Library updates, fixes

SBU-BMI · Jul 29, 2024 · ade3abb · ade3abb
1 parent 54935fb
commit ade3abb
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Showing 13 changed files with 272 additions and 159 deletions.
diff --git a/config/jni-config.json b/config/jni-config.json
@@ -1,8 +1,4 @@
 [
-{
-  "name":"java.io.IOException",
-  "methods":[{"name":"<init>","parameterTypes":["java.lang.String"] }]
-},
 {
   "name":"java.lang.Boolean",
   "methods":[{"name":"getBoolean","parameterTypes":["java.lang.String"] }]

diff --git a/config/reflect-config.json b/config/reflect-config.json
@@ -1,13 +1,4 @@
 [
-{
-  "name":"[[I"
-},
-{
-  "name":"[[J"
-},
-{
-  "name":"[[Lloci.formats.tiff.TiffRational;"
-},
 {
   "name":"boolean",
   "allDeclaredFields":true
@@ -22,6 +13,11 @@
   "queryAllDeclaredConstructors":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"com.beust.jcommander.converters.IntegerConverter",
+  "queryAllDeclaredConstructors":true,
+  "methods":[{"name":"<init>","parameterTypes":["java.lang.String"] }]
+},
 {
   "name":"com.beust.jcommander.validators.NoValidator",
   "methods":[{"name":"<init>","parameterTypes":[] }]
@@ -30,15 +26,34 @@
   "name":"com.beust.jcommander.validators.NoValueValidator",
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"com.sun.xml.internal.stream.XMLInputFactoryImpl",
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"edu.stonybrook.bmi.hatch.HatchParameters",
   "allDeclaredFields":true,
   "queryAllDeclaredMethods":true
 },
+{
+    "name" : "java.util.logging.FileHandler",
+    "methods" : [{ "name" : "<init>", "parameterTypes" : [] }]
+},
 {
   "name":"java.io.File",
   "allDeclaredFields":true
 },
+{
+  "name":"java.lang.Integer",
+  "allDeclaredFields":true
+},
+{
+  "name":"java.security.SecureRandomParameters"
+},
+{
+  "name":"java.util.concurrent.atomic.AtomicReference",
+  "fields":[{"name":"value"}]
+},
 {
   "name":"loci.common.Log4jTools",
   "methods":[{"name":"setRootLevel","parameterTypes":["java.lang.String"] }]
@@ -82,12 +97,6 @@
 {
   "name":"loci.formats.services.JPEGXRServiceImpl"
 },
-{
-  "name":"loci.formats.services.LuraWaveService"
-},
-{
-  "name":"loci.formats.services.LuraWaveServiceImpl"
-},
 {
   "name":"loci.formats.services.MDBService"
 },
@@ -120,21 +129,53 @@
   "name":"loci.formats.services.POIServiceImpl"
 },
 {
-  "name":"loci.formats.services.WlzService"
+  "name":"ome.codecs.services.JAIIIOService"
 },
 {
-  "name":"loci.formats.services.WlzServiceImpl"
+  "name":"ome.codecs.services.JAIIIOServiceImpl"
 },
 {
-  "name":"ome.codecs.services.JAIIIOService"
+  "name":"org.apache.jena.rdfpatch.system.InitPatch"
 },
 {
-  "name":"ome.codecs.services.JAIIIOServiceImpl"
+  "name":"org.apache.jena.rdfs.sys.InitRDFS"
 },
 {
-  "name":"ome.codecs.services.LuraWaveService"
+  "name":"org.apache.jena.riot.system.InitRIOT"
 },
 {
-  "name":"ome.codecs.services.LuraWaveServiceImpl"
+  "name":"org.apache.jena.shacl.sys.InitShacl"
+},
+{
+  "name":"org.apache.jena.shex.sys.InitShex"
+},
+{
+  "name":"org.apache.jena.sparql.system.InitARQ"
+},
+{
+  "name":"org.apache.jena.sys.InitJenaCore"
+},
+{
+  "name":"org.apache.jena.tdb1.sys.InitTDB"
+},
+{
+  "name":"org.apache.jena.tdb2.sys.InitTDB2"
+},
+{
+  "name":"org.apache.log4j.Level"
+},
+{
+  "name":"org.apache.xerces.jaxp.SAXParserFactoryImpl"
+},
+{
+  "name":"org.slf4j.simple.SimpleServiceProvider"
+},
+{
+  "name":"sun.security.provider.NativePRNG",
+  "methods":[{"name":"<init>","parameterTypes":[] }, {"name":"<init>","parameterTypes":["java.security.SecureRandomParameters"] }]
+},
+{
+  "name":"sun.security.provider.SHA",
+  "methods":[{"name":"<init>","parameterTypes":[] }]
 }
 ]
diff --git a/config/resource-config.json b/config/resource-config.json
@@ -1,27 +1,58 @@
 {
