VAMDC and PDL co-integration

A brief introduction to PDL

The Parameter Description Language (PDL) is intended to be a lingua franca for describing parameters:

• Describes params with a fine grained granularity

  • Physical properties (Nature, Meaning, unit, precision,...),
  • Computing properties (Type, Skos concept, UCD, ...),

• Also has capabilities do describe constraints on parameters

  • Physical
  • Arbitrary (including mathematical formulas).

• Not a description of parameters values

The PDL descriptions are typically an XML file.

PDL is in RFC phase for becoming an IVOA standard. Click here for the IVOA official document.

VAMDC exposed as PDL service

Exposing VAMDC infrastructure as a PDL service allows to take advantage of PDL feature with few efforts.

The following schema explains which VAMDC elements compose the exposed PDL service:

The PDL description associated to this service is here.

You can interact with this client with two tools:

• The Java Swing client (cf. Task 1);
• The Taverna Plugin (cf. Task 2).

Task 1: Running the PDL client

Download the client application: client zip file

Double click on the jar. The client will launch :

• Enter your e-mail.
• In the upper-left window, click on AtomsDetail, MoleculesDetails,... This permits you to browse all the available parameters. You will remark that this is the same kind of information you have to provide on the portal.
• Choose H in the field AtomsDetail then click on the Validate button. Then click on Run computation.
• Check your mail and follow the link contained into the received mail.
• When the end of the job is notified, download the tar files containing the XSAMS files.
• Repeat the three previous steps, replacing H by He as atom symbol

Task2: Running the Taverna Plugin

Dependencies for this part are not easy to install (Taverna with AstroTaverna extension). We are going to have this part of the tutorial together.

You can download the file related to the presented workflow here

If you feel brave:

• You can download taverna Workbench from http://www.taverna.org.uk/download/.
• You have then to install the latest version of astrotaverna plugin. You can see the general instructions to install a new plugin here.
• When you click on the “Find New Plugins” button, add the following link: http://wf4ever.github.io/astrotaverna/

Then, select astrotaverna and install it. After installing, you will have to restart taverna to be able to run the workflow.

Task3: Bonus, invoking the VAMDC service from the command line or from a Browser

It is possible to call the service from a browser or using the command line. This is the same mechanism used by the Swing client or the Taverna plugin. We are going to discover how it works:

• Open the PDL description associated with the VAMDC service (cf. VAMDC exposed as PDL service)

• Find into this file :

  • the content of the ServiceId tag. This is the first part of the url to compose
  • the name of the parameters you want to set (tag Name, inside the tag Parameter). The last part of the url is ?Parameter1=Value1&Parameter2=Value2.

• Use the same input as in Task1 and compose the string to copy into the browser for submitting the job

• Example: http://pdl-calc2.obspm.fr:8081/vamdc/OnlineCode?mail=your.mail.com&AtomSymbol=H.

• submit your job through a browser, or using the curl or wget unix commands.