http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/NOTICE ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/NOTICE b/modules/distribution/src/main/resources/NOTICE deleted file mode 100644 index fa7cba5..0000000 --- a/modules/distribution/src/main/resources/NOTICE +++ /dev/null @@ -1,163 +0,0 @@ -Apache Airavata -Copyright 2014 The Apache Software Foundation - -This product includes software developed at -The Apache Software Foundation (http://www.apache.org/). - -=============================================================================== -Apache Xerces Java Notice: - - Portions of this software were originally based on the following: - - software copyright (c) 1999, IBM Corporation., http://www.ibm.com. - - software copyright (c) 1999, Sun Microsystems., http://www.sun.com. - - voluntary contributions made by Paul Eng on behalf of the - Apache Software Foundation that were originally developed at iClick, Inc., - software copyright (c) 1999. - -================================================================================ -Apache XmlBeans Notice: - - Portions of this software were originally based on the following: - - software copyright (c) 2000-2003, BEA Systems, <http://www.bea.com/>. - - Aside from contributions to the Apache XMLBeans project, this - software also includes: - - - one or more source files from the Apache Xerces-J and Apache Axis - products, Copyright (c) 1999-2003 Apache Software Foundation - - - W3C XML Schema documents Copyright 2001-2003 (c) World Wide Web - Consortium (Massachusetts Institute of Technology, European Research - Consortium for Informatics and Mathematics, Keio University) - - - resolver.jar from Apache Xml Commons project, - Copyright (c) 2001-2003 Apache Software Foundation - - - Piccolo XML Parser for Java from http://piccolo.sourceforge.net/, - Copyright 2002 Yuval Oren under the terms of the Apache Software License 2.0 - - - JSR-173 Streaming API for XML from http://sourceforge.net/projects/xmlpullparser/, - Copyright 2005 BEA under the terms of the Apache Software License 2.0 - -========================================================================================= -Apache Axis2 Notice: (axis2-*, mex-1.5.1-impl) - -Portions Copyright 2006 International Business Machines Corp. -Portions Copyright 2005-2007 WSO2, Inc. - -This product also includes schemas and specification developed by: -- the W3C consortium (http://www.w3c.org) - -This product also includes WS-* schemas developed by International -Business Machines Corporation, Microsoft Corporation, BEA Systems, -TIBCO Software, SAP AG, Sonic Software, and VeriSign - -This product also includes a WSDL developed by salesforce.com -- Copyright 1999-2006 salesforce.com, inc. -Portions of the included xmlbeans library were originally based on the following: -- software copyright (c) 2000-2003, BEA Systems, <http://www.bea.com/>. - -==================================================================================== -Apache Derby Notice: - -Portions of Derby were originally developed by -International Business Machines Corporation and are -licensed to the Apache Software Foundation under the -"Software Grant and Corporate Contribution License Agreement", -informally known as the "Derby CLA". -The following copyright notice(s) were affixed to portions of the code -with which this file is now or was at one time distributed -and are placed here unaltered. - -(C) Copyright 1997,2004 International Business Machines Corporation. All rights reserved. - -(C) Copyright IBM Corp. 2003. - -======================= - -The portion of the functionTests under 'nist' was originally -developed by the National Institute of Standards and Technology (NIST), -an agency of the United States Department of Commerce, and adapted by -International Business Machines Corporation in accordance with the NIST -Software Acknowledgment and Redistribution document at -http://www.itl.nist.gov/div897/ctg/sql_form.htm - -======================== - -The JDBC apis for small devices and JDBC3 (under java/stubs/jsr169 and -java/stubs/jdbc3) were produced by trimming sources supplied by the -Apache Harmony project. In addition, the Harmony SerialBlob and -SerialClob implementations are used. The following notice covers the Harmony sources: - -Portions of Harmony were originally developed by -Intel Corporation and are licensed to the Apache Software -Foundation under the "Software Grant and Corporate Contribution -License Agreement", informally known as the "Intel Harmony CLA". - -============================================================================= -Apache Woden Notice: - - This product also includes software developed by : - - - IBM Corporation (http://www.ibm.com), - WSDL4J was the initial code contribution for the Apache Woden - project and some of the WSDL4J design and code has been reused. - - The W3C Consortium (http://www.w3c.org), - Common W3C XML Schema and DTD files are packaged with Apache Woden. - - Please read the different LICENSE files present in the root directory of - this distribution. - -========================================================================= -Woodstox Notice: - -This product includes software developed by the Woodstox Project -(http://woodstox.codehaus.org/) - -This product currently only contains code developed by authors -of specific components, as identified by the source code files. - -Since product implements StAX API, it has dependencies to StAX API -classes. - -For additional credits (generally to people who reported problems) -see CREDITS file. - -=========================================================================== -Apache xml-commons xml-apis Notice: - - Portions of this software were originally based on the following: - - software copyright (c) 1999, IBM Corporation., http://www.ibm.com. - - software copyright (c) 1999, Sun Microsystems., http://www.sun.com. - - software copyright (c) 2000 World Wide Web Consortium, http://www.w3.org - -================================================================================================ -Apache Xalan Notice: - -Portions of this software was originally based on the following: - - software copyright (c) 1999-2002, Lotus Development Corporation., http://www.lotus.com. - - software copyright (c) 2001-2002, Sun Microsystems., http://www.sun.com. - - software copyright (c) 2003, IBM Corporation., http://www.ibm.com. - - voluntary contributions made by Ovidiu Predescu ([email protected]) on behalf of the - Apache Software Foundation and was originally developed at Hewlett Packard Company. -================================================================================================ -Apache OpenJPA Notice: - -OpenJPA includes software developed by the SERP project -Copyright (c) 2002-2006, A. Abram White. All rights reserved. - -OpenJPA includes the persistence and orm schemas from the JPA specifications. -Copyright 2005-2009 Sun Microsystems, Inc. All rights reserved. -OpenJPA elects to include this software in this distribution under the -CDDL license. You can obtain a copy of the License at: - https://glassfish.dev.java.net/public/CDDL+GPL.html -The source code is available at: - https://glassfish.dev.java.net/source/browse/glassfish/ - -OpenJPA includes software written by Miroslav Nachev -OpenJPA uses test code written by Charles Tillman. -================================================================================================ -Apache XmlSchema Notice: - -Portions Copyright 2006 International Business Machines Corp. -================================================================================================
