init

.gitignore

+##########################
+## Java
+##########################
+*.class
+.mtj.tmp/
+*.jar
+*.war
+*.ear
+hs_err_pid*
+
+##########################
+## Maven
+##########################
+target/
+pom.xml.tag
+pom.xml.releaseBackup
+pom.xml.versionsBackup
+pom.xml.next
+release.properties
+.mvn
+##########################
+## IntelliJ
+##########################
+*.iml
+.idea/
+*.ipr
+*.iws
+out/
+.idea_modules/
+
+##########################
+## Eclipse
+##########################
+.metadata
+.classpath
+.project
+.settings/
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.loadpath
+
+##########################
+## NetBeans
+##########################
+nbproject/private/
+build/
+nbbuild/
+dist/
+nbdist/
+nbactions.xml
+nb-configuration.xml
+
+##########################
+## OS X
+##########################
+.DS_Store

cbioondemandK8S/.gitignore

+/target/
+!.mvn/wrapper/maven-wrapper.jar
+
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### IntelliJ IDEA ###
+.idea
+*.iws
+*.iml
+*.ipr
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+/build/

cbioondemandK8S/Dockerfile

+FROM maven:3.6.0-jdk-8-alpine AS build
+WORKDIR /app
+COPY . /app
+RUN cd /app && \
+    mvn clean package && \
+    mv target/cbioondemandK8S-1.0.0-SNAPSHOT.jar /app/
+
+
+FROM openjdk:8-jre-alpine
+WORKDIR /app
+COPY --from=build /app/cbioondemandK8S-1.0.0-SNAPSHOT.jar /app
+EXPOSE 8080
+CMD ["java","-jar","cbioondemandK8S-1.0.0-SNAPSHOT.jar"]

