Description and Discovery of Type Adaptors for Web Services Workflow

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

Presentation Outline Contemporary workflow Design Discovery of services using semantics Problem description Type conversion requirements Describing Type Adaptor capabilities Using WSDL Discovering Type Adaptors Implementation Example Using bespoke mapping language FXML-M GRIMOIRES Registry

In Silico Experimentation Computational experimentation Access to resources provided by Web Services Users map experimental process to workflow Tasks are realised by service instances

Service Discovery Users need to find services to fulfill given tasks e.g. Retrieve sequence data Sequence alignment (Blast) There are lots of services ! Interface definitions can be terse, often un-documented and sometimes cryptic Limited semantic value Manual discovery not ideal

Semantic Discovery Support users in the discovery of services according to domain specific terminology Annotate service descriptions with concepts from an ontology (PEDRO) Input and output types assigned a semantic type by a reference to an ontology concept Discover services by: Task performed Resources used Input and output semantic types

Semantically Driven Workflow Design When building workflows, users connect services because they are deemed semantically compatible: Output semantic type equivalent to input semantic type

Syntactic Compatibility However, semantically compatible service interfaces may not be syntactically compatible (i.e. different data formats)

Syntactic Mediation When a mismatch in data formats occurs within a workflow, a translation component is required These Type Adaptors come in a variety of guises Translation Scripts (e.g. XSLT) Bespoke Code (JAVA and PERL) Web Services Current solutions are manual Identify when mismatch occurs How to resolve it What translation components are suitable Create new translation components if necessary How can we describe Type Adaptors?

WSDL Overview WSDL is a declarative language used to specify program capabilities through the definition of end-points Programs expose operations Operations are specified in terms of messages Messages contain parts (each with syntactic type) XML Schema can be used to describe data formats Abstract definition separated from concrete implementation Binding defines invocation method and data encoding

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="JavaBinding" type="tns:DDBJPortType"> <java:binding/> <format:typeMapping encoding="Java" style="Java"> <format:typeMap typeName=”DDBJ:DDBJXML" formatType=”DDBJXML.SequenceData"/> <format:typeMap typeName=”DDBJ:ACCESSION" formatType="java.lang.String"/> </format:typeMapping> <operation name=”GetEntry"> <java:operation methodName=”GetEntry” methodType="instance"/> <input name="getEntryIn"/> <output name=“getEntryOut”/> </operation> </binding> </definitions> http://ws.apache.org/wsif/providers/wsdl_extensions/java_extension.html

WSDL Conclusions Can be used to describe many implementations Transport not necessarily SOAP over HTTP Data encoding does not have to be XML Java Objects String formats (e.g. csv) Binary Files Other WSDL Bindings: XQuery [Onose and Simeon 2004] EJB, JMS, J2EE Connector Architecture (e.g. Cobol): from Apache WSIF Anything you like…

Type Adaptors Type Adaptors are components that: consume an input (source type) produce an output (destination type) Functionality can be described at an abstract level: what goes in what comes out Actual implementation can be described using a binding, e.g. XSLT script location Java Class used Hence, we use WSDL to describe Type Adaptors

Simple solution: Adaptor for each compatible data format O(n 2 ) Poor Scalability Alternative: Introduce intermediate representation O(n) Less effort introducing new formats Type Adaptor Approaches f c e b d a f c e b d a

Intermediate Representation Use OWL ontologies to capture semantics and structure of data formats Proven technique TAMBIS Project [Stevens et al 2003] Complex query formulation over diverse information sources SEEK Project [Bowers and Ludascher 2004] An ontology-driven framework for data transformation in scientific workflows

Implementation Type Adaptor approach: Using OWL as intermediate representation Transformation Technology: Using bespoke mapping language FXML-M Registry Technology: GRIMOIRES Advertise Discover

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

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/$

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

Transformation Technology Bespoke Mapping Language (FXML-M) Declarative Statements map schema elements from source to destination Mappings are combined in an M-Binding Document Composable M-Bindings can include statements from other M-Bindings Predicate support (for complex relations) Asymmetric relations (one-to-many, many-to-one) Implementation (FXML-T) Consumes M-Bindings, schemas and source document Produces destination document

Mappings with OWL Our Type Adaptor approach uses OWL for an intermediate representation But our transformation technology is XML to XML Solution, use canonical XML representation for OWL concept instances OWL Instance Schema Automatically generated from OWL ontology Concept hierarchies calculated Elements for each concept and property

Bio Example <ddbj:DDBJXML> <ddbj:ACCESSION>AB000059</ddbj:ACCESSION> <ddbj:FEATURES> <ddbj:source> <ddbj:location>1..1755</ddbj:location> <ddbj:qualifiers name="isolate">Som1</ddbj:qualifiers> <ddbj:qualifiers name="lab_host">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

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

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>

Conclusions Type Adaptors come in many flavours, all can be described using WSDL GRIMOIRES can be used to advertise and discover WSDL Type Adaptors We have shown this to work with our own Mapping Language (FXML-M) Practical Scalable

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

Description and Discovery of Type Adaptors for Web Services Workflow

More Related Content

What's hot (19)

Viewers also liked (11)

Similar to Description and Discovery of Type Adaptors for Web Services Workflow (20)

Recently uploaded (20)

Description and Discovery of Type Adaptors for Web Services Workflow

Editor's Notes