http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/README ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/README b/modules/distribution/src/main/resources/README deleted file mode 100644 index c2223ff..0000000 --- a/modules/distribution/src/main/resources/README +++ /dev/null @@ -1,145 +0,0 @@ -Apache Airavata Source - README.txt -Licensed under Apache License 2.0 - http://www.apache.org/licenses/LICENSE-2.0 --------------------------------------------------------------------------------- - -About -===== -Apache Airavata, a software framework to executing and managing computational jobs on -distributed computing resources including local clusters, supercomputers, national grids, -academic and commercial clouds. Airavata builds on general concepts of service oriented computing, -distributed messaging, and workflow composition and orchestration. Airavata bundles a server package -with an API, client software development Kits and a general purpose GUI XBaya as a application registration, workflow -construction execution and monitoring. XBaya GUI also provides capabilities to access the workflow -produced data. - -Contact -======== -For additional information about Apache Airavata, please contact the user or dev mailing lists: -http://airavata.apache.org/community/mailing-lists.html - -Description of Airavata Directory Structure -================================== - - airavata-api - This directory contains Airavata API related data models, api methods, generated server skeletons, client stubs, server implementations and client samples. - - - modules - This contains the source code of all the airavata maven projects organized as libraries, services and distributions - - - samples - This contains all the system wide samples provided in Airavata distribution. All the sample are having its README file - So users have to refer each readme file before running each sample. - - - tools - This contains source code libraries that can enhance Airavata features. - - - README - This document. - - - RELEASE_NOTES - The describe the key features and know issues with the current release. - - - INSTALL - This document will contain information on installing Apache-Airavata. - -Airavata Source Distribution Directory Structure -================================================ - - AIRAVATA_MASTER - âââ airavata-api - âââ modules - â âââ airavata-client - â âââ app-catalog - â âââ commons - â â âââ gfac-schema - â â âââ utils - â â âââ workflow-execution-context - â â âââ workflow-tracking - â âââ credential-store-service - â âââ distribution - â â âââ api-server - â â âââ client - â â âââ gfac-server - â â âââ orchestrator-server - â â âââ server - â â âââ release - â â âââ xbaya-gui - â âââ gfac - â â âââ airavata-gfac-service - â â âââ gfac-bes - â â âââ gfac-core - â â âââ gfac-ec2 - â â âââ gfac-gram - â â âââ gfac-gsissh - â â âââ gfac-hadoop - â â âââ gfac-local - â â âââ gfac-monitor - â â âââ gfac-ssh - â â âââ gfac-thrift-descriptions - â âââ integration-tests - â âââ messaging - â âââ orchestrator - â âââ registry - â â âââ airavata-jpa-registry - â â âââ registry-cpi - â âââ security - â âââ credential-store - â âââ server - â âââ test-suite - â âââ workflow-model - â â âââ workflow-engine - â â âââ workflow-model-component-node - â â âââ workflow-model-core - â âââ ws-messenger - â â âââ commons - â â âââ distribution - â â âââ messagebox - â â âââ messagebroker - â â âââ message-monitor - â â âââ samples - â âââ xbaya-gui - âââ samples - âââ tools - â âââ gsissh - â âââ gsissh-cli-tools - â âââ phoebus-integration - â âââ registry-migrate - âââ INSTALL - âââ LICENSE - âââ NOTICE - âââ README - âââ RELEASE_NOTES - -Available Binary Distributions -============================== - -Server Distributions --------------------- -* Airavata Server - The Airavata Server binary distribution allows you to run a standalone Airavata Server which includes all the airavata services - shipped with a default derby database as the backend registry. For stable purposes, a mysql configuration is recommended. - -* Airavata API Server - This is the server that contains Airavata API Server. - -* Airavata Orchestrator Server - This is the stand-alone orchestrator server - -* Airavata GFac Server - This is the standalone GFac Server - -Client Distributions --------------------- -* Airavata XBaya - The Airavata XBaya distribution is a client GUI application with features to register applications as web services, construct workflows, - execute and monitor workflows and browse the generated results from the airavata registry. - -* Airavata Client - The Airavata Client distribution is a set of libraries and configurations files that allow a 3rd party application to programatically - access Airavata functionality through Airavata API. - - How to test and run samples -=========================== -* If you built Airavata from source, and if you see "BUILD SUCCESS", then the test cases should have passes. -* The test cases are beyond unit level, they startup embedded services and run through basic workflow use cases. -* To walk through Airavata features, follow "XBAYA Quick-Start Tutorial" tutorial at https://cwiki.apache.org/confluence/display/AIRAVATA/XBAYA+Quick-Start+Tutorial. -* For advanced use cases, please contact mailing lists - http://airavata.apache.org/community/mailing-lists.html http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/airavata-server-start.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/airavata-server-start.sh b/modules/distribution/src/main/resources/bin/airavata-server-start.sh deleted file mode 100644 index f44661b..0000000 --- a/modules/distribution/src/main/resources/bin/airavata-server-start.sh +++ /dev/null @@ -1,123 +0,0 @@ -#!