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From samin...@apache.org
Subject [23/50] [abbrv] git commit: Updates to PHP Samples
Date Tue, 22 Jul 2014 15:05:48 GMT
Updates to PHP Samples


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/6a4b162f
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/6a4b162f
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/6a4b162f

Branch: refs/heads/workflow-support
Commit: 6a4b162fb8617b31e2698bc13d048d93b8417d13
Parents: 92244d6
Author: Suresh Marru <smarru@apache.org>
Authored: Sun Jul 13 00:25:24 2014 -0400
Committer: Suresh Marru <smarru@apache.org>
Committed: Sun Jul 13 00:25:24 2014 -0400

----------------------------------------------------------------------
 .../conf/airavata-client-properties.ini         |   4 +-
 .../resources/conf/app-catalog-identifiers.ini  |  20 ++-
 .../php-cli-samples/createExperiment.php        | 168 ++++++++-----------
 .../resources/php-cli-samples/createProject.php |  44 ++---
 .../getAllExperimentsInProject.php              |  46 ++---
 .../php-cli-samples/getAllUserProjects.php      |  35 ++--
 .../getApplicationDeployedResources.php         |  32 +---
 .../php-cli-samples/getApplicationInputs.php    |  37 ++--
 .../php-cli-samples/getApplicationModule.php    |  23 +--
 .../php-cli-samples/getApplicationOutputs.php   |  37 ++--
 .../resources/php-cli-samples/getExperiment.php |  72 +++-----
 .../php-cli-samples/getExperimentOutputs.php    |  76 +++------
 .../php-cli-samples/getExperimentStatus.php     |  64 ++-----
 .../php-cli-samples/launchExperiment.php        |  49 ++----
 .../resources/php-cli-samples/updateProject.php |  42 ++---
 .../tools/RegisterSampleApplications.java       |  34 ++--
 16 files changed, 282 insertions(+), 501 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/airavata-client-properties.ini
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/airavata-client-properties.ini
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/airavata-client-properties.ini
index b16d3c4..0f298da 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/airavata-client-properties.ini
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/airavata-client-properties.ini
@@ -8,7 +8,7 @@ THRIFT_LIB_DIR = "../lib/Thrift/"
 AIRAVATA_PHP_STUBS_DIR = "../lib/Airavata/"
 
 ; Host which runs the Airavata Server
-AIRAVATA_SERVER = "gw111.iu.xsede.org"
+AIRAVATA_SERVER = "gw127.iu.xsede.org"
 ;AIRAVATA_SERVER = "localhost"
 
 ; Airavata Server thrift port
@@ -17,3 +17,5 @@ AIRAVATA_PORT = 9930
 
 ; Time out value to give enough breathing room for client to get synchronous responses back
 AIRAVATA_TIMEOUT = 50000
+
+AIRAVATA_CREDENTIAL_STORE_TOKEN = 2c308fa9-99f8-4baa-92e4-d062e311483c

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
index ee2ddd3..3b3cb85 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini
@@ -1,8 +1,14 @@
 #Apache Airavata Gateway to Airavata Deployment Identifiers
-#Fri Jul 11 18:09:20 EDT 2014
-trestlesResourceId=trestles.sdsc.xsede.org_be1e9355-467c-4e71-b030-1f0ac76091d5
-bigredResourceId=bigred2.uits.iu.edu_866a6c6a-1387-4f87-b7e3-ba6f95c5c652
-stampedeResourceId=stampede.tacc.xsede.org_4a92a63c-be81-422d-a9be-121d35e04af9
-amberInterfaceId=Amber_26a0dec3-eb94-4f2c-9dfc-8a837bf4fbba
-wrfInterfaceId=WRF_9a1de5fb-8f90-4e32-96cb-c06bc1333274
-echoInterfaceId=Echo_b35ac096-808a-494e-94d1-0d20021c43f9
+#Sat Jul 12 18:13:37 EDT 2014
+espressoInterfaceId=ESPRESSO_a9c3acd6-4403-445b-b555-d4dbcc53afdb
+amberInterfaceId=Amber_26a8a2eb-a5a1-460f-a9c3-9bc5899433b3
+gromacsInterfaceId=GROMACS_c720c8f6-8b70-40be-b228-5f9ea72869f9
+trinityInterfaceId=Trinity_6068b270-157e-4ea0-9ec8-b2757b33a147
+stampedeResourceId=stampede.tacc.xsede.org_3da3cb46-851e-4124-a7bd-37449ca057a8
+bigredResourceId=bigred2.uits.iu.edu_fa40aa10-3703-48c6-a14c-c186d772cd58
+trestlesResourceId=trestles.sdsc.xsede.org_30fb9af6-7cd3-4373-87e4-9987e43cc904
+wrfInterfaceId=WRF_c3c67d74-5e60-4ec6-b50d-9a5d61843296
+autoDockInterfaceId=AutoDock_22c4cbbf-7785-4f96-85c6-8fe8404df6c8
+nwChemInterfaceId=NWChem_574c944e-b376-4e83-9871-96e4c9559a89
+lammpsInterfaceId=LAMMPS_752f3ea6-4ae5-4636-9dba-a6efeb1c4da9
+echoInterfaceId=Echo_c024a9c1-29b2-444d-b523-0729c6679ebb

