Merge pull request ebremer#8 from ebremer/develop

Develop
SBU-BMI · Feb 18, 2022 · e2f7b54 · e2f7b54
2 parents 8c6a71e + fdcb561
commit e2f7b54
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Showing 17 changed files with 952 additions and 344 deletions.
diff --git a/config/jni-config.json b/config/jni-config.json
@@ -1,4 +1,7 @@
 [
+{
+ "name":"[Lsun.java2d.loops.GraphicsPrimitive;"
+},
 {
  "name":"com.sun.imageio.plugins.jpeg.JPEGImageReader",
  "methods":[
@@ -24,14 +27,6 @@
  {"name":"writeOutputData","parameterTypes":["byte[]","int","int"] }
  ]
 },
-{
- "name":"java.awt.AWTEvent",
- "fields":[
- {"name":"bdata"}, 
- {"name":"consumed"}, 
- {"name":"id"}
- ]
-},
 {
  "name":"java.awt.AlphaComposite",
  "fields":[
@@ -65,28 +60,12 @@
  ]
 },
 {
- "name":"java.awt.Font",
- "fields":[
- {"name":"pData"}, 
- {"name":"size"}, 
- {"name":"style"}
- ],
- "methods":[
- {"name":"getFamily_NoClientCode","parameterTypes":[] }, 
- {"name":"getFontPeer","parameterTypes":[] }
- ]
-},
-{
- "name":"java.awt.event.InputEvent",
- "fields":[{"name":"modifiers"}]
+ "name":"java.awt.GraphicsEnvironment",
+ "methods":[{"name":"isHeadless","parameterTypes":[] }]
 },
 {
  "name":"java.awt.event.KeyEvent",
- "fields":[
- {"name":"isProxyActive"}, 
- {"name":"keyChar"}, 
- {"name":"keyCode"}
- ]
+ "fields":[{"name":"isProxyActive"}]
 },
 {
  "name":"java.awt.geom.AffineTransform",
@@ -189,13 +168,24 @@
  {"name":"maxBitSize"}
  ]
 },
+{
+ "name":"java.lang.Boolean",
+ "methods":[{"name":"getBoolean","parameterTypes":["java.lang.String"] }]
+},
 {
  "name":"java.lang.ClassLoader",
  "methods":[
  {"name":"getPlatformClassLoader","parameterTypes":[] }, 
  {"name":"loadClass","parameterTypes":["java.lang.String"] }
  ]
 },
+{
+ "name":"java.lang.System",
+ "methods":[
+ {"name":"load","parameterTypes":["java.lang.String"] }, 
+ {"name":"setProperty","parameterTypes":["java.lang.String","java.lang.String"] }
+ ]
+},
 {
  "name":"javax.imageio.plugins.jpeg.JPEGHuffmanTable",
  "fields":[
@@ -211,7 +201,7 @@
  "name":"jdk.internal.loader.ClassLoaders$PlatformClassLoader"
 },
 {
- "name":"org.graalvm.nativebridge.jni.JNIExceptionWrapperEntryPoints",
+ "name":"org.graalvm.jniutils.JNIExceptionWrapperEntryPoints",
  "methods":[{"name":"getClassName","parameterTypes":["java.lang.Class"] }]
 },
 {
@@ -380,9 +370,6 @@
  "name":"sun.java2d.loops.GraphicsPrimitiveMgr",
  "methods":[{"name":"register","parameterTypes":["sun.java2d.loops.GraphicsPrimitive[]"] }]
 },
-{
- "name":"sun.java2d.loops.GraphicsPrimitive[]"
-},
 {
  "name":"sun.java2d.loops.MaskBlit",
  "methods":[{"name":"<init>","parameterTypes":["long","sun.java2d.loops.SurfaceType","sun.java2d.loops.CompositeType","sun.java2d.loops.SurfaceType"] }]

diff --git a/config/reflect-config.json b/config/reflect-config.json
@@ -1,28 +1,4 @@
 [
-{
- "name":"ch.qos.logback.classic.pattern.DateConverter",
- "methods":[{"name":"<init>","parameterTypes":[] }]
-},
-{
- "name":"ch.qos.logback.classic.pattern.LevelConverter",
- "methods":[{"name":"<init>","parameterTypes":[] }]
-},
-{
- "name":"ch.qos.logback.classic.pattern.LineSeparatorConverter",
- "methods":[{"name":"<init>","parameterTypes":[] }]
-},
-{
- "name":"ch.qos.logback.classic.pattern.LoggerConverter",
