R/getDatabase.R

In egonw/BridgeDbR: Code for using BridgeDb identifier mapping framework from within R

getDatabase <- function(organism, location = NA, website = "https://bridgedb.github.io/data/gene_database/") {
    if (is.na(location)) location <- tempdir()

    code <- getOrganismCode(organism)
    names <- getBridgeNames(code, website = website)
    dates <- c()
    i <- 1
    for (name in names) {
        dates[i] <- substr(name, 10, 17)
        i <- i + 1
    }
    j <- 1
    c <- 1
    current <- dates[1]
    for (date in dates) {
        if (date > current) {
            current <- date
            c <- j
        }
        j <- j + 1
    }

    pattern <- paste("http[^\"]*\">", names[c], sep = "")
    lines <- readLines(curl(website))

    i <- 1
    result <- c()

    for (line in lines) {
        expr <- gregexpr(pattern, line, perl = TRUE)
        matches <- expr[[1]]
        matchLengths <- attributes(matches)$match.length
        for (matchCounter in 1:length(matches)) {
            start <- matches[matchCounter]
            stop <- start + matchLengths[matchCounter] - (nchar(names[c]) + 3)
            matchedString <- substr(line, start, stop)
            if (nchar(matchedString) > 0) {
                result[i] <- matchedString
                i <- i + 1
            }
        }
    }

    url <- result[1]
    file <- paste(location, "/", name, sep = "")
    download.file(url, file, mode = "wb")
    file
}