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createExperiment.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createExperiment.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createExperiment.php
index e765c91..fef338f 100755
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createExperiment.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createExperiment.php
@@ -24,118 +24,94 @@ use Airavata\Model\Workspace\Experiment\UserConfigurationData;
 use Airavata\Model\Workspace\Experiment\ComputationalResourceScheduling;
 use Airavata\Model\Workspace\Experiment\DataType;
 
-$appId = 'SimpleEcho3_ca40f7c6-69ba-4f89-918d-9937cea0ca8f';
-$hostID = 'stampede.tacc.xsede.org_8f20b832-c11a-444b-8e73-bf15f4760b9a';
+try {
+    if ($argc < 4) {
+        echo "Usage: php createExperiment.php <username> <experiment_name> <project_ID>
\n";
+    } else {
+
+        /* User provides input values */
+        $userName = $argv[1];
+        $experimentName = $argv[2];
+        $projectId = $argv[3];
+
+        /**
+         * Configure Experiment by selecting application and configuring its input values.
+         *   This sample scripts executes a simple Echo command on one of the remote machines
as a illustrations.
+         *   The getAllApplicationInterfaceNames.php scripts will list other available samples
applications.
+         *   Examples include Amber, AutoDock, ESPRESSO, GROMACS, LAMMPS, NWChem, Trinity
and WRF.
+         */
+
+        $applicationId = $appcatalogdocs['echoInterfaceId'];
+
+        $applicationInput = new DataObjectType();
+        $applicationInput->key = "Input_to_Echo";
+        $applicationInput->value = "Hello World";
+        $experimentInputs = array($applicationInput);
+
+        /**
+         *  NOTE: For convenience, all the computational hosts are provided.
+         *        Comment/Uncomment appropriately to schedule on alternative resources
+         *        If all hosts are uncommented, the last one will be picked.
+         */
+
+        $scheduling = new ComputationalResourceScheduling();
+
+        /* IU BigRed II Cluster */
+        $scheduling->resourceHostId = $appcatalogdocs['bigredResourceId'];
+
+        /* TACC Stampede Cluster */
+        $scheduling->resourceHostId = $appcatalogdocs['stampedeResourceId'];
+        $scheduling->ComputationalProjectAccount = "TG-STA110014S";
+
+        /* SDSC Trestles Cluster */
+        $scheduling->resourceHostId = $appcatalogdocs['trestlesResourceId'];
+        $scheduling->ComputationalProjectAccount = "sds128";
+
+        /* Job dimensions and resource queue */
+        $scheduling->totalCPUCount = 1;
+        $scheduling->nodeCount = 1;
+        $scheduling->wallTimeLimit = 15;
+        $scheduling->queueName = "normal";
 
