similar to: question about SSOAP

I recently started trying R and SSOAP and was able to successfully try a "hello world" service. I am now trying to get a more complicated interface to work with SSOAP and so far failed miserably at that and so need any help I can get from here. The service I am attaching is a prototype for a full service that would take information to identify a data source and a query to run and return

Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Thanks very much. Regards

Dear list, I've been using R for a while, but am new to web services. I'm a relatively novice programmer; advance apologies for incorrect terminology. I'm trying to send queries and get results back from a SOAP server, using the SSOAP package. My code contains sensitive API keys and URLs, and unfortunately I'm unable to share it uncensored. I have not been able to reproduce the

Hi again, On Tue, 2010-06-22 at 10:02 +0200, Steffen Neumann wrote: > 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 ? Well, it's not possible, at least for me. This is as far as I got, any help

First of all, let me confess that I am a newbie to R and don't know much about the language or the environment. We have a need for plugging in R in our production runtime and need the ability to pull data out of our existing services. I am trying to see if I can take advantage of SSOAP such that we can expose the data via webservices and use SSOAP to call into them. Our runtime is mostly

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

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

Hi, so, last post from here unless I can provide any more input to fix the upstream package. On Tue, 2010-06-22 at 10:02 +0200, Steffen Neumann wrote: > So I got a bit further, the reason for the error is > that the WSDL *does not have* any <wsdl:types>...</wsdl:types>, I created a local copy and inserted a dummy <wsdl:types>...</wsdl:types> element. Then, my

Dear community, has anyone managed to get SSOAP working with the ChemSpider Web APIs, using functions which need the security token? I use SSOAP 0.9-0 from the OmegaHat repository. In the example code from SSOAP there is a sample which uses a token function. Interestingly, it checks if(!is.character(token)) first (and proceeds if the token is NOT character.) I can't test that function since I

Dear list, I am trying to use the SSOAP package to access a very simple SOAP service, included as a demonstrator in the axis2 Apache package: "Version" (takes no input parameters and should return a string with the version number). The web service itself seems to be working as I could access it using an other client (eclipse Web Server tester). You will find the service wsdl here:

Hi, I have a SOAP service, provided by BioMoby which I'd like to call via SSOAP. My service breaks during genSOAPClientInterface() genSOAPClientInterface(def=service, verbose = TRUE) Operation MassBank_Simple_2 Error: Cannot resolve SOAP type in empty context Problem seems to be that there are no <types> defined in the WSDL, and that the service passes input/output as a single

Hi: I am trying to search PubMed abstracts which contains BOTH two terms: COL4A1 AND Ocular. I am using the following code: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300", sep="") docId <- xmlTreeParse(getURL(paste(url, search, sep="")),

Hi: I am trying to query pubmed abstracts using the following syntax: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax=100&usehistory=y", sep="") docId <-

I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse("

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only

Duncan, you are a king! Thanks a lot for this cookie. It really helped me. Thanks for the code as well as detailed explanation at the end. >Hi Gregor. > >Here is a function that will collect all of the nodes in the >XML document whose names are in the vector elementNames > >getElements = >function(elementNames) >{ > els = list() > > startElement = function(node,

Hi, I am trying to learn how to from within R access web services. I am also interested in having R be a client and from within R access data on other web services. Specifically the web services I would like to access from within R are “http://water.sdsc.edu/waterOneFlow/NWIS/DailyValues.asmx?WSDL” Therefor, I wrote the following code into R program: > library(SSOAP) >

Hi, I'm having a bit of trouble using SSOAP to send requests containing complex types. It seems as though processWSDL does not generate functions for converting the generated types into SOAP requests, but it does generate them for converting **from** SOAP requests to the complex types. The error that I get when trying to pass an object of type "LoginReq" (as generated by

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:

Hi, I'm trying to use the XML-RPC client in the SSOAP package to connect to a service that I have created. From other languages (Perl, Python, Ruby) this is not a problem but the SSOAP client gives the following error: Error in .XMLRPC("http://localhost:9000", "Cytoscape.test", .opts = list(verbose = TRUE)) : Failed to parse XML-RPC request: Content is not allowed in