/usr/bin/env bash - -# 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. - -. `dirname $0`/setenv.sh -cd ${AIRAVATA_HOME}/bin -LOGO_FILE="logo.txt" - -JAVA_OPTS="" -AIRAVATA_COMMAND="" -EXTRA_ARGS="" -SERVERS="" -IS_DAEMON_MODE=false -LOGO=true -IS_SUBSET=false -SUBSET="" - -# parse command arguments -for var in "$@" -do - case ${var} in - -xdebug) - AIRAVATA_COMMAND="${AIRAVATA_COMMAND}" - JAVA_OPTS="$JAVA_OPTS -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=y,address=8000" - shift - ;; - -security) - JAVA_OPTS="${JAVA_OPTS} -Djava.security.manager -Djava.security.policy=${AIRAVATA_HOME}/conf/axis2.policy -Daxis2.home=${AIRAVATA_HOME}" - shift - ;; - apiserver | gfac | orchestrator | credentialstore | regserver) - if [ -z ${SERVERS} ] ; then - SERVERS="${var}" - else - SERVERS="${SERVERS},${var}" - fi - shift - ;; - all | api-orch | execution ) - IS_SUBSET=true - SUBSET="${var}" - shift - ;; - -d) - IS_DAEMON_MODE=true - shift - ;; - -nologo) - LOGO=false - shift - ;; - -h) - echo "Usage: airavata-server-start.sh [server-name/s] [command-options]" - echo "Server names:" - echo " apiserver Start apiserver" - echo " gfac Start gfac server" - echo " orchestrator Start orchestrator server" - echo " credentialstore Start credentialstore server" - echo " regserver Start registry server" - echo " all Start all servers in one JVM" - - echo "command options:" - echo " -d Start server in daemon mode" - echo " -xdebug Start Airavata Server under JPDA debugger" - echo " -nologo Do not show airavata logo" - echo " -security Enable Java 2 security" - echo " --<key>[=<value>] Server setting(s) to override or introduce (overrides values in airavata-server.properties)" - echo " -h Display this help and exit" - shift - exit 0 - ;; - *) - EXTRA_ARGS="${EXTRA_ARGS} ${var}" - shift - ;; - esac -done - -#Construct Airavata command arguments in proper order. -if ${IS_SUBSET} ; then - AIRAVATA_COMMAND="--servers=${SUBSET} ${AIRAVATA_COMMAND} ${EXTRA_ARGS}" -else - if [ -z ${SERVERS} ] ; then - echo "You should provide at least one server component to start the airavata server. Please use -h option to get more details." - exit -1 - else - AIRAVATA_COMMAND="--servers=${SERVERS} ${AIRAVATA_COMMAND} ${EXTRA_ARGS}" - fi -fi - -#print logo file -if ${LOGO} ; then - if [ -e ${LOGO_FILE} ] - then - cat ${LOGO_FILE} - fi -fi - - -if ${IS_DAEMON_MODE} ; then - echo "Starting airavata server/s in daemon mode..." - nohup java ${JAVA_OPTS} -classpath "${AIRAVATA_CLASSPATH}" \ - org.apache.airavata.server.ServerMain ${AIRAVATA_COMMAND} $* > /dev/null 2>&1 & -else - java ${JAVA_OPTS} -classpath "${AIRAVATA_CLASSPATH}" \ - org.apache.airavata.server.ServerMain ${AIRAVATA_COMMAND} $* -fi - http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/airavata-server-stop.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/airavata-server-stop.sh b/modules/distribution/src/main/resources/bin/airavata-server-stop.sh deleted file mode 100644 index 7f83f48..0000000 --- a/modules/distribution/src/main/resources/bin/airavata-server-stop.sh +++ /dev/null @@ -1,71 +0,0 @@ -#!/usr/bin/env bash - -# 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. - -. `dirname $0`/setenv.sh -cd ${AIRAVATA_HOME}/bin - -JAVA_OPTS="" -AIRAVATA_COMMAND="" -FORCE=false - -for var in "$@" -do - case ${var} in - -f | --force) - FORCE=true - shift - ;; - -h) - echo "Usage: airavata-server-stop.sh [command-options]" - echo "command options:" - echo " -f , --force Force stop all airavata servers." - echo " --<key>[=<value>] Server setting(s) to override or introduce (overrides values in airavata-server.properties)" - echo " -h Display this help and exit" - shift - exit 0 - ;; - *) - shift - esac -done - -if ${FORCE} ; then - for f in `find . -name "server_start_*"`; do - # split file name using "_" underscore - f_split=(${f//_/ }); - echo "Found process file : $f" - echo -n " Sending kill signals to process ${f_split[2]}..." - out=`kill -9 ${f_split[2]} 2>&1` - if [ -z "$out" ]; then - echo "done" - else - echo "failed (REASON: $out)" - fi - echo -n " Removing process file..." - out=`rm ${f} 2>&1` - if [ -z "$out" ]; then - echo "done" - else - echo "failed (REASON: $out)" - fi - done -else - java ${JAVA_OPTS} -classpath "${AIRAVATA_CLASSPATH}" \ - org.apache.airavata.server.ServerMain stop ${AIRAVATA_COMMAND} $* -fi http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/airavata-server.bat ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/airavata-server.bat b/modules/distribution/src/main/resources/bin/airavata-server.bat deleted file mode 100644 index be2c584..0000000 --- a/modules/distribution/src/main/resources/bin/airavata-server.bat +++ /dev/null @@ -1,55 +0,0 @@ -@echo off -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. - -setlocal EnableDelayedExpansion - -call "%~dp0"setenv.bat - -:loop -if ""%1""==""-xdebug"" goto xdebug -if ""%1""==""-security"" goto security -if ""%1""=="""" goto run -goto help - -:xdebug -set JAVA_OPTS= %JAVA_OPTS% -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=y,address=8000 -shift -goto loop - -:security -set JAVA_OPTS=%JAVA_OPTS% -Djava.security.manager -Djava.security.policy=%AIRAVATA_HOME%\conf\axis2.policy -Daxis2.home=%AIRAVATA_HOME% -shift -goto loop - -:help -echo Usage: %0 [-options] -echo. -echo where options include: -echo -xdebug Start Airavata Server under JPDA debugger -echo -security Enable Java 2 security -echo -h Help -goto end - -:run -cd "%AIRAVATA_HOME%\bin" -set LOGO_FILE="logo.txt" -if exist "%LOGO_FILE%" type "%LOGO_FILE%" - -java %JAVA_OPTS% -classpath "%AIRAVATA_CLASSPATH%" org.apache.airavata.server.ServerMain %* - -:end http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/derby.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/derby.sh b/modules/distribution/src/main/resources/bin/derby.sh deleted file mode 100644 index 134f7b9..0000000 --- a/modules/distribution/src/main/resources/bin/derby.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/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. - -. `dirname $0`/setenv.sh -export DERBY_HOME=$AIRAVATA_HOME/standalone-server -cd $AIRAVATA_HOME/bin -./startNetworkServer $* \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/logo.txt ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/logo.txt b/modules/distribution/src/main/resources/bin/logo.txt deleted file mode 100644 index e886438..0000000 --- a/modules/distribution/src/main/resources/bin/logo.txt +++ /dev/null @@ -1,34 +0,0 @@ -...._....................._..............._...._......................_......... -.../ \..._.__...__._..___| |__...___...../ \..(_)_.__.__.___...____._|.|_.__._.. -../ _ \.| '_ \./ _` |/ __| '_ \./ _ \.../ _ \.| | '__/ _` \ \./ / _` | __/ _` |. -./ ___ \| |_) | (_| | (__| |.| | __/../ ___ \| | |.| (_| |\ V / (_| | || (_| |. -/_/...\_\ .__/.\__,_|\___|_|.|_|\___|./_/...\_\_|_|..\__,_|.\_/.\__,_|\__\__,_|. -........|_|..................................................................... -................................................................................ -................,+????++~..