Adapt latest Mastodon version beta 28 #4

maarzt · 2024-02-09T13:59:05Z

Fixes #3

The API of mastodon core components changed with the recent Mastodon releases (1.0.0-beta-27 and beta-28). This PR updates mastodon-git to be compatible with these changes.

Overview of the code changes

In many places classes MamutAppModel and WindowManager where replaced with ProjectModel.

Mastodon-git requires the ability to reload the currently open Mastodon project from disk. In the past this was implemented with a simple call to windowManager.getProjectManager().openWithDialog( project );. But this API was changed in beta-27. The projectmanager no longer exists. The open method is now a static method of the ProjectLoader an can not any longer be used to reload the project. The new "reload from disk" approach: is to use the projectModel.getModel().loadRaw(...) method. See:

mastodon-git/src/main/java/org/mastodon/mamut/collaboration/utils/ReloadFromDiskUtils.java

Lines 25 to 31 in 76233bf

    
           public static void reloadFromDisk( ProjectModel projectModel ) throws IOException 
        
           { 
        
           	try (MamutProject.ProjectReader reader = projectModel.getProject().openForReading()) 
        
           	{ 
        
           		projectModel.getModel().loadRaw( reader ); 
        
           	} 
        
           }

This new approach has the advantage that the AppModel/ProjectModel remains the same. And now BDV/TrackScheme windows remain open. But there is a bug in mastodon-collection which must be fixed for this to work.

Unit tests where added to make sure that mastodon-git still works after all the changes. See MastodonGitRepositoryTest
Two bugs where found when implementing the unit tests, these are now fixed.
- "Reset to remote banch" didn't work after creating and pushing a new branch.
- Conflict tags sets are now automatically removed, when merging two branches finishes without conflicts.
There is a class ModelAsserts, which allows to compare to Mastodon Models. This class is used in the new unit tests.
There is a class CopyModelUtils. Which was used in the unit test but is no longer required. I still want to keep it, because I know it can be useful.

1. ModelAsserts.assertModelEquals() Now compares a string with line breaks, rather than a List<String> this improves the readability of error messages when running the unit test from IntelliJ. 2. The ModelAsserts.assertModelEquals() method is changed. It now only compares the spot labels, if an actual label was set. A label is ignored if it matches the internal pool id.

Turns out the the implementation of a reload from disk functionality can be largely simplified and optimized. The method Model.loadRad(...) that is the standard for opening a Mastodon Model, can also be used for reloading the Model. This should also be way more robust.

Previously there where no tests for the MastodonGitRepository class. Now the test coverage is more than 90%. Two bugs where also discovered and are fixed. First Bug: The pull() method would not set the upstream branch, but without the upstream branch, the resetToRemoteBranch() method would fail. Second Bug: Conflict tag sets where created when merging branches, even if the merge was successful without conflicts.

…tests

The fix depends on this commit in mastodon-collections: mastodon-sc/mastodon-collection@5747775 When reloading from disk, the undo/redo history needs to be cleared, this is achieved be wrapping the reload method as if it would be a model importer.

stefanhahmann

The unit tests added by this PR are very valuable and increase the test coverage to ~50%. There is a lot of UI stuff, which is still not tested. However, testing this is very difficult. So this is from my perspective fine to omit from testing.

I think, it would be still good, if the following would be covered more by the tests:

package credentials
package exceptions
MastodonGitController

Some of the new classes in this PR seem to me very valuable for the Mastodon project as a whole. I would love to see them in the core (CopyModelUtils, ReloadFromDiskUtils, ModelAsserts).

src/main/java/org/mastodon/mamut/collaboration/utils/CopyModelUtils.java

pom.xml

stefanhahmann · 2024-03-13T09:01:19Z

src/main/java/org/mastodon/mamut/collaboration/utils/ReloadFromDiskUtils.java

+	 * Reloads the model from disk.
+	 * <p>
+	 * It does so by opening the Mastodon project again, and copying all the
+	 * spots and links from the new model to the existing one.