   "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"
-    }
-  ]},
-  "bundles":[]
+  "includes":[{
+    "pattern":"\\QMETA-INF/services/java.lang.System$LoggerFinder\\E"
+  }, {
+    "pattern":"\\QMETA-INF/services/java.util.spi.ResourceBundleControlProvider\\E"
+  }, {
+    "pattern":"\\QMETA-INF/services/javax.xml.parsers.SAXParserFactory\\E"
+  }, {
+    "pattern":"\\QMETA-INF/services/javax.xml.stream.XMLInputFactory\\E"
+  }, {
+    "pattern":"\\QMETA-INF/services/org.apache.jena.sys.JenaSubsystemLifecycle\\E"
+  }, {
+    "pattern":"\\QMETA-INF/services/org.slf4j.spi.SLF4JServiceProvider\\E"
+  }, {
+    "pattern":"\\Qetc/location-mapping.rdf\\E"
+  }, {
+    "pattern":"\\Qetc/location-mapping.ttl\\E"
+  }, {
+    "pattern":"\\Qlocation-mapping.rdf\\E"
+  }, {
+    "pattern":"\\Qlocation-mapping.ttl\\E"
+  }, {
+    "pattern":"\\Qloci/common/services/services.properties\\E"
+  }, {
+    "pattern":"\\Qloci/formats/FormatTools.class\\E"
+  }, {
+    "pattern":"\\Qlogging.properties\\E"
+  }, {
+    "pattern":"\\Qorg/apache/jena/ext/xerces/impl/xpath/regex/message.properties\\E"
+  }, {
+    "pattern":"\\Qorg/apache/jena/ext/xerces/impl/xpath/regex/message_en.properties\\E"
+  }, {
+    "pattern":"\\Qorg/apache/jena/ext/xerces/impl/xpath/regex/message_en_US.properties\\E"
+  }, {
+    "pattern":"\\Qorg/joda/time/tz/data/America/New_York\\E"
+  }, {
+    "pattern":"\\Qorg/joda/time/tz/data/ZoneInfoMap\\E"
+  }, {
+    "pattern":"\\Qsimplelogger.properties\\E"
+  }, {
+    "pattern":"java.logging:\\Qsun/util/logging/resources/logging_en.properties\\E"
+  }, {
+    "pattern":"java.logging:\\Qsun/util/logging/resources/logging_en_US.properties\\E"
+  }, {
+    "pattern":"java.xml:\\Qjdk/xml/internal/jdkcatalog/JDKCatalog.xml\\E"
+  }]},
+  "bundles":[{
+    "name":"org.apache.jena.ext.xerces.impl.xpath.regex.message",
+    "locales":["en-US"]
+  }, {
+    "name":"sun.text.resources.cldr.FormatData",
+    "locales":["en", "en-US", "und"]
+  }, {
+    "name":"sun.util.resources.cldr.CalendarData",
+    "locales":["und"]
+  }]
 }
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -45,7 +45,7 @@
           </plugin>
           <plugin>
             <artifactId>maven-shade-plugin</artifactId>
-            <version>3.5.1</version>
+            <version>3.5.2</version>
             <executions>
               <execution>
                 <phase>package</phase>
@@ -87,7 +87,7 @@
           <plugin>
             <groupId>org.graalvm.buildtools</groupId>
             <artifactId>native-maven-plugin</artifactId>
-            <version>0.10.0</version>
+            <version>0.10.1</version>
             <extensions>true</extensions>
             <executions>
               <execution>
@@ -146,6 +146,6 @@
     <twelvemonkeys.version>3.10.1</twelvemonkeys.version>
     <maven.compiler.source>21</maven.compiler.source>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-    <ver.bioformats>7.2.0</ver.bioformats>
+    <ver.bioformats>7.3.0</ver.bioformats>
   </properties>
 </project>
diff --git a/error.log b/error.log
@@ -0,0 +1,2 @@
+2024-05-15 12:34:25 SEVERE edu.stonybrook.bmi.hatch.Validate.file: D:\bad\dest\Image_01_M200_40X_A36.tif ==> index >= numImages (0 >= 0) 
+2024-05-15 12:34:25 SEVERE edu.stonybrook.bmi.hatch.Validate.file: D:\bad\dest\ugh.tif ==> Invalid TIFF byte order mark 'sd', expected: 'II' or 'MM' 
diff --git a/nbactions-hatchjar.xml b/nbactions-hatchjar.xml
@@ -12,7 +12,7 @@
             <properties>
                 <exec.vmArgs></exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.appArgs>-v -src D:\HalcyonStorage\hamid -dest D:\HalcyonStorage\hamid\tif</exec.appArgs>
+                <exec.appArgs>-v -src D:\bad\src -dest D:\bad\dest -validate</exec.appArgs>
                 <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