-$stampedeResourceId = $appcatalogdocs['stampedeResourceId'];
-
-echo "stampede resource if $stampedeResourceId \n";
-
-try
-{
-    if ($argc != 4)
-    {
-        echo 'php createExperiment.php <username> <experiment_name> <project_ID>';
-    }
-    else
-    {
-        /* ComputationalResourceScheduling data for Trestles*/
-        $cmRST = new ComputationalResourceScheduling();
-        $cmRST->resourceHostId = $hostID;
-        $cmRST->ComputationalProjectAccount = "sds128";
-        $cmRST->totalCPUCount = 1;
-        $cmRST->nodeCount = 1;
-        $cmRST->numberOfThreads = 0;
-        $cmRST->queueName = "normal";
-        $cmRST->wallTimeLimit = 15;
-        $cmRST->jobStartTime = 0;
-        $cmRST->totalPhysicalMemory = 0;
-
-        /* ComputationalResourceScheduling data for Stampede */
-        $cmRSS = new ComputationalResourceScheduling();
-        $cmRSS->resourceHostId = $hostID;
-        $cmRSS->ComputationalProjectAccount = "TG-STA110014S";
-        $cmRSS->totalCPUCount = 1;
-        $cmRSS->nodeCount = 1;
-        $cmRSS->numberOfThreads = 0;
-        $cmRSS->queueName = "normal";
-        $cmRSS->wallTimeLimit = 15;
-        $cmRSS->jobStartTime = 0;
-        $cmRSS->totalPhysicalMemory = 0;
-
-        /* UserConfigurationData using either Trestles or Stampede*/
-        $cmRS = $cmRSS;
-	// $cmRS = $cmRST;
         $userConfigurationData = new UserConfigurationData();
         $userConfigurationData->airavataAutoSchedule = 0;
         $userConfigurationData->overrideManualScheduledParams = 0;
-        $userConfigurationData->computationalResourceScheduling = $cmRS;
-        //var_dump($cmRS);
-        //var_dump($userConfigurationData);
-
-        /*Application ID for Trestles or Stamepede */
-        //$appId_trestles = "SimpleEcho2";
-        //$appId_stampede = "SimpleEcho3";
-        //$appId = $appId_stampede;
-        //$appId = $appId_trestles;
-
-        /* Experiment input and output data. */
-        $input = new DataObjectType();
-        $input->key = "echo_input";
-        $input->value = "echo_output=Hello World";
-        $input->type = DataType::STRING;
-        $exInputs = array($input);
-
-        $output = new DataObjectType();
-        $output->key = "echo_output";
-        $output->value = "";
-        $output->type = DataType::STRING;
-        $exOutputs = array($output);
-
-        /* Create Experiment: needs to update using unique project ID. */
-        $user = $argv[1];
-        $exp_name = $argv[2];
-        $proj = $argv[3];
+        $userConfigurationData->computationalResourceScheduling = $scheduling;
+
+        /**
+         * An experiment is created within Airavata and all the provided inputs and configurations
are persisted
+         *  within the Airavata Registry.
+         *
+         * NOTE: Airavata uses a 2 step launch process. The creation just creates the experiment.
The launch step
+         *   executes the created experiment.
+         */
 
         $experiment = new Experiment();
-        $experiment->projectID = $proj;
-        $experiment->userName = $user;
-        $experiment->name = $exp_name;
-        $experiment->applicationId = $appId;
+        $experiment->projectID = $projectId;
+        $experiment->userName = $userName;
+        $experiment->name = $experimentName;
+        $experiment->applicationId = $applicationId;
         $experiment->userConfigurationData = $userConfigurationData;
-        $experiment->experimentInputs = $exInputs;
-        $experiment->experimentOutputs = $exOutputs;
+        $experiment->experimentInputs = $experimentInputs;
 
-        $expId = $airavataclient->createExperiment($experiment);
+        $experimentId = $airavataclient->createExperiment($experiment);
 
-        if ($expId)
-        {
+        if ($experimentId) {
             var_dump($experiment);
-            echo "Experiment $expId created! \n    ";
-        }
-        else
-        {
+            echo "Experiment $experimentId is created! \n    ";
+        } else {
             echo "Failed to create experiment. \n";
         }
     }
 
-
-}
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
-}
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
 }
 
-
 $transport->close();
 
 ?>
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createProject.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createProject.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createProject.php
index da631c8..a5e0b75 100755
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createProject.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/createProject.php
@@ -14,46 +14,30 @@ use Airavata\API\Error\InvalidRequestException;
 
 use Airavata\Model\Workspace\Project;
 
-try
-{
-    if ($argc != 3)
-    {
-        echo 'php createProject.php <owner> <project_name>';
-    }
-    else
-    {
+try {
+    if ($argc < 3) {
+        echo 'php createProject.php <user_name> <project_name>';
+        echo 'php createProject.php <user_name> <project_name>';
+    } else {
         $project = new Project();
         $project->owner = $argv[1];
         $project->name = $argv[2];
 
         $projId = $airavataclient->createProject($project);
 
-        if ($projId)
-        {
-            echo "Project $projId is created!\n";
-        }
-        else
-        {
+        if ($projId) {
+            echo "Project $projId is successfully created!\n";
+        } else {
             echo "Project creation Failed.\n";
         }
     }
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
 }
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
-}
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
-}
-
-
-
-
 
