Return-Path: X-Original-To: apmail-airavata-commits-archive@www.apache.org Delivered-To: apmail-airavata-commits-archive@www.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id C079010A49 for ; Tue, 10 Dec 2013 20:52:50 +0000 (UTC) Received: (qmail 17734 invoked by uid 500); 10 Dec 2013 20:52:50 -0000 Delivered-To: apmail-airavata-commits-archive@airavata.apache.org Received: (qmail 17676 invoked by uid 500); 10 Dec 2013 20:52:50 -0000 Mailing-List: contact commits-help@airavata.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@airavata.apache.org Delivered-To: mailing list commits@airavata.apache.org Received: (qmail 17669 invoked by uid 99); 10 Dec 2013 20:52:49 -0000 Received: from athena.apache.org (HELO athena.apache.org) (140.211.11.136) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 10 Dec 2013 20:52:49 +0000 X-ASF-Spam-Status: No, hits=-2000.0 required=5.0 tests=ALL_TRUSTED X-Spam-Check-By: apache.org Received: from [140.211.11.4] (HELO eris.apache.org) (140.211.11.4) by apache.org (qpsmtpd/0.29) with ESMTP; Tue, 10 Dec 2013 20:52:46 +0000 Received: from eris.apache.org (localhost [127.0.0.1]) by eris.apache.org (Postfix) with ESMTP id 12C1423889E0; Tue, 10 Dec 2013 20:52:26 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: svn commit: r1549966 [2/2] - in /airavata/trunk/modules: distribution/airavata-server/src/main/resources/conf/ gfac-core/ gfac/ gfac/gfac-core/ gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/ gfac/gfac-core/src/main/java/org/apa... Date: Tue, 10 Dec 2013 20:52:25 -0000 To: commits@airavata.apache.org From: lahiru@apache.org X-Mailer: svnmailer-1.0.9 Message-Id: <20131210205226.12C1423889E0@eris.apache.org> X-Virus-Checked: Checked by ClamAV on apache.org Added: airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/errors.properties URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/errors.properties?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/errors.properties (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/errors.properties Tue Dec 10 20:52:23 2013 @@ -0,0 +1,197 @@ +# +# +# 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. +# + +# Directly copied from jglobus. Not a good way to manager error properties. +1 = Parameter not supported +2 = The RSL length is greater than the maximum allowed +3 = No resources available +4 = Bad directory specified +5 = The executable does not exist +6 = Insufficient funds +7 = Authentication with the remote server failed +8 = Job cancelled by user +9 = Job cancelled by system + +10 = Data transfer to the server failed +11 = The stdin file does not exist +12 = The connection to the server failed (check host and port) +13 = The provided RSL 'maxtime' value is invalid (not an integer or must be greater than 0) +14 = The provided RSL 'count' value is invalid (not an integer or must be greater than 0) +15 = The job manager received an invalid RSL +16 = Could not connect to job manager +17 = The job failed when the job manager attempted to run it +18 = Paradyn error +19 = The provided RSL 'jobtype' value is invalid + +20 = The provided RSL 'myjob' value is invalid +21 = The job manager failed to locate an internal script argument file +22 = The job manager failed to create an internal script argument file +23 = The job manager detected an invalid job state +24 = The job manager detected an invalid script response +25 = The job manager detected an invalid job state +26 = The provided RSL 'jobtype' value is not supported by this job manager +27 = Unimplemented +28 = The job manager failed to create an internal script submission file +29 = The job manager cannot find the user proxy + +30 = The job manager failed to open the user proxy +31 = The job manager failed to cancel the job as requested +32 = System memory allocation failed +33 = The interprocess job communication initialization failed +34 = The interprocess job communication setup failed +35 = The provided RSL 'host count' value is invalid +36 = One of the provided RSL parameters is unsupported +37 = The provided RSL 'queue' parameter is invalid +38 = The provided RSL 'project' parameter is invalid +39 = The provided RSL string includes variables that could not be identified + +40 = The provided RSL 'environment' parameter is invalid +41 = The provided RSL 'dryrun' parameter is invalid +42 = The provided RSL is invalid (an empty string) +43 = The job manager failed to stage the executable +44 = The job manager failed to stage the stdin file +45 = The requested job manager type is invalid +46 = The provided RSL 