MyGene_S4_beginning.R

library(IRanges)
library(httr)
library(jsonlite)

version <- '0.3'

collapse <- function(...) {
    paste(unlist(list(...)), sep=",", collapse=",")
}

MyGene <- setClass("MyGene",
    slots=list(base.url="character", delay="numeric", step="numeric", agent="character"),
    prototype=list(base.url="http://mygene.info/v2", delay=1, step=1000, agent=sprintf('R-httr_mygene.R/httr.%s', version)))

validMyGeneObject <- function(object) {
    errors <- character(0)
    for (sn in c("base.url", "delay", "step", "agent")) {
        if (length(slot(object, sn)) != 1)
            errors <- c(errors, sprintf("Slot %s must have length 1", sn))
    }
    if (length(errors) > 0)
        errors
    else
        TRUE
}

setValidity("MyGene", validMyGeneObject)

.Get <- function(mygene, path, params=list()) {
    url <- paste([email protected], path, sep="")
    res <- GET(url, query=params, config=add_headers(c(`User-Agent`=mygene@agent)))
    str(res)
    if (res$status_code != 200)
        stop("Request returned unexpected status code ", res$status_code)
    content(res, "text")
}

.Post <- function(mygene, path, params=list()) {
    url <- paste([email protected], path, sep="")
    res <- POST(url, query=params, config=add_headers(c(`User-Agent`=mygene@agent)))
    str(res)
    if (res$status_code != 200)
        stop("Request returned unexpected status code ", res$status_code)
    content(res, "text")
}

setMethod("metadata", c(x="MyGene"), function(x, ...) {
    .Get(x, "/metadata")
})

available.fields <- function(mygene) {
    fromJSON(metadata(mygene))$available_fields
}

setGeneric("getGene", signature=c("mygene"),
           function(geneid, fields, ..., return.as=c("JSON", "text"), mygene) standardGeneric("getGene"))

setMethod("getGene", c(mygene="MyGene"), function(geneid, fields, ..., return.as=c("JSON", "text"), mygene) {
    return.as <- match.arg(return.as)
    params <- list(...)
    params$fields <- collapse(fields)
    res <- .Get(mygene, paste("/gene/", geneid, sep=""), params)
    switch(return.as,
           JSON=fromJSON(res),
           text=res)
})

## If nothing is passed for the mygene argument, just construct a
## default MyGene object and use it.
setMethod("getGene", c(mygene="missing"), function(geneid, fields, ..., return.as=c("JSON", "text"), mygene) {
    mygene <- MyGene()
    getGene(geneid, fields, ..., mygene=mygene)
})


mg <- MyGene()
metadata(mg)
available.fields(mg)
getGene("1017", fields = 'symbol,name,taxid,entrezgene')