cbioondemandK8S/mvnw

+#!/bin/sh
+# ----------------------------------------------------------------------------
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you 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
+#
+#    http://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.
+# ----------------------------------------------------------------------------
+
+# ----------------------------------------------------------------------------
+# Maven2 Start Up Batch script
+#
+# Required ENV vars:
+# ------------------
+#   JAVA_HOME - location of a JDK home dir
+#
+# Optional ENV vars
+# -----------------
+#   M2_HOME - location of maven2's installed home dir
+#   MAVEN_OPTS - parameters passed to the Java VM when running Maven
+#     e.g. to debug Maven itself, use
+#       set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
+#   MAVEN_SKIP_RC - flag to disable loading of mavenrc files
+# ----------------------------------------------------------------------------
+
+if [ -z "$MAVEN_SKIP_RC" ] ; then
+
+  if [ -f /etc/mavenrc ] ; then
+    . /etc/mavenrc
+  fi
+
+  if [ -f "$HOME/.mavenrc" ] ; then
+    . "$HOME/.mavenrc"
+  fi
+
+fi
+
+# OS specific support.  $var _must_ be set to either true or false.
+cygwin=false;
+darwin=false;
+mingw=false
+case "`uname`" in
+  CYGWIN*) cygwin=true ;;
+  MINGW*) mingw=true;;
+  Darwin*) darwin=true
+    # Use /usr/libexec/java_home if available, otherwise fall back to /Library/Java/Home
+    # See https://developer.apple.com/library/mac/qa/qa1170/_index.html
+    if [ -z "$JAVA_HOME" ]; then
+      if [ -x "/usr/libexec/java_home" ]; then
+        export JAVA_HOME="`/usr/libexec/java_home`"
+      else
+        export JAVA_HOME="/Library/Java/Home"
+      fi
+    fi
+    ;;
+esac
+
+if [ -z "$JAVA_HOME" ] ; then
+  if [ -r /etc/gentoo-release ] ; then
+    JAVA_HOME=`java-config --jre-home`
+  fi
+fi
+
+if [ -z "$M2_HOME" ] ; then
+  ## resolve links - $0 may be a link to maven's home
+  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"`/$link"
+    fi
+  done
+
+  saveddir=`pwd`
+
+  M2_HOME=`dirname "$PRG"`/..
+
+  # make it fully qualified
+  M2_HOME=`cd "$M2_HOME" && pwd`
+
+  cd "$saveddir"
+  # echo Using m2 at $M2_HOME
+fi
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+  [ -n "$M2_HOME" ] &&
+    M2_HOME=`cygpath --unix "$M2_HOME"`
+  [ -n "$JAVA_HOME" ] &&
+    JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+  [ -n "$CLASSPATH" ] &&
+    CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
+fi
+
+# For Mingw, ensure paths are in UNIX format before anything is touched
+if $mingw ; then
+  [ -n "$M2_HOME" ] &&
+    M2_HOME="`(cd "$M2_HOME"; pwd)`"
+  [ -n "$JAVA_HOME" ] &&
+    JAVA_HOME="`(cd "$JAVA_HOME"; pwd)`"
+  # TODO classpath?
+fi
+
+if [ -z "$JAVA_HOME" ]; then
+  javaExecutable="`which javac`"
+  if [ -n "$javaExecutable" ] && ! [ "`expr \"$javaExecutable\" : '\([^ ]*\)'`" = "no" ]; then
+    # readlink(1) is not available as standard on Solaris 10.
+    readLink=`which readlink`
+    if [ ! `expr "$readLink" : '\([^ ]*\)'` = "no" ]; then
+      if $darwin ; then
+        javaHome="`dirname \"$javaExecutable\"`"
+        javaExecutable="`cd \"$javaHome\" && pwd -P`/javac"
+      else
+        javaExecutable="`readlink -f \"$javaExecutable\"`"
+      fi
+      javaHome="`dirname \"$javaExecutable\"`"
+      javaHome=`expr "$javaHome" : '\(.*\)/bin'`
+      JAVA_HOME="$javaHome"
+      export JAVA_HOME
+    fi
+  fi
+fi
+
+if [ -z "$JAVACMD" ] ; then
+  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
+  else
+    JAVACMD="`which java`"
+  fi
+fi
+
+if [ ! -x "$JAVACMD" ] ; then
+  echo "Error: JAVA_HOME is not defined correctly." >&2
+  echo "  We cannot execute $JAVACMD" >&2
+  exit 1
+fi
+
+if [ -z "$JAVA_HOME" ] ; then
+  echo "Warning: JAVA_HOME environment variable is not set."
+fi
+
+CLASSWORLDS_LAUNCHER=org.codehaus.plexus.classworlds.launcher.Launcher
+
+# traverses directory structure from process work directory to filesystem root
+# first directory with .mvn subdirectory is considered project base directory
+find_maven_basedir() {
+
+  if [ -z "$1" ]
+  then
+    echo "Path not specified to find_maven_basedir"
