Upgrade to Gradle 7.4

build.gradle

@@ -1,6 +1,4 @@
 allprojects  {
-  apply plugin: 'maven'
-
   group = 'org.insightcentre'
   version = '1.1'
 }

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.8-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4-bin.zip
 zipStoreBase=GRADLE_USER_HOME
-8ipStorePath=wrapper/dists
+zipStorePath=wrapper/dists

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='"-Xmx64m"'
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD="maximum"
@@ -66,6 +82,7 @@ esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
+
 # Determine the Java command to use to start the JVM.
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
@@ -109,10 +126,11 @@ 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"`
 
     # We build the pattern for arguments to be converted via cygpath
@@ -138,19 +156,19 @@ 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 +177,9 @@ 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
@@ -13,15 +29,18 @@ 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="-Xmx64m"
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
 
 @rem Find java.exe
 if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if "%ERRORLEVEL%" == "0" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -35,7 +54,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -45,28 +64,14 @@ echo location of your Java installation.
 
 goto fail
 
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
 :execute
 @rem Setup the command line
 
 set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
+
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
 
 :end
 @rem End local scope for the variables with windows NT shell

naisc-cili/build.gradle

@@ -10,30 +10,34 @@ buildscript {
 }
 
 plugins {
-    id "org.jetbrains.kotlin.jvm" version "1.3.50"
+    id "org.jetbrains.kotlin.jvm" version "1.6.10"
 }
 apply plugin: 'kotlin'
 repositories {
     mavenCentral()
 }
-dependencies {
-    compile "org.jetbrains.kotlin:kotlin-stdlib-jdk8:$kotlin_version"
-}
-compileKotlin {
-    kotlinOptions {
-        jvmTarget = "1.8"
-    }
-}
-compileTestKotlin {
-    kotlinOptions {
-        jvmTarget = "1.8"
-    }
-}
+//dependencies {
+//    implementation "org.jetbrains.kotlin:kotlin-stdlib-jdk8:$kotlin_version"
+//}
+//compileKotlin {
+//    kotlinOptions {
+//        jvmTarget = "1.8"
+//    }
+//}
+//compileTestKotlin {
+//    kotlinOptions {
+//        jvmTarget = "1.8"
+//    }
+//}
 
 dependencies {
-    compile project(':naisc-core')
-    testCompile 'junit:junit:4.13.1'
-    compile group: 'org.xerial', name: 'sqlite-jdbc', version: '3.28.0'
+    implementation project(':naisc-core')
+    implementation 'it.unimi.dsi:fastutil:7.0.11'
+    implementation 'org.apache.jena:jena-arq:3.9.0'
+    implementation group: 'org.apache.jena', name: 'jena-rdfconnection', version: '3.9.0'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.9'
+    testImplementation 'junit:junit:4.13.1'
+    implementation group: 'org.xerial', name: 'sqlite-jdbc', version: '3.28.0'
 }
 
 
@@ -43,8 +47,9 @@ task jarWithDeps(type: Jar, dependsOn:build) {
         	'Implementation-Version': version,
         	'Main-Class': 'org.insightcentre.uld.naisc.cili.MainKt'
     }
+    duplicatesStrategy = DuplicatesStrategy.INCLUDE
     baseName = project.name + '-all'
-    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
+    from { configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) } }
     with jar
 }
 

naisc-core/build.gradle

@@ -1,18 +1,18 @@
 dependencies {
-    compile 'com.fasterxml.jackson.core:jackson-annotations:2.10.0.pr2'
-    compile 'com.fasterxml.jackson.core:jackson-databind:2.10.0.pr2'
-    compile 'com.fasterxml.jackson.core:jackson-core:2.10.0.pr2'
-    compile 'org.apache.commons:commons-math3:3.5'
-    compile 'net.sf.jopt-simple:jopt-simple:4.9'
-    compile 'it.unimi.dsi:fastutil:7.0.11'
-    testCompile 'junit:junit:4.13.1'
-    compile 'org.apache.commons:commons-lang3:3.4'
-    compile 'org.apache.jena:jena-arq:3.9.0'
-    compile 'tw.edu.ntu.csie:libsvm:3.17'
-    compile 'org.slf4j:slf4j-nop:1.7.25'
-    compile 'org.apache.commons:commons-text:1.7'
-    compile group: 'org.jetbrains', name: 'annotations', version: '19.0.0'
-    compile group: 'org.apache.jena', name: 'jena-rdfconnection', version: '3.9.0'
+    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.10.0.pr2'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.10.0.pr2'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.10.0.pr2'
+    implementation 'org.apache.commons:commons-math3:3.5'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.9'
+    implementation 'it.unimi.dsi:fastutil:7.0.11'
+    testImplementation 'junit:junit:4.13.1'
+    implementation 'org.apache.commons:commons-lang3:3.4'
+    implementation 'org.apache.jena:jena-arq:3.9.0'
+    implementation 'tw.edu.ntu.csie:libsvm:3.17'
+    implementation 'org.slf4j:slf4j-nop:1.7.25'
+    implementation 'org.apache.commons:commons-text:1.7'
+    implementation group: 'org.jetbrains', name: 'annotations', version: '19.0.0'
+    implementation group: 'org.apache.jena', name: 'jena-rdfconnection', version: '3.9.0'
 }
 
