Question: Problems Accessing The Soaplab Newcpgreport Webservice
0
gravatar for herderbezem
7.7 years ago by
herderbezem0 wrote:

I'm trying to use the NewCpGReport webservice to find CpGIslands in nucleotide sequences. However, I'm having problems with the input format.

I'm using SOAPpy in Python to access the wsdl

http://www.ebi.ac.uk/soaplab/services/nucleic_cpg_islands.newcpgreport?wsdl

and trying to use "createAndRun" but so far I can only get the following error:

faultType: <Fault soapenv:Server.userException:
org.soaplab.share.SoaplabException: Soaplab::NotValidInputs [sequence]
Input is mandatory and cannot remain empty. : <SOAPpy.Types.structType
detail at 181263052>: {'hostname': 'ves-oy-2b.ebi.ac.uk'}>

Problem is, in the discription, which is the only documentation I've been able to find which discusses input from a webservice point of view, there are 3 input options which I've all tried but I still get the same error.

 <input name = "sequence_usa" type = "string" mandatory = "false ></input>
 <input name = "sequence_direct_data" type = "string" mandatory = "false"></input>
 <input name = "sformat_sequence" type = "string" mandatory = "false">

So far I've tried setting the input up in multiple ways, trying to copy the input format EMBL used in other tools of theirs but I'm at a loss for ideas how to get it running properly.

• 1.6k views
ADD COMMENTlink modified 6.9 years ago by Biostar ♦♦ 20 • written 7.7 years ago by herderbezem0
0
gravatar for Michael Dondrup
7.7 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

Did you try to test the service in SoapUI first? It is a good way of testing services if they work at all and the example XML it generates could show you which field is missing, this is specifically tricky should the field be named "sequence", because <sequence> is used in XML schema types, too. From what I can see with SoapUI, this service needs to be called in a very particular way, like all soaplab services. It accepts key, value pairs as input. The list of possible keys can be fetched from invoking the "describe" operation.

Following that, the following is a valid invocation (not necessarily sensible):

<soapenv:Envelope xmlns:xsi="&lt;a href=" http:="" www.w3.org="" 2001="" XMLSchema-instance"="" rel="nofollow">http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:axis="http://axis1.protocol.services.soaplab.org">
   <soapenv:Header/>
   <soapenv:Body>
      <axis:createAndRun soapenv:encodingStyle="&lt;a href=" http:="" schemas.xmlsoap.org="" soap="" encoding="" "="" rel="nofollow">http://schemas.xmlsoap.org/soap/encoding/">
         <inputs xsi:type="x-:Map" xs:type="type:Map" xmlns:x-="&lt;a href=" http:="" xml.apache.org="" xml-soap"="" rel="nofollow">http://xml.apache.org/xml-soap" xmlns:xs="http://www.w3.org/2000/XMLSchema-instance">
            
            <item xsi:type="x-:mapItem" xs:type="type:mapItem">
               <key xsi:type="xsd:string">sequence_usa</key>
               <value xsi:type="xsd:string">acgt</value>
            </item>
         </inputs>
      </axis:createAndRun>
   </soapenv:Body>
</soapenv:Envelope>

Response:

<soapenv:Envelope xmlns:soapenv="&lt;a href=" http:="" schemas.xmlsoap.org="" soap="" envelope="" "="" rel="nofollow">http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
   <soapenv:Body>
      <ns1:createAndRunResponse soapenv:encodingStyle="&lt;a href=" http:="" schemas.xmlsoap.org="" soap="" encoding="" "="" rel="nofollow">http://schemas.xmlsoap.org/soap/encoding/" xmlns:ns1="http://axis1.protocol.services.soaplab.org">
         <createAndRunReturn xsi:type="xsd:string">[nucleic_cpg_islands.newcpgreport]_1f702357.13847d191e5._5189</createAndRunReturn>
      </ns1:createAndRunResponse>
   </soapenv:Body>
</soapenv:Envelope>

Use the jobid retrieved to call other methods in the work-flow.

Btw, this should be covered by the documentation, shouldn't it?

ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Michael Dondrup47k
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