+    return 1
+  fi
+
+  basedir="$1"
+  wdir="$1"
+  while [ "$wdir" != '/' ] ; do
+    if [ -d "$wdir"/.mvn ] ; then
+      basedir=$wdir
+      break
+    fi
+    # workaround for JBEAP-8937 (on Solaris 10/Sparc)
+    if [ -d "${wdir}" ]; then
+      wdir=`cd "$wdir/.."; pwd`
+    fi
+    # end of workaround
+  done
+  echo "${basedir}"
+}
+
+# concatenates all lines of a file
+concat_lines() {
+  if [ -f "$1" ]; then
+    echo "$(tr -s '\n' ' ' < "$1")"
+  fi
+}
+
+BASE_DIR=`find_maven_basedir "$(pwd)"`
+if [ -z "$BASE_DIR" ]; then
+  exit 1;
+fi
+
+##########################################################################################
+# Extension to allow automatically downloading the maven-wrapper.jar from Maven-central
+# This allows using the maven wrapper in projects that prohibit checking in binary data.
+##########################################################################################
+if [ -r "$BASE_DIR/.mvn/wrapper/maven-wrapper.jar" ]; then
+    if [ "$MVNW_VERBOSE" = true ]; then
+      echo "Found .mvn/wrapper/maven-wrapper.jar"
+    fi
+else
+    if [ "$MVNW_VERBOSE" = true ]; then
+      echo "Couldn't find .mvn/wrapper/maven-wrapper.jar, downloading it ..."
+    fi
+    jarUrl="https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.4.2/maven-wrapper-0.4.2.jar"
+    while IFS="=" read key value; do
+      case "$key" in (wrapperUrl) jarUrl="$value"; break ;;
+      esac
+    done < "$BASE_DIR/.mvn/wrapper/maven-wrapper.properties"
+    if [ "$MVNW_VERBOSE" = true ]; then
+      echo "Downloading from: $jarUrl"
+    fi
+    wrapperJarPath="$BASE_DIR/.mvn/wrapper/maven-wrapper.jar"
+
+    if command -v wget > /dev/null; then
+        if [ "$MVNW_VERBOSE" = true ]; then
+          echo "Found wget ... using wget"
+        fi
+        wget "$jarUrl" -O "$wrapperJarPath"
+    elif command -v curl > /dev/null; then
+        if [ "$MVNW_VERBOSE" = true ]; then
+          echo "Found curl ... using curl"
+        fi
+        curl -o "$wrapperJarPath" "$jarUrl"
+    else
+        if [ "$MVNW_VERBOSE" = true ]; then
+          echo "Falling back to using Java to download"
+        fi
+        javaClass="$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.java"
+        if [ -e "$javaClass" ]; then
+            if [ ! -e "$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.class" ]; then
+                if [ "$MVNW_VERBOSE" = true ]; then
+                  echo " - Compiling MavenWrapperDownloader.java ..."
+                fi
+                # Compiling the Java class
+                ("$JAVA_HOME/bin/javac" "$javaClass")
+            fi
+            if [ -e "$BASE_DIR/.mvn/wrapper/MavenWrapperDownloader.class" ]; then
+                # Running the downloader
+                if [ "$MVNW_VERBOSE" = true ]; then
+                  echo " - Running MavenWrapperDownloader.java ..."
+                fi
+                ("$JAVA_HOME/bin/java" -cp .mvn/wrapper MavenWrapperDownloader "$MAVEN_PROJECTBASEDIR")
+            fi
+        fi
+    fi
+fi
+##########################################################################################
+# End of extension
+##########################################################################################
+
+export MAVEN_PROJECTBASEDIR=${MAVEN_BASEDIR:-"$BASE_DIR"}
+if [ "$MVNW_VERBOSE" = true ]; then
+  echo $MAVEN_PROJECTBASEDIR
+fi
+MAVEN_OPTS="$(concat_lines "$MAVEN_PROJECTBASEDIR/.mvn/jvm.config") $MAVEN_OPTS"
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+  [ -n "$M2_HOME" ] &&
+    M2_HOME=`cygpath --path --windows "$M2_HOME"`
+  [ -n "$JAVA_HOME" ] &&
+    JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
+  [ -n "$CLASSPATH" ] &&
+    CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
+  [ -n "$MAVEN_PROJECTBASEDIR" ] &&
+    MAVEN_PROJECTBASEDIR=`cygpath --path --windows "$MAVEN_PROJECTBASEDIR"`
+fi
+
+WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
+
+exec "$JAVACMD" \
+  $MAVEN_OPTS \
+  -classpath "$MAVEN_PROJECTBASEDIR/.mvn/wrapper/maven-wrapper.jar" \
+  "-Dmaven.home=${M2_HOME}" "-Dmaven.multiModuleProjectDirectory=${MAVEN_PROJECTBASEDIR}" \
+  ${WRAPPER_LAUNCHER} $MAVEN_CONFIG "$@"