'arguments' parameter is invalid +47 = The gatekeeper failed to run the job manager +48 = The provided RSL could not be properly parsed +49 = There is a version mismatch between GRAM components + +50 = The provided RSL 'arguments' parameter is invalid +51 = The provided RSL 'count' parameter is invalid +52 = The provided RSL 'directory' parameter is invalid +53 = The provided RSL 'dryrun' parameter is invalid +54 = The provided RSL 'environment' parameter is invalid +55 = The provided RSL 'executable' parameter is invalid +56 = The provided RSL 'host_count' parameter is invalid +57 = The provided RSL 'jobtype' parameter is invalid +58 = The provided RSL 'maxtime' parameter is invalid +59 = The provided RSL 'myjob' parameter is invalid + +60 = The provided RSL 'paradyn' parameter is invalid +61 = The provided RSL 'project' parameter is invalid +62 = The provided RSL 'queue' parameter is invalid +63 = The provided RSL 'stderr' parameter is invalid +64 = The provided RSL 'stdin' parameter is invalid +65 = The provided RSL 'stdout' parameter is invalid +66 = The job manager failed to locate an internal script +67 = The job manager failed on the system call pipe() +68 = The job manager failed on the system call fcntl() +69 = The job manager failed to create the temporary stdout filename + +70 = The job manager failed to create the temporary stderr filename +71 = The job manager failed on the system call fork() +72 = The executable file permissions do not allow execution +73 = The job manager failed to open stdout +74 = The job manager failed to open stderr +75 = The cache file could not be opened in order to relocate the user proxy +76 = Cannot access cache files in ~/.globus/.gass_cache, check permissions, quota, and disk space +77 = The job manager failed to insert the contact in the client contact list +78 = The contact was not found in the job manager's client contact list +79 = Connecting to the job manager failed. Possible reasons: job terminated, invalid job contact, network problems, ... + +80 = The syntax of the job contact is invalid +81 = The executable parameter in the RSL is undefined +82 = The job manager service is misconfigured. condor arch undefined +83 = The job manager service is misconfigured. condor os undefined +84 = The provided RSL 'min_memory' parameter is invalid +85 = The provided RSL 'max_memory' parameter is invalid +86 = The RSL 'min_memory' value is not zero or greater +87 = The RSL 'max_memory' value is not zero or greater +88 = The creation of a HTTP message failed +89 = Parsing incoming HTTP message failed + +90 = The packing of information into a HTTP message failed +91 = An incoming HTTP message did not contain the expected information +92 = The job manager does not support the service that the client requested +93 = The gatekeeper failed to find the requested service +94 = The jobmanager does not accept any new requests (shutting down) +95 = The client failed to close the listener associated with the callback URL +96 = The gatekeeper contact cannot be parsed +97 = The job manager could not find the 'poe' command +98 = The job manager could not find the 'mpirun' command +99 = The provided RSL 'start_time' parameter is invalid" +100 = The provided RSL 'reservation_handle' parameter is invalid + +101 = The provided RSL 'max_wall_time' parameter is invalid +102 = The RSL 'max_wall_time' value is not zero or greater +103 = The provided RSL 'max_cpu_time' parameter is invalid +104 = The RSL 'max_cpu_time' value is not zero or greater +105 = The job manager is misconfigured, a scheduler script is missing +106 = The job manager is misconfigured, a scheduler script has invalid permissions +107 = The job manager failed to signal the job +108 = The job manager did not recognize/support the signal type +109 = The job manager failed to get the job id from the local scheduler + +110 = The job manager is waiting for a commit signal +111 = The job manager timed out while waiting for a commit signal +112 = The provided RSL 'save_state' parameter is invalid +113 = The provided RSL 'restart' parameter is invalid +114 = The provided RSL 'two_phase' parameter is invalid +115 = The RSL 'two_phase' value is not zero or greater +116 = The provided RSL 'stdout_position' parameter is invalid +117 = The RSL 'stdout_position' value is not zero or greater +118 = The provided RSL 'stderr_position' parameter is invalid +119 = The RSL 'stderr_position' value is not zero or greater + +120 = The job manager restart attempt failed +121 = The job state file doesn't exist +122 = Could not read the