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Airavata PHP Command Line Student Tutorial

Update

The PHP command line scripts have been moved to the Apache Airavata git repository.

Introduction

An Airavata user or a gateway developer can also exercise using PHP client through command line to execute jobs in the computational Resources.

Prerequisites

1. Make sure you have PHP & GIT  installed in your machine.  
   NOTE: The tutorial steps are given for Linux environment.

You Will Learn

1. Execution of Airavata API methods using PHP client-command line.
2. How to enter/modify input parameters for the methods in command-line.

Tutorial I - Preparation

1. Create a folder (ex: SciGaP) in a preferable location in your local machine to clone download the PHP samples from GitHub. Open the created SciGaP folder (...../ cd SciGaP) and clone the files using GitHuB ‘HTTPS clone URL’    
   git clone https://git-wip-usdist.apache.org/repos/asf?p=airavata.git
   Once the cloning is completed you would get a completed message. /dist/dev/airavata/0.13/RC0/. 
2. In the given location download the apache-airavata-php-sdk-0.13-SNAPSHOT-bin.tar.gz
3. Open the folder which contains the PHP sample scripts. 
   SciGaP → airavata/apache-airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-php-sdk-0.13-SNAPSHOT/php-cli-samples
4. client-samples  folder contains PHP scripts to exercise currently existing Airavata API methods;
   1. add-compute-resources.php
      
   2. 1. GetAPIVersion.php (a sanity check)
   3. 1.  
   4. 1. createProject.php
      2. updateProject.php
      3. getAllUserProjects.php
      4. createExperiment.php
      5. getExperiment.php
      6. updateExperiment.php
      7. cloneExperiment.php
      8. getAllExperimentsInProject.php
      9. getAllUserExperiments.php
      10. search_experiments_by_name.php
   launchExperiment
   5. 1. search_experiments_by_description.php
   getExperimentStatus
   6. 1. search_experiments_by_application.php
   getExperimentOutputs
   7. 1. launchExperiment.php
      2. terminateExperiment.php 
   list-application-interfaces
   8. 1. getExperimentStatus.php
   list-compute-resources
   9. 1. getExperimentOutputs.php
   airavata-client-api-tester
   10. 1. registerComputeResource.php
5. Apart for the scripts for the API methods the folder contains;
   1. airavata-client-properties.ini - contains the server. port and timeout period information
   2. README-PHP-CLI-Examples.txt - Gives the script execution order
6. Navigation to working directory; 
   cd SciGaP/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples

Tutorial II - Sanity Check

1. Get Airavata Version 
   Execute php getAPIVersion.php and confirm the Airavata API version.

Tutorial III - Create, Update & List Projects

Create Project

...

1. Format;
   php createProject.php<space><project_owner><space><project_name>

...

1. Sample values;
   project_owner: Thomas   
   project_name: Test_Project

...

1. 1. 1. getAllComputeResourceNames.php

      2. getComputeResource.php

      3. deleteComputeResource.php

      4. registerApplicationModule.php
      5. getApplicationModule.php
      6. getApplicationDeployedResources.php
         
      7. registerApplicationInterface.php
      8. updateApplicationInterface.php
      9. getAllApplicationInterfaceNames.php
      10. deleteApplicationInterface.php
      11. getAvailableAppInterfaceComputeResources.php
      12. registerApplicationDeployment.php
      13. getApplicationDeployment.php

      14. getApplicationInputs.php

      15. getApplicationOutputs.php
      16. deleteGatewayComputeResourcePreference.php
      17. getGatewayComputeResourcePreference.php
          
      18. airavata-client-api-tester.php
2. Apart for the scripts for the API methods the folder contains;
   1. getAiravataClient.php - This script is referred by all other scripts to obtain Airavata client. Not for stand alone execution.
   2. README.txt - Gives an introduction to the scripts and also reference links to wiki pages with command line script execution information
3. Navigation to working directory; 
   cd SciGaP/airavata/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/php-cli-samples

Tutorial II - Sanity Check

1. Get Airavata Version 
   Execute php getAPIVersion.php and confirm the Airavata API version.

Tutorial III - Create, Update & List Projects

Create Project

1. Use; createProject.php to create new projects.
   project_owner and project_name can be given

...