cbioondemandK8S/mvnw.cmd

+@REM ----------------------------------------------------------------------------
+@REM Licensed to the Apache Software Foundation (ASF) under one
+@REM or more contributor license agreements.  See the NOTICE file
+@REM distributed with this work for additional information
+@REM regarding copyright ownership.  The ASF licenses this file
+@REM to you under the Apache License, Version 2.0 (the
+@REM "License"); you may not use this file except in compliance
+@REM with the License.  You may obtain a copy of the License at
+@REM
+@REM    http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM Unless required by applicable law or agreed to in writing,
+@REM software distributed under the License is distributed on an
+@REM "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+@REM KIND, either express or implied.  See the License for the
+@REM specific language governing permissions and limitations
+@REM under the License.
+@REM ----------------------------------------------------------------------------
+
+@REM ----------------------------------------------------------------------------
+@REM Maven2 Start Up Batch script
+@REM
+@REM Required ENV vars:
+@REM JAVA_HOME - location of a JDK home dir
+@REM
+@REM Optional ENV vars
+@REM M2_HOME - location of maven2's installed home dir
+@REM MAVEN_BATCH_ECHO - set to 'on' to enable the echoing of the batch commands
+@REM MAVEN_BATCH_PAUSE - set to 'on' to wait for a key stroke before ending
+@REM MAVEN_OPTS - parameters passed to the Java VM when running Maven
+@REM     e.g. to debug Maven itself, use
+@REM set MAVEN_OPTS=-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=8000
+@REM MAVEN_SKIP_RC - flag to disable loading of mavenrc files
+@REM ----------------------------------------------------------------------------
+
+@REM Begin all REM lines with '@' in case MAVEN_BATCH_ECHO is 'on'
+@echo off
+@REM set title of command window
+title %0
+@REM enable echoing my setting MAVEN_BATCH_ECHO to 'on'
+@if "%MAVEN_BATCH_ECHO%" == "on"  echo %MAVEN_BATCH_ECHO%
+
+@REM set %HOME% to equivalent of $HOME
+if "%HOME%" == "" (set "HOME=%HOMEDRIVE%%HOMEPATH%")
+
+@REM Execute a user defined script before this one
+if not "%MAVEN_SKIP_RC%" == "" goto skipRcPre
+@REM check for pre script, once with legacy .bat ending and once with .cmd ending
+if exist "%HOME%\mavenrc_pre.bat" call "%HOME%\mavenrc_pre.bat"
+if exist "%HOME%\mavenrc_pre.cmd" call "%HOME%\mavenrc_pre.cmd"
+:skipRcPre
+
+@setlocal
+
+set ERROR_CODE=0
+
+@REM To isolate internal variables from possible post scripts, we use another setlocal
+@setlocal
+
+@REM ==== START VALIDATION ====
+if not "%JAVA_HOME%" == "" goto OkJHome
+
+echo.
+echo Error: JAVA_HOME not found in your environment. >&2
+echo Please set the JAVA_HOME variable in your environment to match the >&2
+echo location of your Java installation. >&2
+echo.
+goto error
+
+:OkJHome
+if exist "%JAVA_HOME%\bin\java.exe" goto init
+
+echo.
+echo Error: JAVA_HOME is set to an invalid directory. >&2
+echo JAVA_HOME = "%JAVA_HOME%" >&2
+echo Please set the JAVA_HOME variable in your environment to match the >&2
+echo location of your Java installation. >&2
+echo.
+goto error
+
+@REM ==== END VALIDATION ====
+
+:init
+
+@REM Find the project base dir, i.e. the directory that contains the folder ".mvn".
+@REM Fallback to current working directory if not found.
+
+set MAVEN_PROJECTBASEDIR=%MAVEN_BASEDIR%
+IF NOT "%MAVEN_PROJECTBASEDIR%"=="" goto endDetectBaseDir
+
+set EXEC_DIR=%CD%
+set WDIR=%EXEC_DIR%
+:findBaseDir
+IF EXIST "%WDIR%"\.mvn goto baseDirFound
+cd ..
+IF "%WDIR%"=="%CD%" goto baseDirNotFound
+set WDIR=%CD%
+goto findBaseDir
+
+:baseDirFound
+set MAVEN_PROJECTBASEDIR=%WDIR%
+cd "%EXEC_DIR%"
+goto endDetectBaseDir
+
+:baseDirNotFound
+set MAVEN_PROJECTBASEDIR=%EXEC_DIR%
+cd "%EXEC_DIR%"
+
+:endDetectBaseDir
+
+IF NOT EXIST "%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config" goto endReadAdditionalConfig
+
+@setlocal EnableExtensions EnableDelayedExpansion
+for /F "usebackq delims=" %%a in ("%MAVEN_PROJECTBASEDIR%\.mvn\jvm.config") do set JVM_CONFIG_MAVEN_PROPS=!JVM_CONFIG_MAVEN_PROPS! %%a
+@endlocal & set JVM_CONFIG_MAVEN_PROPS=%JVM_CONFIG_MAVEN_PROPS%
+
+:endReadAdditionalConfig
+
+SET MAVEN_JAVA_EXE="%JAVA_HOME%\bin\java.exe"
+set WRAPPER_JAR="%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.jar"
+set WRAPPER_LAUNCHER=org.apache.maven.wrapper.MavenWrapperMain
+
+set DOWNLOAD_URL="https://repo.maven.apache.org/maven2/io/takari/maven-wrapper/0.4.2/maven-wrapper-0.4.2.jar"
+FOR /F "tokens=1,2 delims==" %%A IN (%MAVEN_PROJECTBASEDIR%\.mvn\wrapper\maven-wrapper.properties) DO (
+	IF "%%A"=="wrapperUrl" SET DOWNLOAD_URL=%%B 
+)
+
+@REM Extension to allow automatically downloading the maven-wrapper.jar from Maven-central
+@REM This allows using the maven wrapper in projects that prohibit checking in binary data.
+if exist %WRAPPER_JAR% (
+    echo Found %WRAPPER_JAR%
+) else (
+    echo Couldn't find %WRAPPER_JAR%, downloading it ...
+	echo Downloading from: %DOWNLOAD_URL%
+    powershell -Command "(New-Object Net.WebClient).DownloadFile('%DOWNLOAD_URL%', '%WRAPPER_JAR%')"
+    echo Finished downloading %WRAPPER_JAR%
+)
+@REM End of extension
+
+%MAVEN_JAVA_EXE% %JVM_CONFIG_MAVEN_PROPS% %MAVEN_OPTS% %MAVEN_DEBUG_OPTS% -classpath %WRAPPER_JAR% "-Dmaven.multiModuleProjectDirectory=%MAVEN_PROJECTBASEDIR%" %WRAPPER_LAUNCHER% %MAVEN_CONFIG% %*
+if ERRORLEVEL 1 goto error
+goto end
+
+:error
+set ERROR_CODE=1
+
+:end
+@endlocal & set ERROR_CODE=%ERROR_CODE%
+
+if not "%MAVEN_SKIP_RC%" == "" goto skipRcPost
+@REM check for post script, once with legacy .bat ending and once with .cmd ending
+if exist "%HOME%\mavenrc_post.bat" call "%HOME%\mavenrc_post.bat"
+if exist "%HOME%\mavenrc_post.cmd" call "%HOME%\mavenrc_post.cmd"
+:skipRcPost
+
+@REM pause the script if MAVEN_BATCH_PAUSE is set to 'on'
+if "%MAVEN_BATCH_PAUSE%" == "on" pause
+
+if "%MAVEN_TERMINATE_CMD%" == "on" exit %ERROR_CODE%
+
+exit /B %ERROR_CODE%

