R/handleLtFindtags.R

In jbrzusto/motusServer: Operate a server to process data for http://motus.org

#' run the tag finder on all files from a Lotek receiver
#'
#' Called by \code{\link{processServer}}. After running the tag
#' finder, queues a new subjob that exports data.
#'
#' @param j, the job.  It has these properties:
#' \enumerate{
#' \item serno: serial number of receiver; "Lotek-NNN"
#' \item tsStart: earliest timestamp of a detection in a file
#' with new data.  Not used at present, but might
#' allow for pause/resume later.
#' }
#'
#' @return
#'
#' @note if topJob(j) contains fields motusUserID and motusProjectID, these are
#' recorded in the receiver database for the batch generated by this call.
#'
#' @note if topJob(j) contains the field "paramOverrides", then it is treated
#' as a string of parameter overrides for the tag finder.
#'
#' @seealso \link{\code{processServer}}
#'
#' @export
#'
#' @author John Brzustowski \email{jbrzusto@@REMOVE_THIS_PART_fastmail.fm}

handleLtFindtags = function(j) {

    serno = j$serno
    jobLog(j, paste0("Running tag finder on receiver ", serno))

    if (updateTagDeployments())
        jobLog(j, "Some tag deployment metadata were updated from motus.org")

    ## lock this receiver's database
    lockSymbol(serno)

    ## make sure we unlock the receiver DB when this function exits, even on error
    ## NB: the runMotusProcessServer script also drops any locks held by a given
    ## processServer after the latter exits.

    on.exit(lockSymbol(serno, lock=FALSE))

    tj = topJob(j)
    src = getRecvSrc(serno)

    ## get parameter overrides
    por = getParamOverrides(serno, tsStart=Sys.time(), motusProjectID = tj$motusProjectID)

    ## get job-specific parameter overrides
    por2 = tj$paramOverrides
    if (isTRUE(nchar(por2) > 0)) {
        por = paste(por, por2)
    }

    if (por != "")
        jobLog(j, paste0("Got parameter overrides: ", por))

    rv = ltFindTags(src, MOTUS_METADB_CACHE, par=paste(ltDefaultFindTagsParams, por))

    if (! is.null(rv)) {
        ## record motus user and project IDs for this batch, which may
        ## be present in the top job (typically an "uploadFile" job)

        muid = tj$motusUserID
        mpid = tj$motusProjectID
        if (!isTRUE(muid > 0))
            muid = "null"
        if (!isTRUE(mpid > 0))
            mpid = "null"
        dbGetQuery(src$con, sprintf("update batches set motusUserID=%s, motusProjectID=%s, motusJobID=%d where batchID in (%s)", muid, mpid, as.integer(j), paste(rv$batchID, collapse=",")))
    }

    closeRecvSrc(src)
    jobLog(j, paste0("Got ", sum(rv$numHits), " tag detections."))

    return(TRUE)
}