Update Project

1. Use; updateProject.php to modify or add project description.
   project_ID and project_description are passed into the script as command line arguments.
   1. Format;
      php updateProjectcreateProject.php<space><project_ID><space><projectowner><space><project_description>name>
2. When creating new projects both project_owner and project_name When updating Projects currently user can only update the project description. Description cannot contain spaces.
   1. Sample values;
      project_owner: Thomas   
      project_IDname: Test_Project_4063b440-332a-49af-a6de-aea21d77bb2f
      project_description: Test_Airavata_Project
3. Successful creation Successful modification of project will give confirmation message with the Project ID 
   Project<space><project_id><space>successfully<space>modified.ID><space>is<space>created! 
4. Tutorial tryout; 
   Add project name description as a command-line argument to the existing updateProjectcreateProject.php script and execute.
   

...

Update Project

1. Verify the existence of the above created project by using getAllUserProjects.php file 
2. User = Project owner who creates the Project. User name is given as a command line argumentUse; updateProject.php to modify or add project description.
   project_ID and project_description are passed into the script as command line arguments.
   1. Format;
      php getAllUserProjectsupdateProject.php <space><user>
   2. Sample values;
      user: Thomas
3. Execute the file; all the projects created by the given user will get listed with project information.

Image Removed

Image - Project Detail Listing

Tutorial IV - Create, View , Update & Clone Experiment

Create Experiment

1. 1. <space><project_ID><space><project_description>
2. When updating Projects currently user can only update the project description. Use quotes around the description to include spaces.
   1. Sample values;
      project_ID: Test_Project_4063b440-332a-49af-a6de-aea21d77bb2f
      project_description: Test_Airavata_Project
3. Successful modification of project will give confirmation message with the Project ID 
   Project<space><project_id><space>successfully<space>modified.
4. Tutorial tryout; 
   Add project name as a command-line argument to the existing updateProject.php script and execute.

List Project

1. Verify the existence of the above created project by using getAllUserProjects.php file 
2. User = Project owner who creates the Project. User name is given as a command line argumentCreate an experiment with above created project using createExperiment.php script. When creating experiment User, Experiment name and Project ID (username, experiment_name, project_ID) are passed as arguments to the script.
   1. Format;
      php createExperimentgetAllUserProjects.php<space><username><space><experiment_name><space><project_ID>
   Changing other parameters require opening the script and modifying and saving values inside the script. 
   
   1. <space><user>
   2. Sample values;
      user: Peter
3. Execute the file; all the projects created by the given user will get listed with project information.
   Image Added
   Image - Project Detail Listing
   

Tutorial IV - Create, View , Update & Clone Experiment

Create Experiment

1. Create an experiment with above created project using createExperiment.php script. When creating experiment User, Experiment name and Project ID (username, experiment_name, project_ID) are passed as arguments to the script.
   1. Format;
      php createExperiment.php<space><username><space><experiment_name><space><project_ID>
2. Changing other parameters require opening the script and modifying and saving values inside the script. 
   Sample values;

    

   Parameter	Sample Values	NOTE
   Project ID	PHP_EXP1_17a34aa5-68cb-41e6-b189-dc94548660a6	Project iD is validated against existing projects Passed as an argument to the script
   Creating User	Donald	Users are validated against existing Airavata gateway users. Passed as an argument to the script
   Experiment Name	PHP_EXP	Not a unique value. Use can enter any value Passed as an argument to the script
   Resource Host ID		From Application Catalog
   Total CPU Count	10	Number of CPUs required for the experiment
   nodeCount	10	Number of nodes required in each CPU
   Queue Name	normal	if left blank it will pick default queue
   Wall Time Limit	10	This is given in minutes
   Application ID		From Application Catalog
   Input Key	echo_input
   Input Value	echo_output=Hello World

3. Script has all the resource listed; User has to select a resource to run the experiment and comment the others. User can change existing other parameters as well in the script.

