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Commit 65e14345 authored by Philipp Spohr's avatar Philipp Spohr
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Back to the primitive: 

Converted back to "raw" maven as osgi plugin in gradle is not really working as intended and cytoscape strongly suggests using their maven archetype (future versions will drop support for other solutions)
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.gitignore
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# Gradle
.gradle
/build/
#Maven
/target
# Java
*.class
......@@ -11,3 +10,4 @@
/.settings/org.eclipse.buildship.core.prefs
/.settings/org.eclipse.jdt.core.prefs
/bin/de
/.gradle/
build.gradle deleted 100644 → 0
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plugins {
id 'maven'
}
apply plugin: 'java'
group = 'de.hhu.bcs'
version = '0.0.1-SNAPSHOT'
description = """yoshikoWrapper"""
sourceCompatibility = 1.8
targetCompatibility = 1.8
repositories {
maven { url "http://code.cytoscape.org/nexus/content/repositories/snapshots/" }
maven { url "http://code.cytoscape.org/nexus/content/repositories/releases/" }
maven { url "http://repo.maven.apache.org/maven2" }
}
dependencies {
compile group: 'org.osgi', name: 'org.osgi.core', version:'4.2.0'
compile group: 'org.cytoscape', name: 'service-api', version:'3.5.0-RC2'
compile group: 'org.cytoscape', name: 'swing-application-api', version:'3.5.0-RC2'
compile group: 'org.cytoscape', name: 'session-api', version:'3.5.0-RC2'
compile group: 'org.ops4j.pax.logging', name: 'pax-logging-api', version:'1.5.2'
}
gradle/wrapper/gradle-wrapper.jar deleted 100644 → 0
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File deleted
gradle/wrapper/gradle-wrapper.properties deleted 100644 → 0
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#Fri Jul 28 17:36:49 CEST 2017
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-3.4-bin.zip
gradlew deleted 100755 → 0
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#!/usr/bin/env sh
##############################################################################
##
## Gradle start up script for UN*X
##
##############################################################################
# Attempt to set APP_HOME
# Resolve links: $0 may be a link
PRG="$0"
# Need this for relative symlinks.
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '/.*' > /dev/null; then
PRG="$link"
else
PRG=`dirname "$PRG"`"/$link"
fi
done
SAVED="`pwd`"
cd "`dirname \"$PRG\"`/" >/dev/null
APP_HOME="`pwd -P`"
cd "$SAVED" >/dev/null
APP_NAME="Gradle"
APP_BASE_NAME=`basename "$0"`
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
DEFAULT_JVM_OPTS=""
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD="maximum"
warn ( ) {
echo "$*"
}
die ( ) {
echo
echo "$*"
echo
exit 1
}
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
nonstop=false
case "`uname`" in
CYGWIN* )
cygwin=true
;;
Darwin* )
darwin=true
;;
MINGW* )
msys=true
;;
NONSTOP* )
nonstop=true
;;
esac
CLASSPATH=$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
# IBM's JDK on AIX uses strange locations for the executables
JAVACMD="$JAVA_HOME/jre/sh/java"
else
JAVACMD="$JAVA_HOME/bin/java"
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
JAVACMD="java"
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
# Increase the maximum file descriptors if we can.
if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
MAX_FD_LIMIT=`ulimit -H -n`
if [ $? -eq 0 ] ; then
if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
MAX_FD="$MAX_FD_LIMIT"
fi
ulimit -n $MAX_FD
if [ $? -ne 0 ] ; then
warn "Could not set maximum file descriptor limit: $MAX_FD"
fi
else
warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
fi
fi
# For Darwin, add options to specify how the application appears in the dock
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 $cygwin ; then
APP_HOME=`cygpath --path --mixed "$APP_HOME"`
CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
JAVACMD=`cygpath --unix "$JAVACMD"`
# We build the pattern for arguments to be converted via cygpath
ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
SEP=""
for dir in $ROOTDIRSRAW ; do
ROOTDIRS="$ROOTDIRS$SEP$dir"
SEP="|"
done
OURCYGPATTERN="(^($ROOTDIRS))"
# Add a user-defined pattern to the cygpath arguments
if [ "$GRADLE_CYGPATTERN" != "" ] ; then
OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
fi
# Now convert the arguments - kludge to limit ourselves to /bin/sh
i=0
for arg in "$@" ; do
CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
else
eval `echo args$i`="\"$arg\""
fi
i=$((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" ;;
esac
fi
# Escape application args
save ( ) {
for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
echo " "
}
APP_ARGS=$(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" "$@"
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@if "%DEBUG%" == "" @echo off
@rem ##########################################################################
@rem
@rem Gradle startup script for Windows
@rem
@rem ##########################################################################
@rem Set local scope for the variables with windows NT shell
if "%OS%"=="Windows_NT" setlocal
set DIRNAME=%~dp0
if "%DIRNAME%" == "" set DIRNAME=.
set APP_BASE_NAME=%~n0
set APP_HOME=%DIRNAME%
@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=
@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
echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.
goto fail
:findJavaFromJavaHome
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
if exist "%JAVA_EXE%" goto init
echo.
