BioMOBY

What is passed into the service in the SOAP payload takes the following structure:

       <?xml version="1.0" encoding="UTF-8"?>
       <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
          <moby:mobyContent>
              <moby:mobyData queryID=''>
                    <!-- articles (Simple/Collection/Secondary Parameter) 
                            required for first service invocation -->
              </moby:mobyData>
              [<moby:mobyData queryID=''>
                    <!-- articles required for second service invocation -->
               </moby:mobyData>]
               ...

               ...
           </moby:mobyContent>
       </moby:MOBY>

This message takes the form of a number of nested XML tags. The mobyContent envelope exists primarily as a container for possible future use.

The mobyData tags delimit the set of inputs to a single invocation of the service, though there may be multiple invocations in a single message, each contained within its own enumerated mobyData block. The contents of this block may be a Primary article (Simple, or Collection), or a Secondary article, which are Parameters used to modify the service behaviour.

Any request sent to a service with no mobyData blocks must be replied to with a MOBY payload containing no mobyData blocks). This is considered a basic "ping" functionality all MOBY-S Services must implement.

The queryID has no intrinsic meaning

Enumeration of mobyData elements is achieved by the queryID attribute of the mobyData element, whose value has no intrinsic meaning. The client program should choose it be any legal XML attribute value, such that it is unique to each mobyData in the message. Service providers should not attempt to interpret the value of queryID; it is simply an identifier. The service provider must assign the same queryID to the associated mobyData element in their response message (described below). This allows the client program to match each query with its corresponding response.

The articleName attribute of the Simple and/or Collection elements is optional (it may or may not be there, and if there, it may or may not have a non-null value), and is used to invoke services that have named arguments; a single queryInput may contain multiple Simple and/or Collection articles that need to be differentiated by name.

How to invoke a service with a Simple Article

For example, the retrieveSequence service registered above, that accepts a single Simple article as its input, would accept either of the following SOAP message payloads for its service invocation:

       <?xml version="1.0" encoding="UTF-8"?>
       <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
          <moby:mobyContent>
              <moby:mobyData queryID='a1'>
                   <Simple articleName='input1'>
                      <Object namespace="NCBI_gi" id="163483"/>
                   </Simple>
              </moby:mobyData>
          </moby:mobyContent>
       </moby:MOBY>

For multiple invocations, the form is similar, except that the mobyData entity contains more than one Simple.

       <?xml version="1.0" encoding="UTF-8"?>
       <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
          <moby:mobyContent>
              <moby:mobyData queryID='a1'>
                   <Simple articleName='input1'>
                      <Object namespace="NCBI_gi" id="163483"/>
                   </Simple>
              </moby:mobyData>
              <moby:mobyData queryID='a2'>
                   <Simple articleName='input1'>
                      <Object namespace="NCBI_gi" id="124454"/>
                   </Simple>
              </moby:mobyData>
          </moby:mobyContent>
       </moby:MOBY>

How to invoke a service with a Collection Article

You invoke a service that requires a Collection article in a similar way to invoking one that requires just a Simple article:

       <?xml version="1.0" encoding="UTF-8"?>
       <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
         <moby:mobyContent>
          <moby:mobyData  queryID='b1'>
              <Collection articleName="mySequenceCollection">
                 <Simple>
                  <Object namespace="NCBI_gi" id="163483"/>
                 </Simple>
                 <Simple>
                  <Object namespace="NCBI_gi" id="244355"/>
                 </Simple>
                 <Simple>
                  <Object namespace="NCBI_gi" id="533253"/>
                 </Simple>
                 <Simple>
                  <Object namespace="NCBI_gi" id="745290"/>
                 </Simple>
               </Collection>
          </moby:mobyData>
          <moby:mobyData  queryID='b2'>
              <Collection articleName="mySequenceCollection">
                 <Simple>
                  <Object namespace="NCBI_gi" id="868483"/>
                 </Simple>
                 <Simple>
                  <Object namespace="NCBI_gi" id="2492355"/>
                 </Simple>
               </Collection>
          </moby:mobyData>
         </moby:mobyContent>
       </moby:MOBY>

How to invoke a service with Parameters

A message to a service that requires Secondary Articles is invoked as like this:

       <?xml version="1.0" encoding="UTF-8"?>
       <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
          <moby:mobyContent>
              <moby:mobyData queryID='a1'>
                   <Simple articleName='input1'>
                      <Object namespace="NCBI_gi" id="163483"/>
                   </Simple>

                   <Parameter articleName='cutoff'>
                                <Value>34</Value>
                   </Parameter>

              </moby:mobyData>
          </moby:mobyContent>
       </moby:MOBY>

Note that, even if present, the CRIB and PIB blocks of input MOBY objects should be ignored by the service. They may safely be stripped out of the input client-side prior to service invocation.