[TAVERNA-14] Nested XML input splitters wrongly escapes incoming XML

• Type: Bug
• Status: To Do
• Priority: Blocker
• Resolution: Unresolved
• Component/s: Taverna Common Activities
• Labels: wsdl
• Assignee: Unassigned
• Reporter: Stian Soiland-Reyes
• Created: 10/Oct/13 14:03
• Updated: 28/Apr/15 11:42

Description

For services that need a series of XML Input splitters, such as the EBI Interproscan service "run" from http://www.ebi.ac.uk/Tools/services/soap/iprscan?wsdl - when the second input splitter takes an input from the first, it wrongfully escapes the incoming XML.

From the attached wfbundle, built from scratch in Taverna 3, the output run_input_output shows:

<parameters xmlns="http://soap.jdispatcher.ebi.ac.uk"><email xmlns="">[e-mail]</email>
 <parameters xmlns="">&lt;parameters&gt;&lt;sequence&gt;&amp;gt;sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1&#xD;
..
LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE&lt;/sequence&gt;&lt;/parameters&gt;</parameters></parameters>

Notice that inner & thingie there.

The bug happens also if you open the equivalent Taverna 2 workflow (Attached) - however in Taverna 2 you get:

<parameters xmlns="http://soap.jdispatcher.ebi.ac.uk"><email xmlns="">[e-mail]</email>
 <parameters xmlns=""><sequence>&gt;sp|Q9BTV4|TMM43_HUMAN Transmembrane protein 43 OS=Homo sapiens GN=TMEM43 PE=1 SV=1&#xD;
..
LLTVAAGWLFYRPLWALLIAGLALVPILVARTRVPAKKLE</sequence></parameters></parameters>

The bug is probably related to the "syntacticType" being "text/xml" on the output port - this is somewhat passed down into the wsdl-generic in Taverna 2 through a setting on the activity port, but is done in a different way in Taverna 3 (just added to the JSON config of the splitter), which probably contains the bug.

Notice that it is correct in this case to have double set of <parameters> as one of the parameters is called "parameters" - as shopwn by "error" outputting a job ID in Taverna 2:

<ns2:runResponse xmlns:ns2="http://soap.jdispatcher.ebi.ac.uk"><jobId>iprscan-S20131010-140020-0402-76128981-pg</jobId></ns2:runResponse>