add maven transformer for n5 compression to trakem2 module (should ha…

…ve done this when the problem was fixed for the other modules)
tpietzsch · Sep 9, 2024 · b714212 · b714212
1 parent d055aa9
commit b714212
Showing 1 changed file with 37 additions and 2 deletions.
diff --git a/trakem2-scripts/pom.xml b/trakem2-scripts/pom.xml
@@ -30,6 +30,35 @@
 
                             <outputFile>target/render-ws_trakem2_plugins-${project.version}.jar</outputFile>
 
+                            <transformers>
+
+                                <!--
+                                    Compression implementations defined in org.janelia.saalfeldlab:n5,
+                                    org.janelia.saalfeldlab:n5-blosc, and org.janelia:n5-zstandard get built/serialized
+                                    into META-INF/json/org.janelia.saalfeldlab.n5.Compression$CompressionType files by
+                                    https://github.com/scijava/scijava-common/blob/master/src/main/java/org/scijava/annotations/AnnotationCombiner.java
+
+                                    The serializations need to be combined into a single resource for this fat jar
+                                    ( see https://imagej.net/imagej-wiki-static/Uber-JAR ).
+
+                                    Note that the org.janelia.saalfeldlab:n5-blosc implementation is excluded in the
+                                    filters area below because we don't currently need it.
+                                -->
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer"
+                                             combine.children="append">
+                                    <resource>META-INF/json/org.janelia.saalfeldlab.n5.Compression$CompressionType</resource>
+                                </transformer>
+
+                                <!-- copied these transformers from hot-knife pom.xml -->
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                                    <resource>META-INF/json/org.scijava.plugin.Plugin</resource>
+                                </transformer>
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                                    <resource>META-INF/json/mpicbg.spim.data.generic.sequence.ImgLoaderIo</resource>
+                                </transformer>
+
+                            </transformers>
+
                             <filters>
 
                                 <!-- filter out overlapping or irrelevant resources and classes -->
@@ -67,10 +96,16 @@
                                         <exclude>*.jq</exclude>
                                     </excludes>
                                 </filter>
+                                <!--
+                                    Filter out org.janelia.saalfeldlab:n5-blosc compression support because
+                                    we don't currently need it.
+                                    It produces distracting java.lang.UnsatisfiedLinkError warning messages in
+                                    environments where blosc is not independently installed.
+                                -->
                                 <filter>
-                                    <artifact>org.janelia.saalfeldlab:n5-*</artifact>
+                                    <artifact>org.janelia.saalfeldlab:n5-blosc</artifact>
                                     <excludes>
-                                        <exclude>META-INF/json/org.janelia.saalfeldlab.n5.Compression*</exclude>
+                                        <exclude>META-INF/json/org.janelia.saalfeldlab.n5.Compression$CompressionType</exclude>
                                     </excludes>
                                 </filter>
                             </filters>