From 10c65bc98dd0810d362f05a3d67848a3dece8bce Mon Sep 17 00:00:00 2001
From: philipp <spohr.philipp@web.de>
Date: Fri, 28 Jul 2017 18:53:24 +0200
Subject: [PATCH] Beginning to write a gradle script that fetches git data (and
hopefully compiles it eventually/ resolves all dependencies)
---
build.gradle | 52 ++++++
gradlew | 172 ++++++++++++++++++
gradlew.bat | 84 +++++++++
pom.xml | 142 +++++++++++++++
settings.gradle | 1 +
.../yoshikoWrapper/internal/CyActivator.java | 14 ++
6 files changed, 465 insertions(+)
create mode 100644 build.gradle
create mode 100755 gradlew
create mode 100644 gradlew.bat
create mode 100644 pom.xml
create mode 100644 settings.gradle
create mode 100644 src/main/java/de/hhu/bcs/yoshikoWrapper/internal/CyActivator.java
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 0000000..cfc1d03
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,52 @@
+plugins {
+ id 'org.ajoberstar.grgit' version '1.7.2'
+ //id 'fr.echoes.gradle.cpp' version '1.2.9'
+}
+
+apply plugin: 'java'
+apply plugin: 'maven'
+//apply plugin: 'org.ajoberstar.grgit'
+
+group = 'de.hhu.bcs'
+version = '0.0.1-SNAPSHOT'
+description = """yoshikoWrapper"""
+
+sourceCompatibility = 1.8
+targetCompatibility = 1.8
+
+def yoshikoDir = 'build/yoshikoSource'
+
+/*
+Clone task to fetch the required C++ code from the yoshiko repository
+*/
+task cloneYoshikoCode {
+
+
+
+ description = 'Fetches the Yoshiko Source from the github repository for further processing'
+ doLast{
+ if (!(file(yoshikoDir).exists())){
+ logger.info("Yoshiko source files don't exist yet, cloning ...")
+ org.ajoberstar.grgit.Grgit.clone(dir: file(yoshikoDir), uri: 'https://github.com/spqrPh/yoshiko')
+ }
+ }
+}
+
+compileJava.dependsOn(cloneYoshikoCode)
+
+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" }
+ maven { url "https://plugins.gradle.org/m2/" }
+}
+
+
+
+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'
+}
diff --git a/gradlew b/gradlew
new file mode 100755
index 0000000..4453cce
--- /dev/null
+++ b/gradlew
@@ -0,0 +1,172 @@
+#!/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" "$@"
diff --git a/gradlew.bat b/gradlew.bat
new file mode 100644
index 0000000..e95643d
--- /dev/null
+++ b/gradlew.bat
@@ -0,0 +1,84 @@
+@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
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..2d67244
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,142 @@
+<?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">
+
+ <properties>
+ <bundle.symbolicName>de.hhu.bcs.yoshikoWrapper</bundle.symbolicName>
+ <bundle.namespace>de.hhu.bcs.yoshikoWrapper</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>de.hhu.bcs</groupId>
+ <artifactId>yoshikoWrapper</artifactId>
+ <version>0.0.1-SNAPSHOT</version>
+
+ <name>yoshikoWrapper</name>
+
+ <build>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ </resource>
+ </resources>
+ <!-- Cytoscape requires Java 1.8 -->
+ <plugins>
+ <plugin>
+ <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>
+ <configuration>
+ <source>1.8</source>
+ <target>1.8</target>
+ <optimize>true</optimize>
+ <showWarnings>true</showWarnings>
+ <showDeprecation>true</showDeprecation>
+ <compilerArguments>
+ <Xmaxwarns>10000</Xmaxwarns>
+ <Xmaxerrs>10000</Xmaxerrs>
+ </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>
+ <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>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <!-- Links to the Cytoscape Maven repositories. -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+ <url>http://code.cytoscape.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ </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>
+ </dependency>
+
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>service-api</artifactId>
+ <version>3.5.0-RC2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>swing-application-api</artifactId>
+ <version>3.5.0-RC2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>session-api</artifactId>
+ <version>3.5.0-RC2</version>
+ </dependency>
+
+ <!-- Logging -->
+ <dependency>
+ <groupId>org.ops4j.pax.logging</groupId>
+ <artifactId>pax-logging-api</artifactId>
+ <version>1.5.2</version>
+ <scope>provided</scope>
+ </dependency>
+
+ </dependencies>
+
+ <description>A Java Application that wraps the yoshiko algorithm implemented in C++</description>
+</project>
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 0000000..83349fd
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1 @@
+rootProject.name = 'yoshikoWrapper'
diff --git a/src/main/java/de/hhu/bcs/yoshikoWrapper/internal/CyActivator.java b/src/main/java/de/hhu/bcs/yoshikoWrapper/internal/CyActivator.java
new file mode 100644
index 0000000..5746dab
--- /dev/null
+++ b/src/main/java/de/hhu/bcs/yoshikoWrapper/internal/CyActivator.java
@@ -0,0 +1,14 @@
+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 {
+ //DONOTHINGYET
+ }
+
+}
--
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