[R] SSOAP & chemspider

[Duncan Temple Lang]

Hi Paul

 I've been gradually filling in the XMLSchema packages for different cases that arise.
My development versions of SSOAP and XMLSchema get a long way further and I have been trying
to find time to finish them off.  Fortunately, it is on my todo list for the next few weeks.
I have released new (source) versions of the packages (XMLSchema 0.2-0 and SSOAP 0.6-0)
on the Omegahat repository.

These succeed in the genSOAPClientInterface(, processWSDL( url )) for each of the 3 WSDLs
in your email

Also, there are numerous WSDLs in the source of the package and also mentioned in the
Todo.xml file and the code works for almost all of those.

 Thanks for the report

   D.




On 8/2/11 9:10 AM, Benton, Paul wrote:
> Has anyone got SSOAP working on anything besides KEGG?
> 
> I just tried another 3 SOAP servers. Both the WSDL and constructing the .SOAP call. Again the perl and ruby interface worked without any hitches.
> 
> Paul
> 
>> library(SSOAP)
>> massBank<-processWSDL("http://www.massbank.jp/api/services/MassBankAPI?wsdl")
> Error in parse(text = paste(txt, collapse = "\n")) : 
>   <text>:1:29: unexpected input
> 1: function(x, ..., obj = new( ‚
>                                ^
> In addition: Warning message:
> In processWSDL("http://www.massbank.jp/api/services/MassBankAPI?wsdl") :
>   Ignoring additional <service><port> ... elements
>>
> 
>> metlin<-processWSDL("http://metlin.scripps.edu/soap/metlin.wsdl")
> Error in parse(text = paste(txt, collapse = "\n")) : 
>   <text>:1:29: unexpected input
> 1: function(x, ..., obj = new( ‚
>                                ^
>> pubchem<-processWSDL("http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl")
> Error in parse(text = paste(txt, collapse = "\n")) : 
>   <text>:1:29: unexpected input
> 1: function(x, ..., obj = new( ‚
>                                ^
> 
> 
> 
> On 20 Jul 2011, at 01:54, Benton, Paul wrote:
> 
>> Dear all,
>>
>> I've been trying on and off for the past few months to get SSOAP to work with chemspider. First I tried the WSDL file:
>>
>> cs<-processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL")
>> Error in parse(text = paste(txt, collapse = "\n")) : 
>>  <text>:1:29: unexpected input
>> 1: function(x, ..., obj = new( ‚
>>                               ^
>> In addition: Warning message:
>> In processWSDL("http://www.chemspider.com/MassSpecAPI.asmx?WSDL") :
>>  Ignoring additional <service><port> ... elements
>>
>> Next I've tried using just the pure .SOAP to call the database. 
>>
>> s <- SOAPServer("http://www.chemspider.com/MassSpecAPI.asmx")
>> csid<- .SOAP(s, "SearchByMass2", mass=89.04767, range=0.01,
>>        action = I("http://www.chemspider.com/SearchByMass2"),
>>        xmlns = c("http://www.chemspider.com"), .opts = list(verbose = TRUE))
>>
>> This seems to work and gives back a result. However, this result isn't the right result. It's seems to have converted the mass into 0. When I run the similar program in perl I get the correct id's. So this isn't a server side problem but SSOAP. Any thoughts or suggestions on other packages to use?
>> Further infomation about the SeachByMass2 method and it's xml that it's expecting.
>> http://www.chemspider.com/MassSpecAPI.asmx?op=SearchByMass2
>>
>> Cheers,
>>
>>
>> Paul
>>
>>
>> PS Placing a fake error in the .SOAP code I can look at the xml it's sending to the server:
>> Browse[1]> doc
>> <?xml version="1.0"?>
>> <SOAP-ENV:Envelope xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/" xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/">
>>  <SOAP-ENV:Body>
>>    <ns:SearchByMass2 xmlns:ns="http://www.chemspider.com">
>>      <ns:mass>89.04767</ns:mass>
>>      <ns:range>0.01</ns:range>
>>    </ns:SearchByMass2>
>>  </SOAP-ENV:Body>
>> </SOAP-ENV:Envelope>
> 
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