4.  

   Parameter	Sample Values	NOTE
   Project ID	Test_Project_4063b440-332a-49af-a6de-aea21d77bb2f	Project iD is validated against existing projects Passed as an argument to the script
   Creating User	Thomas	Users are validated against existing Airavata gateway users. Passed as an argument to the script
   Experiment Name	Exp_Test_Project_1	Not a unique value. Use can enter any value Passed as an argument to the script
   Resource Host ID	trestles.sdsc.edu stampede.tacc.xsede.org
   Computational Project Account
   Total CPU Count	10	Number of CPUs required for the experiment
   nodeCount	10	Number of nodes required in each CPU
   Number of Threads	10	Number of threads per node
   Queue Name	normal	if left blank it will pick default queue
   Wall Time Limit	10	This is given in minutes
   JobStartTime	0
   Total Physical Memory	0
   Application ID	SimpleEcho2	Existing application in the selected resource
   Input Key	echo_input
   Input Value	echo_output=Hello World
   Output Key	echo_output

   Depending on the computational resource used the resource scheduling data part need to be entered by the user. Other defined resource scheduling parts should be commented. 
   Image Removed
   Image - PHP Script Sample
   Execute the file; experiment will be created and experiment ID will be generated; ID is the unique value which identifies the experiment in Airavata.
5. Experiment creation confirmation message;
   Experiment<space><exp_ID><space>created!

View Experiment (Search by Experiment ID)

1. To search and view above created experiment use getExperiment.php. 
2. This would list experiment parameters and information about the experiment such as output, number of nodes, status, etc…  
3. To view the experiment use;
   1. php getExperiment.php
   2. Format:
      php getExperiment.php<space><exp_ID>
4. All experiment related information will be listed along with experiment ID, experiment name, resource, application , user configuration data, etc…

Update Experiment

1. To update above created experiment use updateExperiment.php. 
2. Currently the script modifies only the experiment name, by adding a generated text at the end of the name.  
3. To modify the experiment use;
   1. php updateExperiment.php
   2. Format:
      php updateExperiment.php<space><exp_ID>
4. Once executed experiment details will be displayed along with the new experiment name.
5. Tutorial tryout; 
   1. Modifying the script to update more data in the experiment the same way; Try updating exp_description.  
   2. Update the script to modify existing configuration data by feeding the new values as command line arguments.

Clone Experiment

1. To clone above modified experiment use cloneExperiment.php.
2. Cloning will create exact copy of the existing experiment with a new experiment ID, new experiment name in CREATED state. 
3. To clone the experiment use;
   1. php cloneExperiment.php
   2. Format:
      php cloneExperiment.php<space><exp<space><experiment_ID>id>
4. Experiment modification confirmation message;
   1. Experiment<space><exp_ID><space>cloned!

      Created<space>clone<space>with<space>ID<space><Experiment_id><space>named<space><experiment_name>

5. User can clone any experiment created by him/her irrespective of the experiment status.
6. User can change existing information by updating the newly created experiment.
7. Tutorial tryout;
   1. Try adding parameters to the script to change other data in the new experiment. E.g.: Exp name, Application, Resource, etc… and execute.

Tutorial V - Search Experiments

Get All Experiments In Project

1. To view all experiments created under one project we use getAllExperimentsInProject.php.
   1. Format:
      php getAllExperimentsInProject.php<space><project_ID>
2. All the experiments and their details created using the given project_ID will be listed.

Get All Experiments by User

1. To view all experiments created by a single user we use getAllUserExperiments.php.
   1. Format:
      php getAllUserExperiments.php<space><username>
2. All the experiments and their details created by the given user/username will be listed.

Search Experiments by Experiment Name

1. Experiments can be searched by providing username along with experiment name or part of the experiment name.
   1. Format;
      php search_experiments_by_name.php<space><username><space><experiment_name>
   2. Example;
      php search_experiments_by_name.php Test_User Exp
2. When the script is executed; all the experiments which has the given text as part of the name will be listed along with all experiment information.
   