- "methods":[{"name":"<init>","parameterTypes":[] }]
-},
-{
- "name":"ch.qos.logback.classic.pattern.MessageConverter",
- "methods":[{"name":"<init>","parameterTypes":[] }]
-},
-{
- "name":"ch.qos.logback.classic.pattern.ThreadConverter",
- "methods":[{"name":"<init>","parameterTypes":[] }]
-},
 {
  "name":"java.awt.image.AffineTransformOp"
 },
@@ -51,9 +27,6 @@
 {
  "name":"java.security.AllPermission"
 },
-{
- "name":"java.security.MessageDigestSpi"
-},
 {
  "name":"java.security.SecureRandomParameters"
 },
@@ -68,9 +41,9 @@
 },
 {
  "name":"javax.imageio.spi.ImageReaderWriterSpi",
- "methods":[
+ "methods":[{"name":"getFormatNames","parameterTypes":[] }],
+ "queriedMethods":[
  {"name":"getFileSuffixes","parameterTypes":[] }, 
- {"name":"getFormatNames","parameterTypes":[] }, 
  {"name":"getMIMETypes","parameterTypes":[] }
  ]
 },
@@ -172,10 +145,6 @@
 {
  "name":"ome.codecs.services.LuraWaveServiceImpl"
 },
-{
- "name":"sun.awt.X11GraphicsEnvironment",
- "methods":[{"name":"<init>","parameterTypes":[] }]
-},
 {
  "name":"sun.java2d.marlin.DMarlinRenderingEngine",
  "methods":[{"name":"<init>","parameterTypes":[] }]

diff --git a/config/resource-config.json b/config/resource-config.json
@@ -1,14 +1,33 @@
 {
  "resources":{
  "includes":[
- {"pattern":"\\Qloci/common/services/services.properties\\E"}, 
- {"pattern":"\\Qloci/formats/FormatTools.class\\E"}, 
- {"pattern":"\\Qorg/joda/time/tz/data/America/Chicago\\E"}, 
- {"pattern":"\\Qorg/joda/time/tz/data/America/Denver\\E"}, 
- {"pattern":"\\Qorg/joda/time/tz/data/America/Los_Angeles\\E"}, 
- {"pattern":"\\Qorg/joda/time/tz/data/America/New_York\\E"}, 
- {"pattern":"\\Qorg/joda/time/tz/data/ZoneInfoMap\\E"}, 
- {"pattern":"\\Qorg/slf4j/impl/StaticLoggerBinder.class\\E"}
+ {
+ "pattern":"\\Qloci/common/services/services.properties\\E"
+ }, 
+ {
+ "pattern":"\\Qloci/formats/FormatTools.class\\E"
+ }, 
+ {
+ "pattern":"\\Qorg/joda/time/tz/data/America/Chicago\\E"
+ }, 
+ {
+ "pattern":"\\Qorg/joda/time/tz/data/America/Denver\\E"
+ }, 
+ {
+ "pattern":"\\Qorg/joda/time/tz/data/America/Los_Angeles\\E"
+ }, 
+ {
+ "pattern":"\\Qorg/joda/time/tz/data/America/New_York\\E"
+ }, 
+ {
+ "pattern":"\\Qorg/joda/time/tz/data/ZoneInfoMap\\E"
+ }, 
+ {
+ "pattern":"\\Qorg/slf4j/impl/StaticLoggerBinder.class\\E"
+ }
  ]},
- "bundles":[{"name":"sun.awt.resources.awt"}]
+ "bundles":[{
+ "name":"sun.awt.resources.awt",
+ "classNames":["sun.awt.resources.awt"]
+ }]
 }
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -3,7 +3,7 @@
  <modelVersion>4.0.0</modelVersion>
  <groupId>edu.stonybrook.bmi</groupId>
  <artifactId>hatch</artifactId>
- <version>1.1.1</version>
+ <version>1.1.3</version>
  <build>
  <plugins>
  <plugin>
@@ -56,8 +56,8 @@
  </repository>
  </repositories>
  <properties>
- <maven.compiler.target>17</maven.compiler.target>
- <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>11</maven.compiler.source>
  <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
  <ver.bioformats>6.7.0</ver.bioformats>
  </properties>

diff --git a/hatch.build_artifacts.txt b/hatch.build_artifacts.txt
@@ -0,0 +1,3 @@
+[EXECUTABLE]
+hatch
+
diff --git a/nbactions.xml b/nbactions.xml
