R/make_entrez_query.r

In rentrez: Entrez in R

#Create a URL for the EUtils API. 
#
# This function is usde by all the API-querying functions in rentrez to build
# the appropriate url. Required arguments for each rentrez are handled in each
# function. Those arguments that either ID(s) or are WebEnv cookie can be set
# by passing a string or two argument names to `make_entrez_query`
#
#
# efetch_url <- make_entrez_query("efetch", require_one_of=c("id", "WebEnv"), 
#                                 id=c(23310964,23310965), db="pubmed",
#                                 rettype="xml")
#

make_entrez_query <- function(util, require_one_of=NULL, ...){
    args <- list(..., email=entrez_email, tool=entrez_tool)
    arg_names <- names(args)
    
    if(length(require_one_of) > 1 ){
        if(!any(require_one_of %in% arg_names)){
            msg <- paste("Function requires either", require_one_of[1], "or",
                         require_one_of[2], "to be set as arguments\n")
            stop(msg)
        }
    }
    
    if("id" %in% arg_names){
        args[["id"]] = paste(args[["id"]], collapse=",")
      
    }
    base_url <- paste("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/", util, ".fcgi?", sep="")
    url_args <- paste(paste(arg_names, args, sep="="), collapse="&")
    query <- paste(base_url, url_args, sep="&")
    return(query)
}