OpenSPIM update site needs to reconsider micromanager-dev dependency

[hinerm]

The auto-enabling of the micromanager-dev update site is confusing, as there is no indication that it is tied to OpenSPIM.

When disabling micromanager-dev without disabling OpenSPIM, micromanager attempts to reinstall itself on Fiji restart.

See:
http://fiji.sc/bugzilla/show_bug.cgi?id=1075
https://list.nih.gov/cgi-bin/wa.exe?A2=ind1505&L=IMAGEJ&F=&S=&P=181254

So, we certainly need update site dependencies, but this silent work-around is problematic - especially given that micromanager-dev is not a public update site (e.g. not on the wiki or publicized anywhere else from what I can tell).

Also, to uninstall OpenSPIM I have to:

1. Turn off the OpenSPIM update site
2. Turn off micromanager-dev

If I try disabling both OpenSPIM and micromanager-dev simultaneously I get:

[ERROR] Cannot create plugin: class='org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage', name='JavaScript', priority=0.0, enabled=true, pluginType=ScriptLanguage
java.lang.NullPointerException
    at org.scijava.script.AdaptedScriptLanguage.<init>(AdaptedScriptLanguage.java:63)
    at org.scijava.script.AdaptedScriptLanguage.<init>(AdaptedScriptLanguage.java:73)
    at org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage.<init>(JavaScriptScriptLanguage.java:59)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:408)
    at java.lang.Class.newInstance(Class.java:438)
    at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:302)
    at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:236)
    at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:225)
    at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:216)
    at org.scijava.plugin.AbstractSingletonService.initInstances(AbstractSingletonService.java:114)
    at org.scijava.plugin.AbstractSingletonService.getInstances(AbstractSingletonService.java:72)
    at org.scijava.script.DefaultScriptService.initScriptLanguageIndex(DefaultScriptService.java:342)
    at org.scijava.script.DefaultScriptService.scriptLanguageIndex(DefaultScriptService.java:307)
    at org.scijava.script.DefaultScriptService.getIndex(DefaultScriptService.java:117)
    at org.scijava.script.DefaultScriptService.canHandleFile(DefaultScriptService.java:233)
    at org.scijava.script.ScriptFinder.discoverScripts(ScriptFinder.java:131)
    at org.scijava.script.ScriptFinder.discoverScripts(ScriptFinder.java:125)
    at org.scijava.script.ScriptFinder.findScripts(ScriptFinder.java:93)
    at org.scijava.script.DefaultScriptService.initScripts(DefaultScriptService.java:391)
    at org.scijava.script.DefaultScriptService.scripts(DefaultScriptService.java:325)
    at org.scijava.script.DefaultScriptService.getScripts(DefaultScriptService.java:167)
    at net.imagej.legacy.LegacyService.getScriptsAndNonLegacyCommands(LegacyService.java:627)
    at net.imagej.legacy.IJ1Helper.addMenuItems(IJ1Helper.java:630)
    at net.imagej.legacy.LegacyService.initialize(LegacyService.java:501)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:353)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
    at org.scijava.Context.<init>(Context.java:267)
    at org.scijava.Context.<init>(Context.java:224)
    at org.scijava.Context.<init>(Context.java:163)
    at org.scijava.Context.<init>(Context.java:119)
    at org.scijava.Context.<init>(Context.java:107)
    at net.imagej.ImageJ.<init>(ImageJ.java:82)
    at net.imagej.Main.launch(Main.java:61)
    at net.imagej.Main.main(Main.java:73)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:483)
    at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
    at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
    at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
java.net.MalformedURLException
    at java.net.URL.<init>(URL.java:620)
    at java.net.URL.<init>(URL.java:483)
    at java.net.URL.<init>(URL.java:432)
    at net.imagej.updater.util.Downloader.download(Downloader.java:106)
    at net.imagej.updater.util.Downloader.start(Downloader.java:98)
    at net.imagej.updater.Installer.start(Installer.java:154)
    at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:629)
    at net.imagej.ui.swing.updater.UpdaterFrame$13.run(UpdaterFrame.java:566)
Caused by: java.lang.NullPointerException
    at java.net.URL.<init>(URL.java:525)

[ctrueden]

Cannot create plugin: class='org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage', name='JavaScript', priority=0.0, enabled=true, pluginType=ScriptLanguage
java.lang.NullPointerException
    at org.scijava.script.AdaptedScriptLanguage.<init>(AdaptedScriptLanguage.java:63)

This first exception is imagej/ImageJ#116.

[dscho]

OpenSPIM simply requires Micro-Manager. The users should not have reported this as a Fiji problem, because they clearly set up an OpenSPIM software. Not your fault, @hinerm & @ctrueden!

[dscho]

@hkmoon as a clue bat, maybe you could insert something like

Helper.log("Enabling the Micro-Manager-dev update site because OpenSPIM requires it!");

before

openspim-app/src/main/java/org/openspim/app/OpenSPIMService.java

Line 57 in 4469e05

if (siteMM != null) {

, and insert

public static void log(final String msg) {
   IJ.log(msg);
}

into https://github.com/openspim/openspim-app/blob/4469e05bca800b3957b4f12cc64a6f80ae48add3/src/main/java/org/openspim/app/Helper.java ... we cannot use ImageJ 1.x classes in the OpenSPIMService class directly because then they would be loaded already when loading (as opposed to running) the OpenSPIMService class, which would prevent the legacy support from runtime-patching the ImageJ 1.x classes.

[hkmoon]

@dscho Actually, do you want me to put those codes in the master branch?

[dscho]

Sorry for the late response: yep, on master. We will also have to upload a new build to the update site after that.