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From lah...@apache.org
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 GMT
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<InputParameterType> inputList = new ArrayList<InputParameterType>();
+
+        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<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+        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 @@
+<!-- ~ 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. -->
+    
+<GFac>
+    <GlobalHandlers>
+        <InHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.AppDescriptorCheckHandler">
+                    <property name="name" value="value"/>
+            </Handler>
+        </InHandlers>
+        <OutHandlers></OutHandlers>
+    </GlobalHandlers>
+    <Provider class="org.apache.airavata.gfac.provider.impl.LocalProvider" host="org.apache.airavata.schemas.gfac.impl.HostDescriptionTypeImpl">
+        <InHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.LocalDirectorySetupHandler"/>
+        </InHandlers>
+    </Provider>
+    <Provider class="org.apache.airavata.gfac.provider.impl.GramProvider" host="org.apache.airavata.schemas.gfac.impl.GlobusHostTypeImpl">
+        <property name="name" value="value"/>
+        <InHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler">
+                    <property name="name" value="value"/>
+            </Handler>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPInputHandler"/>
+        </InHandlers>
+        <OutHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
+        </OutHandlers>
+    </Provider>
+      <Provider class="org.apache.airavata.gfac.provider.impl.BESProvider" host="org.apache.airavata.schemas.gfac.impl.UnicoreHostTypeImpl">
+        <InHandlers>
+        	<Handler class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler"/>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPInputHandler"/>
+        </InHandlers>
+        <OutHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
+        </OutHandlers>
+    </Provider>
+
+    <Provider class="org.apache.airavata.gfac.ec2.EC2Provider" host="org.apache.airavata.schemas.gfac.impl.Ec2HostTypeImpl">
+        <InHandlers/>
+        <OutHandlers/>
+    </Provider>
+
+    <Provider class="org.apache.airavata.gfac.provider.impl.HadoopProvider" host="org.apache.airavata.schemas.gfac.impl.HadoopHostTypeImpl">
+        <InHandlers>
+        	<Handler class="org.apache.airavata.gfac.handler.HadoopDeploymentHandler"/>
+            <Handler class="org.apache.airavata.gfac.handler.HDFSDataMovementHandler"/>
+        </InHandlers>
+        <OutHandlers/>
+    </Provider>
+
+    <Application name="UltraScan">
+        <InHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler"/>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPInputHandler"/>
+        </InHandlers>
+        <OutHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
+        </OutHandlers>
+    </Application>
+
+     <Provider class="org.apache.airavata.gfac.provider.impl.SSHProvider" host="org.apache.airavata.schemas.gfac.impl.SSHHostTypeImpl">
+         <InHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.SCPDirectorySetupHandler"/>
+            <Handler class="org.apache.airavata.gfac.handler.SCPInputHandler"/>
+        </InHandlers>
+        <OutHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.SCPOutputHandler"/>
+        </OutHandlers>
+    </Provider>
+     <Provider class="org.apache.airavata.gfac.provider.impl.GSISSHProvider" host="org.apache.airavata.schemas.gfac.impl.GsisshHostTypeImpl">
+         <InHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.SCPDirectorySetupHandler"/>
+            <Handler class="org.apache.airavata.gfac.handler.SCPInputHandler"/>
+        </InHandlers>
+        <OutHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.SCPOutputHandler"/>
+        </OutHandlers>
+    </Provider>
+</GFac>
\ 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;



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