job state file +123 = Could not write the job state file +124 = The old job manager is still alive +125 = The job manager state file TTL expired +126 = It is unknown if the job was submitted +127 = The provided RSL 'remote_io_url' parameter is invalid +128 = Could not write the remote io url file +129 = The standard output/error size is different + +130 = The job manager was sent a stop signal (job is still running) +131 = The user proxy expired (job is still running) +132 = The job was not submitted by original jobmanager +133 = The job manager is not waiting for that commit signal +134 = The provided RSL scheduler specific parameter is invalid +135 = The job manager could not stage in a file +136 = The scratch directory could not be created +137 = The provided 'gass_cache' parameter is invalid +138 = The RSL contains attributes which are not valid for job submission +139 = The RSL contains attributes which are not valid for stdio update + +140 = The RSL contains attributes which are not valid for job restart +141 = The provided RSL 'file_stage_in' parameter is invalid +142 = The provided RSL 'file_stage_in_shared' parameter is invalid +143 = The provided RSL 'file_stage_out' parameter is invalid +144 = The provided RSL 'gass_cache' parameter is invalid +145 = The provided RSL 'file_cleanup' parameter is invalid +146 = The provided RSL 'scratch_dir' parameter is invalid +147 = The provided scheduler-specific RSL parameter is invalid +148 = A required RSL attribute was not defined in the RSL spec +149 = The gass_cache attribute points to an invalid cache directory + +150 = The provided RSL 'save_state' parameter has an invalid value +151 = The job manager could not open the RSL attribute validation file +152 = The job manager could not read the RSL attribute validation file +153 = The provided RSL 'proxy_timeout' is invalid +154 = The RSL 'proxy_timeout' value is not greater than zero +155 = The job manager could not stage out a file +156 = The job contact string does not match any which the job manager is handling +157 = Proxy delegation failed +158 = The job manager could not lock the state lock file + +1000 = Failed to start up callback handler +1003 = Job contact not set Added: airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/service.properties URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/service.properties?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/service.properties (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/main/resources/service.properties Tue Dec 10 20:52:23 2013 @@ -0,0 +1,67 @@ +# +# +# 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. +# +# + +# +# Properties for JCR Registry interface. By default, Apache Jackrabbit is used. +# +# org.apache.jackrabbit.repository.uri=http://localhost:8080/rmi +# jcr.class=org.apache.jackrabbit.rmi.repository.RmiRepositoryFactory +jcr.class=org.apache.jackrabbit.core.RepositoryFactoryImpl +jcr.user=admin +jcr.pass=admin + + +# +# Class which implemented Scheduler interface. It will be used to determine a Provider +# +scheduler.class= org.apache.airavata.core.gfac.scheduler.impl.SchedulerImpl + +# +# Data Service Plugins classes +# +datachain.classes= org.apache.airavata.core.gfac.extension.data.RegistryDataService + +# +# Pre execution Plugins classes. For example, GridFTP Input Staging +# +prechain.classes= org.apache.airavata.core.gfac.extension.pre.GridFtpInputStaging +prechain.classes= org.apache.airavata.core.gfac.extension.pre.HttpInputStaging + +# +# Post execution Plugins classes. For example, GridFTP Output Staging +# +postchain.classes= org.apache.airavata.core.gfac.extension.post.GridFtpOutputStaging +postchain.classes= org.apache.airavata.core.gfac.extension.post.OutputRegister + +# +# SSH private key location. It will be used by SSHProvider +# +# ssh.key=/home/user/.ssh/id_rsa +# ssh.keypass= +# ssh.username=usernameAtHost + +# +# MyProxy credential. It will be used by GridFTP Plugins and GramProvider. +# +# myproxy.server=myproxy.teragrid.org +# myproxy.user=username +# myproxy.pass=password +# myproxy.life=3600 \ No newline at end of file Added: airavata/trunk/modules/gfac/gfac-ec2/src/test/java/org/apache/airavata/gfac/ec2/EC2ProviderTest.java URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/test/java/org/apache/airavata/gfac/ec2/EC2ProviderTest.java?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/test/java/org/apache/airavata/gfac/ec2/EC2ProviderTest.java (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/test/java/org/apache/airavata/gfac/ec2/EC2ProviderTest.java Tue Dec 10 20:52:23 2013 @@ -0,0 +1,171 @@ +/* + * + * 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.ec2; + +import org.apache.airavata.commons.gfac.type.