mastodon-sc / mastodon-ctc Goto Github PK

• organize better the menu items -- there are multiple import/export functions scattered around
• show time decimated lineage in a new window (GraphStreamer) is no longer functional
• export/import points could have richer dialogs (provide time span, import spot radius, delimiter...)

check the original issue: CellTrackingChallenge/CTC-FijiPlugins#24

from CellTrackingChallenge/CTC-FijiPlugins#20

As of 5-Feb-2024 the CTC plugins and Mastodon plugins distributed through the Fiji updater are incompatible.

When starting Mastodon v1.0.0-beta-28 the following stack trace is generated:

[WARNING] 2 exceptions occurred during plugin discovery.
Exception in thread "Thread-8" java.lang.NoClassDefFoundError: org/mastodon/mamut/plugin/MamutPluginAppModel
	at org.mastodon.ctc.CTC_Plugins.setAppPluginModel(CTC_Plugins.java:56)
	at org.mastodon.mamut.ProjectModel.lambda$discoverPlugins$1(ProjectModel.java:208)
	at org.mastodon.app.plugin.PluginUtils.lambda$forEachDiscoveredPlugin$0(PluginUtils.java:63)
	at org.mastodon.app.plugin.PluginUtils.forEachDiscoveredPlugin(PluginUtils.java:96)
	at org.mastodon.app.plugin.PluginUtils.forEachDiscoveredPlugin(PluginUtils.java:64)
	at org.mastodon.mamut.ProjectModel.discoverPlugins(ProjectModel.java:211)
	at org.mastodon.mamut.ProjectModel.<init>(ProjectModel.java:132)
	at org.mastodon.mamut.ProjectModel.create(ProjectModel.java:250)
	at org.mastodon.mamut.io.ProjectLoader.open(ProjectLoader.java:193)
	at org.mastodon.mamut.launcher.LauncherUtil.openWithDialog(LauncherUtil.java:332)
	at org.mastodon.mamut.launcher.MastodonLauncher.lambda$loadMastodonProject$19(MastodonLauncher.java:556)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.ClassNotFoundException: org.mastodon.mamut.plugin.MamutPluginAppModel
	at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
	... 12 more

Disabling the CTC update site allows Mastodon to function as expected. With the CTC plugins installed it cannot open any new or existing Mastodon project.

CTC update site provides:

mastodon-ctc-0.1.2.jar

Mastodon update site provides:

mastodon-1.0.0-beta-28.jar

I presume this is due to a binary incompatible API change in Mastodon. Hopefully the fix is a simple recompile with a compatible CTC change and redistribute.

Note: This may require a downstream change to the plugin discovery mechanism in Mastodon to catch errors, log them, but continue without the incompatible plugins. Currently Mastodon does not gracefully handle incompatible plugins.

Let me know if I should cascade this issue to Mastodon.

 src/main/java/org/mastodon/tomancak/PlainTextFileExport.java
		//open a folder choosing dialog
		final File selectedFile = FileChooser.chooseFile(null, null,
				new ExtensionFileFilter("txt"),
				"Choose TXT file to write tracks into:",
				FileChooser.DialogType.SAVE,
				FileChooser.SelectionMode.FILES_ONLY);

@imagejan imagejan on Apr 27, 2020

You could use UIService#chooseFile() here (and improve the SciJava API in case it doesn't meet your requirements ;-)

@xulman xulman on Apr 27, 2020 Author Member

thanks @imagejan... I actually did not know about it and was anyway blindly following example of how to open file from some other Mastodon code,
I'll fix it... on my TODO list now ;-)

...and add visualization of them

originally from: CellTrackingChallenge/CTC-FijiPlugins#10

originating from the idea of @aherbert in #8 :

PS: You're right, maybe we should aim at detecting broken plugins on the Mastodon side.. although, I'm not sure how that should be achieved. Do you happen to have an idea?

I don't think this can be done from Mastodon's side. It would have to know all possible downstream users of the API. From the plugin side you could use GitHub's dependabot to notify you of new releases for Mastodon. This will raise a PR with the code updated to the latest Mastodon version whenever a release happens. In this case the PR would break as the API is incompatible and you should be sent a notification.

I've experienced dependabot working on repositories where it watches all your dependencies and can get very noisy with constant PRs for releases of minor revisions. For the mastodon-ctc repo there are only 3 direct dependencies so the noise should be low. You can configure dependabot to ignore dependencies if you only wish to watch mastodon.

See Configuration options for the dependabot.yml file

taken from @aherbert from PR #9

Note: CTC-Measures use SimplifiedIO which includes some loci code. The new Mastodon beta-28 brings in Bioformats via a dependency which includes a lot of the same class files. I added an exclusion in the pom for the loci jar to get this to build. If you remove the exclusion and run:

mvn compile
the duplicates will be shown by the maven enforcer plugin used by scijava-pom.

I did not investigate updating CTC-Measures to see if there is a way to avoid SimplifiedIO and Bioformats clashing. I also did not check that all the classes used by SimplifiedIO are duplicated in the Bioformats jars. You can view the transitive dependencies using:

mvn dependency:tree
from this project and the CTC-Measures project.

It indeed must not be forgotten and should be fixed eventually....