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Commit 8d9d3a91 authored by Matija Obreza's avatar Matija Obreza
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Merge branch '33-upgrade-to-j11' into 'master' 

Resolve "Upgrade to J11"

Closes #33

See merge request !28
parents 6344fee7 ca262204
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.gitlab-ci.yml 0 → 100644
View file @ 8d9d3a91
# This template will build and test your projects
# * Caches downloaded dependencies and plugins between invocation.
# * Verify but don't deploy merge requests.
# * Deploy built artifacts from master branch only.
variables:
# This will suppress any download for dependencies and plugins or upload messages which would clutter the console log.
# `showDateTime` will show the passed time in milliseconds. You need to specify `--batch-mode` to make this work.
MAVEN_OPTS: "-Dhttps.protocols=TLSv1.2 -Dmaven.repo.local=$CI_PROJECT_DIR/.m2/repository -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=WARN -Dorg.slf4j.simpleLogger.showDateTime=true -Djava.awt.headless=true"
# As of Maven 3.3.0 instead of this you may define these options in `.mvn/maven.config` so the same config is used
# when running from the command line.
# `installAtEnd` and `deployAtEnd` are only effective with recent version of the corresponding plugins.
MAVEN_CLI_OPTS: "--batch-mode --errors --fail-at-end --show-version -DinstallAtEnd=true -DdeployAtEnd=true"
# This template uses jdk8 for verifying and deploying images
image: maven:3-openjdk-11
# Cache downloaded dependencies and plugins between builds.
# To keep cache across branches add 'key: "$CI_JOB_NAME"'
cache:
paths:
- .m2/repository
stages:
- test
# Always verify
verify:
stage: test
script:
- mvn $MAVEN_CLI_OPTS test -B -U
# only:
# - master
# - tags
anno-docs/pom.xml
View file @ 8d9d3a91
......@@ -4,7 +4,7 @@
<parent>
<groupId>org.genesys-pgr</groupId>
<artifactId>anno</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>anno-docs</artifactId>
<name>Genesys Uploader documentation</name>
......
anno-docs/src/docs/asciidoc/manual.adoc
View file @ 8d9d3a91
......@@ -21,11 +21,11 @@ Genesys Anno User Manual
Introduction
------------
The Genesys upload tool *Anno* is a standalone Java application for managing accession-level data on
The Genesys Uploader *Anno* is a standalone Java application for managing accession-level data on
Genesys PGR - a global database on plant genetic resources in the world's genebanks. The Genesys database is
accessible at https://www.genesys-pgr.org.
The Anno application allows users to map their Excel XLSX files, CSV files or database SQL queries to Multi-Crop
The Anno application allows you to map your Excel XLSX files, CSV files or database SQL queries to Multi-Crop
Passport Descriptor (MCPD) format and push the mapped data to Genesys for publication.
*Genesys Sandbox*, a playground instance of the Genesys
......
anno-docs/src/docs/asciidoc/sections/download.adoc
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......@@ -3,11 +3,11 @@
== Installing Anno
Anno is an open-source project, licensed under the Apache License v2.
Anno requires the Java 8 Run-Time Environment (JRE) to run.
Anno requires https://adoptopenjdk.net/?variant=openjdk11&jvmVariant=hotspot[Java 11] to run.
NOTE: Make sure you don't allow the Java JRE installer to install browser toolbars like Ask.com or make any other changes to your default browser configuration.
NOTE: Make sure you don't allow the Java JRE installer to install browser toolbars or make any other changes to your default browser configuration.
WARNING: Disable Java in all Internet browsers on your computer. Java applet technology has been marked for deprecation and is seldom used today.
WARNING: Disable Java in all Internet browsers on your computer.
If downloading pre-compiled binaries, make sure to download the latest version of Anno for your platform.
......@@ -29,12 +29,11 @@ Extract, if necessary, and run the executable for your platform.
== Troubleshooting
The **WinRun4J** wrapper used for Windows OS may fail to automatically detect the Java run-time environment and fail with "Fail to find Java VM" error message.
The **WinRun4J** wrapper used for Windows may fail to automatically detect the Java run-time environment and fail with "Fail to find Java VM" error message.
In this case you will need to update the `Genesys Magic.ini` file and configure the `vm.location` property:
In this case you will need to update the `Genesys Magic.ini` file and configure the `vm.location` property to point to the `bin\client\jvm.dll` of your
OpenJDK installation:
```
vm.location=C:\Program Files\Java\jre-9.0.4\bin\server\jvm.dll
vm.location=C:\Program Files\AdoptOpenJDK\jdk-11.0.10.9-hotspot\bin\client\jvm.dll
```
Source: https://stackoverflow.com/questions/28229792/winrun4j-auto-detect-jvm[Stackoverflow]
anno-gui-macosx/ICONS.md 0 → 100644
View file @ 8d9d3a91
# Icons
mkdir anno.iconset
# Generate
for I in 16 256 512 128 32 64; do echo $I; sips -z $I $I ../../../../anno-gui/src/main/resources/icon/appicon.png --out anno.iconset/icon_$Ix$I.png; done
# Convert
iconutil -c icns -o anno.icns anno.iconset
anno-gui-macosx/pom.xml
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......@@ -3,7 +3,7 @@