 $transport->close();
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllExperimentsInProject.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllExperimentsInProject.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllExperimentsInProject.php
index 07cd96d..1590053 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllExperimentsInProject.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllExperimentsInProject.php
@@ -17,37 +17,23 @@ use Thrift\Transport\TBufferedTransport;
 use Thrift\Transport\TSocket;
 use Airavata\API\AiravataClient;
 
-try
-{
-
-   if ($argc != 2) {
-		echo 'php getAllExperimentsInProject.php <project_ID>';
-	}
-
-	else {
-	    $projectExperiments = $airavataclient->getAllExperimentsInProject($argv[1]);
-   	  echo '# of project experiments = ' . sizeof($projectExperiments) . '         <br><br>';
-    	  var_dump($projectExperiments);
-   }
-
-
-}
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
+try {
+
+    if ($argc != 2) {
+        echo 'Usage: php getAllExperimentsInProject.php <project_ID>';
+    } else {
+        $projectExperiments = $airavataclient->getAllExperimentsInProject($argv[1]);
+        echo '# of project experiments = ' . sizeof($projectExperiments);
+        var_dump($projectExperiments);
+    }
+
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
 }
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
-}
-
-
-
-
 
 $transport->close();
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllUserProjects.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllUserProjects.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllUserProjects.php
index c8c43da..3088435 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllUserProjects.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getAllUserProjects.php
@@ -17,37 +17,22 @@ use Thrift\Transport\TBufferedTransport;
 use Thrift\Transport\TSocket;
 use Airavata\API\AiravataClient;
 
-try
-{
-    if ($argc != 2)
-    {
-        echo 'php getAllUserProjects.php <user>';
-    }
-    else
-    {
+try {
+    if ($argc != 2) {
+        echo "Usage: php getAllUserProjects.php <user> \n";
+    } else {
         $userProjects = $airavataclient->getAllUserProjects($argv[1]);
         echo '# of user projects = ' . sizeof($userProjects) . '       ';
         var_dump($userProjects);
     }
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
 }
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
-}
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
-}
-
-
-
-
 
 $transport->close();
 
 ?>
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployedResources.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployedResources.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployedResources.php
index ccad572..e12bb9e 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployedResources.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationDeployedResources.php
@@ -21,9 +21,8 @@ use Thrift\Transport\TBufferedTransport;
 use Thrift\Transport\TSocket;
 use Airavata\API\AiravataClient;
 
-if ($argc != 2)
-{
-    exit("php getApplicationDeployedResources.php <appModuleID> \n");
+if ($argc != 2) {
+    exit("Usage: php getApplicationDeployedResources.php <appModuleID> \n");
 }
 
 $appModuleId = $argv[1];
@@ -52,32 +51,19 @@ function get_application_deployed_resources($appModuleId)
 {
     global $airavataclient;
 
-    try
-    {
+    try {
         return $airavataclient->getAppModuleDeployedResources($appModuleId);
-    }
-    catch (InvalidRequestException $ire)
-    {
+    } catch (InvalidRequestException $ire) {
         echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
-    }
-    catch (ExperimentNotFoundException $enf)
-    {
+    } catch (ExperimentNotFoundException $enf) {
         echo 'ExperimentNotFoundException!<br><br>' . $enf->getMessage();
-    }
-    catch (AiravataClientException $ace)
-    {
+    } catch (AiravataClientException $ace) {
         echo 'AiravataClientException!<br><br>' . $ace->getMessage();
-    }
-    catch (AiravataSystemException $ase)
-    {
+    } catch (AiravataSystemException $ase) {
         echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
-    }
-    catch (TTransportException $tte)
-    {
+    } catch (TTransportException $tte) {
         echo 'TTransportException!<br><br>' . $tte->getMessage();
-    }
-    catch (\Exception $e)
-    {
+    } catch (\Exception $e) {
         echo 'Exception!<br><br>' . $e->getMessage();
     }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationInputs.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationInputs.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationInputs.php
index 433dcb0..c8d853a 100755
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationInputs.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationInputs.php
@@ -14,14 +14,11 @@ use Airavata\API\Error\InvalidRequestException;
 use Thrift\Exception\TTransportException;
 use Airavata\Model\AppCatalog\AppInterface\DataType;
 
-try
-{
+try {
 
-    if ($argc < 1)
-    {
+    if ($argc < 1) {
         echo 'php getApplicationInputs.php <appInterfaceId>';
-    }
-    else {
+    } else {
 
         $appInterfaceId = $argv[1];
 
