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![Example (continued) <portType name="Blast"> <operation name="searchSimple" parameterOrder="program database query"> <documentation>Execute Blast</documentation> <input name="searchSimple1In" message="tns:searchSimple1In" /> <output name="searchSimple1Out" message="tns:searchSimple1Out" /> </operation> ….[other operations] </portType>](https://image.slidesharecdn.com/websvcs-240925155037-4c09b243/75/Introduction-to-Web-Services-Architecture-33-2048.jpg)
![Using SOAP:Lite sub Blast_SOAP{ local $query_file = @_[0]; $service = SOAP::Lite -> service('http://xml.nig.ac.jp/wsdl/Blast.wsdl'); $service->proxy('http://localhost/', timeout => 60*60); return $service->searchSimple("blastn", “ddbjhum",$query_file); } $service connects to Blast web service at DDBJ site blastn is program, ddbjhum is database, $query_file contains sequence](https://image.slidesharecdn.com/websvcs-240925155037-4c09b243/75/Introduction-to-Web-Services-Architecture-36-2048.jpg)
Introduction to Web Services - Architecture
- 1.
- 2. What is aWeb Service? • Piece of software available over Internet • Uses standardized (i.e., XML) messaging system • More general definition: collection of protocols and standards used for exchanging data between applications or systems
- 3. Web Services Architecture •Technologies capable of – Exchanging messages – Describing Web services – Publishing and discovering Web service descriptions
- 4. An Example: EMBL •EMBL nucleotide sequence database • http://www.ebi.ac.uk/cgi-bin/dbfetch – X12399
- 5. Another Example: NOAA •Oceanographic data • Water level, currents data, etc. • http://opendap.co-ops.nos.noaa.gov/axis/
- 6. A service example •Previous two examples provide data • Web services can also perform analysis • Example: sequence similarity using ClustalW: – http://www.ebi.ac.uk/clustalw/
- 7. Observations • Web servicesuseful for both retrieval and analysis – Leverage existing programs/data – “Service-oriented science” • What if I want to analyze 100s of objects?
- 8. Service-Oriented Science • Idea:need standards and interfaces to encapsule information tools as services • No knowledge of inner workings required • Service oriented architecture: systems as networks of loosely-coupled, communicating services • Service oriented science: scientific research enabled by networks of interoperating services
- 9. Advantages for Scientists •Data on the web, not in the lab • Automate time-consuming activities • Infrastructure issues – Share compute resources • Automation – Enables programs to process large volumes of data quickly
- 10. Creating and SharingServices • Describe operations service supports • Define protocol to invoke services over Internet • Operate server to process incoming requests
- 11. Web Service Challenges •Interoperability • Scale • Management • Quality Control • Incentives
- 12. Interoperability • Need standards •Why is this useful? – Automate processing of requests – Common interface to a variety of services – Need common protocols, data formats, and semantics
- 13. Scale • Services mustdeal with: – Large volumes of data – High computational demands – Many users • May require access to high-performance resources
- 14. Management and QualityControl • Management – who uses services and for what purpose? – Prevent overloading • Quality control – metadata and lineage info – Allow users to determine quality of data • Incentives – Sharing data – Overhead of developing web service
- 15. Infrastructure • Idea: domainindependent functions and resources can be handed off to specialized providers • Scientists can focus on domain-specific data and software • Example: – Open Science Grid (OSG) – “SourceForge for scientists”
- 16. Approaches to Scaling •1. Cookie-cutter approach – Researchers create dedicated domain-specific infrastructures – Standardized domain specific software – Examples: • Bioinformatics Research Network • Network for Earthquake Engineering Simulation • PlanetLab – High degree of central control and uniformity – But high cost of expansion, requires new hardware
