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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
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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
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• 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?
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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.
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Genome Atlas online documentation - like Jasper - there should be one online!
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Creating a new project
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Labeling the project and adding WSDL
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Default request are made automatically
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We provide a genbank accession to ‘getSeq’
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http://www.cbs.dtu.dk/ws/RNAmmer
RNAmmer online documentation
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Adding a new WSDL to the project
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Adding a new WSDL to the project
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Copy the genome sequence from ‘getSeq’
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Paste genome sequence in RNAmmer ‘runService’
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Adding a new WSDL to the project
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Submit and acquire jobid
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Poll queue until job finished
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Poll queue until job finished
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Fetch the result, suing ‘fetchResult’
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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.
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Inspecting Service Description
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Pro features
• Forms ( reading enumerations from XSD)
• Workflows/testcases
• Scripting language (GroovyScript)
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scripting
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Export workflow results into any database (provided JDBC driver),
Excel sheet, script, or raw file
Exporting
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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