*; +import org.apache.airavata.gfac.GFacAPI; +import org.apache.airavata.gfac.GFacConfiguration; +import org.apache.airavata.gfac.GFacException; +import org.apache.airavata.gfac.context.ApplicationContext; +import org.apache.airavata.gfac.context.JobExecutionContext; +import org.apache.airavata.gfac.context.MessageContext; +import org.apache.airavata.schemas.gfac.*; +import org.junit.Assert; +import org.junit.Before; +import org.junit.Test; + +import java.io.File; +import java.net.URL; +import java.util.ArrayList; +import java.util.List; + +/** + * Your Amazon instance should be in a running state before running this test. + */ +public class EC2ProviderTest { + private JobExecutionContext jobExecutionContext; + + private static final String hostName = "ec2-host"; + + private static final String hostAddress = "ec2-address"; + + private static final String sequence1 = "RR042383.21413#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATA" + + "CTCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCCTGCGCCCATTGACCAATATTCCTCA" + + "CTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGC" + + "CTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAG" + + "GCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCCGCCGGTCGCCATCAGTCTTAGCAAGCTAAGACCATGCTGCCCCTGACTTGCATGT" + + "GTTAAGCCTGTAGCTTAGCGTTC"; + + private static final String sequence2 = "RR042383.31934#CTGGCACGGAGTTAGCCGATCCTTATTCATAAAGTACATGCAAACGGGTATCCATA" + + "CCCGACTTTATTCCTTTATAAAAGAAGTTTACAACCCATAGGGCAGTCATCCTTCACGCTACTTGGCTGGTTCAGGCTCTCGCCCATTGACCAATATTCCTCA" + + "CTGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGC" + + "CTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAAATCTTCCTTTCAGAA" + + "GGCTATCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCGTGCG"; + + /* Following variables are needed to be set in-order to run the test. Since these are account specific information, + I'm not adding the values here. It's the responsibility of the person who's running the test to update + these variables accordingly. + */ + + /* Username used to log into your ec2 instance eg.ec2-user */ + private String userName = ""; + + /* Secret key used to connect to the image */ + private String secretKey = ""; + + /* Access key used to connect to the image */ + private String accessKey = ""; + + /* Instance id of the running instance of your image */ + private String instanceId = ""; + + @Before + public void setUp() throws Exception { + URL resource = EC2ProviderTest.class.getClassLoader().getResource("gfac-config.xml"); + assert resource != null; + System.out.println(resource.getFile()); + GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()), null, null); + + /* EC2 Host */ + HostDescription host = new HostDescription(Ec2HostType.type); + host.getType().setHostName(hostName); + host.getType().setHostAddress(hostAddress); + + /* App */ + ApplicationDescription ec2Desc = new ApplicationDescription(Ec2ApplicationDeploymentType.type); + Ec2ApplicationDeploymentType ec2App = (Ec2ApplicationDeploymentType)ec2Desc.getType(); + + String serviceName = "Gnome_distance_calculation_workflow"; + ec2Desc.getType().addNewApplicationName().setStringValue(serviceName); + ec2App.setJobType(JobTypeType.EC_2); + ec2App.setExecutable("/home/ec2-user/run.sh"); + ec2App.setExecutableType("sh"); + + /* Service */ + ServiceDescription serv = new ServiceDescription(); + serv.getType().setName("GenomeEC2"); + + List inputList = new ArrayList(); + + InputParameterType input1 = InputParameterType.Factory.newInstance(); + input1.setParameterName("genome_input1"); + input1.setParameterType(StringParameterType.Factory.newInstance()); + inputList.add(input1); + + InputParameterType input2 = InputParameterType.Factory.newInstance(); + input2.setParameterName("genome_input2"); + input2.setParameterType(StringParameterType.Factory.newInstance()); + inputList.add(input2); + + InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList.size()]); + + List outputList = new ArrayList(); + OutputParameterType output = OutputParameterType.Factory.newInstance(); + output.setParameterName("genome_output"); + output.setParameterType(StringParameterType.Factory.newInstance()); + outputList.add(output); + + OutputParameterType[] outputParamList = outputList + .toArray(new OutputParameterType[outputList.size()]); + + serv.getType().setInputParametersArray(inputParamList); + serv.getType().setOutputParametersArray(outputParamList); + + jobExecutionContext = new JobExecutionContext(gFacConfiguration,serv.getType().getName()); + ApplicationContext applicationContext = new ApplicationContext(); + jobExecutionContext.setApplicationContext(applicationContext); + applicationContext.setServiceDescription(serv); + applicationContext.setApplicationDeploymentDescription(ec2Desc); + applicationContext.setHostDescription(host); + + AmazonSecurityContext amazonSecurityContext = + new AmazonSecurityContext(userName, accessKey, secretKey, instanceId); + jobExecutionContext.addSecurityContext(AmazonSecurityContext.AMAZON_SECURITY_CONTEXT, amazonSecurityContext); + + MessageContext inMessage = new MessageContext(); + ActualParameter genomeInput1 = new ActualParameter(); + ((StringParameterType)genomeInput1.getType()).setValue(sequence1); + inMessage.addParameter("genome_input1", genomeInput1); + + ActualParameter genomeInput2 = new ActualParameter(); + ((StringParameterType)genomeInput2.getType()).setValue(sequence2); + inMessage.addParameter("genome_input2", genomeInput2); + + MessageContext outMessage = new MessageContext(); + ActualParameter echo_out = new ActualParameter(); + outMessage.addParameter("distance", echo_out); + + jobExecutionContext.setInMessageContext(inMessage); + jobExecutionContext.setOutMessageContext(outMessage); + } + + @Test + public void testGramProvider() throws GFacException { + GFacAPI gFacAPI = new GFacAPI(); + gFacAPI.submitJob(jobExecutionContext); + MessageContext outMessageContext = jobExecutionContext.getOutMessageContext(); + Assert.assertEquals(MappingFactory. + toString((ActualParameter) outMessageContext.getParameter("genome_output")), "476"); + } +} + + Added: airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-client.properties URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-client.properties?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-client.properties (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-client.properties Tue Dec 10 20:52:23 2013 @@ -0,0 +1,73 @@ +# +# +# 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. +# + +########################################################################### +# +# This properties file provides configuration for Airavata Clients: +# XBaya and Airavata API +# +########################################################################### + +###---------------------------REGISTRY API IMPLEMENTATION---------------------------### + +class.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.registry.accessor=org.apache.airavata.rest.client.RegistryClient + +###---------------------REGISTRY API IMPLEMENTATION - CUSTOM SETTINGS----------------------### + +#for mysql [AiravataJPARegistry] +#registry.jdbc.driver=com.mysql.jdbc.Driver +#registry.jdbc.url=jdbc:mysql://localhost:3306/persistent_data + +#for derby [AiravataJPARegistry] +registry.jdbc.driver=org.apache.derby.jdbc.ClientDriver +registry.jdbc.url=jdbc:derby://localhost:1527/persistent_data;create=true;user=airavata;password=airavata +registry.jdbc.user=airavata +registry.jdbc.password=airavata +start.derby.server.mode=true + +default.registry.user=admin +default.registry.password=admin +default.registry.password.hash.method=SHA +default.registry.gateway=default + +#for xbaya +xbaya.registry.user=admin +xbaya.registry.url=http://localhost:8080/airavata/services/registry +xbaya.default.gateway=default + +trust.store=aiaravata.jks +trust.store.password=airavata + +#user defined registry accessor classes +#class.provenance.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.configuration.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.descriptor.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.project.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.user.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.published.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry + +################################################################################### +# Thrift configuration +################################################################################### +thrift.server.port=6060 + +class.execution.service.impl=org.apache.airavata.client.impl.ExecutionManagerImpl +#class.execution.service.impl=org.apache.airavata.client.impl.ExecutionManagerThriftImpl \ No newline at end of file Added: airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-server.properties URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-server.properties?