Don't minify the jar, possible fix for errors with parsing some files

build.gradle

@@ -3,13 +3,13 @@ plugins {
     id 'application'
     id 'maven'
     id 'idea'
-    id 'com.github.johnrengelman.shadow' version '4.0.3'
+    id 'com.github.johnrengelman.shadow' version '4.0.4'
     id 'edu.sc.seis.launch4j' version '2.4.4'
     id "com.github.ben-manes.versions" version '0.20.0'
 }
 
 group = 'com.dmtavt'
-version = '1.1'
+version = '1.2.b03'
 
 description = """DeltaMass - detection and visualization of common mass shifts in proteomic searches."""
 
@@ -29,12 +29,18 @@ jar {
 
 shadowJar {
     classifier = null
-    minimize {
-        exclude(dependency('javax.xml.bind:jaxb-api:.*'))
-        exclude(dependency('org.glassfish.jaxb:jaxb-runtime:.*'))
-        exclude(dependency('javax.activation:javax.activation-api:.*'))
-        exclude(dependency('com.sun.istack:istack-commons-runtime:.*'))
-    }
+//    minimize {
+//        exclude(dependency("javax.xml.bind:jaxb-api:.*"))
+//        exclude(dependency("javax.activation:javax.activation-api:.*"))
+//        exclude(dependency("org.glassfish.jaxb:jaxb-runtime:.*"))
+//        exclude(dependency("javax.xml.bind:jaxb-api:.*"))
+//        exclude(dependency("org.glassfish.jaxb:txw2:.*"))
+//        exclude(dependency("com.sun.istack:istack-commons-runtime:.*"))
+//        exclude(dependency("org.jvnet.staxex:stax-ex:.*"))
+//        exclude(dependency("com.sun.xml.fastinfoset:FastInfoset:.*"))
+//        exclude(dependency("javax.activation:javax.activation-api:.*"))
+        //exclude(dependency(""))
+//    }
 }
 
 launch4j {
@@ -89,5 +95,5 @@ dependencies {
     // test
     testCompile(group: 'org.apache.maven', name: 'maven-model', version: '3.6.0')
     testCompile group: 'junit', name: 'junit', version: '4.12'
-    testCompile("org.assertj:assertj-core:3.11.1")
+    testCompile("org.assertj:assertj-core:3.12.0")
 }

src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java

@@ -20,7 +20,7 @@ public final class DeltaMassInfo {
   private static final EventBus bus = EventBus.getDefault();
 
   public static final String Name = "DeltaMass";
-  public static final String Ver = "1.1";
+  public static final String Ver = "1.2.b03";
 
   private static final String PROP_VER = "deltamass.version.current";
   private static final String PROP_DOWNLOAD_URL = "deltamass.download.url";

src/main/resources/logback.xml

@@ -1,13 +1,13 @@
 <configuration>
 
-  <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
-    <!-- encoders are assigned the type ch.qos.logback.classic.encoder.PatternLayoutEncoder by default -->
-    <encoder>
-      <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
-    </encoder>
-  </appender>
+<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
+  <!-- encoders are assigned the type ch.qos.logback.classic.encoder.PatternLayoutEncoder by default -->
+  <encoder>
+    <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
+  </encoder>
+</appender>
 
-  <root level="info">
-    <appender-ref ref="STDOUT" />
-  </root>
+<root level="info">
+  <appender-ref ref="STDOUT" />
+</root>
 </configuration>