- 17. Approaches to Scaling •2. Bottom-up approach – Researchers develop service ecologies – agreements on interfaces – Participants provide content and function as they see fit – Each site responsible for its own equipment – Examples: • Earth System Grid • myGrid – biological workflows – Low cost of entry, but may not scale
- 18. Approaches to Scaling •3. General-purpose infrastructure – Discipline independent resources or functions – Access to monitoring functions, simulation codes, etc. – Examples: • TeraGrid • Campus Grids
- 19. Summary • Benefits ofservice-oriented science: – Access to data – Access to programs to analyze data – Automatic processing • Challenges: – Interoperability, scalability, quality – Individual communities need to outsource infrastructure functions and resources
- 20. Some Web ServiceStandards • REST (Representational State Transfer) – Architecture style of networked systems • SOAP (Simple Object Access Protocol) – Standard for sending messages between applications • WSDL (Web Service Description Language) – Standard for describing web services and their capabilities
- 21. REST • Representational StateTransfer • Architectural style (technically not a standard) • Idea: a network of web pages where the client progresses through an application by selecting links • When client traverses link, accesses new resource (i.e., transfers state) • Uses existing standards, e.g., HTTP
- 22. REST Characteristics • Client-Server:Clients pull representations • Stateless: each request from client to server must contain all needed information. • Uniform interface: all resources are accessed with a generic interface (HTTP-based) • Interconnected resource representations • Layered components - intermediaries, such as proxy servers, cache servers, to improve performance, security
- 23. REST examples • TheWeb is RESTful (a bunch of HTTP links) • EBI (European Bioinformatics Institute) – http://www.ebi.ac.uk/xembl • Dbfetch – retrieve entries from EMBL nucleotide sequence database – http://www.ebi.ac.uk/cgi-bin/dbfetch? db=embl&id=x12399&format=default
- 24. SOAP • Simple ObjectAccess Protocol • Format for sending messages over Internet between programs • XML-based • Platform and language independent • Simple and extensible • Stateless, one-way – But applications can create more complex interaction patterns
- 25. SOAP Building Blocks •Envelope (required) – identifies XML document as SOAP message • Header (optional) – contains header information • Body (required) –call and response information • Fault (optional) – errors that occurred while processing message
- 26. Simple Example “Get theprice of apples” <?xml version="1.0"?> <soap:Envelope xmlns:soap="http://www.w3.org/2001/12/soap- envelope" soap:encodingStyle="http://www.w3.org/2001/12/soap- encoding"> <soap:Body> <m:GetPrice xmlns:m="http://www.w3schools.com/prices"> <m:Item>Apples</m:Item> </m:GetPrice> </soap:Body> </soap:Envelope> Note:GetPrice and Item are application-specific (not part of SOAP)
- 27. Summary: SOAP vs.REST • REST – clients submit requests to Web services as HTTP requests • SOAP – clients submit request in form of XML document
- 28. SOAP vs. REST •SOAP advantages: – Widely used and supported – Supports variety of protocols (network transfer, authentication, encryption) • REST advantages: – Simple, relies only on HTTP protocol – Performance and reliability • Many sites support both SOAP and RESTful interfaces – Amazon.com, XEMBL from EBI
- 29. WSDL (Web ServiceDescription Language) • Standard method of describing Web Services and their capabilities • Idea: Automate details involved in applications communication • Operations and messages are described abstractly • Bound to a concrete network protocol and message format to define an endpoint • Provide documentation for distributed systems
- 30. WSDL Details • AWSDL document defines services • Services are collection of network endpoints (ports) • Abstract definition of endpoints and messages is separated from their concrete network deployment or data format bindings • Allows the reuse of abstract definitions: – messages -abstract descriptions of data being exchanged – port types -abstract collections of operations – concrete protocol and data format specifications for a particular port type constitutes a reusable binding