~~++..+????????+??++.++~...~+=???+++................. -..............:???????....:::...~??????????????.~..::...=????????............... -............????????..~~..?????..??????????????.?????..~~~.~???????............. -...........?????????I,~I~~??????.+????????????.~??????~=~..?????????~........... -.........?????++??????..????????:.??????????I..????????..????????+????.......... -........??.....???????....???????...???????+..+??????+.I.????????.....?,........ -........????==????????..??..?????..=???????=..?????,.=+?.?????????===??=........ -......=??????????+????..+??=.???=.~??????????,.???=,???,.????=+??????????....... -....??????????+...+I++..???,=...:??????????????.....+??..++I?+..,??????????..... -....???????=??..........??..+??.:=:.???????......??..??=..........?=???????=.... -....??????..?...........+?..???.....???????......???.??...........~=.??????=.... -....~???~.~..............?..???.~=..,??????...7..???.?.:..............~????:.... -...7....7 ...............?..????. ...??????... .????.?.?.............I ..:.:.... -.....+7=,.+?................????:,I...?????..=.?????.?.............??~.=7+...... -..........????..............??????~...~??..~~??????..?...........+???,.......... -...........???............=.+???????,.?+:.?????????..+...........???+........... -............??............?,.??????.,??..??????????.,............???............ -...........??,.............=.,????.?+....????????I.I..............=?............ -..........I?..................+??.:?~.....=??????..................??........... -..........??...?...............??.:?=......??????..............?...??........... -............++?..............?.????...?....??????.+..............++I............ -.............................?.??????~....???????.?............................. -............................~~.??????......??????............................... -.............................=???????......???????+............................. -..........................=I??++?+++?......?+++++++?+........................... -..........................,..77..77......... .. ...7.......................... -................................................................................ http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/setenv.bat ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/setenv.bat b/modules/distribution/src/main/resources/bin/setenv.bat deleted file mode 100644 index 5f1fda1..0000000 --- a/modules/distribution/src/main/resources/bin/setenv.bat +++ /dev/null @@ -1,33 +0,0 @@ -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. - -@echo off - -:initialize -if "%AIRAVATA_HOME%"=="" set AIRAVATA_HOME=%~sdp0.. -SET curDrive=%cd:~0,1% -SET airavataDrive=%AIRAVATA_HOME:~0,1% -if not "%curDrive%" == "%airavataDrive%" %airavataDrive%: -goto updateClasspath - -rem ----- update classpath ----------------------------------------------------- -:updateClasspath -cd %AIRAVATA_HOME% -set AIRAVATA_CLASSPATH= -FOR %%C in ("%AIRAVATA_HOME%\lib\*.jar") DO set AIRAVATA_CLASSPATH=!AIRAVATA_CLASSPATH!;..\lib\%%~nC%%~xC - -:end \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/setenv.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/setenv.sh b/modules/distribution/src/main/resources/bin/setenv.sh deleted file mode 100755 index 9e894e1..0000000 --- a/modules/distribution/src/main/resources/bin/setenv.sh +++ /dev/null @@ -1,46 +0,0 @@ -#!/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. - -# resolve links - $0 may be a softlink -PRG="$0" - -while [ -h "$PRG" ]; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '.*/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`/"$link" - fi -done - -PRGDIR=`dirname "$PRG"` - -# Only set AIRAVATA_HOME if not already set -[ -z "$AIRAVATA_HOME" ] && AIRAVATA_HOME=`cd "$PRGDIR/.." ; pwd` - -AIRAVATA_CLASSPATH="" - -for f in "$AIRAVATA_HOME"/lib/*.jar -do - AIRAVATA_CLASSPATH="$AIRAVATA_CLASSPATH":$f -done - -export AIRAVATA_HOME -export AIRAVATA_CLASSPATH http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/bin/startNetworkServer ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/bin/startNetworkServer b/modules/distribution/src/main/resources/bin/startNetworkServer deleted file mode 100644 index 808566c..0000000 --- a/modules/distribution/src/main/resources/bin/startNetworkServer +++ /dev/null @@ -1,189 +0,0 @@ -#!/bin/sh - -# Licensed to the Apache Software Foundation (ASF) under one -# or more contributor license agreements. See the NOTICE file -# distributed with this work for additional information -# regarding copyright ownership. The ASF licenses this file -# to you under the Apache License, Version 2.0 (the -# "License"); you may not use this file except in compliance -# with the License. You may obtain a copy of the License at - -# http://www.apache.org/licenses/LICENSE-2.0 - -# Unless required by applicable law or agreed to in writing, -# software distributed under the License is distributed on an -# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY -# KIND, either express or implied. See the License for the -# specific language governing permissions and limitations -# under the License. - -if [ -n "$derby_common_debug" ] ; then - set -x -fi - -# OS specific support. $var _must_ be set to either true or false. -cygwin=false; -darwin=false; -case "`uname`" in - CYGWIN*) cygwin=true ;; - Darwin*) darwin=true - if [ -z "$JAVA_HOME" ] ; then - JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Home - fi - ;; -esac - -if [ -z "$DERBY_HOME" -o ! -d "$DERBY_HOME" ] ; then - ## resolve links - $0 may be a link to derby's home - PRG="$0" - progname=`basename "$0"` - - # need this for relative symlinks - while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi - done - - DERBY_HOME=`dirname "$PRG"`/.. - - # make it fully qualified - DERBY_HOME=`cd "$DERBY_HOME" && pwd` -fi - -# For Cygwin, ensure paths are in UNIX format before anything is touched -if $cygwin ; then - [ -n "$DERBY_HOME" ] && - DERBY_HOME=`cygpath --unix "$DERBY_HOME"` - [ -n "$JAVA_HOME" ] && - JAVA_HOME=`cygpath --unix "$JAVA_HOME"` -fi - -# set DERBY_LIB location -DERBY_LIB="${DERBY_HOME}/lib" - -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="$JAVA_HOME/bin/java" - fi - else - JAVACMD=`which java 2> /dev/null ` - if [ -z "$JAVACMD" ] ; then - JAVACMD=java - fi - fi -fi - -if [ ! -x "$JAVACMD" ] ; then - echo "Error: JAVA_HOME is not defined correctly." - echo " We cannot execute $JAVACMD" - exit 1 -fi - -# set local classpath, don't overwrite the user's -LOCALCLASSPATH=$DERBY_LIB/derby.jar:$DERBY_LIB/derbynet.jar:$DERBY_LIB/derbytools.jar:$DERBY_LIB/derbyclient.jar - -# if CLASSPATH_OVERRIDE env var is set, LOCALCLASSPATH will be -# user CLASSPATH first and derby-found jars after. -# In that case, the user CLASSPATH will override derby-found jars -# -# if CLASSPATH_OVERRIDE is not set, we'll have the normal behaviour -# with derby-found jars first and user CLASSPATH after -if [ -n "$CLASSPATH" ] ; then - # merge local and specified classpath - if [ -z "$LOCALCLASSPATH" ] ; then - LOCALCLASSPATH="$CLASSPATH" - elif [ -n "$CLASSPATH_OVERRIDE" ] ; then - LOCALCLASSPATH="$CLASSPATH:$LOCALCLASSPATH" - else - LOCALCLASSPATH="$LOCALCLASSPATH:$CLASSPATH" - fi - - # remove class path from launcher -cp option - CLASSPATH="" -fi - -# For Cygwin, switch paths to appropriate format before running java -# For PATHs convert to unix format first, then to windows format to ensure -# both formats are supported. Probably this will fail on directories with ; -# in the name in the path. Let's assume that paths containing ; are more -# rare than windows style paths on cygwin. -if $cygwin; then - if [ "$OS" = "Windows_NT" ] && cygpath -m .