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
echo.
echo Please set the JAVA_HOME variable in your environment to match the
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%
:end
@rem End local scope for the variables with windows NT shell
if "%ERRORLEVEL%"=="0" goto mainEnd
:fail
rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
rem the _cmd.exe /c_ return code!
if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
exit /b 1
:mainEnd
if "%OS%"=="Windows_NT" endlocal
:omega
pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<properties>
<bundle.symbolicName>de.hhu.bcs.yoshikoWrapper</bundle.symbolicName>
<bundle.namespace>de.hhu.bcs.yoshikoWrapper</bundle.namespace>
<bundle.symbolicName>org.cytoscape.sample-control-panel</bundle.symbolicName>
<bundle.namespace>org.cytoscape.sample.internal</bundle.namespace>
<cytoscape.api.version>3.0.0</cytoscape.api.version>
<maven-bundle-plugin.version>2.3.4</maven-bundle-plugin.version>
<osgi.api.version>4.2.0</osgi.api.version>
</properties>
<modelVersion>4.0.0</modelVersion>
<groupId>de.hhu.bcs</groupId>
<groupId>de.hhu.ba</groupId>
<artifactId>yoshikoWrapper</artifactId>
<version>0.0.1-SNAPSHOT</version>
<version>0.0.1</version>
<name>yoshikoWrapper</name>
<name>YoshikoWrapper</name>
<build>
<resources>
<resource>
<directory>src/main/resources</directory>
</resource>
</resources>
<!-- Cytoscape requires Java 1.8 -->
<plugins>
<plugin>
<inherited>true</inherited>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>2.3.2</version>
<executions>
<execution>
<id>default-testCompile</id>
<phase>test-compile</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>default-compile</id>
<phase>compile</phase>
<goals>
<goal>compile</goal>
</goals>
</execution>
</executions>
<version>3.0</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<source>1.6</source>
<target>1.6</target>
<optimize>true</optimize>
<showWarnings>true</showWarnings>
<showDeprecation>true</showDeprecation>
......@@ -53,27 +35,18 @@
</compilerArguments>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.7.1</version>
<configuration>
<redirectTestOutputToFile>true</redirectTestOutputToFile>
</configuration>
</plugin>
<!-- Generates the OSGi metadata based on the osgi.bnd file. -->
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>2.3.7</version>
<version>${maven-bundle-plugin.version}</version>
<extensions>true</extensions>
<configuration>
<instructions>
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
<Bundle-Version>${project.version}</Bundle-Version>
<Export-Package>${bundle.namespace}</Export-Package>
<Private-Package>${bundle.namespace}.internal.*</Private-Package>
<Bundle-Activator>${bundle.namespace}.internal.CyActivator</Bundle-Activator>
<Export-Package>!${bundle.namespace}.*</Export-Package>
<Private-Package>${bundle.namespace}.*</Private-Package>
<Bundle-Activator>${bundle.namespace}.CyActivator</Bundle-Activator>
</instructions>
</configuration>
</plugin>
......@@ -85,6 +58,7 @@
<repository>
<id>cytoscape_snapshots</id>
<snapshots>
<enabled>true</enabled>
</snapshots>
<releases>
<enabled>false</enabled>
......@@ -98,45 +72,62 @@
<enabled>false</enabled>
</snapshots>
<releases>
<enabled>true</enabled>
</releases>
<name>Cytoscape Releases</name>
<url>http://code.cytoscape.org/nexus/content/repositories/releases/</url>
</repository>
</repositories>
<!-- Dependencies needed to compile this project. -->
<dependencies>
<dependency>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.core</artifactId>
<version>4.2.0</version>
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
<version>${cytoscape.api.version}</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>service-api</artifactId>
<version>3.5.0-RC2</version>
<artifactId>work-api</artifactId>
<version>${cytoscape.api.version}</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
<version>3.5.0-RC2</version>
<artifactId>service-api</artifactId>
<version>${cytoscape.api.version}</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>session-api</artifactId>
<version>3.5.0-RC2</version>
<groupId>org.osgi</groupId>
<artifactId>org.osgi.core</artifactId>
<version>${osgi.api.version}</version>
</dependency>
<!-- Logging -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.8.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.8.5</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.ops4j.pax.logging</groupId>
<artifactId>pax-logging-api</artifactId>
<version>1.5.2</version>
<scope>provided</scope>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>service-api</artifactId>