 task jarWithDeps(type: Jar, dependsOn: build) {
@@ -21,8 +21,9 @@ task jarWithDeps(type: Jar, dependsOn: build) {
             'Implementation-Version': version,
             'Main-Class': 'org.insightcentre.uld.naisc.main.Main'
     }
+    duplicatesStrategy = DuplicatesStrategy.INCLUDE
     baseName = project.name + '-all'
-    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
+    from { configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) } }
     with jar
 }
 

naisc-elexis/build.gradle

@@ -5,7 +5,7 @@ plugins {
 }
 
 group = 'naisc'
-sourceCompatibility = '1.8'
+//sourceCompatibility = '1.8'
 
 repositories {
     mavenCentral()

naisc-meas/build.gradle

@@ -1,13 +1,15 @@
 dependencies {
-    compile project(':naisc-core')
-    testCompile 'junit:junit:4.13.1'
-    compile 'org.hamcrest:hamcrest-core:1.3'
-    compile 'commons-fileupload:commons-fileupload:1.3.3'
-    compile 'org.xerial:sqlite-jdbc:3.25.2'
-    compile 'org.eclipse.jetty:jetty-annotations:9.4.34.v20201102'    
-    compile 'org.eclipse.jetty:jetty-webapp:9.4.34.v20201102'    
-    compile 'org.eclipse.jetty:apache-jsp:9.4.34.v20201102'    
-    compile 'org.eclipse.jetty:apache-jstl:9.4.34.v20201102'    
+    implementation project(':naisc-core')
+    testImplementation 'junit:junit:4.13.1'
+    implementation 'org.hamcrest:hamcrest-core:1.3'
+    implementation 'commons-fileupload:commons-fileupload:1.3.3'
+    implementation 'org.xerial:sqlite-jdbc:3.25.2'
+    implementation 'org.eclipse.jetty:jetty-annotations:9.4.34.v20201102'    
+    implementation 'org.eclipse.jetty:jetty-webapp:9.4.34.v20201102'    
+    implementation 'org.eclipse.jetty:apache-jsp:9.4.34.v20201102'    
+    implementation 'org.eclipse.jetty:apache-jstl:9.4.34.v20201102'    
+    implementation 'org.apache.jena:jena-arq:3.9.0'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.9'
 }
 
 task jarWithDeps(type: Jar, dependsOn:build) {
@@ -16,8 +18,9 @@ task jarWithDeps(type: Jar, dependsOn:build) {
         	'Implementation-Version': version,
         	'Main-Class': 'org.insightcentre.uld.naisc.meas.Launch'
     }
+    duplicatesStrategy = DuplicatesStrategy.INCLUDE
     baseName = project.name + '-all'
-    from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
+    from { configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) } }
     with jar
 }
 

naisc-meas/src/main/java/org/insightcentre/uld/naisc/meas/execution/Execution.java

@@ -432,7 +432,7 @@ public static List<Meas.CompareResultRow> loadCompare(String id1, String id2) {
 
                     }
                 }
-            } catch(SQLException|JsonProcessingException x) {
+            } catch(SQLException|IOException x) {
                 throw new RuntimeException(x);
             }
         }

naisc-meas/src/main/webapp/compare.jsp

@@ -53,11 +53,9 @@
                 </table>
             </div>
         </div>
-        <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/jquery-3.3.1.min.js"
-                integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8="
-                crossorigin="anonymous"></script>
-    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/popper.min.js" integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous"></script>
-    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/bootstrap.min.js" integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous"></script>
+        <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/jquery-3.3.1.min.js"></script>
+    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/popper.min.js"></script>
+    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/bootstrap.min.js"></script>
     <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/vue.js"></script>
     <script>
 var data = {

naisc-meas/src/main/webapp/index.jsp

@@ -355,10 +355,9 @@
 
     <script
   src="<%= System.getProperties().getProperty("base.url", "")  %>/js/jquery-3.3.1.min.js"
-  integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8="
-  crossorigin="anonymous"></script>
-    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/popper.min.js" integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous"></script>
-    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/bootstrap.min.js" integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous"></script>
+  ></script>
+    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/popper.min.js" ></script>
+    <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/bootstrap.min.js" ></script>
     <script src="<%= System.getProperties().getProperty("base.url", "")  %>/js/vue.js"></script>
 
     <script>var data = <%= Meas.json() %>;</script>
@@ -806,4 +805,4 @@ var app = new Vue({
 })
 </script>
   </body>
-</html>
+</html>