>/dev/null 2>/dev/null ; then - format=mixed - else - format=windows - fi - DERBY_HOME=`cygpath --$format "$DERBY_HOME"` - DERBY_LIB=`cygpath --$format "$DERBY_LIB"` - if [ -n "$JAVA_HOME" ]; then - JAVA_HOME=`cygpath --$format "$JAVA_HOME"` - fi - LCP_TEMP=`cygpath --path --unix "$LOCALCLASSPATH"` - LOCALCLASSPATH=`cygpath --path --$format "$LCP_TEMP"` - if [ -n "$CLASSPATH" ] ; then - CP_TEMP=`cygpath --path --unix "$CLASSPATH"` - CLASSPATH=`cygpath --path --$format "$CP_TEMP"` - fi - CYGHOME=`cygpath --$format "$HOME"` -fi - -# add a second backslash to variables terminated by a backslash under cygwin -if $cygwin; then - case "$DERBY_HOME" in - *\\ ) - DERBY_HOME="$DERBY_HOME\\" - ;; - esac - case "$CYGHOME" in - *\\ ) - CYGHOME="$CYGHOME\\" - ;; - esac - case "$LOCALCLASSPATH" in - *\\ ) - LOCALCLASSPATH="$LOCALCLASSPATH\\" - ;; - esac - case "$CLASSPATH" in - *\\ ) - CLASSPATH="$CLASSPATH\\" - ;; - esac -fi - -# Readjust classpath for MKS -# expr match -if [ \( "`expr $SHELL : '.*sh.exe$'`" -gt 0 \) -a \( "$cygwin" = "false" \) ]; then - LOCALCLASSPATH=`echo $LOCALCLASSPATH | sed -E 's/([\d\w]*):([\d\w]*)/\1;\2/g -'` -fi -#!/bin/sh - -# Licensed to the Apache Software Foundation (ASF) under one -# or more contributor license agreements. See the NOTICE file -# distributed with this work for additional information -# regarding copyright ownership. The ASF licenses this file -# to you under the Apache License, Version 2.0 (the -# "License"); you may not use this file except in compliance -# with the License. You may obtain a copy of the License at - -# http://www.apache.org/licenses/LICENSE-2.0 - -# Unless required by applicable law or agreed to in writing, -# software distributed under the License is distributed on an -# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY -# KIND, either express or implied. See the License for the -# specific language governing permissions and limitations -# under the License. - -derby_exec_command="exec \"$JAVACMD\" $DERBY_OPTS -classpath \"$LOCALCLASSPATH\" org.apache.derby.drda.NetworkServerControl start $@" -eval $derby_exec_command http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/registerSample.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/samples/registerSample.sh b/modules/distribution/src/main/resources/samples/registerSample.sh deleted file mode 100644 index 384ec0e..0000000 --- a/modules/distribution/src/main/resources/samples/registerSample.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/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. - -. `dirname $0`/../bin/setenv.sh -JAVA_OPTS="" - -java -classpath "$AIRAVATA_CLASSPATH" \ - org.apache.airavata.client.samples.RegisterSampleData $* http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/add.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/samples/scripts/add.sh b/modules/distribution/src/main/resources/samples/scripts/add.sh deleted file mode 100755 index daa140b..0000000 --- a/modules/distribution/src/main/resources/samples/scripts/add.sh +++ /dev/null @@ -1,21 +0,0 @@ -#!/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. - -# add two numbers -sleep 10 -/bin/echo "Result=`expr $1 + $2`" http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/echo.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/samples/scripts/echo.sh b/modules/distribution/src/main/resources/samples/scripts/echo.sh deleted file mode 100755 index 9dbaab9..0000000 --- a/modules/distribution/src/main/resources/samples/scripts/echo.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/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. - -#echo wrapper -sleep 10 -/bin/echo "Echoed_Output=$1" http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/multiply.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/samples/scripts/multiply.sh b/modules/distribution/src/main/resources/samples/scripts/multiply.sh deleted file mode 100755 index a5b5f7f..0000000 --- a/modules/distribution/src/main/resources/samples/scripts/multiply.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/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. - -# mutiply two numbers -sleep 10 -/bin/echo "Result=`expr $1 \* $2`" http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/distribution/src/main/resources/samples/scripts/subtract.sh ---------------------------------------------------------------------- diff --git a/modules/distribution/src/main/resources/samples/scripts/subtract.sh b/modules/distribution/src/main/resources/samples/scripts/subtract.sh deleted file mode 100755 index a21bec7..0000000 --- a/modules/distribution/src/main/resources/samples/scripts/subtract.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/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. - -# substract two numbers -sleep 10 -/bin/echo "Result=`expr $1 - $2`" http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-application-specific-handlers/pom.xml ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-application-specific-handlers/pom.xml b/modules/gfac/gfac-application-specific-handlers/pom.xml deleted file mode 100644 index 662a871..0000000 --- a/modules/gfac/gfac-application-specific-handlers/pom.xml +++ /dev/null @@ -1,30 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!