error_foo <- function() {
    cat(geterrmessage(), file = stderr())
    q("no", 1, F)
}
options(show.error.messages = F, error = error_foo)

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

suppressPackageStartupMessages({
    library("pathview")
    library("optparse")
})

sessionInfo()

option_list <- list(
    make_option(c("--pathway_id"), type = "character", default = NULL, help = "Path to tabular file with gene data"),
    make_option(c("--pathway_id_fp"), type = "character", default = NULL, help = "Path to tabular file with pathway ids"),
    make_option(c("--pathway_id_header"), type = "logical", default = FALSE, help = "Header for tabular file with pathway ids"),
    make_option(c("--species"), type = "character", default = "hsa", help = "KEGG code, scientific name or the common name of the species"),
    make_option(c("--gene_data"), type = "character", default = NULL, help = "Path to tabular file with gene data"),
    make_option(c("--gd_header"), type = "logical", default = FALSE, help = "Header for the gene data file"),
    make_option(c("--gene_idtype"), type = "character", default = "entrez", help = "ID type used for the gene data"),
    make_option(c("--cpd_data"), type = "character", default = NULL, help = "Path to tabular file with compound data"),
    make_option(c("--cpd_header"), type = "logical", default = FALSE, help = "Header for the compound data file"),
    make_option(c("--cpd_idtype"), type = "character", default = "kegg", help = "ID type used for the compound data"),
    make_option(c("--multi_state"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"),
    make_option(c("--match_data"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"),
    make_option(c("--kegg_native"), type = "logical", default = TRUE, help = "Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"),
    make_option(c("--same_layer"), type = "logical", default = TRUE, help = "Plot on same layer?"),
    make_option(c("--map_null"), type = "logical", default = TRUE, help = "Map the NULL gene or compound data to pathway?"),
    make_option(c("--split_group"), type = "logical", default = FALSE, help = "Split node groups into individual nodes?"),
    make_option(c("--expand_node"), type = "logical", default = FALSE, help = "Expand multiple-gene nodes into single-gene nodes?"),
    make_option(c("--sign_pos"), type = "character", default = "bottomright", help = "Position of pathview signature")
)

parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
args <- parse_args(parser)
print(args)

read_table <- function(fp, header, rownames = 1, colclasses = NA) {
    table <- read.table(fp, header = header, sep = "\t", row.names = rownames, colClasses = colclasses)
    # transform to vector if only one column
    if (dim(table)[2] == 1) {
        names <- rownames(table)
        table <- table[, 1]
        names(table) <- names
    }
    return(table)
}

get_table <- function(fp, header) {
    table <- NULL
    if (!is.null(fp)) {
        table <- read_table(fp, header, rownames = 1)
    }
    return(table)
}

# load gene_data file
gene_data <- get_table(args$gene_data, args$gd_header)

# load compound data file
cpd_data <- get_table(args$cpd_data, args$cpd_header)

run_pathview <- function(pathway_id) {
    pathview(
        pathway.id = pathway_id,
        gene.data = gene_data,
        gene.idtype = args$gene_idtype,
        cpd.data = cpd_data,
        cpd.idtype = args$cpd_idtype,
        species = args$species,
        multi.state = args$multi_state,
        match.data = args$match_data,
        kegg.native = args$kegg_native,
        same.layer = args$same_layer,
        split.group = args$split_group,
        expand.node = args$expand_node,
        sign.pos = args$sign_pos,
        map.null = args$map_null
    )
}

# get pathway ids
if (!is.null(args$pathway_id)) {
    run_pathview(args$pathway_id)
} else {
    pthws <- read_table(args$pathway_id_fp, args$pathway_id_header, rownames = NULL, colclasses = "character")
    for (p in pthws) {
        run_pathview(p)
    }
}