Investigating Web Services with SoapUI

Peter Fischer Hallin, Center for Biological Sequence AnalysisEMBRACE Workshop on Client Side Scripting for Web Services

February 6, 2008

What is SoapUI?

• Java based stand-alone software for inspecting, invoking, and testing Web Services.

• Downloadable from http://www.soapui.org free of charge.

• ‘pro’ edition available for purchase having extended features

• Ideal for development/testing of Web Services: Provide the raw XML request/response to/from your server. It allows you to view HTTP headers, attachments etc.

• Construct template/default request messages based on the WSDL/XSD

• SoapUIs strength is inspection and manually invoking of operations, however the Pro edition supports workflows/test cases!

• Handling multiple WSDLs with a project, and multiple projects within a session

Why SoapUI?

Example: inspecting two Web Services

• Genome Atlas 3.3 (http://www.cbs.dtu.dk/ws/GenomeAtlas/) Various database tools accessing prokaryotic genomes sequences

• RNAmmer 1.2b (http://www.cbs.dtu.dk/ws/RNAmmer) Predicts ribosomal RNA genes in full genome sequences.

Genome Atlas online documentation - like Jasper - there should be one online!

Creating a new project

Labeling the project and adding WSDL

Default request are made automatically

We provide a genbank accession to ‘getSeq’

http://www.cbs.dtu.dk/ws/RNAmmer

RNAmmer online documentation

Adding a new WSDL to the project

Adding a new WSDL to the project

Copy the genome sequence from ‘getSeq’

Paste genome sequence in RNAmmer ‘runService’

Adding a new WSDL to the project

Submit and acquire jobid

Poll queue until job finished

Poll queue until job finished

Fetch the result, suing ‘fetchResult’

RNAmmer output, detailed

•Gene entries found in output->entries->entry•Contains query (gene) sequence•The matches to the Hidden Markov Model•Details like E-value, scores, start-stop postion etc.

Inspecting Service Description

Pro features

• Forms ( reading enumerations from XSD)

• Workflows/testcases

• Scripting language (GroovyScript)

scripting

Export workflow results into any database (provided JDBC driver),

Excel sheet, script, or raw file

Exporting

Live demo• Search for protein EGFR_HUMAN using

‘efetch’ (http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/efetch.wsdl)

• Predict the presence of signal peptides usign SignalP: http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1.wsdl

• Validation

• http://api.bioinfo.no/wsdl/JasparDB.wsdl, Id:MA0003, format:PFM, db:CORE