support for unique file naming using UUIDs to prevent overwriting files with identical names in the backup directory. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Introduced UI functionality (only during opening) for saving, restoring, reviewing and discarding changes with accurate commit details retrieval. [#2961](https://github.com/JabRef/jabref/issues/2961)
+- Enabled a "Restore" button to recover specific backup versions. [#2961](https://github.com/JabRef/jabref/issues/2961)


Some user facing information should be kept, e.g. "enhanced backup and restore functionality".

subhramit · 2024-12-05T11:30:14Z

CHANGELOG.md

@@ -52,6 +57,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv

 ### Changed

+- Refactored backup-related components to integrate with the new BackupManagerGit, replacing the older BackupManager logic. [#2961](https://github.com/JabRef/jabref/issues/2961)


Internal implementation, not relevant to user-side. Remove.

subhramit · 2024-12-05T11:43:56Z

src/main/java/org/jabref/gui/autosaveandbackup/BackupManagerGit.java

+        String normalized = lines
+                .map(String::trim) // Supprimer les espaces en début et fin de ligne
+                .filter(line -> !line.isBlank()) // Supprimer les lignes vides
+                .collect(Collectors.joining("\n")); // Réassembler avec des sauts de ligne


Avoid magic strings. Put \n into a constant named LINE_BREAK.

subhramit · 2024-12-05T11:48:19Z

src/test/java/org/jabref/gui/autosaveandbackup/BackupManagerGitTest.java

+        mockDatabaseContext1 = mock(BibDatabaseContext.class);
+        mockDatabaseContext2 = mock(BibDatabaseContext.class);


You don't need to mock multiple instances of the same class.
If you actually want variation, make different entries/set of entries and generate a database context from them.

subhramit · 2024-12-05T11:48:50Z

src/test/java/org/jabref/gui/autosaveandbackup/BackupManagerGitTest.java

+        mockLibraryTab = mock(LibraryTab.class);
+        mockDatabaseContext1 = mock(BibDatabaseContext.class);
+        mockDatabaseContext2 = mock(BibDatabaseContext.class);
+        mockEntryTypesManager = mock(BibEntryTypesManager.class);


You can make an actual instance instead of mocking this.

subhramit · 2024-12-05T11:52:27Z

src/test/java/org/jabref/gui/autosaveandbackup/BackupManagerGitTest.java

+             .map(Path::toFile)
+             .forEach(file -> {
+                 if (!file.delete()) {
+                     file.deleteOnExit();


@koppor Not sure about this one, I think using @TempDir would take care of the deletion?

subhramit · 2024-12-05T11:58:44Z

src/main/java/org/jabref/gui/dialogs/BackupUIManager.java

+                                                                             GuiPreferences preferences,
+                                                                             List<BackupEntry> backups) {
+        return UiTaskExecutor.runInJavaFXThread(
+                () -> dialogService.showCustomDialogAndWait(new BackupChoiceDialog(preferences.getFilePreferences().getBackupDirectory(), backups)));


Pass preferences.getFilePreferences().getBackupDirectory() via constructor and use it here for better abstraction (detailed reason in similar review comment above).

Also, is this supposed to be GuiPreferences or CliPreferences?

Its fine in the FilePreferences/GuiPreferences. You only need the backup in the ui mode.

Its fine in the FilePreferences/GuiPreferences. You only need the backup in the ui mode.

The rest of their changes involve clipreferences

guipreferences is a superset of clipreferences.

subhramit · 2024-12-05T12:04:29Z

By the way, really good work guys.

Please also take a look at the failing tests and try to fix them.
https://devdocs.jabref.org/code-howtos/faq.html will help you.

Co-authored-by: Subhramit Basu Bhowmick <[email protected]>

subhramit · 2024-12-11T22:11:47Z

Hey team, good job fixing the tests.
The maintainers are currently a bit busy, and will get to your PR as soon as they find time.

khola22 · 2024-12-13T21:58:44Z

Hello @subhramit ,
We wanted to let you know that we have carefully reviewed all your comments and made the necessary adjustments. Thank you for taking the time to provide your feedback—it is greatly appreciated.

nawalchahboune and others added 30 commits October 23, 2024 20:18

l'ajout de la classe BackUpManagerJGit

094252c

l'ajout de la classe BackUpManagerJGit

d0f6346

Merge remote-tracking branch 'origin/main'