             </properties>
@@ -29,7 +29,7 @@
             <properties>
                 <exec.vmArgs>-agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
-                <exec.appArgs>-v -src D:\HalcyonStorage\hamid -dest D:\HalcyonStorage\hamid\tif</exec.appArgs>
+                <exec.appArgs>-v -src D:\bad\src -dest D:\bad\dest -validate</exec.appArgs>
                 <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
@@ -49,7 +49,7 @@
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.mainClass>edu.stonybrook.bmi.hatch.Hatch</exec.mainClass>
                 <exec.executable>java</exec.executable>
-                <exec.appArgs>-v -src D:\HalcyonStorage\hamid -dest D:\HalcyonStorage\hamid\tif</exec.appArgs>
+                <exec.appArgs>-v -src D:\bad\src -dest D:\bad\dest -validate</exec.appArgs>
             </properties>
         </action>
     </actions>
diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<maven.compiler.source>21</maven.compiler.source>
 		<maven.compiler.target>21</maven.compiler.target>
-		<ver.bioformats>7.2.0</ver.bioformats>
+		<ver.bioformats>7.3.0</ver.bioformats>
                 <twelvemonkeys.version>3.10.1</twelvemonkeys.version>
 	</properties>
 	<dependencies>
@@ -26,9 +26,9 @@
                 </exclusions>
             </dependency>
             <dependency>
-                <groupId>com.beust</groupId>
+                <groupId>org.jcommander</groupId>
                 <artifactId>jcommander</artifactId>
-                <version>1.82</version>
+                <version>1.83</version>
             </dependency>
             <dependency>
                 <groupId>com.twelvemonkeys.imageio</groupId>
@@ -41,7 +41,11 @@
                 <version>5.0.0</version>
                 <type>pom</type>
             </dependency>
-            <!--
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>slf4j-simple</artifactId>
+                <version>2.0.12</version>
+            </dependency>            <!--
             <dependency>
                 <groupId>com.ebremer.HalcyonProject</groupId>
                 <artifactId>halcyon-core</artifactId>
@@ -85,6 +89,9 @@
         <profiles>
             <profile>
                 <id>hatchjar</id>
+                <activation>
+                    <activeByDefault>true</activeByDefault>
+                </activation>
                 <build>
                     <finalName>hatch-${project.version}</finalName>
                     <plugins>
@@ -109,7 +116,7 @@
                         <plugin>
                             <groupId>org.apache.maven.plugins</groupId>
                             <artifactId>maven-shade-plugin</artifactId>
-                            <version>3.5.1</version>
+                            <version>3.5.2</version>
                             <configuration>
                                 <shadedArtifactAttached>false</shadedArtifactAttached>
                                 <transformers>
@@ -151,7 +158,7 @@
                         <plugin>
                             <groupId>org.graalvm.buildtools</groupId>
                             <artifactId>native-maven-plugin</artifactId>
-                            <version>0.10.0</version>
+                            <version>0.10.1</version>
                             <extensions>true</extensions>
                             <executions>
                                 <execution>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		2024-05-15 12:34:25 SEVERE edu.stonybrook.bmi.hatch.Validate.file: D:\bad\dest\Image_01_M200_40X_A36.tif ==> index >= numImages (0 >= 0)
		2024-05-15 12:34:25 SEVERE edu.stonybrook.bmi.hatch.Validate.file: D:\bad\dest\ugh.tif ==> Invalid TIFF byte order mark 'sd', expected: 'II' or 'MM'