R/gmql_read.R

In DEIB-GECO/RGMQL: GenoMetric Query Language for R/Bioconductor

#' Function read
#'
#' It reads a GMQL dataset, as a folder containing some homogenus samples on 
#' disk or as a GRangesList, saving it in Scala memory in a way that can be 
#' referenced in R. It is also used to read a repository dataset in case of
#' remote processing.
#' 
#' @importFrom rJava J .jnull .jarray
#' @importFrom methods is
#' 
#' @param dataset folder path for GMQL dataset or dataset name on repository
#' @param parser string used to parsing dataset files.
#' The Parsers available are:
#' \itemize{
#' \item{BedParser}
#' \item{BroadPeakParser}
#' \item{NarrowPeakParser}
#' \item{CustomParser}
#' }
#' Default is CustomParser.
#' @param is_local logical value indicating local or remote dataset
#' 
#' @return GMQLDataset object. It contains the value to use as input 
#' for the subsequent GMQLDataset method
#' 
#' @details
#' Normally, a GMQL dataset contains an XML schema file that contains
#' name of region attributes. (e.g chr, start, stop, strand)
#' The CustomParser reads this XML schema; 
#' if you already know what kind of schema your files have, use one of the 
#' parsers defined, without reading any XML schema.
#' 
#' If GRangesList has no metadata: i.e. metadata() is empty, two metadata are
#' generated:
#' \itemize{
#' \item{"provider" = "PoliMi"}
#' \item{"application" = "RGMQL"}
#' }
#'
#' NOTE: 
#' The folder layout must obey the following rules and adopt 
#' the following layout:
#' The dataset folder can have any name, but must contains the 
#' sub-folders named: "files".
#' The sub-folder "files" contains the dataset files and 
#' the schema xml file.
#' The schema files adopt the following the naming conventions:
#' 
#' - "schema.xml"
#' - "test.schema"
#' 
#' The names must be in LOWERCASE. Any other schema file 
#' will not be conisdered, if both are present, "test.schema" will be used. 
#'
#' @examples
#' 
#' ## This statement initializes and runs the GMQL server for local execution 
#' ## and creation of results on disk. Then, with system.file() it defines 
#' ## the path to the folder "DATASET" in the subdirectory "example" 
#' ## of the package "RGMQL" and opens such folder as a GMQL dataset 
#' ## named "data" using CustomParser
#' 
#' init_gmql()
#' test_path <- system.file("example", "DATASET", package = "RGMQL")
#' data = read_gmql(test_path)
#' 
#' ## This statement opens such folder as a GMQL dataset named "data" using 
#' ## "NarrowPeakParser" 
#' dataPeak = read_gmql(test_path,"NarrowPeakParser")
#' 
#' ## This statement reads a remote public dataset stored into GMQL system 
#' ## repository. For a public dataset in a (remote) GMQL repository the 
#' ## prefix "public." is needed before dataset name
#' 
#' remote_url = "http://www.gmql.eu/gmql-rest/"
#' login_gmql(remote_url)
#' data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)
#' 
#' 
#' @name read_gmql
#' @rdname read-function
#' @export
#'
read_gmql <- function(
    dataset, 
    parser = "CustomParser",
    is_local = TRUE
) {
    .check_input(dataset)
    .check_logical(is_local)
    WrappeR <- J("it/polimi/genomics/r/Wrapper")
    parser_name <- .check_parser(parser)
    if(is_local) {
        if(!dir.exists(dataset))
            stop("folder does not exist")
        
        dataset <- sub("/*[/]$","",dataset)
        if(basename(dataset) !="files")
            dataset <- file.path(dataset,"files")
        
        schema_XML <- .retrieve_schema(dataset, TRUE)
        
        schema_matrix <- .jnull("java/lang/String")
        url <- .jnull("java/lang/String")
        coords_sys <- .jnull("java/lang/String")
        type <- .jnull("java/lang/String")
    } else {
        
        if(!exists("GMQL_credentials", envir = .GlobalEnv))
            stop("You have to log on using login function")
        
        credential <- get("GMQL_credentials", envir = .GlobalEnv)
        url <- credential$remote_url
        if(is.null(url))
            stop("You have to log on using login function")
        
