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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