Error opening OME-Zarr v0.2

[tischi]

@KateMoreva
Could you please have a look why we get an error when opening this file?
/g/cba/exchange/ome-zarr/2022/v0.2-mobie-error.zarr

(Fiji Is Just) ImageJ 2.3.0/1.53f51; Java 1.8.0_202 [64-bit]; Mac OS X 10.14.6; 475MB of 8405MB (5%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:68)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303)
	... 5 more
Caused by: java.lang.RuntimeException: Module threw exception
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	... 1 more
Caused by: java.lang.NullPointerException
	at org.embl.mobie.io.ome.zarr.util.ZArrayAttributes.getDatasetAttributes(ZArrayAttributes.java:69)
	at org.embl.mobie.io.ome.zarr.readers.N5OmeZarrReader.getDatasetAttributes(N5OmeZarrReader.java:232)
	at org.embl.mobie.io.ome.zarr.loaders.N5OMEZarrImageLoader.getDatasetAttributes(N5OMEZarrImageLoader.java:248)
	at org.embl.mobie.io.ome.zarr.loaders.N5OMEZarrImageLoader.initSetups(N5OMEZarrImageLoader.java:185)
....

[constantinpape]

Just for some context: this is an ome.zarr file with format version 0.2. And we are not 100% sure if there is an issue with MoBIE opening version 0.2 files in general or something wrong with this particular file.

[KateMoreva]

The problem was that there was no information about compression. PR fixes this issue.

[constantinpape]

@tischi I have merged #75 where this should be fixed. Could you make sure to also include this in the release?

[tischi]

Yes, I will.

I am starting an off-topic issue here:

I wonder whether we should be more generous with bumping the versions in mobie-io and mobie-fiji. What about whenever we merge something as significant as a bug fix also bump the minor version? Then it is easier to see, e.g., whether what we ship with Fiji is the same thing as what we have somewhere else.

What do you think?

[tischi]

ping @constantinpape @K-Meech @KateMoreva ☝️

[constantinpape]

I wonder whether we should be more generous with bumping the versions in mobie-io and mobie-fiji. What about whenever we merge something as significant as a bug fix also bump the minor version? Then it is easier to see, e.g., whether what we ship with Fiji is the same thing as what we have somewhere else.

I agree, we can bump the version more frequently for smaller fixes. But note that you can also bump the patch version, i.e. the z in x.y.z. Especially when a project still has a zero major (x) version it's best practice to bump the patch version frequently, and bump the minor version (y) when something in the design changes or new functionality is added.

[tischi]

Sorry, I meant the patch version!

[K-Meech]

Yes - sounds good!

[constantinpape]

I think the issue is solved two, but do we also have a test for this? cc @K-Meech @KateMoreva

[K-Meech]

I think this was fixed by @KateMoreva here: #75. I'm not sure there's a test though?

[constantinpape]

Yes, I couldn't find a test either. I will close this for now; I will open another issue about tests since it would be good to systematize this a bit; but this can wait till after the release.