1. Description and Discovery of Type Adaptors for Web Services Workflow Martin Szomszor ( [email_address] )

11. WSDL Examples: <definitions> <message name='getEntryIn'> <part name='accession_id' element='DDBJ:ACCESSION'/> </message> <message name='getEntryOut'> <part name='record' element='DDBJ:DDBJXML'/> </message> <portType name='DDBJPortType'> <operation name='GetEntry'> <input name='getEntryIn' message='tns:getEntryIn'/> <output name='getEntryOut' message='tns:getEntryOut'/> </operation> </portType> SOAP <binding name='DDBJBinding' type='tns:DDBJPortType'> <soap:binding style='document' transport='http://schemas.xmlsoap.org/soap/http'/> <operation name='GetEntry'> <soap:operation soapAction='GetEntry'/> <input name='getEntryIn'> <soap:body use='literal'/> </input> <output name='getEntryOut'> <soap:body use='literal'/> </output> </operation> </binding> </definitions> JAVA <binding name=&quot;JavaBinding&quot; type=&quot;tns:DDBJPortType&quot;> <java:binding/> <format:typeMapping encoding=&quot;Java&quot; style=&quot;Java&quot;> <format:typeMap typeName=”DDBJ:DDBJXML&quot; formatType=”DDBJXML.SequenceData&quot;/> <format:typeMap typeName=”DDBJ:ACCESSION&quot; formatType=&quot;java.lang.String&quot;/> </format:typeMapping> <operation name=”GetEntry&quot;> <java:operation methodName=”GetEntry” methodType=&quot;instance&quot;/> <input name=&quot;getEntryIn&quot;/> <output name=“getEntryOut”/> </operation> </binding> </definitions> http://ws.apache.org/wsif/providers/wsdl_extensions/java_extension.html

14. WSDL for Type Adaptors

15. Discovery of Type Adaptors

19. Mapping Mechanics <S> <X>foo</X> <X>bar</X> </S> <D> <Y>foo</Y> <Y>bar</Y> </D> Source Document Destination Document m 1 : S/X -> D/Y m 2 : X/$ -> Y/$ Mappings

20. Mapping Mechanics S X “ foo” S/* S/* xsd:string xsd:string X “ bar” D Y “ foo” D/* D/* xsd:string xsd:string Y “ bar” m 1 : S/X -> D/Y m 2 : X/$ -> Y/$

21. Example M-Binding <binding xmlns=&quot;http://www.ecs.soton.ac.uk/~mns03r/mapping/example&quot; xmlns:sns=&quot;http://jaco.ecs.soton.ac.uk/schema/source&quot; xmlns:dns=&quot;http://jaco.ecs.soton.ac.uk/schema/destination&quot;> <mapping id= &quot;1&quot; > <source match= &quot;sns:S/sns:X&quot; /> <destination create= &quot;dns:D[join]/dns:Y[branch]&quot; /> </mapping> <mapping id= ”2&quot; > <source match= &quot;sns:X/$&quot; /> <destination create= &quot;dns:Y[join]/$&quot; /> </mapping> </binding>

24. Bio Example <ddbj:DDBJXML> <ddbj:ACCESSION>AB000059</ddbj:ACCESSION> <ddbj:FEATURES> <ddbj:source> <ddbj:location>1..1755</ddbj:location> <ddbj:qualifiers name=&quot;isolate&quot;>Som1</ddbj:qualifiers> <ddbj:qualifiers name=&quot;lab_host&quot;>Felis domesticus</ddbj:qualifiers> </ddbj:source> </ddbj:FEATURES> </ddbj:DDBJXML> <ont:Sequence_Data_Record> <ont:accession_id>AB000059</ont:accession_id> <ont:has_feature> <ont:Feature_Source> <ont:isolate>Som1</ont:isolate> <ont:lab_host>Felis domesticus</ont:lab_host> <ont:location> <ont:Feature_Location> <ont:start>1</ont:start> <ont:end>1755</ont:end> </ont:Feature_Location> </ont:location> </ont:Feature_source> </ont:has_feature> </ont:Sequence_Data_Record> Simple One-to-One Element and literal Many-to-Many Split literal value Predicate evaluation

