[R] SSOAP & chemspider

[Benton, Paul]

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>