@@ -36,26 +33,16 @@ try
         } else {
             echo "\n Failed to fetch application interface Inputs. \n";
         }
-}
-}
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
-}
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
-}
-catch (TTransportException $tte)
-{
+    }
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
+} catch (TTransportException $tte) {
     echo 'TTransportException!<br><br>' . $tte->getMessage();
-}
-catch (\Exception $e)
-{
+} catch (\Exception $e) {
     echo 'Exception!<br><br>' . $e->getMessage();
 }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
index e28dbac..dfbc650 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationModule.php
@@ -37,28 +37,17 @@ function get_appModule($appModuleId)
 {
     global $airavataclient;
 
-    try
-    {
+    try {
         return $airavataclient->getApplicationModule($appModuleId);
-    }
-    catch (InvalidRequestException $ire)
-    {
+    } catch (InvalidRequestException $ire) {
         echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
-    }
-    catch (AiravataClientException $ace)
-    {
+    } catch (AiravataClientException $ace) {
         echo 'AiravataClientException!<br><br>' . $ace->getMessage();
-    }
-    catch (AiravataSystemException $ase)
-    {
+    } catch (AiravataSystemException $ase) {
         echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
-    }
-    catch (TTransportException $tte)
-    {
+    } catch (TTransportException $tte) {
         echo 'TTransportException!<br><br>' . $tte->getMessage();
-    }
-    catch (\Exception $e)
-    {
+    } catch (\Exception $e) {
         echo 'Exception!<br><br>' . $e->getMessage();
     }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationOutputs.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationOutputs.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationOutputs.php
index fd8e83f..ed57ac1 100755
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationOutputs.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getApplicationOutputs.php
@@ -14,14 +14,11 @@ use Airavata\API\Error\InvalidRequestException;
 use Thrift\Exception\TTransportException;
 use Airavata\Model\AppCatalog\AppInterface\DataType;
 
-try
-{
+try {
 
-    if ($argc < 1)
-    {
+    if ($argc < 1) {
         echo 'php getApplicationOutputs.php <appInterfaceId>';
-    }
-    else {
+    } else {
 
         $appInterfaceId = $argv[1];
 
@@ -35,26 +32,16 @@ try
         } else {
             echo "\n Failed to fetch application interface Outputs. \n";
         }
-}
-}
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
-}
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
-}
-catch (TTransportException $tte)
-{
+    }
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
+} catch (TTransportException $tte) {
     echo 'TTransportException!<br><br>' . $tte->getMessage();
-}
-catch (\Exception $e)
-{
+} catch (\Exception $e) {
     echo 'Exception!<br><br>' . $e->getMessage();
 }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperiment.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperiment.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperiment.php
index 24371bd..bdda534 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperiment.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperiment.php
@@ -20,61 +20,29 @@ use Thrift\Transport\TBufferedTransport;
 use Thrift\Transport\TSocket;
 use Airavata\API\AiravataClient;
 
-
-if (count($argv) < 2) {
-    exit("Please provide an experimentID. \n");
+try {
+    if (count($argv) < 2) {
+        exit("Please provide an experimentID. Usage: \n");
+    } else {
+        $experimentId = $argv[1];
+        $experiment = $airavataclient->getExperiment($experimentId);
+        var_dump($experiment);
+    }
+} catch (InvalidRequestException $ire) {
+    echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
+} catch (ExperimentNotFoundException $enf) {
+    echo 'ExperimentNotFoundException!<br><br>' . $enf->getMessage();
+} catch (AiravataClientException $ace) {
+    echo 'AiravataClientException!<br><br>' . $ace->getMessage();
+} catch (AiravataSystemException $ase) {
+    echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
+} catch (TTransportException $tte) {
+    echo 'TTransportException!<br><br>' . $tte->getMessage();
+} catch (\Exception $e) {
+    echo 'Exception!<br><br>' . $e->getMessage();
 }
 
-$expId = $argv[1];
-
-
-$experiment = get_experiment($expId);
-
-var_dump($experiment);
-
-
 $transport->close();
 
