<div dir="ltr">Hi Pietro,<div><br></div><div><div><div>> java.lang.IllegalArgumentException: No compatible service:</div><div>> io.scif.SCIFIOService</div></div><div><br></div><div>You have been bitten by the annotation combining problem: many of the JAR files you are trying to combine have a file at META-INF/json/org.scijava.plugin.Plugin, which lists the plugins included in that JAR file. All of these files need to be appended to one another and stored within your uber-JAR, or else plugins will not be discoverable. The scheme you are using to build your uberjar is likely not merging these files as needed.</div><div><br></div><div>We provide some code in scijava-common to facilitate combining this metadata in the correct way. If you are using Maven to build, you can use it via the following configuration in your pom.xml:</div><div><br></div><div> <a href="https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-22/pom.xml#L577-L594">https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-22/pom.xml#L577-L594</a><br></div><div><br></div><div>See also:</div><div><a href="https://github.com/scijava/scijava-common/issues/37">https://github.com/scijava/scijava-common/issues/37</a><br></div><div><br></div><div>Regards,</div><div>Curtis</div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 15, 2015 at 7:02 AM, Pietro Incardona <span dir="ltr"><<a href="mailto:incardon@mpi-cbg.de" target="_blank">incardon@mpi-cbg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Hi Curtis<br>
<br>
I already strongly suggest to use Fiji/ImageJ2, but I would like (if
reasonably possible) to maintain an imageJ version<br>
<br>
I packed this in the jar file<br>
<br>
/imglib2-2.0.0-beta-26.jar<br>
/imglib2-2.0.0-SNAPSHOT.jar<br>
/imglib2-algorithms-2.0.0-beta-26.jar<br>
/imglib2-algorithms-gpl-2.0.0-beta-26.jar<br>
/imglib2-algorithms-legacy-2.0.0-beta-26.jar<br>
/imglib2-ij-2.0.0-beta-26.jar<br>
/imglib2-meta-2.0.0-beta-26.jar<br>
/imglib2-ops-2.0.0-beta-26.jar<br>
/imglib2-realtransform-2.0.0-beta-26.jar<br>
/imglib2-ui-2.0.0-SNAPSHOT.jar<br>
/scifio-0.16.5.jar<br>
/scifio-bf-compat-1.8.4.jar<br>
/scifio-cli-0.1.0.jar<br>
/scifio-jai-imageio-1.1.0.jar<br>
/scifio-lifesci-0.5.2.jar<br>
/scifio-ome-xml-0.9.2.jar<br>
/scifio-tools-0.14.0.jar<br>
/scijava-common-2.33.0.jar<br>
/scijava-plugins-commands-0.1.7.jar<br>
/scijava-plugins-platforms-0.1.2.jar<br>
/scijava-plugins-text-markdown-0.1.1.jar<br>
/scijava-plugins-text-plain-0.1.1.jar<br>
/scijava-ui-awt-0.1.2.jar<br>
/scijava-ui-swing-0.3.0.jar<br>
<br>
<br>
Apparently it crashes on the instruction<br>
<br>
// create the ImgOpener<br>
ImgOpener imgOpener = new ImgOpener();<br>
<br>
ImageJ 1.48v; Java 1.6.0_24 [64-bit]; Linux 3.16.3-200.fc20.x86_64;
10MB of 455MB (2%)<br>
<br>
java.lang.IllegalArgumentException: No compatible service:
io.scif.SCIFIOService<br>
at
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:242)<br>
at
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:193)<br>
at
org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:169)<br>
at org.scijava.Context.<init>(Context.java:234)<br>
at org.scijava.Context.<init>(Context.java:195)<br>
at org.scijava.Context.<init>(Context.java:138)<br>
at org.scijava.Context.<init>(Context.java:126)<br>
at
io.scif.img.AbstractImgIOComponent.<init>(AbstractImgIOComponent.java:57)<br>
at io.scif.img.ImgOpener.<init>(ImgOpener.java:94)<br>
at
mosaic.core.utils.MosaicTest.processResult(MosaicTest.java:178)<br>
at mosaic.core.utils.MosaicTest.testPlugin(MosaicTest.java:335)<br>
at mosaic.plugins.test.Jtest.naturalization(Jtest.java:32)<br>
at mosaic.plugins.Jtest.setup(Jtest.java:39)<br>
at
ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:47)<br>
at ij.IJ.runUserPlugIn(IJ.java:201)<br>
at ij.IJ.runPlugIn(IJ.java:163)<br>
at ij.Executer.runCommand(Executer.java:131)<br>
at ij.Executer.run(Executer.java:64)<br>
at java.lang.Thread.run(Thread.java:662)<br>
<br>
<br>
Cheers<span class="HOEnZb"><font color="#888888"><br>
Pietro</font></span><div><div class="h5"><br>
<br>
<div>On 01/14/2015 05:07 PM, Curtis Rueden
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Pietro,
<div><br>
</div>
<div>
<div>> Is there any way to pack a jar with SCIFIO included
that work also in</div>
<div>> imageJ1</div>
</div>
<div><br>
</div>
<div>Certainly. But it would help to be more specific about what
you are trying to do.</div>
<div><br>
</div>
<div>By "pack a jar with SCIFIO" do you mean "create an uber-JAR
with dependencies embedded"? Or something else?</div>
<div><br>
</div>
<div>By "ImageJ1" do you mean the vanilla ImageJ1 distribution
from <a href="http://imagej.nih.gov" target="_blank">imagej.nih.gov</a>?
If so, you can do it, but I would recommend saving yourself a
lot of work and just recommending people use ImageJ2, which
comes with SCIFIO already bundled. But if you really want to
go that route, look at the maven-shade-plugin or
maven-assembly-plugin [1].</div>
<div><br>
</div>
<div>Regards,</div>
<div>Curtis</div>
<div><br>
</div>
<div>[1] Here is a starting point for how we create an ImageJ2
uber-JAR with dependencies: <a href="https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-22/pom.xml#L421-L648" target="_blank">https://github.com/imagej/imagej/blob/imagej-2.0.0-rc-22/pom.xml#L421-L648</a>.
Your use case would likely be simpler.</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jan 14, 2015 at 7:18 AM, Pietro
Incardona <span dir="ltr"><<a href="mailto:incardon@mpi-cbg.de" target="_blank">incardon@mpi-cbg.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi All<br>
<br>
Is there any way to pack a jar with SCIFIO included that
work also in imageJ1<br>
<br>
Cheers<br>
Pietro<br>
<br>
<br>
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</blockquote>
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</div></div></div>
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