Merge pull request #12 from chris-allan/omero56-bf64

OMERO 5.6.x support

README.md

@@ -6,7 +6,7 @@ Annotation converter to and from OME-XML
 Requirements
 ============
 
-* OMERO 5.4.x+
+* OMERO 5.6.x+
 * Java 8+
 
 Workflow

build.gradle

@@ -1,7 +1,6 @@
 plugins {
     id 'application'
     id 'eclipse'
-    id 'java'
 }
 
 group = 'com.glencoesoftware.roitool'
@@ -25,57 +24,35 @@ repositories {
 
 configurations.all {
     resolutionStrategy.cacheChangingModulesFor 0, 'minutes'
-    exclude group: 'OME'
-    exclude group: 'antlr'
-    exclude group: 'asm'
-    exclude group: 'backport-util-concurrent'
-    exclude group: 'batik'
-    exclude group: 'cglib'
-    exclude group: 'checkstyle'
+    exclude group: 'com.drewnoakes'
     exclude group: 'com.jamonapi'
     exclude group: 'com.mortennobel'
-    exclude group: 'com.zeroc', module: 'freeze'
-    exclude group: 'com.zeroc', module: 'icefreeze'
-    exclude group: 'com.zeroc', module: 'icegrid'
     exclude group: 'com.zeroc', module: 'icestorm'
     exclude group: 'commons-beanutils'
     exclude group: 'commons-codec'
-    exclude group: 'commons-collections'
-    exclude group: 'commons-io'
-    exclude group: 'commons-lang'
-    exclude group: 'commons-pool'
-    exclude group: 'dom4j'
-    exclude group: 'edu.ucar'
-    exclude group: 'freemarker'
+    exclude group: 'geronimo-spec'
     exclude group: 'gnu.getopt'
-    exclude group: 'hsqldb'
-    exclude group: 'javassist'
-    exclude group: 'javax.jts'
-    exclude group: 'jmock'
-    exclude group: 'net.sourceforge.findbugs'
-    exclude group: 'org.apache.ant'
-    exclude group: 'org.apache.lucene'
+    exclude group: 'net.sf.ehcache'
+    exclude group: 'org.apache.commons'
     exclude group: 'org.apache.httpcomponents'
+    exclude group: 'org.apache.pdfbox'
+    exclude group: 'org.apache.xmlgraphics'
     exclude group: 'org.ini4j'
-    exclude group: 'org.uncommons'
+    exclude group: 'org.javassist'
+    exclude group: 'org.quartz-scheduler'
     exclude group: 'org.subethamail'
-    exclude group: 'pdfbox'
-    exclude group: 'quartz'
     exclude group: 'xerces'
     exclude group: 'xalan'
-    exclude group: 'xml-apis'
-    exclude group: 'zeroc', module: 'ice-db'
 }
 
 dependencies {
-    compile ('omero:blitz:5.4.10-ice36-b105') {
-        exclude group: 'org.testng', module: 'testng'
-    }
-    compile 'ch.qos.logback:logback-classic:1.1.7'
-    compile 'ch.qos.logback:logback-core:1.1.7'
-    compile 'net.sourceforge.argparse4j:argparse4j:0.7.0'
-    compile 'info.picocli:picocli:3.9.3'
-    testCompile 'org.testng:testng:6.10'
+    implementation 'org.openmicroscopy:omero-blitz:5.5.6'
+    implementation 'com.zeroc:icegrid:3.6.4'
+    implementation 'org.slf4j:slf4j-api:1.7.30'
+    implementation 'org.slf4j:log4j-over-slf4j:1.7.30'
+    implementation 'ch.qos.logback:logback-classic:1.2.3'
+    implementation 'info.picocli:picocli:3.9.3'
+    testImplementation 'org.testng:testng:6.10'
 }
 
 jar {

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.3-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.1-bin.zip

gradlew

@@ -1,5 +1,21 @@
 #!/usr/bin/env sh
 
+#
+# Copyright 2015 the original author or authors.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      https://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
 ##############################################################################
 ##
 ##  Gradle start up script for UN*X
@@ -28,7 +44,7 @@ APP_NAME="Gradle"
 APP_BASE_NAME=`basename "$0"`
 
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS=""
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
@@ -109,8 +125,8 @@ if $darwin; then
     GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
 fi
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
     APP_HOME=`cygpath --path --mixed "$APP_HOME"`
     CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
     JAVACMD=`cygpath --unix "$JAVACMD"`
@@ -138,19 +154,19 @@ if $cygwin ; then
         else
             eval `echo args$i`="\"$arg\""
         fi
-        i=$((i+1))
+        i=`expr $i + 1`
     done
     case $i in
-        (0) set -- ;;
-        (1) set -- "$args0" ;;
-        (2) set -- "$args0" "$args1" ;;
-        (3) set -- "$args0" "$args1" "$args2" ;;
-        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+        0) set -- ;;
+        1) set -- "$args0" ;;
+        2) set -- "$args0" "$args1" ;;
+        3) set -- "$args0" "$args1" "$args2" ;;
+        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
     esac
 fi
 
@@ -159,14 +175,9 @@ save () {
     for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
     echo " "
 }
-APP_ARGS=$(save "$@")
+APP_ARGS=`save "$@"`
 
 # Collect all arguments for the java command, following the shell quoting and substitution rules
 eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
 
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
-  cd "$(dirname "$0")"
-fi
-
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -1,3 +1,19 @@
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
 @if "%DEBUG%" == "" @echo off
 @rem ##########################################################################
 @rem
@@ -13,8 +29,11 @@ if "%DIRNAME%" == "" set DIRNAME=.
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
 @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS=
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome