Merge branch 'development'

.gitignore

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+.history
 *.iml
 atlassian-ide-plugin.xml
 java_pid*.hprof

karma-app/.gitignore

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+target/*

karma-app/README.md

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+Karma-app
+=========
+Karma desktop app for linux, windows and mac using which you can easily launch Karma.
+
+![](http://i.imgur.com/LtQcfmi.png)
+
+##Installation
+Download [karma app](https://github.com/usc-isi-i2/Web-Karma/releases) for your operating system. Then, install [java](https://www.java.com/en/download/help/download_options.xml) if you don't already have it. Installation of the right version of java is important. For instance, if you are running a 64bit windows, you have to download 64bit java for windows.
+###Linux
+Run `./Karma` on terminal.
+###Mac
+Navigate to the folder and open `Karma.app`
+###Windows
+First [set JRE_HOME](https://confluence.atlassian.com/doc/setting-the-java_home-variable-in-windows-8895.html) environmment variable. Then, navigate to the folder and open `Karma.exe`
+
+##Usage
+Once Karma app is opened, it automatically starts the server and launches on a web browser (It can take sometime the first time). In order to open a new instance on the browser, you can either click on "Open New Window" on the app or open `localhost:8080` on a new window in the browser.
+
+##Configuration
+You can set maximum heap size for karma on the main window. Once you change it, you need to __restart karma__.
+
+![](http://i.imgur.com/zMUotto.png)
+
+
+##Building the app from code.
+
+1. Install:
+
+  1. latest [node](https://nodejs.org/en/) 
+  2. electron-packager - `sudo npm install -g electron-packager`
+  3. wget - `brew install wget`
+  4. wine -
+      * if building on Mac[](https://www.davidbaumgold.com/tutorials/wine-mac/)
+
+        ```
+        brew doctor
+        brew update
+        brew tap caskroom/cask
+        brew cask install xquartz
+        brew install wine     
+        ```
+      * if building on Linux: `sudo apt-get install wine`
+      
+2. Clone this repository and navigate to `karma-app` folder.
+3. Make sure the npm python points to 2.7 version `npm config set python python2.7`
+4. Run `./build --archive` to build and generate the zip files for all OS
+5. The builds for all operating systems will be found in the target folder in `karma-app` folder.
+
+Karma app is built for linux, windows and mac for both ia32 and x64 versions as follows when `./build` is run:
+
+1. Navigates to karma-web directory and creates a shaded .war file.
+2. Copies the .war snapshot and other .war files in external_webapps to the target folder.
+3. Downloads apache tomcat.
+4. Copies the war files to webapps folder in tomcat.
+5. Copies conf files to tomcat folder.
+6. Navigates to the electron app folder (desktop) and copies the tomcat folder to app directory.
+7. Then we install all the dependencies and create a pre-release.
+8. We then use electron-packager to create packages for all the OSes and their flavors.
+9. The packages built are then copied to the target folder.
+10. If the build script is run wit `--archive` option, it will create zip archives of all the builds.

karma-app/build

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+#!/bin/bash
+
+########################################
+# This build script:
+# 1. Navigates to karma-web directory and creates a shaded .war file.
+# 2. Copies the .war snapshot and other .war files in external_webapps to the target folder.
+# 3. Downloads apache tomcat.
+# 4. Copies the war files to webapps folder.
+# 5. Copies conf files to tomcat folder.
+# 6. Navigates to the electron app folder and copies the tomcat folder to app/app directory.
+# 7. Runs the release script there to build karma app for linux, windows and mac.
+########################################
+
+CURRENT=`pwd`
+rm -rf target
+mkdir target
+
+cd ..
+mvn clean install -Dmaven.test.skip=true
+cd karma-web/
+mvn package -Pshaded
+cp target/karma-web*.war $CURRENT/target/ROOT.war
+cp external_webapps/* $CURRENT/target/
+
+mv $CURRENT/target/cluster*.war $CURRENT/target/clusterService.war
+
+cd $CURRENT/target
+
+# download tomcat binary
+wget http://apache.cs.utah.edu/tomcat/tomcat-7/v7.0.72/bin/apache-tomcat-7.0.72.zip -O tomcat.zip
+
+# TODO if this fails, exit
+unzip tomcat.zip
+rm tomcat.zip
+
+mv apache-tomcat* tomcat
+rm -rf tomcat/webapps/*
+mv *.war tomcat/webapps
+chmod +x tomcat/bin/*.sh
+
+cp $CURRENT/conf/* tomcat/conf/
+
+rm -rf $CURRENT/desktop/app/tomcat
+mv tomcat $CURRENT/desktop/app/
+
+cd $CURRENT/desktop
+npm install
+npm run prerelease
+cd app
+electron-packager . --platform=win32 --arch=x64 --icon=../resources/icons/karma.ico --overwrite
+electron-packager . --platform=linux --arch=x64 --icon=../resources/icons/karma.png --overwrite
+electron-packager . --platform=darwin --arch=x64 --icon=../resources/icons/karma.icns --overwrite
+
+cp -rf Karma-darwin* $CURRENT/target/Karma-Mac
+cp -rf Karma-linux* $CURRENT/target/Karma-Linux
+cp -rf Karma-win* $CURRENT/target/Karma-Windows
+rm -rf Karma-*
+
+cd $CURRENT/target
+
+#put our license
+for build_folder in `ls |grep Karma`
+do
+	mv $build_folder/LICENSE $build_folder/LICENSE.electron.packager
+	cp $CURRENT/../LICENSE.txt $build_folder/
+done
+
+if [ "$1" == "--archive" ]
+then
+  for i in `ls |grep 'Karma-*'`
+  do
+    zip -r $i $i
+  done
+fi

karma-app/conf/catalina.properties

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+# 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.
+
+#
+# List of comma-separated packages that start with or equal this string
+# will cause a security exception to be thrown when
+# passed to checkPackageAccess unless the
+# corresponding RuntimePermission ("accessClassInPackage."+package) has
+# been granted.
+package.access=sun.,org.apache.catalina.,org.apache.coyote.,org.apache.jasper.,\
+org.apache.naming.resources.,org.apache.tomcat.
+#
+# List of comma-separated packages that start with or equal this string
+# will cause a security exception to be thrown when
+# passed to checkPackageDefinition unless the
+# corresponding RuntimePermission ("defineClassInPackage."+package) has
+# been granted.
+#
+# by default, no packages are restricted for definition, and none of
+# the class loaders supplied with the JDK call checkPackageDefinition.
+#
+package.definition=sun.,java.,org.apache.catalina.,org.apache.coyote.,\
+org.apache.jasper.,org.apache.naming.,org.apache.tomcat.
+
+#
+#
+# List of comma-separated paths defining the contents of the "common"
+# classloader. Prefixes should be used to define what is the repository type.
+# Path may be relative to the CATALINA_HOME or CATALINA_BASE path or absolute.
+# If left as blank,the JVM system loader will be used as Catalina's "common"
+# loader.
+# Examples:
+#     "foo": Add this folder as a class repository
+#     "foo/*.jar": Add all the JARs of the specified folder as class
+#                  repositories
+#     "foo/bar.jar": Add bar.jar as a class repository
+common.loader=${catalina.base}/lib,${catalina.base}/lib/*.jar,${catalina.home}/lib,${catalina.home}/lib/*.jar
+
+#
+# List of comma-separated paths defining the contents of the "server"
+# classloader. Prefixes should be used to define what is the repository type.
+# Path may be relative to the CATALINA_HOME or CATALINA_BASE path or absolute.
+# If left as blank, the "common" loader will be used as Catalina's "server"
+# loader.
+# Examples:
+#     "foo": Add this folder as a class repository
+#     "foo/*.jar": Add all the JARs of the specified folder as class
+#                  repositories
+#     "foo/bar.jar": Add bar.jar as a class repository
+server.loader=
+
+#
+# List of comma-separated paths defining the contents of the "shared"
+# classloader. Prefixes should be used to define what is the repository type.
+# Path may be relative to the CATALINA_BASE path or absolute. If left as blank,
+# the "common" loader will be used as Catalina's "shared" loader.
+# Examples:
+#     "foo": Add this folder as a class repository
+#     "foo/*.jar": Add all the JARs of the specified folder as class
+#                  repositories
+#     "foo/bar.jar": Add bar.jar as a class repository
+# Please note that for single jars, e.g. bar.jar, you need the URL form
+# starting with file:.
+shared.loader=
+
+# List of JAR files that should not be scanned using the JarScanner
+# functionality. This is typically used to scan JARs for configuration
+# information. JARs that do not contain such information may be excluded from
+# the scan to speed up the scanning process. This is the default list. JARs on
+# this list are excluded from all scans. Scan specific lists (to exclude JARs
+# from individual scans) follow this. The list must be a comma separated list of
+# JAR file names.
+# The JARs listed below include:
+# - Tomcat Bootstrap JARs
+# - Tomcat API JARs
+# - Catalina JARs
+# - Jasper JARs
+# - Tomcat JARs
+# - Common non-Tomcat JARs
+# - Test JARs (JUnit, Cobertura and dependencies)
+tomcat.util.scan.DefaultJarScanner.jarsToSkip=\
+bootstrap.jar,commons-daemon.jar,tomcat-juli.jar,\
+annotations-api.jar,el-api.jar,jsp-api.jar,servlet-api.jar,websocket-api.jar,\
+catalina.jar,catalina-ant.jar,catalina-ha.jar,catalina-tribes.jar,\
+jasper.jar,jasper-el.jar,ecj-*.jar,\
+tomcat-api.jar,tomcat-util.jar,tomcat-coyote.jar,tomcat-dbcp.jar,\
+tomcat-jni.jar,tomcat-spdy.jar,\
+tomcat-i18n-en.jar,tomcat-i18n-es.jar,tomcat-i18n-fr.jar,tomcat-i18n-ja.jar,\
+tomcat-juli-adapters.jar,catalina-jmx-remote.jar,catalina-ws.jar,\
+tomcat-jdbc.jar,\
+tools.jar,\
+commons-beanutils*.jar,commons-codec*.jar,commons-collections*.jar,\
+commons-dbcp*.jar,commons-digester*.jar,commons-fileupload*.jar,\
+commons-httpclient*.jar,commons-io*.jar,commons-lang*.jar,commons-logging*.jar,\
+commons-math*.jar,commons-pool*.jar,\
+jstl.jar,taglibs-standard-spec-*.jar,\
+geronimo-spec-jaxrpc*.jar,wsdl4j*.jar,\
+ant.jar,ant-junit*.jar,aspectj*.jar,jmx.jar,h2*.jar,hibernate*.jar,httpclient*.jar,\
+jmx-tools.jar,jta*.jar,log4j.jar,log4j-1*.jar,mail*.jar,slf4j*.jar,\
+xercesImpl.jar,xmlParserAPIs.jar,xml-apis.jar,\
+junit.jar,junit-*.jar,hamcrest*.jar,org.hamcrest*.jar,ant-launcher.jar,\
+cobertura-*.jar,asm-*.jar,dom4j-*.jar,icu4j-*.jar,jaxen-*.jar,jdom-*.jar,\
+jetty-*.jar,oro-*.jar,servlet-api-*.jar,tagsoup-*.jar,xmlParserAPIs-*.jar,\
+xom-*.jar
+
+# Additional JARs (over and above the default JARs listed above) to skip when
+# scanning for Servlet 3.0 pluggability features. These features include web
+# fragments, annotations, SCIs and classes that match @HandlesTypes. The list
+# must be a comma separated list of JAR file names.
+org.apache.catalina.startup.ContextConfig.jarsToSkip=
+
+# Additional JARs (over and above the default JARs listed above) to skip when
+# scanning for TLDs. The list must be a comma separated list of JAR file names.
+org.apache.catalina.startup.TldConfig.jarsToSkip=tomcat7-websocket.jar
+
+#
+# String cache configuration.
+tomcat.util.buf.StringCache.byte.enabled=true
+#tomcat.util.buf.StringCache.char.enabled=true
+#tomcat.util.buf.StringCache.trainThreshold=500000
+#tomcat.util.buf.StringCache.cacheSize=5000