-
-/**
- * Get the experiment with the given ID
- * @param $expId
- * @return null
- */
-function get_experiment($expId)
-{
-    global $airavataclient;
-
-    try
-    {
-        return $airavataclient->getExperiment($expId);
-    }
-    catch (InvalidRequestException $ire)
-    {
-        echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
-    }
-    catch (ExperimentNotFoundException $enf)
-    {
-        echo 'ExperimentNotFoundException!<br><br>' . $enf->getMessage();
-    }
-    catch (AiravataClientException $ace)
-    {
-        echo 'AiravataClientException!<br><br>' . $ace->getMessage();
-    }
-    catch (AiravataSystemException $ase)
-    {
-        echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
-    }
-    catch (TTransportException $tte)
-    {
-        echo 'TTransportException!<br><br>' . $tte->getMessage();
-    }
-    catch (\Exception $e)
-    {
-        echo 'Exception!<br><br>' . $e->getMessage();
-    }
-
-}
-
 ?>
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentOutputs.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentOutputs.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentOutputs.php
index d8bc0df..e9fc30c 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentOutputs.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentOutputs.php
@@ -14,65 +14,35 @@ use Airavata\API\Error\ExperimentNotFoundException;
 use Airavata\API\Error\InvalidRequestException;
 use Thrift\Exception\TTransportException;
 
-if ($argc != 2)
-{
-    exit("php getExperimentOutputs.php <experiment_id> \n");
-}
+try {
+    if ($argc != 2) {
+        exit("Please specify a Experiment Id. Usage: php getExperimentOutputs.php <experiment_id>
\n");
+    } else {
 
-$expId = $argv[1];
+        $experimentId = $argv[1];
+        $experimentOutputs = $airavataclient->getExperimentOutputs($experimentId);
 
-$outputs = get_experiment_outputs($expId);
+        var_dump($experimentOutputs);
 
-foreach ($outputs as $output)
-{
-    echo "$output->type: $output->value      <br><br>";
+        foreach ($experimentOutputs as $output) {
+            echo "\n$output->key: $output->value \n";
+        }
+    }
+} catch (InvalidRequestException $ire) {
+    echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
+} catch (ExperimentNotFoundException $enf) {
+    echo 'ExperimentNotFoundException!<br><br>' . $enf->getMessage();
+} catch (AiravataClientException $ace) {
+    echo 'AiravataClientException!<br><br>' . $ace->getMessage();
+} catch (AiravataSystemException $ase) {
+    echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
+} catch (TTransportException $tte) {
+    echo 'TTransportException!<br><br>' . $tte->getMessage();
+} catch (\Exception $e) {
+    echo 'Exception!<br><br>' . $e->getMessage();
 }
 
-var_dump($outputs);
-
-
 $transport->close();
 
-
-/**
- * Get the experiment with the given ID
- * @param $expId
- * @return null
- */
-function get_experiment_outputs($expId)
-{
-    global $airavataclient;
-
-    try
-    {
-        return $airavataclient->getExperimentOutputs($expId);
-    }
-    catch (InvalidRequestException $ire)
-    {
-        echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
-    }
-    catch (ExperimentNotFoundException $enf)
-    {
-        echo 'ExperimentNotFoundException!<br><br>' . $enf->getMessage();
-    }
-    catch (AiravataClientException $ace)
-    {
-        echo 'AiravataClientException!<br><br>' . $ace->getMessage();
-    }
-    catch (AiravataSystemException $ase)
-    {
-        echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
-    }
-    catch (TTransportException $tte)
-    {
-        echo 'TTransportException!<br><br>' . $tte->getMessage();
-    }
-    catch (\Exception $e)
-    {
-        echo 'Exception!<br><br>' . $e->getMessage();
-    }
-
-}
-
 ?>
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentStatus.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentStatus.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentStatus.php
index babda01..f357a56 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentStatus.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/getExperimentStatus.php
@@ -19,55 +19,27 @@ use Thrift\Transport\TBufferedTransport;
 use Thrift\Transport\TSocket;
 use Airavata\API\AiravataClient;
 
-if (count($argv) < 2) {
-    exit("Please provide an experimentID. \n");
-}
-
-$expId = $argv[1];   
-
-$experimentStatusString = get_experiment_status($expId);
-echo "experiment status = " . $experimentStatusString . "       \n<br>";
-
+try {
+    if (count($argv) < 2) {
+        exit("Please provide an experimentID. Usage: php getExperimentStatus.php <experimentId>
\n");
+    } else {
 
-$transport->close();
-
-
-/**
- * Get a string containing the given experiment's status
- * @param $expId
- * @return mixed
- */
-function get_experiment_status($expId)
-{
-    global $airavataclient;
+        $experimentId = $argv[1];
+        $experimentStatus = $airavataclient->getExperimentStatus($experimentId);
 