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-server.properties (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/airavata-server.properties Tue Dec 10 20:52:23 2013 @@ -0,0 +1,235 @@ +# +# +# 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. +# + +########################################################################### +# +# This properties file provides configuration for all Airavata Services: +# Registry, Workflow Interpreter, GFac, Message Broker, Message Box +# +########################################################################### + +########################################################################### +# Airavata Embedded-Tomcat Server Configuration +########################################################################### +# By default, tomcat runs on port 80. If the port is changed, it will be +# have to be specified with port properties. This will be picked up by +# the registry service to register the service end-points. + +port=8080 + +# Axis2 server automatically picks up IP address from axis configuration, +# but some DHCP enables machines do not report correct ip addresses, +# in which case, the IP address can be manually specified. + +#ip=192.2.33.12 + + +#This property will enable https and stops http, during the url registration, https urls will be stored and +# http urls will not get registered, because currently airavata supports only one url for each service +#enable.https=false + +########################################################################### +# Airavata Registry Configuration +########################################################################### +system.gateway=default +system.user=admin +system.password=admin +#for derby [AiravataJPARegistry] +registry.jdbc.driver=org.apache.derby.jdbc.ClientDriver +registry.jdbc.url=jdbc:derby://localhost:1527/persistent_data;create=true;user=airavata;password=airavata +# MySql database configuration +#registry.jdbc.driver=com.mysql.jdbc.Driver +#registry.jdbc.url=jdbc:mysql://localhost:3306/persistent_data +registry.jdbc.user=airavata +registry.jdbc.password=airavata +start.derby.server.mode=true +default.registry.user=admin +default.registry.password=admin +default.registry.password.hash.method=SHA +default.registry.gateway=default +validationQuery=SELECT 1 from Configuration +jpa.connection.properties=MaxActive=10,MaxIdle=5,MinIdle=2,MaxWait=60000,testWhileIdle=true,testOnBorrow=true +#for rest [RegistryClient] +#registry.jdbc.url=http://localhost:9080/airavata-services + +#user defined registry accessor classes +#class.provenance.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.configuration.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.descriptor.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.project.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.user.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.published.workflow.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry + +########################################################################### +# Airavata Workflow Interpreter Configurations +########################################################################### + +runInThread=true +provenance=true +provenanceWriterThreadPoolSize=20 +gfac.embedded=true + +# +# Security Configuration used by Airavata Generic Factory Service +# to interact with Computational Resources. +# + +########################################################################### +# Airavata GFac MyProxy GSI credentials to access Grid Resources. +########################################################################### + +myproxy.server=myproxy.teragrid.org +myproxy.user=username +myproxy.pass=password +myproxy.life=3600 +# XSEDE Trusted certificates can be downloaded from https://software.xsede.org/security/xsede-certs.tar.gz +trusted.cert.location=modules/gfac-core/src/test/resources/certificates + +# SSH PKI key pair is SSH based authentication is used. +#ssh.key=/home/user/.ssh/id_rsa +#ssh.keypass= +#ssh.username=usernameAtHost + +########################################################################### +# Airavata Message Broker Basic Configurations. +# the Advanced section provides detailed custom configuration properties. +########################################################################### + +# Default derby database configuration +broker.jdbc.driver=org.apache.derby.jdbc.EmbeddedDriver +broker.jdbc.url=jdbc:derby:wsmg;create=true;user=airavata;password=airavata + +# Note: This database will only be used if 'broker.storage.type=persistent' +# is set in advanced properties below. +# MySql database configuration +#broker.jdbc.driver=com.mysql.jdbc.Driver +#broker.jdbc.url=jdbc:mysql://localhost:3306/wsmg?user=airavata&password=airavata + +########################################################################### +# Airavata Message Box Basic Configurations, +# the Advanced section provides detailed custom configuration properties. +########################################################################### + +# Default derby database +msgBox.jdbc.driver=org.apache.derby.jdbc.EmbeddedDriver +msgBox.jdbc.url=jdbc:derby:wsmg;create=true;user=airavata;password=airavata + +# MySql database configuration +#msgBox.jdbc.driver=com.mysql.jdbc.Driver +#msgBox.jdbc.url=jdbc:mysql://localhost:3306/wsmg?user=airavata&password=airavata + +########################################################################### +# Advance configuration to change service implementations +########################################################################### + +#Update the server context root path if airavata server is deployed under a different context root other than axis2 +server.context-root=airavata-server + +# +# Class which implemented HostScheduler interface. It will determine the which host to submit the request +# +host.scheduler=org.apache.airavata.gfac.scheduler.impl.SimpleHostScheduler + +# +# Data Service Plugins classes +# +datachain.classes= org.apache.airavata.core.gfac.extension.data.RegistryDataService + +# +# Pre execution Plugins classes. For example, GridFTP Input Staging +# +prechain.classes= org.apache.airavata.core.gfac.extension.pre.GridFtpInputStaging +prechain.classes= org.apache.airavata.core.gfac.extension.pre.HttpInputStaging + +# +# Post execution Plugins classes. For example, GridFTP Output Staging +# +postchain.classes= org.apache.airavata.core.gfac.extension.post.GridFtpOutputStaging +postchain.classes= org.apache.airavata.core.gfac.extension.post.OutputRegister + +# +# Advanced Message Broker Configurations +# + +#socket time out in milliseconds for sending messages. (defaults is 20000) +broker.socket.timeout=60000 + +broker.storage.type=persistent +#broker.storage.type=memory + +#specifies wether delivery component should be started or not. +broker.start.delivery.thread=true + +#fixed thread pool based delivery +#broker.delivery.method=pcrew + +#dynamic thread pool based delivery +#broker.delivery.method=parallel + +#single thread delivery +broker.delivery.method=serial + +#number of message delivery failures before a url become black listed (default is 2) +#broker.msg.delivery.retries=2 + +#time period (in seconds) a url will be kept blacklisted (default is 5 seconds) +#consumer.expiration.time.gap=5 + +#maximum number of messages to be send to a one consumer/url at time. +#applicable if 'broker.delivery.method' is 'pcrew' . (default is 10) + +#sending.batch.size=10 + +#size of the thread pool. only applicable if 'broker.delivery.method' is 'pcrew'. (default is 4) +#sending.thread.pool.size=4 + +# +# Advanced Message Box Configurations +# +#trusted.cert.location=/Users/lahirugunathilake/Downloads/certificates +public.ssh.key=/Users/lahirugunathilake/.ssh/id_dsa.pub +# SSH PKI key pair is SSH based authentication is used. +ssh.key=/home/user/.ssh/id_rsa +ssh.username=lginnali +private.ssh.key=/Users/lahirugunathilake/.ssh/id_dsa +ssh.password= +msgBox.usedatabase=true +messagePreservationDays=2 +messagePreservationHours=0 +messagePreservationMinutes=0 +messagePerservationIntervalDays=0 +messagePerservationIntervalHours=1 +messagePerservationIntervalMinutes=0 + +###---------------------------REGISTRY API IMPLEMENTATION---------------------------### + +class.registry.accessor=org.apache.airavata.persistance.registry.jpa.impl.AiravataJPARegistry +#class.registry.accessor=org.apache.airavata.rest.client.RegistryClient + +###---------------------------Computational Middleware Configurations---------------------------### + +#enable.application.job.status.history=true +#http://localhost:8080/axis2/services/RegistryService?wsdl +registry.service.wsdl=http://localhost:${port}/${server.context-root}/services/RegistryService?wsdl + +################################################################################### +# Thrift configuration +################################################################################### +thrift.server.port=6060 \ No newline at end of file Added: airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/echo.bat URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/echo.bat?