<parent>
<groupId>org.genesys-pgr</groupId>
<artifactId>anno</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>anno-gui-macosx</artifactId>
<name>Anno for MacOSX</name>
......@@ -12,7 +12,7 @@
<dependency>
<groupId>org.genesys-pgr</groupId>
<artifactId>anno-gui</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.eclipse.platform</groupId>
......@@ -30,22 +30,38 @@
<build>
<plugins>
<plugin>
<groupId>sh.tak.appbundler</groupId>
<artifactId>appbundle-maven-plugin</artifactId>
<version>1.2.1-SNAPSHOT</version>
<groupId>de.perdian.maven.plugins</groupId>
<artifactId>macosappbundler-maven-plugin</artifactId>
<version>1.10.0</version>
<configuration>
<mainClass>org.genesys2.anno.gui.AppWindow</mainClass>
<bundleName>Genesys Magic</bundleName>
<dictionaryFile>Info.plist</dictionaryFile>
<diskImageInternetEnable>true</diskImageInternetEnable>
<generateDiskImageFile>true</generateDiskImageFile>
<jvmVersion>1.8</jvmVersion>
<jvmOptions>
<jvmOption>
-XstartOnFirstThread
</jvmOption>
</jvmOptions>
<!-- <iconFile>CustomIncon.icns</iconFile> -->
<plist>
<CFBundleIconFile>anno.icns</CFBundleIconFile>
<CFBundleName>Genesys Uploader</CFBundleName>
<CFBundleDisplayName>Genesys Uploader</CFBundleDisplayName>
<CFBundleDevelopmentRegion>English</CFBundleDevelopmentRegion>
<CFBundleURLTypes>
<string>msa</string>
</CFBundleURLTypes>
<JVMMainClassName>org.genesys2.anno.gui.AppWindow</JVMMainClassName>
<JVMVersion>11+</JVMVersion>
<JVMOptions>
<string>-XstartOnFirstThread</string>
</JVMOptions>
<!-- <JVMArguments>
<string>-XstartOnFirstThread</string>
</JVMArguments>
-->
</plist>
<dmg>
<generate>true</generate>
<appendVersion>true</appendVersion>
<additionalResources>
<additionalResource>
<directory>../anno-docs/target/</directory>
<include>anno-manual-3.0-SNAPSHOT.pdf</include>
</additionalResource>
</additionalResources>
</dmg>
</configuration>
<executions>
<execution>
......
anno-gui-macosx/src/main/resources/Info.plist deleted 100644 → 0
View file @ 6344fee7
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>CFBundleDevelopmentRegion</key>
<string>English</string>
<key>CFBundleExecutable</key>
<string>${cfBundleExecutable}</string>
<key>CFBundleIconFile</key>
<string>${iconFile}</string>
<key>CFBundleIdentifier</key>
<string>${mainClass}</string>
<key>CFBundleDisplayName</key>
<string>${bundleName}</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundleName</key>
<string>${bundleName}</string>
<key>CFBundlePackageType</key>
<string>APPL</string>
<key>CFBundleShortVersionString</key>
<string>${version}</string>
<key>CFBundleSignature</key>
<string>????</string>
<key>CFBundleVersion</key>
<string>1</string>
<key>NSHumanReadableCopyright</key>
<string></string>
<key>NSHighResolutionCapable</key>
<true/>
<key>JVMRuntime</key>
<string>${jrePath}</string>
<key>JVMRuntimePath</key>
<string>${jreFullPath}</string>
<key>JVMDebug</key>
<string>${jvmDebug}</string>
<key>JDKPreferred</key>
<string>${jdkPreferred}</string>
<key>JREPreferred</key>
<string>${jrePreferred}</string>
<key>JVMMainClassName</key>
<string>${mainClass}</string>
<key>JVMClassPaths</key>
${classpath}
<key>JVMVersion</key>
<string>${jvmVersion}</string>
<key>JVMOptions</key>
${jvmOptions}
<key>JVMArguments</key>
<array/>
<key>LauncherWorkingDirectory</key>
<string>${workingDirectory}</string>
</dict>
</plist>
\ No newline at end of file
anno-gui-package/bin/Genesys Magic.ini
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main.class=org.genesys2.anno.gui.AppWindow
classpath.1=lib\*.jar
# Update if required
vm.location=C:\Program Files\AdoptOpenJDK\jdk-11.0.10.9-hotspot\bin\client\jvm.dll
anno-gui-package/pom.xml
View file @ 8d9d3a91
......@@ -3,7 +3,7 @@
<parent>
<groupId>org.genesys-pgr</groupId>
<artifactId>anno</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>anno-gui-package</artifactId>
<build>
......@@ -39,7 +39,7 @@
<dependency>
<groupId>org.genesys-pgr</groupId>
<artifactId>anno-gui</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.eclipse.platform</groupId>
......
anno-gui/pom.xml
View file @ 8d9d3a91
......@@ -3,7 +3,7 @@
<parent>
<groupId>org.genesys-pgr</groupId>
<artifactId>anno</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
</parent>
<artifactId>anno-gui</artifactId>
<name>Data annotator GUI</name>
......@@ -45,6 +45,12 @@
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
<version>2.11.0</version>
<exclusions>
<exclusion>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
......@@ -79,7 +85,7 @@
<dependency>
<groupId>org.genesys-pgr</groupId>
<artifactId>genesys-client-api</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>commons-collections</groupId>
......
pom.xml
View file @ 8d9d3a91
......@@ -2,7 +2,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.genesys-pgr</groupId>
<artifactId>anno</artifactId>
<version>2.0-SNAPSHOT</version>
<version>3.0-SNAPSHOT</version>
<packaging>pom</packaging>
<name>Data annotator</name>
......@@ -31,9 +31,9 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.version>1.8</java.version>
<jdk.target>1.8</jdk.target>
<jdk.source>1.8</jdk.source>
<java.version>11</java.version>
<jdk.target>11</jdk.target>
<jdk.source>11</jdk.source>
</properties>
<modules>
......
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