<version>${cytoscape.api.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
</dependencies>
<description>A Java Application that wraps the yoshiko algorithm implemented in C++</description>
<description>A Cytoscape plugin for graph-based clustering that wraps the yoshiko algorithm.</description>
<packaging>bundle</packaging>
</project>
settings.gradle deleted 100644 → 0
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rootProject.name = 'yoshikoWrapper'
src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java 0 → 100644
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View file @ 65e14345
package de.hhu.ba.yoshikoWrapper.gui;
import java.awt.Component;
import javax.swing.Icon;
import javax.swing.JFileChooser;
import javax.swing.JPanel;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.application.swing.CytoPanelName;
/**This class describes the Swing Panel that the user interacts with in cytoscape
* @author Philipp Spohr, Aug 6, 2017
*
*/
public class MainPanel extends JPanel implements CytoPanelComponent {
/**
* Unique identifier for serialization
*/
private static final long serialVersionUID = 6214827920591046457L;
/**
* Main constructor, creates a new Panel and intializes subcomponents
*/
public MainPanel() {
JFileChooser yoshikoNativeChooser = new JFileChooser();
this.add(yoshikoNativeChooser);
this.setVisible(true);
}
public Component getComponent() {
return this;
}
/* (non-Javadoc)
* @see org.cytoscape.application.swing.CytoPanelComponent#getCytoPanelName()
*/
public CytoPanelName getCytoPanelName() {
//By convention most plugins that provide a "toolbox"-like interface use the WEST orientation
return CytoPanelName.WEST;
}
public String getTitle() {
//TODO: Be creative I guess
return "Yoshiko Wrapper Panel";
}
public Icon getIcon() {
//TODO:
return null;
}
}
src/main/java/de/hhu/ba/yoshikoWrapper/internal/CyActivator.java 0 → 100644
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package de.hhu.ba.yoshikoWrapper.internal;
import java.util.Properties;
import org.cytoscape.application.swing.CyAction;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.swing.CytoPanelComponent;
import org.cytoscape.service.util.AbstractCyActivator;
import org.osgi.framework.BundleContext;
import de.hhu.ba.yoshikoWrapper.gui.MainPanel;
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
super();
}
@Override
public void start(BundleContext context) throws Exception {
CySwingApplication cytoscapeDesktopService = getService(context,CySwingApplication.class);
MainPanel mainPanel = new MainPanel();
registerService(context,mainPanel,CytoPanelComponent.class, new Properties());
MainPanelAction controlPanelAction = new MainPanelAction(cytoscapeDesktopService,mainPanel);
registerService(context,controlPanelAction,CyAction.class, new Properties());
}
}
src/main/java/de/hhu/ba/yoshikoWrapper/internal/MainPanelAction.java 0 → 100644
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View file @ 65e14345
package de.hhu.ba.yoshikoWrapper.internal;
import java.awt.event.ActionEvent;
import org.cytoscape.application.swing.AbstractCyAction;
import org.cytoscape.application.swing.CySwingApplication;
//import org.cytoscape.application.swing.CytoPanel;
//import org.cytoscape.application.swing.CytoPanelName;
import de.hhu.ba.yoshikoWrapper.gui.MainPanel;
public class MainPanelAction extends AbstractCyAction {
/**
*
*/
private static final long serialVersionUID = -4710814976875737575L;
//private CySwingApplication desktopApp;
//private final CytoPanel cytoPanelWest;
//private MainPanel mainPanel;
/**Main constructor, generates a new CyAction handling the main panel
* @param desktopApp
* @param mainPanel
*/
public MainPanelAction(
CySwingApplication desktopApp,
MainPanel mainPanel
){
super("Control Panel");
setPreferredMenu("Apps.Clustering");
//this.desktopApp = desktopApp;
//this.cytoPanelWest = this.desktopApp.getCytoPanel(CytoPanelName.WEST);
//this.mainPanel = mainPanel;
}
@Override
public void actionPerformed(ActionEvent e) {
// TODO Auto-generated method stub
}
}
src/main/java/de/hhu/bcs/yoshikoWrapper/internal/CyActivator.java deleted 100644 → 0
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package de.hhu.bcs.yoshikoWrapper.internal;
import org.cytoscape.service.util.AbstractCyActivator;
import org.osgi.framework.BundleContext;
public class CyActivator extends AbstractCyActivator {
@Override
public void start(BundleContext context) throws Exception {
System.loadLibrary("yoshiko");
}
}
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