cbioondemandK8S/pom.xml

+<?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/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>org.springframework.boot</groupId>
+		<artifactId>spring-boot-starter-parent</artifactId>
+		<version>2.1.3.RELEASE</version>
+		<relativePath/>
+	</parent>
+	<groupId>cz.muni.ics.edirex.cbioondemandK8S</groupId>
+	<artifactId>cbioondemandK8S</artifactId>
+	<version>1.0.0-SNAPSHOT</version>
+	<name>cbio-on-demandK8S</name>
+	<description>API for cbio-on-demand implemented with K8S</description>
+
+	<properties>
+		<java.version>1.8</java.version>
+	</properties>
+
+	<dependencies>
+
+
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-web</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-actuator</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-test</artifactId>
+			<scope>test</scope>
+		</dependency>
+
+
+		<dependency>
+			<groupId>io.kubernetes</groupId>
+			<artifactId>client-java</artifactId>
+			<version>4.0.0</version>
+			<scope>compile</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>com.cronutils</groupId>
+			<artifactId>cron-utils</artifactId>
+			<version>8.0.0</version>
+		</dependency>
+
+
+
+		<!---->
+<!--		<dependency>-->
+<!--			<groupId>org.springframework</groupId>-->
+<!--			<artifactId>spring-web</artifactId>-->
+<!--			<version>5.1.2.RELEASE</version>-->
+<!--		</dependency>-->
+	</dependencies>
+
+	<build>
+		<resources>
+			<resource>
+				<directory>${basedir}/src/main/resources</directory>
+				<includes>
+					<include>*</include>
+				</includes>
+			</resource>
+		</resources>