-    try
-    {
-        $experimentStatus = $airavataclient->getExperimentStatus($expId);
-    }
-    catch (InvalidRequestException $ire)
-    {
-        echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
-    }
-    catch (ExperimentNotFoundException $enf)
-    {
-        echo 'ExperimentNotFoundException!<br><br>' . $enf->getMessage();
-    }
-    catch (AiravataClientException $ace)
-    {
-        echo 'AiravataClientException!<br><br>' . $ace->getMessage();
-    }
-    catch (AiravataSystemException $ase)
-    {
-        echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
-    }
-    catch (\Exception $e)
-    {
-        echo 'Exception!<br><br>' . $e->getMessage();
+        echo "experiment status = " . ExperimentState::$__names[$experimentStatus->experimentState]
. "       \n<br>";
     }
 
-    return ExperimentState::$__names[$experimentStatus->experimentState];
+} catch (InvalidRequestException $ire) {
+    echo 'InvalidRequestException!<br><br>' . $ire->getMessage();
+} catch (ExperimentNotFoundException $enf) {
+    echo 'ExperimentNotFoundException!<br><br>' . $enf->getMessage();
+} catch (AiravataClientException $ace) {
+    echo 'AiravataClientException!<br><br>' . $ace->getMessage();
+} catch (AiravataSystemException $ase) {
+    echo 'AiravataSystemException!<br><br>' . $ase->getMessage();
+} catch (\Exception $e) {
+    echo 'Exception!<br><br>' . $e->getMessage();
 }
 
-?>
-
+$transport->close();

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/launchExperiment.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/launchExperiment.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/launchExperiment.php
index b2e7108..49542c4 100755
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/launchExperiment.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/launchExperiment.php
@@ -21,39 +21,26 @@ use Airavata\API\AiravataClient;
 use Airavata\Model\Workspace\Project;
 use Airavata\Model\Workspace\Experiment\Experiment;
 
-try
-{
-   if (count($argv) < 2) {
-	exit("Please provide an experimentID. \n");
-   }
-
-   $expId = $argv[1];	
-   $airavataclient->launchExperiment($expId, '7a8b801f-23e7-465f-b5e4-3cf1e8bee2ab');
-   echo "Experiment $expId is launched.";
-}
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
+try {
+    if (count($argv) < 2) {
+        exit("Please provide the experimentId to be launched. Usage: php launchExperiment.php
<experimentId> \n");
+    } else {
+        $experimentId = $argv[1];
+        $airavataclient->launchExperiment($experimentId, $airavataconfig['AIRAVATA_CREDENTIAL_STORE_TOKEN']);
+        echo "Experiment $experimentId is launched. \n";
+    }
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
+} catch (ExperimentNotFoundException $enf) {
+    print 'Experiment Not Found Exception: ' . $enf->getMessage() . "\n";
+} catch (LaunchValidationException $lve) {
+    print 'Experiment Validation Failed: ' . $lve->getMessage() . "\n";
 }
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
-}
-catch (ExperimentNotFoundException $enf)
-{
-    print 'Experiment Not Found Exception: ' . $enf->getMessage()."\n";
-}
-
-
-
-
-
 
 $transport->close();
 
 ?>
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateProject.php
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateProject.php
b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateProject.php
index 1b9847a..9d870c1 100644
--- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateProject.php
+++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples/updateProject.php
@@ -17,35 +17,23 @@ use Thrift\Transport\TBufferedTransport;
 use Thrift\Transport\TSocket;
 use Airavata\API\AiravataClient;
 
-try 
-{
-		  if($argc != 3) 
-		  {
-					 echo 'php updateProject.php <project_id> <project_description>';
-		  }
-		  else
-		  {
-					 $project=$airavataclient->getProject($argv[1]);
-					 $project->description = $argv[2];
-					 $airavataclient->updateProject($argv[1], $project);
-					 echo 'Project '.$argv[1] . ' succesfully modified.';
-		  }
-}
-
-catch (InvalidRequestException $ire)
-{
-    print 'InvalidRequestException: ' . $ire->getMessage()."\n";
-}
-catch (AiravataClientException $ace)
-{
-    print 'Airavata System Exception: ' . $ace->getMessage()."\n";
-}
-catch (AiravataSystemException $ase)
-{
-    print 'Airavata System Exception: ' . $ase->getMessage()."\n";
+try {
+    if ($argc != 3) {
+        echo 'php updateProject.php <project_id> <project_description>';
+    } else {
+        $project = $airavataclient->getProject($argv[1]);
+        $project->description = $argv[2];
+        $airavataclient->updateProject($argv[1], $project);
+        echo 'Project ' . $argv[1] . ' successfully modified.';
+    }
+} catch (InvalidRequestException $ire) {
+    print 'InvalidRequestException: ' . $ire->getMessage() . "\n";
+} catch (AiravataClientException $ace) {
+    print 'Airavata System Exception: ' . $ace->getMessage() . "\n";
+} catch (AiravataSystemException $ase) {
+    print 'Airavata System Exception: ' . $ase->getMessage() . "\n";
 }
 
