SlideBook .SLD files do not load

[RichardMyers]

After updating to latest FIJI I get the following exception/stack trace; it all worked a few weeks ago when I last updated my local Fiji. This is likely related to PR #118 and I'll need to investigate further. Perhaps updates were made to the other readers that also need to be made to SlideBook6ImgLoader .

SlideBook6Reader initializing C:\Users\Richard Myers\Documents\3i\images\diSPIM\fish-spinal-cord-sm.sld mpicbg.spim.data.SpimDataInstantiationException: could not find XmlIoBasicImgLoader implementation for SlideBook6ImgLoader at mpicbg.spim.data.generic.sequence.ImgLoaders.createXmlIoForImgLoaderClass(ImgLoaders.java:93) at mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription.toXml(XmlIoAbstractSequenceDescription.java:77) at mpicbg.spim.data.generic.XmlIoAbstractSpimData.toXml(XmlIoAbstractSpimData.java:180) at spim.fiji.spimdata.XmlIoSpimData2.toXml(XmlIoSpimData2.java:175) at spim.fiji.spimdata.XmlIoSpimData2.toXml(XmlIoSpimData2.java:45) at mpicbg.spim.data.generic.XmlIoAbstractSpimData.save(XmlIoAbstractSpimData.java:97) at spim.fiji.spimdata.XmlIoSpimData2.save(XmlIoSpimData2.java:112) at spim.fiji.spimdata.SpimData2.saveXML(SpimData2.java:360) at spim.fiji.plugin.Define_Multi_View_Dataset.defineDataset(Define_Multi_View_Dataset.java:140) at spim.fiji.plugin.Data_Explorer.run(Data_Explorer.java:74) at ij.IJ.runUserPlugIn(IJ.java:217) at ij.IJ.runPlugIn(IJ.java:181) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:745)

[RichardMyers]

Hi @StephanPreibisch @ctrueden , It looks like the 5.0.14 SPIM_Registration plugin does not load SLD files, but the 5.0.15 SNAPSHOT works. Perhaps 5.0.14 didn't deploy properly?

I don't see any other changes made to the plugin between the 5.0.14 release and creating the 5.0.15 Snapshot.

[RichardMyers]

I assume this is related to Fiji updating to SciJava 16.1.0 on May 24 and SPIM_Registration updating to SciJava 16.2.0 on July 11.

[StephanPreibisch]

Hi @RichardMyers, I'll make another release just to be sure it's not the reason ...

[StephanPreibisch]

Hi, I do not understand why, but the Travis build often, not always fails because it cannot find the sources. @ctrueden, do you have any idea what's the reason for that? I checked, the file does exist though.

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-deploy-plugin:2.8.2:deploy (default-deploy) on project SPIM_Registration: Failed to deploy artifacts: Could not transfer artifact sc.fiji:SPIM_Registration:jar:sources:5.0.16 from/to imagej.releases (dav:http://maven.imagej.net/content/repositories/releases): Failed to transfer file: http://maven.imagej.net/content/repositories/releases/sc/fiji/SPIM_Registration/5.0.16/SPIM_Registration-5.0.16-sources.jar. Return code is: 400 -> [Help 1]

[StephanPreibisch]

After re-running the build from the travis website it now does not find the jar with the class itself - maybe that is now because this one was deployed before, I am really stuck here ...

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-deploy-plugin:2.8.2:deploy (default-deploy) on project SPIM_Registration: Failed to deploy artifacts: Could not transfer artifact sc.fiji:SPIM_Registration:jar:5.0.16 from/to imagej.releases (dav:http://maven.imagej.net/content/repositories/releases): Failed to transfer file: http://maven.imagej.net/content/repositories/releases/sc/fiji/SPIM_Registration/5.0.16/SPIM_Registration-5.0.16.jar. Return code is: 400 -> [Help 1]

[StephanPreibisch]

Well, I anyway put SPIM_Registration-5.0.16.jar into the Fiji uploader for now. @RichardMyers can you check if it works now again?

[StephanPreibisch]

Travis really only seems to work for Snapshots currently: https://github.com/fiji/SPIM_Registration/commits/master There is again no change except the pom-version itself ... I wonder what's behind that. I am also not sure why it only tries to compile some of the commits, what triggers it? Thanks for any insights in advance @ctrueden

[RichardMyers]

Thanks @StephanPreibisch! that fixed it. Using latest SPIM_Registration-5.0.16.jar SLD files can again be read.

[ctrueden]

Return code is: 400

This happens because you have a release version instead of a SNAPSHOT version. You can only deploy each release version to the repository once. In other words: releases are immutable. It is very important to "bump to next development cycle" after doing a release, changing e.g. 5.0.16 to 5.0.17-SNAPSHOT in the next commit. Otherwise you will receive this error, and your Git history will be ambiguous in that you cannot tell by inspection if a particular commit is the real 5.0.16 or not.

[StephanPreibisch]

Hi, thanks @ctrueden! But this only explains the follow up error, but it really happens for every release that I make, maybe it is best explained with this annotated screenshot: The precise change was:

It feels like I do not understand something conceptually ... thanks so much for your help @ctrueden

[StephanPreibisch]

Another example is release version 5.0.13, exactly same thing, just the version in the pom.xml changed and it does not compile: https://github.com/fiji/SPIM_Registration/commit/2d1d9c4c4e9edd101936252ce6f43649b847afe9

[ctrueden]

Thanks for the clarification, @StephanPreibisch. I took a look earlier this week and it was not immediately obvious to me what the heck is going on. I'm planning to look again in more detail soon, but have a couple of urgent things on my plate to take care of first. I'll follow up again when I can.

[StephanPreibisch]

Thanks a lot @ctrueden! It is not that urgent, things work despite of it. I just kind of want to understand if I do something wrong or if it is a hiccup of travis :)

[StephanPreibisch]

Sorry for forgetting the NOT :)