- 31. An example • FromBLAST service at DDBJ http://xml.nig.ac.jp/wsdl/Blast.wsdl • SearchSimple – function takes as input: – Program – which BLAST program to use – Database – which BLAST database to query – Query – sequence to query • SearchSimple output: – Result – string containing matches
- 32. An example <message name="searchSimple1In"> <partname="program" type="xsd:string" /> <part name="database" type="xsd:string" /> <part name="query" type="xsd:string" /> </message> <message name="searchSimple1Out"> <part name="Result" type="xsd:string" /> </message>
- 33. Example (continued) <portType name="Blast"> <operationname="searchSimple" parameterOrder="program database query"> <documentation>Execute Blast</documentation> <input name="searchSimple1In" message="tns:searchSimple1In" /> <output name="searchSimple1Out" message="tns:searchSimple1Out" /> </operation> ….[other operations] </portType>
- 34. Summary • WSDL documentlists functions supported by each web service, inputs and ouputs • To actually call a web service, need interface or tools: – SOAP:lite (Perl) – Apache Axis (Java) – Many others…
- 35. A WSDL example:DDBJ • http://xml.ddbj.nig.ac.jp/wsdl/index.jsp • Look at the SearchSimple WSDL example • SearchSimple(program,database,query) in BLAST web service • Many other web services available
- 36. Using SOAP:Lite sub Blast_SOAP{ local$query_file = @_[0]; $service = SOAP::Lite -> service('http://xml.nig.ac.jp/wsdl/Blast.wsdl'); $service->proxy('http://localhost/', timeout => 60*60); return $service->searchSimple("blastn", “ddbjhum",$query_file); } $service connects to Blast web service at DDBJ site blastn is program, ddbjhum is database, $query_file contains sequence
- 37. Using Apache Axis publicclass BlastSoap extends SoapMaster{ public BlastSoap(){ super("http://xml.nig.ac.jp/wsdl/Blast.wsdl","http://www.themi ndelectric.com/wsdl/Blast/","Blast","searchSimple"); } public String runBlastSoap(Vector pQuery) throws Exception{ Vector query = new Vector(); query.add("blastn"); query.add(“ddbjhum"); for(int i=0;i< pQuery.size();i++){ query.add(pQuery.elementAt(i)); } return this.runSoap(query);
- 38. How are theseused? Many SOAP and REST based bioinformatics web services, including: • EBI – www.ebi.ac.uk/Tools/webservices/ • NCBI – http://eutils.ncbi.nlm.nih.gov/entrez/query/static/ eutils_help.html . • DNA Databank of Japan (DDBJ) – http://xml.ddbj.nig.ac.jp/soapp.html
- 39. Describing Web Services- UDDI • Universal Description, Discovery, and Integration • Directory for locating Web services • Can be interrogated by SOAP messages and provides access to WSDL documents describing web services in its directory
- 40. Some example webservices • SDSS-based web services • NOAA • Bioinformatics – PubMed – GenBank – BLAST – SwissProt – ClustalW
- 41. SDSS • http://cas.sdss.org/dr5/en/skyserver/ws/ • ImageCutout – get jpg images of parts of the sky: http://casjobs.sdss.org/ImgCutoutDR5/ Imgcutout.asmx • CAS access – submission of SQL queries – http://voservices.net/CasService/ws_v1_0/ CasService.asmx • Many others…
- 42.
- 43. PubMed/Medline • http://www.ncbi.nlm.nih.gov/entrez/ • Comprehensivedatabase of scientific literature in biomedical area • Useful for finding literature on a given topic
- 44. PubMed example Find outabout “dUTPase”
- 45. PubMed Example • http://www.ncbi.nlm.nih.gov/entrez/ •Find out about “dUTPase”
- 46. GenBank • National Institutesof Health (NIH) genetic sequence database • Collection of all known sequences • Each GenBank entry consists of: – Locus name and accession number – Reference section – link to relevant articles – Features – Sequence
- 48. Other scientific domains: •Astronomy: – http://www.atnf.csiro.au/vo/rvs/thumbnail.html – Converts astronomy image to thumbnail • Chemistry: – http://www.liv.ac.uk/Chemistry/Links/webservi ces.html • GIS – http://terraservice.net/webservices.aspx
- 49. Summary • Web servicesprovide standardized interface to data and functionality on web – Access to data – Perform computations • Accessible by machines/programs • Stateless – websites don’t keep track of requests • Preview of things to come: scientific workflows
- 50. Other Web Services •Web services exist in many domains – Stock quotes, conversions, weather… • Web service search engines (e.g., Woogle): http://haydn.cs.washington.edu:8080/won/ wonServlet