karma-app/conf/context.xml

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+<?xml version='1.0' encoding='utf-8'?>
+<!--
+  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.
+-->
+<!-- The contents of this file will be loaded for each web application -->
+<Context>
+
+    <!-- Default set of monitored resources -->
+    <WatchedResource>WEB-INF/web.xml</WatchedResource>
+
+    <!-- Uncomment this to disable session persistence across Tomcat restarts -->
+    <!--
+    <Manager pathname="" />
+    -->
+
+    <!-- Uncomment this to enable Comet connection tacking (provides events
+         on session expiration as well as webapp lifecycle) -->
+    <!--
+    <Valve className="org.apache.catalina.valves.CometConnectionManagerValve" />
+    -->
+
+</Context>

karma-app/desktop/.editorconfig

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+# editorconfig.org
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.json]
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false

karma-app/desktop/.gitignore

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+node_modules
+.DS_Store
+Thumbs.db
+*.log
+*.autogenerated
+
+# ignore everything in 'app' folder what had been generated from 'src' folder
+/app/stylesheets
+/app/app.js
+/app/background.js
+/app/karma.js
+/app/env.json
+/app/**/*.map
+/app/tomcat
+/app/Karma-*
+
+/dist
+*.swp
+*.swo
+*~
+!package.json
+!config

karma-app/desktop/README.md

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+Karma app
+=========
+
+```
+npm install
+npm start
+npm run build
+npm run release
+```