7fd8f89

l'ajout de la classe BackUpManagerJGit

9ab37a2

Add the class JGIT

d8812ef

first git implementation, not tested

af50c7c

ajout de la methide backupGitDiffers

e72d408

Added Pop up to choose backup

d427e05

adding methods 06/11

0737f48

methods aded and changed : retrieveCommitDetails , retreiveCommits

f68236f

I start switching French comments to English

129d175

finish switching comments from French to English

b82682a

Added table

34a2889

Removed BackupManagerJGit to do UI changes

Navigation through dialogs implemented

b299e5f

some modif

d2b3619

some modif

d84fcab

fix some issues

54fa60a

adding date details

9a8e615

Merge branch 'UI' into branch-1

62a8beb

Merge branch 'branch-1' of https://github.com/khola22/jabref into bra…

df21a4d

…nch-1

Revert "Merge branch 'branch-1' of https://github.com/khola22/jabref …

0f9fcb9

…into branch-1" This reverts commit df21a4d, reversing changes made to 62a8beb.

Reapply "Merge branch 'branch-1' of https://github.com/khola22/jabref …

7b6ee3f

…into branch-1" This reverts commit 0f9fcb9.

minor fixes

b67b2d9

Minor Synthax fixes

3f9584e

supression de classe BackupManagerJGit

76b6f92

differenciation BackupManagerOld et BackupManager

fc94296

Corrected errors related to BackupManagerGit class

d6df47a

Start tests

9a07077

OpenDatabaseAction adapted

9c86a64

Start adapting SaveDatabaseAction.java and LibraryTab.java

fa42e86

BackupResolverDialog.java doesn't use the old backup system anymore.

aac4915

change in CHANGELOG.md

a292db3

khola22 marked this pull request as ready for review December 5, 2024 00:44

Updated submodule csl-locales to latest commit

7ae97d1

Merge branch 'main' into branch-1

5bbefcf

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subhramit requested changes Dec 5, 2024

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Update CHANGELOG.md

70b123b

Co-authored-by: Subhramit Basu Bhowmick <[email protected]>

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“Khaoula added 9 commits December 5, 2024 16:22

CHANGELOG.md changes

69ad0f3

Resolve comment on LibraryTab.java and BackupManagerGit.java

a577ad9

Resolve comment on LibraryTab.java and BackupManagerGit.java

e55a831

Resolve comment on BackupUIManager.java

cf23e68

checkstyle

61a1987

Working Tests

b515e51

Add missing submodule configuration

8f06c80

Apply OpenRewrite recipes

d3b6dd3

Correct Unit Tests

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Gillan0 and others added 3 commits December 6, 2024 19:21

Added new UI text to JabRef_en.properties

dbe6f2b

Merge branch 'fix-localization-issues' into branch-1

3d13e22

Resolve comment on BackupManagerGitTest.java and

e065399

nawalchahboune and others added 3 commits December 13, 2024 21:04

Resolve comments on insatantiation within mock

01478c7

Merge branch 'main' into branch-1

e4ad25c

Resolve comment about BackupUIManager.java

da79d5d

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Git Integration and UI Improvements #12252

Git Integration and UI Improvements #12252

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khola22 commented Dec 13, 2024

		@@ -11,6 +11,11 @@ Note that this project does not adhere to [Semantic Versioning](https://semv

		### Added

		- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961](https://github.com/JabRef/jabref/issues/2961)

	- Implemented BackupManagerGit to handle automatic backups of .bib files using Git, ensuring centralized, version-controlled backup management. [#2961](https://github.com/JabRef/jabref/issues/2961)
	- Implemented version-control based backup management of .bib files using Git. [#2961](https://github.com/JabRef/jabref/issues/2961)

		@@ -52,6 +57,7 @@ Note that this project does not adhere to [Semantic Versioning](https://semv

		### Changed

		- Refactored backup-related components to integrate with the new BackupManagerGit, replacing the older BackupManager logic. [#2961](https://github.com/JabRef/jabref/issues/2961)

		mockDatabaseContext1 = mock(BibDatabaseContext.class);
		mockDatabaseContext2 = mock(BibDatabaseContext.class);

Git Integration and UI Improvements #12252

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Git Integration and UI Improvements #12252

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