25. Example M-Binding <binding xmlns=&quot;http://www.ecs.soton.ac.uk/~mns03r/mapping/ddbj-to-ont-mapping&quot; xmlns:sns=&quot;http://jaco.ecs.soton.ac.uk/schema/DDBJ&quot; xmlns:dns=&quot;http://jaco.ecs.soton.ac.uk/ont/sequencedata&quot;> <mapping id=&quot;1&quot;> <source match=&quot;sns:DDBJXML/sns:ACCESSION&quot;/> <destination create=&quot;dns:Sequence_Data_Record[join]/dns:accession_id[branch]/&quot;/> </mapping> <mapping id=“2”> <source match=&quot;sns:ACCESSION/$&quot;/> <destination create=&quot;dns:accession_id[join]/$&quot;/> </mapping> <mapping id=”3&quot;> <source match=&quot;sns:DDBJXML/sns:FEATURES/sns:source&quot;/> <destination create=&quot;dns:Sequence_Data_Record[join]/dns:has_feature[branch]/ dns:Feature_Source[branch]&quot;/> </mapping> <mapping id=”4&quot;> <source match='sns:source/sns:qualifiers[sns:qualifiers/sns:name/$ = &quot;lab_host&quot;]'/> <destination create=&quot;dns:Feature_Source[join]/dns:lab-host[branch]&quot;/> <mapping> <source match=&quot;sns:qualifiers/$&quot;/> <destination create=&quot;dns:lab-host[join]/$&quot;/> </mapping> </mapping> <mapping id=”5&quot;> <source match=&quot;sns:location/$^[^.]+&quot;/> <destination create=&quot;dns:Location[join]/dns:start[branch]/$&quot;/> </mapping> </binding>

26. Configurable Mediator

27. Discovery of M-Bindings

28. Example WSDL <?xml version='1.0' encoding='UTF-8'?> <definitions name='DDBJ-to-sequencedata' targetNamespace='http://jaco.ecs.soton.ac.uk:8080/Bindings/DDBJ-to-sequencedata' ... xmlns='http://schemas.xmlsoap.org/wsdl/'> <types> <xsd:schema targetNamespace='http://jaco.ecs.soton.ac.uk:8080/Bindings/DDBJ-to-sequencedata'> <xsd:import namespace='http://jaco.ecs.soton.ac.uk/schema/DDBJ'/> <xsd:import namespace='http://jaco.ecs.soton.ac.uk/ont/sequencedata'/> </xsd:schema> </types> <message name='sns#DDBJXML-to-dns#Sequence_Data_Record-IN'> <part name='in' element='sns:DDBJXML'/> </message> <message name='sns#DDBJXML-to-dns#Sequence_Data_Record-OUT'> <part name='in' element='dns:Sequence_Data_Record'/> </message> <portType name='TranslationPortType'> <operation name='sns#DDBJXML-to-dns#Sequence_Data_Record'> <input name='sns#DDBJXML-to-dns#Sequence_Data_Record-IN'/> <output name='sns#DDBJXML-to-dns#Sequence_Data_Record-OUT'/> </operation> </portType> <binding name='TranslationBinding' type='tns:TranslationPortType'> <operation name='sns#DDBJXML-to-dns#Sequence_Data_Record'> <input name='sns#DDBJXML-to-dns#Sequence_Data_Record-IN'/> <output name='sns#DDBJXML-to-dns#Sequence_Data_Record-OUT'/> </operation> </binding> <service name='TranslationService'> <port name='TranslationPort' binding='tns:TranslationBinding'> <fxml:binding location='http://jaco.ecs.soton.ac.uk/binding/DDBJ-to-sequencedata.xml'/> </port> </service> </definitions>

30. Questions and Comments?

31. FXML-T Performance

32. FXML-T Performance

33. FXML-T Performance

34. GRIMOIRES Performance 1.81 Total Mediation 0.27 Serialisation Translation 0.23 Serialisation Discovery 0.62 Jena Mediation 0.47 Realisation Translation 0.22 RealisationDiscovery 2.50 DDBJ Execution Average Time (S) Activity