3. To view all experiments created by the user use percentage mark (%) in the place of experiment name. 

Search Experiments by Experiment Description

...

1. Experiments can be searched by providing username along with experiment description or part of the experiment description.
   1. Format;
      php search_experiments_by_description.php<space><username><space><experiment_description>
   2. Example;
      php search_experiments_by_description.php Test_User Test
2. When the script is executed; all the experiments which has the given text as part of the description will be listed along with all experiment information.
3. To view all experiments created by the user use percentage mark (%) in the place of experiment description. This would list experiment which has no description as well.
   

Search Experiments by Application

1. Experiments can be searched by providing username along with applicationId or part of the applicationId.
   1. Format;
      php search_experiments_by_application.php<space><username><space><applicationID>
   2. Example;
      php search_experiments_by_application.php Test_User Echo
2. When the script is executed; all the experiments which has the given text as part of the application ID will be listed along with all experiment information.
3. To view all experiments created by the user use percentage mark (%) in the place of applicationID.

Tutorial VI - Launch & Cancel Experiments

Launch Experiment

1. launchExperiment.php is used to launch individual experiments. 
2. Currently with the scripts to launch an experiment user need to pass only the experiment ID as a command line arguments to the script.
   1. Format;
   2. php launchExperiment.php<space><experiment_id>
3. Upon successful launch a confirmation message will be displayed; 
   Experiment<space><experiment_id><space>is<space>launched!     

Cancel/Terminate the Experiment

1. Experiments which are not in statuses COMPLETED, CANCELED, UNKNOWN can be canceled/terminated. 
2. In order to cancel use;
   1. Format;
      php terminateExperiment.php<space><Experiment ID>
3. User provided with the message; 'If there are no exceptions, assume the experiment terminated successfully'
4. Experiment will be terminated/canceled. The status can be viewed by using the command getExperimentStatus.php. Status will be  immediately changed to CANCELING and then to CANCELED.

Tutorial VII - Get Experiment Results & Status

  Check Experiment Status

1. To check the experiment status;
   1. Format; 
      php getExperimentStatus.php<space><experiment_id>
2. Experiment status will be displayed to the user in the command line.
   1. experiment status = COMPLETED

Check Experiment Output

1. Once the experiment is COMPLETED (Status of the experiment is checked using above getExperimentStatus.php) user can check the output. 
2. To check the output  
   1. Format; 
      php getExperimentOutputs.php<space><experiment_id>
      

...

1. 1. Image Added 

Image - Sample output

Tutorial VIII - Computational Resources

Register Computational Resource

1. To add computational resources use script; registerComputeResource.php
2. In order to run the script hostName and resourceDescription are passed as command line arguments.
   1. Format;
      php registerComputeResource.php<space><hostName><space><resourceDescription>
3. Execute the above and a confirmation message will be prompted along with the resource ID (computResourceId)
   Compute Resource<space><computeResourceId><space>is<space>registered!
4. Tutorial Tryout;
   Add other parameters to the script as command line arguments and improve the script.
   1. hostAliases

   2. ipAddresses

Tutorial IX - Application Modules

Register Application Module

View Computational Resource

1. To view computational resource information after creating above; use the script getComputeResource.php
   1. Format;
   2. php getComputeResource.php<space><computeResourceId>

2. Given information will be available when the script is executed;

   Image Added
   

View All Computational Resources

1. User can view all existing resources linked with the gateway using script; getAllComputeResourceNames.php
2. To add new application module use the script; registerApplicationModule.php
3. Parameters appModuleName, appModuleVersion and appModuleDescription are passed as command line arguments to the script.
   1. Format;
      php registerApplicationModulegetAllComputeResourceNames.php<space><appModuleName><space><appModuleVersion><space><appModuleDescription>
4. Successful execution of the script will display the created application module object along with the confirmation message
   Image Removed
   
5. Confirmation message contains the application module ID generated at module creation.
   Application Module <appModuleId><space>is<space>registered!

