R/choosebank.R

In seqinr: Biological Sequences Retrieval and Analysis

###########################################################################
# 
#                                choosebank
#
# To select an ACNUC database or to get the list of available databases
# from an ACNUC server.
# 
###########################################################################

.seqinrEnv <- new.env()
choosebank <- function(bank = NA,
                       host = "pbil.univ-lyon1.fr",
                       port = 5558,
                       server = FALSE,
                       blocking = TRUE,
                       open = "a+",
                       encoding = "",
                       verbose = FALSE,
                       timeout = 5,
                       infobank = FALSE,
                       tagbank = NA){
    #
    # Print parameter values if verbose mode is on:
    #
    if(verbose){ 
        cat("Verbose mode is on, parameter values are:\n")
        cat(paste("  bank = ", deparse(substitute(bank)), "\n"))
        cat(paste("  host = ", deparse(substitute(host)), "\n"))
        cat(paste("  port = ", deparse(substitute(port)), "\n"))
        cat(paste("  timeout = ", deparse(substitute(timeout)), "seconds \n"))
        cat(paste("  infobank = ", deparse(substitute(infobank)), "\n"))
        cat(paste("  tagbank = ", deparse(substitute(tagbank)), "\n"))
    }
    
    #
    # Check parameter values (to be completed):
    #
    if( !is.na(tagbank) ){
        if(verbose) cat("I'm checking the tagbank parameter value...\n")
        if( !(tagbank %in% c("TEST", "TP", "DEV")) ){
            if(verbose) cat("... and I was able to detect an error.\n")
            stop("non allowed value for tagbank parameter.\n")
        } else {
            if(verbose) cat("... and everything is OK up to now.\n")
        }  
    }
    
    #
    # Check that sockets are available:
    #
    if(verbose) cat("I'm ckecking that sockets are available on this build of R...\n")
    if( !capabilities("sockets") ){
        stop("Sockets are not available on this build of R.")
    } else {
        if(verbose) cat("... yes, sockets are available on this build of R.\n")
    }
    
    # 
    # Try to open socket connection:
    #
    if(verbose) cat("I'm trying to open the socket connection...\n")
    oldtimeout <- getOption("timeout")
    options(timeout = timeout)
    socket <- try( socketConnection( host = host, port = port, server = server,
                                     blocking = blocking, open = open, encoding = encoding))
    options(timeout = oldtimeout)
    if(inherits(socket, "try-error")) {
        errmess <- paste("I wasn't able to open the socket connection:\n",
                         "  o Check that your are connected to the internet.\n",
                         "  o Check that port", port, "is not closed by a firewall.\n",
                         "  o Try to increase timeout value (current is", timeout, "seconds).\n")
        stop(errmess)
    } else {
        if(verbose) cat("... yes, I was able to open the socket connection.\n")
    }
    
    #
    # Read the answer from server:
    #
    if(verbose) cat("I'm trying to read answer from server...\n")
    rep1 <- readLines(socket, n = 1)
    if(verbose) cat(paste("... answer from server is:", rep1, "\n"))
    
    #
    # Send client ID to server:
    #
    clientid(socket = socket, verbose = verbose)
    
    ###############################################################################
    #
    # If no bank name is given, return the list of available banks from server:
    #
    ###############################################################################
    resdf <- kdb(tag = tagbank, socket = socket)
    nbank <- nrow(resdf)
    
    if( is.na(bank) ){
        close(socket) # No more needed
        if(verbose) cat("No bank argument was given...\n")
        if( !infobank ){
            if(verbose) cat("infobank parameter is FALSE, I'm just returning bank names\n")
            return(resdf$bank)
        } else {
            if(verbose) cat("infobank parameter is TRUE, I'm returning all bank infos\n")
            return(resdf) 
        }
    } else {
        
        ###############################################################################
        #
        # If a bank name is given, try to open it from server:
        #
        ###############################################################################
        
        # 
        # Try to open bank from server:
        #
        if(verbose) cat("I'm trying to open the bank from server...\n")
        resacnucopen <- acnucopen(bank, socket)
        if(verbose) cat("... and everything is OK up to now.\n")
        
        #
        # Try to get informations from HELP file: 
        #
        if(verbose) cat("I'm trying to get information on the bank...\n")
        bankhelp <- ghelp(item = "CONT", file = "HELP", socket = socket, catresult = FALSE)
        bankrel <- bankhelp[2]
        if(verbose) cat("... and everything is OK up to now.\n")
        
        #
        # Try to get status info:
        #
        status <- "unknown"
        for(i in seq_len(nbank)){
            if (resdf[i,1] == bank) status <- resdf[i,2]
        }
        
        #
        # Build result and assign it in the global environment:
        #
        res <- list(socket = socket,
                    bankname = bank,
                    banktype = resacnucopen$type,
                    totseqs = resacnucopen$totseqs,
                    totspecs = resacnucopen$totspecs,
                    totkeys = resacnucopen$totkeys,
                    release = bankrel,
                    status = status,
                    details = bankhelp)
        assign("banknameSocket", res, .seqinrEnv)
        invisible(res)
    }
}