R help - Jun 2010 - SSOAP fails with .types[[1]] : subscript out of bounds

Hi,

I am trying to create a BioMoby client in R using SSOAP.
BioMoby is a normal SOAP web service, with request 
and response messages wrapped in BioMoby XML dialect.

Since the particular WSDL I am having problems with 
is autogenerated and used similarly by *many* services,
it would be quite important to a) fix SSOAP or 
b) fix the WSDL generator. 

I am a bit lost how to continue debugging here, 
any clues or help to get me going ?

Thanks in advance,
Yours,
Steffen

The code:

library(SSOAP)
w =
processWSDL("http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_Instruments")
iface = genSOAPClientInterface(def = w, verbose=TRUE)

The output and system info:
> library(SSOAP)
> 
> w =
processWSDL("http://biomoby.org/services/wsdl/ipb-halle.de/MassBank_Instruments")
> iface = genSOAPClientInterface(def = w, verbose=TRUE)
Operation MassBank_Instruments 
Error in .types[[1]] : subscript out of bounds
> 
> traceback()
4: paste(" .elementFormQualified", .elementFormQualified, sep = "
= ")
3: paste("function(", paste(c(sapply(names(.operation at parameters), 
       convertToSName), paste("server = .defaultServer, .convert = ", 
       converter, ", .opts = list(...), ...")), collapse = ",\n\t
"),
       paste(",\n\t nameSpaces = ", ifelse(is.na(nameSpaces),
nameSpaces,
           simple.dQuote(nameSpaces))), if (insertSoapHeader) ",
.soapHeader = NULL",
       ")\n{\n", fixes[1], "\t .SOAP(server, .operation at name,
",
       "\n\t\t", dotArgs, if (length(.operation at parameters))
", " else "",
       "\n\t\t", "action = .operation at action, ",
"\n\t\t", "xmlns = .operation at namespace, ",
       "\n\t\t", ".types = .operation at parameters, ",
"\n\t\t", ".convert = .convert,",
       "\n\t\t", ".header = .header,", "\n\t\t",
".opts = .opts ",
       if (!is.na(.operation at use["input"]) && .operation at
use["input"] ==
           "literal") ",\n\t\t .literal = TRUE", ",
nameSpaces = nameSpaces,",
       paste(" .elementFormQualified", .elementFormQualified, sep =
" = "),
       if (insertSoapHeader) ", .soapHeader = .soapHeader",
")\n",
       fixes[2], "\n}", sep = "")
2: createOperationDefinition(i, server, def at types, env, nameSpaces, 
       addSoapHeader)
1: genSOAPClientInterface(def = w, verbose = TRUE)
> sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SSOAP_0.5-5

loaded via a namespace (and not attached):
[1] RCurl_1.3-0     XML_3.1-0       XMLSchema_0.1-4

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

On Tue, 2010-06-22 at 08:56 +0200, Steffen Neumann
wrote:
> Since the particular WSDL I am having problems with 
> is autogenerated and used similarly by *many* services,
> it would be quite important to a) fix SSOAP or 
> b) fix the WSDL generator. 
So I got a bit further, the reason for the error is 
that the WSDL *does not have* any <wsdl:types>...</wsdl:types>,
and I guess that's because <wsdl:message ...>
has as parameter something as simple as 
<wsdl:part name="data" type="xsd:string"/>
(where "data" is a certain XML document itself, 
 conforming to BioMoby conventions.) 

So, if XMLSchema:::processSchemaTypes() does not find 
any custom/embedded type definitions, is it possibe to "inject" those 
from the http://www.w3.org/2001/XMLSchema.xsd 
into genSOAPClientInterface() instead ? 

Or would I use something different than genSOAPClientInterface() 
in first place ? Or did I get something completely wrong ?

Yours,
Steffen



-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409