Tutorial X - Application Interfaces

Register Application Interface

1. 1. php
2. Computational resource names and their IDs will be listed at the script execution.
   Image Added
   

Delete Computational Resource

1. User can delete existing computational resource form the gateway by using script; deleteComputeResource.php
   1. Format;
      php deleteComputeResource.php <computeResourceId>
2. Once the script is executed user will be prompted a successfully deleted message
   Computational Resource<space><computeResourceId><space>successfully<space>deleted

Tutorial IX - Application Modules

Register Application Module

1. To add new application To register a new application interface using above created application module use the script; registerApplicationInterfaceregisterApplicationModule.php
2. Along with application interface name and description also need to provide application module ID as  command Parameters appModuleName, appModuleVersion and appModuleDescription are passed as command line arguments to the script.
   1. Format;
      php registerApplicationInterfaceregisterApplicationModule.php<space><appName><space><appDescription><space><appModuleId><appModuleName><space><appModuleVersion><space><appModuleDescription>
3. Successful execution of the script will display the created application interface module object along with the confirmation message
   Image RemovedImage Added
   
4. Confirmation message contains the application interface module ID generated at module creation.
   Application Interface <applicationInterfaceId><space>is<space>registeredModule <appModuleId><space>is<space>registered!

...

View Application

...

Module 

1. Gateway user can view a particular application module details using script; getApplicationModule.php

...

1. Use script updateApplicationInterface.php to update the above registered application interface.
   1. Format;
      php updateApplicationInterfacegetApplicationModule.php<space><appInterfaceId>php<space><appModuleID>
2. Execution of Executing the script will update name of the application input and application output.
   Image Removed
   
3. Confirmation message contains the application interface ID generated at update.
   Application Interface <applicationInterfaceId><space>is<space>updated!
   

List Application Interfaces

1. display application module object with Application module ID, Application Module name, Description and version.
   Image Added
   

Search Application Deployments 

1. To view all application deployments of a particle application module use the script; getApplicationDeployedResources.php
2. By providing the application module ID can view all available application deployments of the applicationFor user to view all existing applications and their application interface ID use; getAllApplicationInterfaceNames.php script.
   1. Format;
      php getAllApplicationInterfaceNamesphp getApplicationDeployedResources.php
3. All the applications used within the gateway will be listed along with the application interface ID.
   Image Removed
   

Delete Application Interface

1. 1. <space><appModuleID>
2. Output will look like;
   Image Added
   

Tutorial X - Application Interfaces

Register Application Interface

1. To register a new application interface using above created application module use the script; registerApplicationInterface.php
2. Along with application interface name and description also need to provide application module ID as  command line arguments to the script.User can delete existing application interface by providing the application interface ID as a command line argument to the script; deleteApplicationInterface.php
   1. Format;
      php deleteApplicationInterfaceregisterApplicationInterface.php<space><appInterfaceId>
3. At sucesful execution a confirmation message will be prompted to coinfrm the deletion
   Application Interface <applicationInterfaceId><space>successfully<space>deleted

List Computational Resources by the Application Interface

1. 1. php<space><appName><space><appDescription><space><appModuleId>
2. Successful execution of the script will display the created application interface object along with the confirmation message
   Image Added
   
3. Confirmation message contains the application interface ID generated at creation.
   Application Interface <applicationInterfaceId><space>is<space>registered!

Update Application Interface

1. Application interface registration is required to indicate gateway user, what inputs and outputs required for an application. To register an application interface use script updateApplicationInterface.php to update the above registered application interface.User can view all the computational resources which has a particular Application deployed by using the script; getAvailableAppInterfaceComputeResources.php
   
   1. Format;
      php getAvailableAppInterfaceComputeResourcesupdateApplicationInterface.php<space><appInterfaceId>
2. All the resources with the provided application

Tutorial X - Airavata API tester

1. This special script consist of several API method executions. 
   
   1. Format;
      php airavata-client-api-tester.php<space><username>
2. By this single script user can create project, update the project, create experiment, launch experiment, view experiment, clone experiment, etc... 
3. Explore the script for more infomration and build on this script.
   