@@ -1,55 +1,55 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<actions>
- <action>
- <actionName>run</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
- </goals>
- <properties>
- <exec.vmArgs></exec.vmArgs>
- <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
- <exec.appArgs>-v /vsi/001738-000598_01_01_2019071702.vsi /vsi/final.tif</exec.appArgs>
- <exec.mainClass>edu.stonybrook.bmi.hatch.VSI2TIF</exec.mainClass>
- <exec.executable>java</exec.executable>
- </properties>
- </action>
- <action>
- <actionName>debug</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
- </goals>
- <properties>
- <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
- <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
- <exec.appArgs>-v /vsi/001738-000598_01_01_2019071702.vsi /vsi/final.tif</exec.appArgs>
- <exec.mainClass>edu.stonybrook.bmi.hatch.VSI2TIF</exec.mainClass>
- <exec.executable>java</exec.executable>
- <jpda.listen>true</jpda.listen>
- </properties>
- </action>
- <action>
- <actionName>profile</actionName>
- <packagings>
- <packaging>jar</packaging>
- </packagings>
- <goals>
- <goal>process-classes</goal>
- <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
- </goals>
- <properties>
- <exec.vmArgs></exec.vmArgs>
- <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
- <exec.mainClass>edu.stonybrook.bmi.hatch.VSI2TIF</exec.mainClass>
- <exec.executable>java</exec.executable>
- <exec.appArgs>-v /vsi/001738-000598_01_01_2019071702.vsi /vsi/final.tif</exec.appArgs>
- </properties>
- </action>
- </actions>
+<?xml version="1.0" encoding="UTF-8"?>
+<actions>
+ <action>
+ <actionName>run</actionName>
+ <packagings>
+ <packaging>jar</packaging>
+ </packagings>
+ <goals>
+ <goal>process-classes</goal>
+ <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+ </goals>
+ <properties>
+ <exec.vmArgs></exec.vmArgs>
+ <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+ <exec.appArgs>-v /vsi/PC380089.vsi /vsi/final2.tif</exec.appArgs>
+ <exec.mainClass>edu.stonybrook.bmi.hatch.VSI2TIF</exec.mainClass>
+ <exec.executable>java</exec.executable>
+ </properties>
+ </action>
+ <action>
+ <actionName>debug</actionName>
+ <packagings>
+ <packaging>jar</packaging>
+ </packagings>
+ <goals>
+ <goal>process-classes</goal>
+ <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+ </goals>
+ <properties>
+ <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
+ <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+ <exec.appArgs>-v /vsi/PC380089.vsi /vsi/final2.tif</exec.appArgs>
+ <exec.mainClass>edu.stonybrook.bmi.hatch.VSI2TIF</exec.mainClass>
+ <exec.executable>java</exec.executable>
+ <jpda.listen>true</jpda.listen>
+ </properties>
+ </action>
+ <action>
+ <actionName>profile</actionName>
+ <packagings>
+ <packaging>jar</packaging>
+ </packagings>
+ <goals>
+ <goal>process-classes</goal>
+ <goal>org.codehaus.mojo:exec-maven-plugin:3.0.0:exec</goal>
+ </goals>
+ <properties>
+ <exec.vmArgs></exec.vmArgs>
+ <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
+ <exec.mainClass>edu.stonybrook.bmi.hatch.VSI2TIF</exec.mainClass>
+ <exec.executable>java</exec.executable>
+ <exec.appArgs>-v /vsi/PC380089.vsi /vsi/final2.tif</exec.appArgs>
+ </properties>
+ </action>
+ </actions>