 $transport->close();
 
 ?>
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/6a4b162f/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
----------------------------------------------------------------------
diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
index 5c2c0c3..ddc4848 100644
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
@@ -47,7 +47,7 @@ import org.apache.thrift.TException;
 
 public class RegisterSampleApplications {
 
-    public static final String THRIFT_SERVER_HOST = "gw111.iu.xsede.org";
+    public static final String THRIFT_SERVER_HOST = "gw127.iu.xsede.org";
 //    public static final String THRIFT_SERVER_HOST = "localhost";
     public static final int THRIFT_SERVER_PORT = 9930;
 //    public static final int THRIFT_SERVER_PORT = 8930;
@@ -87,10 +87,10 @@ public class RegisterSampleApplications {
     private static String amberModuleId;
     private static String autoDockModuleId;
     private static String espressoModuleId;
-    private static String gromacsModuleId;
+    private static String gromacsModuleId = "GROMACS_417271fd-7ac1-4f40-b2a5-ed0908a743eb";
     private static String lammpsModuleId;
     private static String nwChemModuleId;
-    private static String trinityModuleId;
+    private static String trinityModuleId = "Trinity_8af45ca0-b628-4614-9087-c7b73f5f2fb6";
     private static String wrfModuleId;
 
     //App Interface Id's
@@ -245,22 +245,22 @@ public class RegisterSampleApplications {
         registerAmberInterface();
 
         //Registering AutoDock
-//        registerAutoDockInterface();
+        registerAutoDockInterface();
 
         //Registering Espresso
-//        registerEspressoInterface();
+        registerEspressoInterface();
 
         //Registering Gromacs
-//        registerGromacsInterface();
+        registerGromacsInterface();
 
         //Registering Lammps
         registerLammpsInterface();
 
         //Registering NWChem
-//        registerNWChemInterface();
+        registerNWChemInterface();
 
         //Registering Trinity
-//        registerTrinityInterface();
+        registerTrinityInterface();
 
         //Registering WRF
         registerWRFInterface();
@@ -418,14 +418,21 @@ public class RegisterSampleApplications {
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Portable_Input_Binary_File",
null,
                     DataType.URI, null, false, "Coordinates velocities, molecular topology
and simulation parameters", null);
 
+            InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("GROMOS_Coordinate_File",
null,
+                    DataType.URI, null, false, "Trajectory Coordinates Molecular Structure
in Gromos87 format", null);
+
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
+            applicationInputs.add(input2);
 
-            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
-                    "", DataType.STRING);
+            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("GROMACS_Execution_Log",null,DataType.URI);
+            OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("Full_Precision_Trajectory_file",null,DataType.URI);
+            OutputDataObjectType output3 = RegisterSampleApplicationsUtils.createAppOutput("Portable_Energy_file",null,DataType.URI);
 
             List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
             applicationOutputs.add(output1);
+            applicationOutputs.add(output2);
+            applicationOutputs.add(output3);
 
             gromacsInterfaceId = airavataClient.registerApplicationInterface(
                     RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(gromacsName,
gromacsDescription,
@@ -505,18 +512,19 @@ public class RegisterSampleApplications {
             InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Left_Input",
null,
                     DataType.URI, null, false, "RNA-Seq Left Library", null);
 
-            InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Left_Input",
null,
+            InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Right_Input",
null,
                     DataType.URI, null, false, "RNA-Seq Right Library", null);
 
             List<InputDataObjectType> applicationInputs = new ArrayList<InputDataObjectType>();
             applicationInputs.add(input1);
             applicationInputs.add(input2);
 
-            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output",
-                    "", DataType.STRING);
+            OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_Execution_Log",null,DataType.URI);
+            OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("Trinity_FASTA_File",null,DataType.URI);
 
             List<OutputDataObjectType> applicationOutputs = new ArrayList<OutputDataObjectType>();
             applicationOutputs.add(output1);
+            applicationOutputs.add(output2);
 
             trinityInterfaceId = airavataClient.registerApplicationInterface(
                     RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(trinityName,
trinityDescription,


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