EMBL-EBI Web Services

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====== soap4r ======

===== Install soap4r =====

The [[http://dev.ctor.org/soap4r|soap4r]] module is bundled with modern versions of [[http://www.ruby-lang.org/|Ruby]]. The latest version is also available as a [[http://rubygems.org/|Ruby Gem]] or as a download from the [[http://dev.ctor.org/soap4r|soap4r]] web site. For package based platforms (e.g. Ubuntu, CentOS, etc.) check if a package exists before installing from a Ruby Gem or download.

===== Using soap4r =====

''SOAP::WSDLDriverFactory.new().create_rpc_driver'' can be used to create a service proxy, from a WSDL document, which provides an interface to the web service. Using the methods provided by the service proxy the service can be used as though it was a local resource.

For example: using [[services:dbfetch|WSDbfetch]] to get fasta formatted sequence for the UniProtKB protein ALK1_HUMAN

Load the soap4r library:
<code ruby>require 'soap/wsdlDriver'</code>

Get the service proxy for the service:
<code ruby>
# URL for the service WSDL
wsdl = 'http://www.ebi.ac.uk/ws/services/WSDbfetch?wsdl'

# Get the object from the WSDL
dbfetchSrv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver
</code>

For debugging it is useful to see the SOAP messages being passed between the client and the server: 
<code ruby>dbfetchSrv.wiredump_dev = STDOUT</code>

Get the data from the service and print it:
<code ruby>puts dbfetchSrv.fetchData("UNIPROT:ADH1A_HUMAN", "fasta", "raw")</code>

All the methods in the [[services:dbfetch|WSDbfetch]] service take simple strings as arguments. For complex data types such as those used in the [[services:fasta|WSFasta]] service nested hash data structures are used to represent the type.

For example: submitting a job to [[services:fasta|WSFasta]]:
<code ruby>
# Query sequence
seq = ">Q8E5Q5_STRA3
MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFI
VAQIVQIVFPVIPGGVTTVAGFLIFGPTLGFIYNYIGIIIGSVILFWLVKFYGRKFVLLF
MDQKTFDKYESKLETSGYEKFFIFCMASPISPADIMVMITGLSNMSIKRFVTIIMITKPI
SIIGYSYLWIYGGDILKNFLN"

# Get the object from the WSDL
fastaSrv = SOAP::WSDLDriverFactory.new(wsdl).create_rpc_driver

# Set the parameters for the job
params = {}  
params['program'] = 'ssearch'
params['database'] = 'swissprot'
params['email'] = 'your@email'
params['async'] = 1
# Build the data structure
data = [{'type'=>'sequence', 'content'=>seq}]

# Submit the job
jobId = fastaSrv.runFasta(params, data)
puts jobId
</code>

Given the job identifier we poll until the job completes:
<code ruby>
# Use the job identifier to check the status of the job
status = 'RUNNING'
while status=='RUNNING'
  sleep 10 
  status = fastaSrv.checkStatus(jobId)
  puts status
end
</code>

And if the job completed successfully, retrieve the result:
<code ruby>
# When finished get the result
if status=='DONE'
  puts fastaSrv.polljob(jobId, 'tooloutput')  
end
</code>

===== Examples =====

  * [[:services:dbfetch|WSDbfetch]]: [[http://www.ebi.ac.uk/Tools/webservices/downloads/ruby/examples/dbfetch_soap4r.rb|dbfetch_soap4r.rb]]
  * [[:services:fasta|WSFasta]]: [[http://www.ebi.ac.uk/Tools/webservices/downloads/ruby/examples/fasta_soap4r.rb|fasta_soap4r.rb]]

===== Sample Clients =====

Most SOAP Web Services at [[http://www.ebi.ac.uk/|EMBL-EBI]] have sample clients which provide command-line access to the service and example code. For Ruby these clients are based on soap4r.

==== Document/literal SOAP ====

^ Service ^ Sample client ^
| [[:services:pfa:iprscan_soap|InterProScan (SOAP)]] | [[http://www.ebi.ac.uk/Tools/webservices/download_clients/ruby/soap4r/iprscan_soap4r.rb|iprscan_soap4r.rb]] |
| [[:services:sss:NCBI BLAST (SOAP)]] | [[http://www.ebi.ac.uk/Tools/webservices/download_clients/ruby/soap4r/ncbiblast_soap4r.rb|ncbiblast_soap4r.rb]] |
| [[:services:dbfetch|WSDbfetch (SOAP)]] | [[http://www.ebi.ac.uk/Tools/webservices/download_clients/ruby/soap4r/wsdbfetch_soap4r.rb|wsdbfetch_soap4r.rb]] |

==== RPC/encoded SOAP ====

^ Service ^ Sample client ^
| [[:services:dbfetch|WSDbfetch]] | [[http://www.ebi.ac.uk/Tools/webservices/downloads/ruby/wsdbfetch.rb|wsdbfetch.rb]] |

\\
^ Up | [[..:..:Ruby]] ^ Contents | [[..:..:..:00_Contents|Contents]] |
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