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/echo.bat (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/echo.bat Tue Dec 10 20:52:23 2013 @@ -0,0 +1,22 @@ +:: +:: +:: 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 off +echo %1^=%2 \ No newline at end of file Added: airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/gfac-config.xml URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/gfac-config.xml?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/gfac-config.xml (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/gfac-config.xml Tue Dec 10 20:52:23 2013 @@ -0,0 +1,90 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file Added: airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/logging.properties URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/logging.properties?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/logging.properties (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/logging.properties Tue Dec 10 20:52:23 2013 @@ -0,0 +1,42 @@ +# +# 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. +# +# +#default/fallback log4j configuration +# + +# Set root logger level to WARN and its only appender to A1. +log4j.rootLogger=INFO, A1, A2 + +# A1 is set to be a rolling file appender with default params +log4j.appender.A1=org.apache.log4j.RollingFileAppender +log4j.appender.A1.File=target/seclogs.txt + +# A1 uses PatternLayout. +log4j.appender.A1.layout=org.apache.log4j.PatternLayout +log4j.appender.A1.layout.ConversionPattern=%d [%t] %-5p %c %x - %m%n + +# A2 is a console appender +log4j.appender.A2=org.apache.log4j.ConsoleAppender + +# A2 uses PatternLayout. +log4j.appender.A2.layout=org.apache.log4j.PatternLayout +log4j.appender.A2.layout.ConversionPattern=%d [%t] %-5p %c{1} %x - %m%n + +log4j.logger.unicore.security=INFO + Added: airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/service.properties URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/service.properties?rev=1549966&view=auto ============================================================================== --- airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/service.properties (added) +++ airavata/trunk/modules/gfac/gfac-ec2/src/test/resources/service.properties Tue Dec 10 20:52:23 2013 @@ -0,0 +1,67 @@ +# +# +# 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. +# +# + +# +# Properties for JCR Registry interface. By default, Apache Jackrabbit is used. +# +# org.apache.jackrabbit.repository.uri=http://localhost:8080/rmi +# jcr.class=org.apache.jackrabbit.rmi.repository.RmiRepositoryFactory +jcr.class=org.apache.jackrabbit.core.RepositoryFactoryImpl +jcr.user=admin +jcr.pass=admin + + +# +# Class which implemented Scheduler interface. It will be used to determine a Provider +# +scheduler.class= org.apache.airavata.core.gfac.scheduler.impl.SchedulerImpl + +# +# Data Service Plugins classes +# +datachain.classes= org.apache.airavata.core.gfac.extension.data.RegistryDataService + +# +# Pre execution Plugins classes. For example, GridFTP Input Staging +# +prechain.classes= org.apache.airavata.core.gfac.extension.pre.GridFtpInputStaging +prechain.classes= org.apache.airavata.core.gfac.extension.pre.HttpInputStaging + +# +# Post execution Plugins classes. For example, GridFTP Output Staging +# +postchain.classes= org.apache.airavata.core.gfac.extension.post.GridFtpOutputStaging +postchain.classes= org.apache.airavata.core.gfac.extension.post.OutputRegister + +# +# SSH private key location. It will be used by SSHProvider +# +# ssh.key=/home/user/.ssh/id_rsa +# ssh.keypass= +# ssh.username=usernameAtHost + +# +# MyProxy credential. It will be used by GridFTP Plugins and GramProvider. +# +# myproxy.server=myproxy.teragrid.org +# myproxy.user=username +# myproxy.pass=password +# myproxy.life=3600 \ No newline at end of file Modified: airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java URL: http://svn.apache.org/viewvc/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java?rev=1549966&r1=1549965&r2=1549966&view=diff ============================================================================== --- airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java (original) +++ airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java Tue Dec 10 20:52:23 2013 @@ -72,7 +72,6 @@ import org.apache.axiom.om.OMFactory; import org.apache.axiom.om.OMNamespace; import org.apache.axiom.om.impl.builder.StAXOMBuilder; import org.apache.axiom.om.impl.llom.util.AXIOMUtil; -import org.jets3t.service.impl.rest.httpclient.GoogleStorageService; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import org.xmlpull.v1.builder.XmlElement;