1. SCI-BUS is supported by the FP7 Capacities Programme under contract nr RI-283481 Creating the Autodock gateway from WS-PGRADE/gUSE and making it cloud-enabled Zoltán Farkas MTA SZTAKI LPDS zoltan.farkas@sztaki.mta.hu

2. Outlines Introduction WS-PGRADE/gUSE layer: – Template creation – Workflow exporting – Local Repository Liferay layer: – End-user role setup – Enable additional login/registration methods – Modify portlets’ visibility

3. Targeted audience, Goals Workflow/Application, Science Gateway Instance developers Create an easily usable portal for an existing workflow Within an hour Without any programming Enable modification of some basic workflow properties: command-line arguments, uploaded files, etc…

4. Keywords Workflow: – Structure: Graph – Properties: Concrete workflow gUSE repository – A way to collaborate with a given gUSE instance’s users – One may export the workflows to it – Others may import workflows from there Template: – A concrete workflow with a restricted set of modifiable properties Liferay user roles „End User” role

5. 5/29/2006SCI-BUS CodeCamp 2012, Budapest5 Concrete Workflow Algorithms, executable Resource references, Inputs Graph Jobs, Edges, Ports Template Constraints, Comments, Form Generators Workflow Instance Running state, Outputs Repository Item Application OR Project OR, Workflow part (G,T,CW) Important high-level graph structures in WS- PGRADE Legend: a b a must reference b a b a may reference b

6. Keywords Liferay user roles – Each Liferay user has a specific set of roles assigned by default – On a normal installation: „Power User” and „User” – On an end-user portal: „End User” „End User” role: – Implies the invisibility of the „Workflow” tab – That is: no workflow creation and editing is possible

7. Normal portal VS End-User

8. AutoDock workflow Run docking simulations AutoGrid: – Role: generator (n job instances) – Creates inputs for AutoDock AutoDock: – Runs as a PS job – Performs the docking simulations Collector: – Examines the results – Collects m best results

9. WS-PGRADE See your portal’s URL at http://goo.gl/rf1E2http://goo.gl/rf1E2 If necessary, you can log in using ssh as well

10. WS-PGRADE – Workflow Import After logging in, import the robot-enabled AutoDock IaaS workflow created during day 4: – Select menu „Workflow”/”Import” – Select „Local Repository” – Click „Refresh/show list” – Select your workflow – Click „Import” Check out the workflow, select menu „Workflow”/”Concrete”

11. WS-PGRADE – Template creation I. We’re going to create the template in this step: – Select menu „Workflow”/”Template” – Next to „Select a concrete workflow as base to create a template”, choose the imported workflow – Set „Name of new template” to something, e.g. „AutoDock” – Click on „Configure”

12. WS-PGRADE – Template creation II. We’re going to configure the template in this step: – By default, all properties are closed – Set some properties to „Free”, for example: „Parameter of binary executable” under job „AutoGrid” – this will enable to set the command-line argument for the job AutoGrid „Recently defined Input File name to Upload” under job „AutoGrid” for input „receptor.pdb” – this will enable to upload a new file for the „receptor.pdb” input … Value of „Label” will be presented for the end-user during the workflow’s configuration (should be short) Value of „Description” will be available as a tooltip (can be long) – Once finished, click „Save” (close to the top of the page)

13. WS-PGRADE – Template exporting I. First, we have to create a new concrete workflow based on the template: – Select menu „Workflow”/”Create Concrete” – Under „Create a new workflow from a”, select „Template”, and the template you have created in the previous step – „Name for the new workflow” can be e.g. „AutoDock_Template” At this point, check out which properties you can modify for the created workflow under the menu „Workflow”/”Concrete”

14. WS-PGRADE – Template exporting II. Finally, we have to export our „templated” workflow: – Select menu „Workflow”/” Concrate” – Click „Export” next to the templated workflow – Select „Local WS-PGRADE/gUSE Community” – Click „Yes” – Export as an application – You can define some optional note if you like – Click „Yes”

15. Status We have created a template based on the original workflow, by allowing end-users to modify only some properties of the original workflow (typically input files, command-line parameters) The templated concrete workflow has been exported, so others can make use of it Next: configure Liferay

16. Liferay – End-user role setup In this step, we’re going to set the end-user role as the default role for new users: – At the top of the portal page, select „Go to”/”Control Panel” – At the left panel, click „Portal Settings” – At the right panel, click „Users” – Select the „Default User Associations” menu – Under „Roles”, enter the text „End User” (remove „Power User” and „User” from here) – At the right panel, click „Save” This way, new users will receive only the „End User” role You can test your settings by adding a new user: select „Users” at the left panel, after click „Add”/”User”, and fill in the form

17. Liferay – Enable registration methods Within the Liferay Control Panel: – At the left tab, select „Portal Settings” – At the right tab, select „Authentication” – Under „General” tab, you should see that anybody is allowed to create accounts – Under the other tabs, you can configure and enable other login methods, e.g. Facebook (you need to register a new application under Facebook for this)

18. Liferay – Modify portlets’ visibility Default portlets in end-user view: Storage/*, Settings, Information, …, Security Let’s say, we don’t need „Security”: – Log in as the portal administrator – At the top, select „Manage”/”Site Pages” – In the left part, click on „Security” – In the top middle, click on „Permissions” – For the „End User” role, uncheck the „View” permission – Click on „Save”

19. Final steps Remove any workflows from the repository that are not needed: – „Workflow” / „Import” / „Local Repository” / „Refresh/show list” – Click on „Delete” next to unneded workflows Promote your portal!

20. End user activities As an end-user check out the usable workflows, and run them: – „End User” / „Import” / „Local Repository” / „Refresh/show list” – Select the workflow, click on „Import” – Go to „End User” / „Configure” / „Configure” button – Override values (if you like, otherwise default values will be used), click on „Save on Server” – Click on „Submit” – Click on „Refresh” until you see the status as „running” – Click on „Details” to check the progress of the workflow

21. Video tutorials Template creation: – http://youtu.be/bmN1ia0evXw http://youtu.be/bmN1ia0evXw Liferay end user mode configuration and new user registration: – http://youtu.be/WrPxbkZvpro http://youtu.be/WrPxbkZvpro