        if(identical(parser_name,"CUSTOMPARSER")) {
            list <- show_schema(url, dataset)
            coords_sys <- list$coordinate_system
            type <- list$type
            schema_names <- vapply(
                list$fields, function(x){ x$name },character(1)
            )
            schema_type <- vapply(
                list$fields, function(x){ x$type },character(1)
            )
            schema_matrix <- cbind(schema_names,schema_type)
            
            if(is.null(schema_matrix) || !length(schema_matrix))
                schema_matrix <- .jnull("java/lang/String")
            else
                schema_matrix <- .jarray(schema_matrix, dispatch = TRUE)
        }
        else
            schema_matrix <- .jnull("java/lang/String")
        
        schema_XML <- .jnull("java/lang/String")
    }
    
    response <- WrappeR$readDataset(
        dataset, 
        parser_name, 
        is_local,
        schema_matrix,
        schema_XML,
        coords_sys, 
        type
    )
    error <- strtoi(response[1])
    data <- response[2]
    if(error)
        stop(data)
    else
        GMQLDataset(data)
}

#' @importFrom S4Vectors metadata
#' @importFrom rJava J .jarray
#' 
#' @param samples GRangesList
#' 
#' @name read_gmql
#' @rdname read-function
#' @export
#'
read_GRangesList <- function(samples) {
    if(!is(samples,"GRangesList"))
        stop("only GrangesList")
    
    meta <- S4Vectors::metadata(samples)
    if(is.null(meta) || !length(meta)) {
        #repeat meta for each sample in samples list
        len <- length(samples)
        warning(
            "No metadata.\nWe provide two metadata for you:
            \n1.provider = PoliMi\n2.application = RGMQL\n"
        )
        index_meta <- rep(seq_len(len),each = len)
        rep_meta <- rep(
            c("provider","PoliMi", "application", "RGMQL"),
            times = len
        )
        meta_matrix <- matrix(rep_meta,ncol = 2,byrow = TRUE)
        meta_matrix <- cbind(index_meta,meta_matrix)
    } else {
        unlist_meta <- unlist(meta)
        names_meta <- names(unlist_meta)
        group_names <- gsub(".*_([0-9]*)\\..*","\\1", names_meta)
        names(unlist_meta) <- NULL
        meta_matrix <- cbind(group_names,names_meta,unlist_meta)
    }
    
    df <- data.frame(samples)
    df <- df[-2] #delete group_name
    len_df <- dim(df)[1] # number of rows
    
    col_types <- vapply(df,class,character(1))
    col_names <- names(col_types)
    #re order the schema?
    # if GTF, change
    if("phase" %in% col_names) {
        col_names <- plyr::revalue(
            col_names,c(type = "feature", phase = "frame", seqnames = "seqname")
        )
        schema_matrix <- cbind(toupper(col_types),col_names)
        schema_matrix<- schema_matrix[
            setdiff(rownames(schema_matrix), c("group","width")),]
    } else {
        col_names <- plyr::revalue(
            col_names,
            c(start = "left", end = "right", seqnames = "chr")
        )
        schema_matrix <- cbind(col_names,toupper(col_types))
        df$start = df$start - 1
        schema_matrix<- schema_matrix[
            setdiff(rownames(schema_matrix),c("group","width")),]
    }
    region_matrix <- as.matrix(vapply(df, as.character,character(len_df)))
    region_matrix[is.na(region_matrix)] <- "NA"
    region_matrix <- region_matrix[,setdiff(colnames(region_matrix),"width")]
    rownames(schema_matrix) <- NULL
    colnames(schema_matrix) <- NULL
    
    schema_matrix <- .jarray(schema_matrix,dispatch = TRUE)
    meta_matrix <- .jarray(meta_matrix,dispatch = TRUE)
    region_matrix <- .jarray(region_matrix,dispatch = TRUE)
    
    WrappeR <- J("it/polimi/genomics/r/Wrapper")
    response <- WrappeR$read(
        meta_matrix,
        region_matrix,
        schema_matrix,
        "default", 
        "TAB"
    )
    
    GMQLDataset(response)
}

.check_parser <- function(parser) {
    parser <- toupper(parser)
    parsers <- c(
        "BEDPARSER",
        "BROADPEAKPARSER",
        "NARROWPEAKPARSER",
        "CUSTOMPARSER"
    )
    
    if(!parser %in% parsers)
        stop("parser not defined")
    
    parser
}