--Licensed to the Apache Software Foundation (ASF) under one or more contributor - license agreements. See the NOTICE file distributed with this work for additional - information regarding copyright ownership. The ASF licenses this file to - you under the Apache License, Version 2.0 (theà "License"); you may not use - this file except in compliance with the License. You may obtain a copy of - the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required - by applicable law or agreed to in writing, software distributed under the - License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS - OF ANY ~ KIND, either express or implied. See the License for the specific - language governing permissions and limitations under the License. --> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd";> - <parent> - <artifactId>airavata-gfac</artifactId> - <groupId>org.apache.airavata</groupId> - <version>0.17-SNAPSHOT</version> - </parent> - <modelVersion>4.0.0</modelVersion> - - <artifactId>airavata-gfac-application-specific-handlers</artifactId> - <dependencies> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-gfac-core</artifactId> - <version>${project.version}</version> - </dependency> - </dependencies> - - -</project> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java b/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java deleted file mode 100644 index 2481ec9..0000000 --- a/modules/gfac/gfac-application-specific-handlers/src/main/java/org/apache/airavata/application/gaussian/handler/GaussianHandler.java +++ /dev/null @@ -1,163 +0,0 @@ -///* -// * -// * 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. -// * -// */ -// -//package org.apache.airavata.application.gaussian.handler; -// -//import org.apache.airavata.gfac.core.context.JobExecutionContext; -//import org.apache.airavata.gfac.core.handler.AbstractHandler; -//import org.apache.airavata.gfac.core.handler.GFacHandlerException; -//import org.apache.airavata.model.appcatalog.appinterface.InputDataObjectType; -//import org.apache.airavata.model.experiment.ComputationalResourceScheduling; -//import org.apache.airavata.registry.cpi.ExperimentCatalogModelType; -//import org.apache.airavata.registry.cpi.RegistryException; -//import org.slf4j.Logger; -//import org.slf4j.LoggerFactory; -// -//import java.io.BufferedReader; -//import java.io.File; -//import java.io.FileReader; -//import java.io.IOException; -//import java.util.HashMap; -//import java.util.Map; -//import java.util.Properties; -// -//public class GaussianHandler extends AbstractHandler { -// -// private static final Logger logger = LoggerFactory.getLogger(GaussianHandler.class); -// public static final String LINK_SECTION = "%"; -// public static final String ROUTE_SECTION = "#"; -// public static final String PROC_SHARED = "procshared"; -// public static final String MEM = "mem"; -// public static final String CHK = "chk"; -// public static final String PROC = "proc"; -// -// public static final String EQUAL = "="; -// public static final String OPEN_PARENTHESES = "("; -// public static final String CLOSE_PARENTHESES = ")"; -// -// private String mainInputFilePath; -// @Override -// public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException { -// super.invoke(jobExecutionContext); -// Map<String, String> configurations; -// Map<String, Object> parameters = jobExecutionContext.getInMessageContext().getParameters(); -// // only get first input file, which is the main input file -// for (Object paraValue : parameters.values()) { -// if (paraValue instanceof InputDataObjectType) { -// InputDataObjectType inputDataObjectType = (InputDataObjectType) paraValue; -// mainInputFilePath = inputDataObjectType.getValue(); -// break; -// } -// } -// if (mainInputFilePath != null) { -// File mainInputFile = new File(mainInputFilePath); -// if (mainInputFile.exists()) { -// try { -// configurations = parseGaussianInputFile(mainInputFile); -// ComputationalResourceScheduling taskScheduling = jobExecutionContext.getTaskData().getTaskScheduling(); -// for (Map.Entry<String, String> inputConfig : configurations.entrySet()) { -// if (inputConfig.getKey().equals(PROC_SHARED)) { -// taskScheduling.setTotalCPUCount(Integer.parseInt(inputConfig.getValue())); -// } else if (inputConfig.getKey().equals(MEM)) { -// int userRequestedMem = Integer.parseInt(inputConfig.getValue()); -// int additionalMem = (int) (userRequestedMem * 0.2); -// // TODO check (userRequestedMem + additionalMem) > maxNode or Queue allowed Mem -// taskScheduling.setTotalPhysicalMemory(userRequestedMem + additionalMem); -// } else if (inputConfig.getKey().equals(PROC)) { -// taskScheduling.setTotalCPUCount(Integer.parseInt(inputConfig.getValue())); -// } else { -// // TODO - handle other input configurations -// } -// logger.info("$$$$$$$$ " + inputConfig.getKey() + " --> " + inputConfig.getValue() + " $$$$$$$$$$$"); -// } -// experimentCatalog.update(ExperimentCatalogModelType.TASK_DETAIL, jobExecutionContext.getTaskData(), jobExecutionContext.getTaskData().getTaskID()); -// } catch (IOException e) { -// throw new GFacHandlerException("Error while reading main input file ", e); -// } catch (RegistryException e) { -// throw new GFacHandlerException("Error while updating task details", e); -// } -// } else { -// throw new GFacHandlerException("Main input file doesn't exists " + mainInputFilePath); -// } -// -// } else { -// throw new GFacHandlerException("Main input file path shouldn't be null"); -// } -// -// } -// -// /* %procshared=6 , put this line to the map key:procshared , value:6 -// keyword = option -// keyword(option) -// keyword=(option1, option2, â¦) -// keyword(option1, option2, â¦)*/ -// // TODO - make this method private -// public Map<String, String> parseGaussianInputFile(File mainInputFile) throws IOException { -// Map<String, String> configs = new HashMap<String, String>(); -// BufferedReader br = new BufferedReader(new FileReader(mainInputFile)); -// String line = br.readLine(); -// while (line != null) { -// line = line.trim(); -// String keyword = null; -// String withoutKeyword = null; -// String option = null; -// if (line.startsWith(LINK_SECTION)) { -// int equalIndex = line.indexOf(EQUAL); -// int openParenthesesIndex = line.indexOf(OPEN_PARENTHESES); -// // read the keyword -// if (equalIndex > 0) { -// keyword = line.substring(1, equalIndex).trim(); -// withoutKeyword = line.substring(equalIndex + 1, line.length()); // remove up to = sign -// } else if (openParenthesesIndex > 0) { -// keyword = line.substring(1, openParenthesesIndex).trim(); -// withoutKeyword = line.substring(openParenthesesIndex, line.length()); // remove left side of ( sign -// } else { -// // TODO - malformed input configuration -// } -// // read the option -// if (openParenthesesIndex > 0) { -// if (withoutKeyword.endsWith(CLOSE_PARENTHESES)) { -// option = withoutKeyword.substring(1, withoutKeyword.length() - 1); -// } else { -// //TODO - malformed input configuration -// } -// } else { -// option = withoutKeyword.trim(); -// } -// configs.put(keyword, option); -// } else if (line.startsWith(ROUTE_SECTION)) { -// // parse the line -// } -// line = br.readLine(); -// } -// return configs; -// } -// -// @Override -// public void initProperties(Properties properties) throws GFacHandlerException { -// -// } -// -// @Override -// public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException { -// // Implement this method if we need safe recover steps before rerun the task. -// } -//} http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/pom.xml ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/pom.xml b/modules/gfac/gfac-bes/pom.xml deleted file mode 100644 index 5f313c0..0000000 --- a/modules/gfac/gfac-bes/pom.xml +++ /dev/null @@ -1,130 +0,0 @@ -<?