I was asking myself, if this method could be used to solve this issue: mastodon-sc/mastodon#246
However, after a short discussion, it turns out, that it cannot do so.

May the javadoc could be a bit more explicite that features and image dataset are excluded from the reload process in this method?

Against the background of the existing issue (mastodon-sc/mastodon#246), one could think of migrating this class to the core. The method needed to solve that issue would match perfectly in this class.

I updated the javadoc. The method reloads only the ModelGraph and tags. It however does not reload the dataset XML, and therefor is not related to mastodon-sc/mastodon#246

src/test/java/org/mastodon/mamut/collaboration/MastodonGitRepositoryTest.java

src/test/java/org/mastodon/mamut/collaboration/utils/ReloadFromDiskUtilsTest.java

src/test/java/org/mastodon/mamut/collaboration/utils/ModelAsserts.java

src/main/java/org/mastodon/mamut/collaboration/MastodonGitRepository.java

maarzt added 8 commits January 17, 2024 11:50

Update dependency to mastodon core 1.0.0-beta-27

bc11430

Implement "reload from disk" functionality

7230b4c

Use "reload from disc" functionality for mastodon git plugin

6907580

Allow to open the a cloned project with dummy data

1ed4fd5

POM: adapt mastodon-1.0.0-beta-28 to fix out of memory exceptions in …

76233bf

…tests

maarzt mentioned this pull request Feb 9, 2024

Adapt to Mastodon's new ProjectModel #3

Closed

8 tasks

maarzt added 2 commits March 8, 2024 14:21

Fix reload from disk

c44e198

The fix depends on this commit in mastodon-collections: mastodon-sc/mastodon-collection@5747775 When reloading from disk, the undo/redo history needs to be cleared, this is achieved be wrapping the reload method as if it would be a model importer.

Fix MastodonGitRepositoryDemo

8016ea7

maarzt self-assigned this Mar 11, 2024

Move the loadModel method to a new class ModelIO

921cdea

maarzt assigned stefanhahmann and unassigned stefanhahmann Mar 11, 2024

maarzt requested a review from stefanhahmann March 12, 2024 12:54

Fix typo improve description of the "share project" command

3a416de

stefanhahmann approved these changes Mar 13, 2024

View reviewed changes

stefanhahmann reviewed Mar 13, 2024

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src/main/java/org/mastodon/mamut/collaboration/MastodonGitRepository.java Outdated Show resolved Hide resolved

maarzt added 10 commits March 22, 2024 18:02

Update dependencies: mastodon and mastodon-tomancak

82a13a9

ReloadFromDiskUtils: update javadoc, make constructor private

61e9e4e

MastodonGitRepository: fix typo

e10e9a3

MastodonGitRepository: refactoring, make parameter names readable

112e0b5

MastodonGitRepositoryDemo: remove unused code

7bdbdf4

MastodonGitRepository: add javadoc to all public methods

dd14287

Remove unused import

dbd1608

MastodonGitRepository: tiny refactoring

aa01f6c

ModelAsserts: add javadoc to clarify properties that are compared

fd683c7

MastodonGitRepositoryTest: set author name before running the tests

19d5af1

maarzt merged commit bf560ae into master Mar 22, 2024

maarzt deleted the adapt-beta-27 branch October 1, 2024 13:48

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Adapt latest Mastodon version beta 28 #4

Adapt latest Mastodon version beta 28 #4

maarzt commented Feb 9, 2024 •

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stefanhahmann left a comment

stefanhahmann Mar 13, 2024

stefanhahmann Mar 13, 2024

maarzt Mar 20, 2024

	public static void reloadFromDisk( ProjectModel projectModel ) throws IOException
	{
	try (MamutProject.ProjectReader reader = projectModel.getProject().openForReading())
	{
	projectModel.getModel().loadRaw( reader );
	}
	}

Adapt latest Mastodon version beta 28 #4

Adapt latest Mastodon version beta 28 #4

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maarzt commented Feb 9, 2024 • edited Loading

Overview of the code changes

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maarzt commented Feb 9, 2024 •

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