Useful Commands

...

Action

...

Command

...

Make a directory

...

mkdir <directory name>

...

Navigate to directory

...

cd <directory name>

...

List directory content

...

ls <directory name>

...

Navigate to a directory giving path

...

cd <..../….../…../ directory name>

cd SciGaP/Airavata-PHP-Client-Samples/client-samples

...

Check for PHP existence

...

php –v

...

Install PHP & GIT

...

sudo apt-get install php5-cli

sudo apt-get install git

...

The given sequence will ensure getting a new copy from git reverting all the local changes have made  to the local scripts

...

git reset --hard HEAD

git pull

1. 1. php<space><appInterfaceId>
2. Execution of the script will update name of the application input and application output.
   Image Added
   
3. Confirmation message contains the application interface ID generated at update.
   Application Interface <applicationInterfaceId><space>is<space>updated!
   

List Application Interfaces

1. For user to view all existing applications and their application interface ID use; getAllApplicationInterfaceNames.php script.
   1. Format;
      php getAllApplicationInterfaceNames.php
2. All the applications used within the gateway will be listed along with the application interface ID.
   Image Added
   

Delete Application Interface

1. User can delete existing application interface by providing the application interface ID as a command line argument to the script; deleteApplicationInterface.php
   1. Format;
      php deleteApplicationInterface.php<space><appInterfaceId>
2. At sucesful execution a confirmation message will be prompted to coinfrm the deletion
   Application Interface <applicationInterfaceId><space>successfully<space>deleted

List Computational Resources by the Application Interface

1. User can view all the computational resources which has a particular Application interface deployed by using the script; getAvailableAppInterfaceComputeResources.php
   1. Format;
      php getAvailableAppInterfaceComputeResources.php<space><appInterfaceId>
2. name and computational resource ID of all the resources which has the provided application deployed will get listed.

Tutorial XI - Application Deployments

Register Application Deployment

1. When an application module is registered in the system AIravat need to register the deployment of the application module in one or many computational resources. In order to do so user can execute the script;
   registerApplicationDeployment.php
   1. Format;
      php registerApplicationDeployment.php<space><appModuleId><space><computeHostId><space><executablePath>
2. In order to do deploy user has to give application module ID, computational Host ID and also the executable path of the application deployment.
3. Tutorial tryout; User can enhance the script to add other parameters such as appDeploymentDescription, libPrependPaths, etc... as command line arguments.

View Application Deployment

1. Execution of getApplicationDeployment.php script will show all the information related to the application deployment.
   1. Format;
      php getApplicationDeployment.php<space>< appDeploymentId>
2. When the script is executed it will show;
   Image Added
   

Tutorial XII - View Application Input & Output

View Application Input

1. In order to view a particular application input data this script can be used with providing application interface ID
   1. Format;
      php getApplicationInputs.php
2. At script execution user will be provided with information on application inputs.
   Sample inout information on Echo application
   Image Added
   
   

View Application Output

1. In order to view a particular application output data this script can be used with providing application interface ID
   1. Format;
      php getApplicationOutputs.php
2. At script execution user will be provided with information on application outputs.
   Sample: Application Output Name: Echoed_Output   Output Type STRING

Tutorial XIII - Gateway Preferences

View Gateway Preference

1. A gateway can have a resource preference to execute an application when the same application is available in multiple reseoruces.
2. To find out the gateway preference user can use getGatewayComputeResourcePreference.php script.
   1. Format;
   2. php getGatewayComputeResourcePreference.php<space> <gateway id><space><compute resource id>

Delete Gateway Preference

1. To delete an existing gateway preference one can use deleteGatewayComputeResourcePreference.php script.

Tutorial XIV - Airavata API tester

1. This special script consist of several API method executions. 
   
   1. Format;
      php airavata-client-api-tester.php<space><username>
2. By this single script user can create project, update the project, create experiment, launch experiment, view experiment, clone experiment, etc... 
3. Explore the script for more infomration and build on this script.

...