SSOAP & chemspider
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>