R/chemQueries.R

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# .ChemQ: Create gtoxLoadChem query string 
#-------------------------------------------------------------------------------

.ChemQ <- function(field, val, exact) {

    qformat <-
        "
        SELECT * FROM 
        (
        SELECT 
            spid, 
            chemical.*
        FROM chemical 
        LEFT JOIN sample ON sample.chid = chemical.chid
        UNION ALL
        SELECT 
            spid, 
            chemical.*
        FROM sample
        LEFT JOIN chemical ON sample.chid = chemical.chid
        WHERE  chemical.chid IS NULL
        ) AS cs 
        "

    if (getOption("TCPL_DRVR") == "SQLite") exact <- TRUE

    if (!is.null(field)) {

        nfld <- switch(
            field,
            spid="spid",
            chid="chid",
            casn="casn",
            code="casn",
            "chnm"
        )

        if (field == "code") val <- suppressWarnings(sapply(val, gtoxCode2CASN))

        qformat <- paste(qformat, "WHERE")

        if (nfld == "chnm") {
            if (exact) {
                qformat <- paste(qformat, "chnm IN (%s);")
                val <- paste0("\"", val, "\"", collapse=",")
                qstring <- sprintf(qformat, val, val)
            } else {
                qformat <- paste(qformat, "chnm RLIKE %s;")
                val <- paste0("\"", paste(val, collapse="|"), "\"")
                qstring <- sprintf(qformat, val, val)
            }
        } else {
            qformat <- paste(qformat, nfld, "IN (%s)")
            qstring <- sprintf(qformat, paste0("\"", val, "\"", collapse=","))
        }

    } else {
        qstring <- qformat
    }
    qstring
}

#-------------------------------------------------------------------------------
# END .ChemQ
#-------------------------------------------------------------------------------

#-------------------------------------------------------------------------------
# .ClibQ: Create gtoxLoadClib query string 
#-------------------------------------------------------------------------------

.ClibQ <- function(field, val) {

    qformat <- "SELECT chid, clib FROM chemical_library"

    if (!is.null(field)) {

        nfld <- switch(
            field,
            chid="chid",
            clib="clib"
        )

        qformat <- paste(qformat, "WHERE %s IN (%s);")
        qstring <- sprintf(
            qformat, nfld,
            paste0("\"", val, "\"", collapse=",")
        )

    } else {
        qstring <- paste0(qformat, ";")
    }
    qstring
}

#-------------------------------------------------------------------------------
# END .ClibQ
#-------------------------------------------------------------------------------