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 (theà "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. --> - -<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";> - <parent> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-gfac</artifactId> - <version>0.17-SNAPSHOT</version> - <relativePath>../pom.xml</relativePath> - </parent> - - <modelVersion>4.0.0</modelVersion> - <artifactId>airavata-gfac-bes</artifactId> - <name>Airavata GFac BES implementation</name> - <description>This is the extension of GFAC to use GRAM </description> - <url>http://airavata.apache.org/</url> - - <dependencies> - - <!-- Logging --> - <dependency> - <groupId>org.slf4j</groupId> - <artifactId>slf4j-api</artifactId> - </dependency> - - <!-- GFAC schemas --> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-gfac-core</artifactId> - <version>${project.version}</version> - </dependency> - <!-- Credential Store --> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-credential-store</artifactId> - <version>${project.version}</version> - <exclusions> - <exclusion> - <groupId>org.bouncycastle</groupId> - <artifactId>bcprov-jdk16</artifactId> - </exclusion> - </exclusions> - </dependency> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-server-configuration</artifactId> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.apache.airavata</groupId> - <artifactId>airavata-client-configuration</artifactId> - <scope>test</scope> - </dependency> - - - <!-- Test --> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.testng</groupId> - <artifactId>testng</artifactId> - <version>6.1.1</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.slf4j</groupId> - <artifactId>jcl-over-slf4j</artifactId> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.slf4j</groupId> - <artifactId>slf4j-log4j12</artifactId> - <scope>test</scope> - </dependency> - - <!-- gsi-ssh api dependencies --> - <dependency> - <groupId>org.apache.xmlbeans</groupId> - <artifactId>xmlbeans</artifactId> - <version>${xmlbeans.version}</version> - </dependency> - <!-- Unicore dependencies --> - <dependency> - <groupId>commons-httpclient</groupId> - <artifactId>commons-httpclient</artifactId> - <version>3.1</version> - </dependency> - <dependency> - <groupId>eu.unicore</groupId> - <artifactId>unicore-client-wrapper</artifactId> - <version>1.7.2_1</version> - <exclusions> - <!-- <exclusion> - <groupId>org.apache.santuario</groupId> - <artifactId>xmlsec</artifactId> - </exclusion> --> - <exclusion> - <groupId>net.sf.saxon</groupId> - <artifactId>saxon</artifactId> - </exclusion> - <exclusion> - <groupId>net.sf.saxon</groupId> - <artifactId>saxon-dom</artifactId> - </exclusion> - <exclusion> - <groupId>net.sf.saxon</groupId> - <artifactId>saxon-xpath</artifactId> - </exclusion> - </exclusions> - </dependency> - <dependency> - <groupId>net.sf.saxon</groupId> - <artifactId>Saxon-HE</artifactId> - <version>9.6.0-1</version> - </dependency> - </dependencies> -</project> http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java deleted file mode 100644 index faab749..0000000 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/AbstractSMSHandler.java +++ /dev/null @@ -1,171 +0,0 @@ -/* -* -* 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. -* -*/ - -package org.apache.airavata.gfac.bes.handlers; - -import java.io.PrintWriter; -import java.io.StringWriter; -import java.util.Properties; - -import org.apache.airavata.registry.cpi.AppCatalogException; -import org.apache.airavata.gfac.core.GFacException; -import org.apache.airavata.gfac.bes.security.UNICORESecurityContext; -import org.apache.airavata.gfac.bes.security.X509SecurityContext; -import org.apache.airavata.gfac.bes.utils.BESConstants; -import org.apache.airavata.gfac.bes.utils.DataTransferrer; -import org.apache.airavata.gfac.bes.utils.SecurityUtils; -import org.apache.airavata.gfac.bes.utils.StorageCreator; -import org.apache.airavata.gfac.core.context.JobExecutionContext; -import org.apache.airavata.gfac.core.handler.GFacHandler; -import org.apache.airavata.gfac.core.handler.GFacHandlerException; -import org.apache.airavata.gfac.core.GFacUtils; -import org.apache.airavata.model.appcatalog.computeresource.*; -import org.apache.airavata.model.experiment.CorrectiveAction; -import org.apache.airavata.model.experiment.ErrorCategory; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; -import org.w3.x2005.x08.addressing.EndpointReferenceType; - -import de.fzj.unicore.uas.client.StorageClient; -import eu.unicore.util.httpclient.DefaultClientConfiguration; - -public abstract class AbstractSMSHandler implements BESConstants, GFacHandler{ - - private final Logger log = LoggerFactory.getLogger(this.getClass()); - - protected DefaultClientConfiguration secProperties; - - protected StorageClient storageClient; - - protected DataTransferrer dataTransferrer; - - @Override - public void initProperties(Properties properties) - throws GFacHandlerException { - - } - - @Override - public void invoke(JobExecutionContext jobExecutionContext) - throws GFacHandlerException { - try { - initSecurityProperties(jobExecutionContext); - JobSubmissionInterface preferredJobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface(); - JobSubmissionProtocol protocol = preferredJobSubmissionInterface.getJobSubmissionProtocol(); - String interfaceId = preferredJobSubmissionInterface.getJobSubmissionInterfaceId(); - String factoryUrl = null; - if (protocol.equals(JobSubmissionProtocol.UNICORE)) { - UnicoreJobSubmission unicoreJobSubmission = GFacUtils.getUnicoreJobSubmission(interfaceId); - factoryUrl = unicoreJobSubmission.getUnicoreEndPointURL(); - } - storageClient = null; - - if (!isSMSInstanceExisting(jobExecutionContext)) { - EndpointReferenceType eprt = EndpointReferenceType.Factory.newInstance(); - eprt.addNewAddress().setStringValue(factoryUrl); - StorageCreator storageCreator = new StorageCreator(secProperties, factoryUrl, 5, null); - try { - storageClient = storageCreator.createStorage(); - } catch (Exception e2) { - log.error("Cannot create storage.."); - throw new GFacHandlerException("Cannot create storage..", e2); - } - jobExecutionContext.setProperty(PROP_SMS_EPR, storageClient.getEPR()); - } else { - EndpointReferenceType eprt = (EndpointReferenceType) jobExecutionContext.getProperty(PROP_SMS_EPR); - try { - storageClient = new StorageClient(eprt, secProperties); - } catch (Exception e) { - throw new GFacHandlerException("Cannot create storage..", e); - } - } - dataTransferrer = new DataTransferrer(jobExecutionContext, storageClient); - } catch (AppCatalogException e) { - throw new GFacHandlerException("Error occurred while retrieving unicore job submission interface..", e); - } - } - - protected void initSecurityProperties(JobExecutionContext jobExecutionContext) throws GFacHandlerException{ - log.debug("Initializing SMSInHandler security properties .."); - if (secProperties != null) { - secProperties = secProperties.clone(); - return; - } - UNICORESecurityContext unicoreContext; - try { - if (jobExecutionContext.getSecurityContext(X509SecurityContext.X509_SECURITY_CONTEXT) == null ) { - SecurityUtils.addSecurityContext(jobExecutionContext); - log.info("Successfully added the UNICORE Security Context"); - } - }catch (Exception e) { - log.error(e.getMessage()); - try { - StringWriter errors = new StringWriter(); - e.printStackTrace(new PrintWriter(errors)); - GFacUtils.saveErrorDetails(jobExecutionContext, errors.toString(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR); - } catch (GFacException e1) { - log.error(e1.getLocalizedMessage()); - } - throw new GFacHandlerException("Error while creating UNICORESecurityContext", e, e.getLocalizedMessage()); - } - - try { - unicoreContext = (UNICORESecurityContext) jobExecutionContext.getSecurityContext(X509SecurityContext.X509_SECURITY_CONTEXT); - log.info("Successfully retrieved the UNICORE Security Context"); - } catch (GFacException e) { - throw new GFacHandlerException(e); - } - if(log.isDebugEnabled()) { - log.debug("Generating client's default security configuration.."); - } - //TODO: check what kind of credential (server signed or myproxy) should be used - try { - secProperties = unicoreContext.getDefaultConfiguration(false); - } catch (Exception e) { - throw new GFacHandlerException(e); - } - if(log.isDebugEnabled()) { - log.debug("Security properties are initialized."); - } - jobExecutionContext.setProperty(PROP_CLIENT_CONF, secProperties); - } - - protected boolean isSMSInstanceExisting(JobExecutionContext jec){ - boolean hasSMS = true; - if((null == jec.getProperty(PROP_SMS_EPR))) { - hasSMS = false; - } - return hasSMS; - } - - /** - * It checks whether the SMSByteIO protocol is used during the creation - * of the job execution context. - * */ - protected boolean isSMSEnabled(JobExecutionContext jobExecutionContext){ -// if(((UnicoreHostType)jobExecutionContext.getApplicationContext().getHostDescription().getType()).getJobDirectoryMode() == JobDirectoryMode.SMS_BYTE_IO) { -// return true; -// } - return false; - } - - -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java deleted file mode 100644 index add8cb1..0000000 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOInHandler.java +++ /dev/null @@ -1,55 +0,0 @@ -/* -* -* 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. -* -*/ - -package org.apache.airavata.gfac.bes.handlers; - - -import org.apache.airavata.gfac.core.context.JobExecutionContext; -import org.apache.airavata.gfac.core.handler.GFacHandler; -import org.apache.airavata.gfac.core.handler.GFacHandlerException; -import org.apache.airavata.gfac.core.provider.GFacProviderException; - -/** - * Download upload job's input files to the temporary SMS directory. - * - * */ -public class SMSByteIOInHandler extends AbstractSMSHandler implements GFacHandler { - - - @Override - public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException { - super.invoke(jobExecutionContext); - if(jobExecutionContext.getInMessageContext().getParameters().size() < 1) return; - try{ - dataTransferrer.uploadLocalFiles(); - } catch (GFacProviderException e) { - throw new GFacHandlerException("Cannot upload local data",e); - } - - } - - @Override - public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException { - // TODO: Auto generated method body. - } - - -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java deleted file mode 100644 index 1baa2d9..0000000 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSByteIOOutHandler.java +++ /dev/null @@ -1,93 +0,0 @@ -/* -* -* 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. -* -*/ - -package org.apache.airavata.gfac.bes.handlers; - - - -import org.apache.airavata.gfac.bes.utils.ActivityInfo; -import org.apache.airavata.gfac.core.context.JobExecutionContext; -import org.apache.airavata.gfac.core.handler.GFacHandler; -import org.apache.airavata.gfac.core.handler.GFacHandlerException; -import org.apache.airavata.gfac.core.provider.GFacProviderException; -import org.ggf.schemas.bes.x2006.x08.besFactory.ActivityStateEnumeration; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; - -public class SMSByteIOOutHandler extends AbstractSMSHandler implements GFacHandler{ - - // TODO: later use AbstractHandler, which cannot be used due to error in RegistryFactory - private final Logger log = LoggerFactory.getLogger(this.getClass()); - - @Override - public void invoke(JobExecutionContext jobExecutionContext) - throws GFacHandlerException { - super.invoke(jobExecutionContext); - - ActivityInfo activityInfo = (ActivityInfo)jobExecutionContext.getProperty(PROP_ACTIVITY_INFO); - try { - if(activityInfo == null) { - log.error("No ActivityInfo instance found. The activity execution is ended due to an exception, see provider logs"); - return; - } - - if ((activityInfo.getActivityStatus().getState() == ActivityStateEnumeration.FAILED)) { - try {Thread.sleep(5000);}catch (InterruptedException e){} - - try { - dataTransferrer.downloadStdOuts(); - } catch (GFacProviderException e) { - throw new GFacHandlerException("Cannot download stdout data",e); - } - } - else if (activityInfo.getActivityStatus().getState() == ActivityStateEnumeration.FINISHED) { - try {Thread.sleep(5000);}catch (InterruptedException e){} - - try { - if (activityInfo.getActivityStatus().getExitCode() == 0) { - dataTransferrer.downloadRemoteFiles(); - } else { - dataTransferrer.downloadStdOuts(); - } - } catch (GFacProviderException e) { - throw new GFacHandlerException( - "Cannot download stdout data", e); - } - } - } finally { - try { - if (storageClient != null) { - storageClient.destroy(); - } - } catch (Exception e) { - log.warn("Cannot destroy temporary SMS instance", e); - } - - } - - } - - @Override - public void recover(JobExecutionContext jobExecutionContext) throws GFacHandlerException { - // TODO: Auto generated method body. - } -} - http://git-wip-us.apache.org/repos/asf/airavata-php-gateway/blob/488b772f/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java b/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java deleted file mode 100644 index 13393c9..0000000 --- a/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/handlers/SMSDirectoryHandler.java +++ /dev/null @@ -1,26 +0,0 @@ -/* -* -* 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. -* -*/ - -package org.apache.airavata.gfac.bes.handlers; - -public class SMSDirectoryHandler { - -}
