R/download_ctd.R

In isglobal-brge/CTDquerier: Package for CTDbase data query, visualization and downstream analysis

.get_cache <- function( verbose = FALSE, ask = TRUE ) {
    #path <- file.path(tempdir(), "tempCTDquerierCacheDir")
    #bfc <- BiocFileCache::BiocFileCache( path )
    if( verbose ) {
        cache <- tools::R_user_dir("CTDquerier", which = "cache")
        bfc <- BiocFileCache::BiocFileCache( cache, ask = ask )
    } else {
        suppressMessages( suppressWarnings({
            cache <- tools::R_user_dir("CTDquerier", which = "cache")
            bfc <- BiocFileCache::BiocFileCache( cache )
        } ) )
    }
    return( bfc )
}

#' Function to download genes available in CTDbase
#'
#' This function download the "Gene vocabulary" file (\code{CTD_genes.tsv.gz})
#' from \code{http://ctdbase.org/downloads}.
#'
#' @details The field included in the file (\code{CTD_genes.tsv.gz}) are:
#' \enumerate{
#'  \item GeneSymbol
#'  \item GeneName
#'  \item GeneID (NCBI Gene identifier)
#'  \item AltGeneIDs (alternative NCBI Gene identifiers; '|'-delimited list)
#'  \item Synonyms ('|'-delimited list)
#'  \item BioGRIDIDs ('|'-delimited list)
#'  \item PharmGKBIDs ('|'-delimited list)
#'  \item UniprotIDs ('|'-delimited list)
#' }
#'
#' @param verbose (default \code{FALSE}) If set to \code{TRUE} is shows relevant
#' information of each step.
#' @param ask (default \code{TRUE}) If \code{TRUE} it asks the the persistent
#' location must be used.
#' @return Passed name into \code{filename} argument if it could be download
#' \code{1} otherwise.
#' @examples
#' download_ctd_genes()
#' @export download_ctd_genes
download_ctd_genes <- function( verbose = FALSE, ask = TRUE ) {
    fileURL <- "http://ctdbase.org/reports/CTD_genes.tsv.gz"
    bfc <- .get_cache( verbose, ask )

    if( nrow( BiocFileCache::bfcquery(bfc, "CTD_genes") ) == 0 ) {
        if( verbose ) message( "Downloading GENE vocabulary from CTDbase" )
        rst <- tryCatch({
            BiocFileCache::bfcadd(bfc, "CTD_genes", fileURL )
            TRUE
        }, error=function(e) {
            warning( "\nGENE vocabulary could not be downloaded from CTDbase" )
            FALSE
        })
        return(rst)
    } else {
        return(TRUE)
    }
}

#' Function to download checmicals available in CTDbase
#'
#' This function download the "Chemical vocabulary" file (\code{CTD_chemicals.tsv.gz})
#' from \code{http://ctdbase.org/downloads}.
#'
#' @details The field included in the file (\code{CTD_chemicals.tsv.gz}) are:
#' \enumerate{
#'  \item ChemicalName
#'  \item ChemicalID (MeSH identifier)
#'  \item CasRN (CAS Registry Number, if available)
#'  \item Definition
#'  \item ParentIDs (identifiers of the parent terms; '|'-delimited list),
#'  \item TreeNumbers (identifiers of the chemical's nodes; '|'-delimited list),
#'  \item ParentTreeNumbers (identifiers of the parent nodes; '|'-delimited list),
#'  \item Synonyms ('|'-delimited list)
#'  \item DrugBankIDs ('|'-delimited list)
#'  }
#'
#' @param verbose (default \code{FALSE}) If set to \code{TRUE} is shows relevant
#' information of each step.
#' @param ask (default \code{TRUE}) If \code{TRUE} it asks the the persistent
#' location must be used.
#' @return Passed name into \code{filename} argument if it could be download
#' \code{1} otherwise.
#' @examples
#' download_ctd_chem()
#' file.exists( "CTD_chemicals.tsv.gz" )
#' @export download_ctd_chem
download_ctd_chem <- function( verbose = FALSE, ask = TRUE ) {
    fileURL <- "http://ctdbase.org/reports/CTD_chemicals.tsv.gz"
    bfc <- .get_cache( verbose, ask )

    if( nrow( BiocFileCache::bfcquery(bfc, "CTD_chemicals") ) == 0 ) {
        if( verbose ) message( "Downloading CHEMICAL vocabulary from CTDbase" )
        rst <- tryCatch({
            BiocFileCache::bfcadd(bfc, "CTD_chemicals", fileURL )
            TRUE
        }, error = function(e) {
            warning( "\nCHEMICAL vocabulary could not be downloaded from CTDbase" )
            FALSE
        })
        return(rst)
    } else {
        return(TRUE)
    }
}

#' Function to download diseases available in CTDbase
#'
#' This function download the "Disease vocabulary" file (\code{CTD_diseases.tsv.gz})
#' from \code{http://ctdbase.org/downloads}.
#'
#' @details The field included in the file (\code{CTD_diseases.tsv.gz}) are:
#' \enumerate{
#'  \item DiseaseName
#'  \item DiseaseID (MeSH or OMIM identifier)
#'  \item Definition
#'  \item AltDiseaseIDs (alternative identifiers; '|'-delimited list)
#'  \item ParentIDs (identifiers of the parent terms; '|'-delimited list)
#'  \item TreeNumbers (identifiers of the disease's nodes; '|'-delimited list)
#'  \item ParentTreeNumbers (identifiers of the parent nodes; '|'-delimited list)
#'  \item Synonyms ('|'-delimited list)
#'  \item SlimMappings (MEDIC-Slim mappings; '|'-delimited list)
#'  }
#'
#' @param verbose (default \code{FALSE}) If set to \code{TRUE} is shows relevant
#' information of each step.
#' @param ask (default \code{TRUE}) If \code{TRUE} it asks the the persistent
#' location must be used.
#' @return Passed name into \code{filename} argument if it could be download
#' \code{1} otherwise.
#' @examples
#' download_ctd_dise()
#' file.exists( "CTD_diseases.tsv.gz" )
#' @export download_ctd_dise
download_ctd_dise <- function( verbose = FALSE, ask = TRUE ) {
    fileURL <- "http://ctdbase.org/reports/CTD_diseases.tsv.gz"
    bfc <- .get_cache( verbose, ask )

    if( nrow( BiocFileCache::bfcquery(bfc, "CTD_diseases") ) == 0 ) {
        if( verbose ) message( "Downloading DISEASE vocabulary from CTDbase" )
        rst <- tryCatch({
            BiocFileCache::bfcadd(bfc, "CTD_diseases", fileURL )
            TRUE
        }, error = function(e) {
            warning( "\nDISEASE vocabulary could not be downloaded from CTDbase" )
            FALSE
        })
        return(rst)
    } else {
        return(TRUE)
    }
}