Apache

Description Usage Arguments Details Value Author(s) Examples

The generateFunctionMap function generates java wrapper functions for a list of R functions. It also generates java beans and R–Java data type conversions for any R data types that are related to the function but unavailable in the environment lookup. This function also updates environments lookup and cvtImport (see arguments below) as a side effect.

generateFunctionMap(rTypeInfo, genTest = TRUE, workDir = getwd(),
                    verbose = FALSE,
                    deployModeName = "jms", typeModeName = "javalib",
                    wsdlStyle = "WRAPPED", wsdlUse = "LITERAL",
                    extraClasses = "", pkgRoot="org.bioconductor", ...)

`rTypeInfo`	a list, each component is an instance of `RJavaSignature-class` and represents the signature of a R function.
`genTest`	logical, TRUE if want to generate a java program to test the java wrapper functions generated by `generateFunctionMap`, FALSE otherwise.
`workDir`	a character string, the path of the directory where this function generates all its outputs.
`verbose`	logical, TRUE if want to print out debug information, FALSE otherwise.
`deployModeName`	Character, either "demo" or "jms". How the service will be deployed. "demo" is no longer supported.
`typeModeName`	Character, either "robject" or "javalib". How Java objects should be generated; see `generateDataMap` and `converters`
`wsdlStyle`	Style of wsdl to create. A value of “WRAPPED” adds “_PortType” to the short name of the main service interface; all other values do not add “_PortType”.
`wsdlUse`	Whether SOAP bindings are document/literal (value “LITERAL” or document/encoded (any other value). Only “LITERAL” is currently supported.
`extraClasses`	character. Extra classes requied to convert function argument or return values, e.g., an argument of type `list` might require information about the classes present in the list. Usually this argument is not required, as S4 classes are parsed to their constituent parts
`pkgRoot`	character. Root package name of the java classes classes being created. It should be a sequence of one or more character strings delimited by dot, and no dot after the last string
`...`	Additional arguments, to be compatiable with `createMap`.

The java mappings generated under workDir are organized as following:

biocJavaMap The base directory
biocJavaMap/package1 Java mappings for functions and data types defined in R package1
biocJavaMap/package1/data Java beans and java <-> R mapping functions (in R) for data types defined in pacakge1
biocJavaMap/package1/function Java wrapper functions for functions defined in package1
biocJavaMap/package2 Java mappings for functions and data types defined in package2
biocJavaMap/mainService Main java API, which invokes the java mapping functions for package1, package2, etc. mainService value is provided by user as input.

A list, each component is an instance of RJavaSignature-class and represents the signature of a java wrapper function. The return value has a one-to-one mapping relation with input parameter rTypeInfo, i.e. the java wrapper function that is represented by the ith component in the return list, is the wrapper for the R function that is represend by the ith component in rTypeInfo.

Nianhua Li