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Posted to commits@airavata.apache.org by sm...@apache.org on 2014/07/13 06:25:33 UTC
git commit: Updates to PHP Samples
Repository: airavata
Updated Branches:
refs/heads/master 92244d67e -> 6a4b162fb
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/master
Commit: 6a4b162fb8617b31e2698bc13d048d93b8417d13
Parents: 92244d6
Author: Suresh Marru <sm...@apache.org>
Authored: Sun Jul 13 00:25:24 2014 -0400
Committer: Suresh Marru <sm...@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,