R/getRun.r
In jwist/request: What the Package Does (One Line, Title Case)
#' #' create configuration files
#' #' @param selectedSamples - the selected samples for run
#' #' @param type - the type of run
#' #' @param matrixName - the id of the samples matrix
#' #' @param deviceName - the id of the device to run the experiments
#' #' @param methodName - the id of the method to be run
#' #' @param cohortName - the name of the cohort to run
#' #' @param projectName - the name of the project
#' #' @param runID - the name of the run
#' #' @param options - options
#' #' @return the name of the device
#' #' @export
#' getRun <- function(selectedSamples,
#' type,
#' matrixName,
#' deviceName,
#' methodName,
#' cohortName,
#' projectName,
#' runID,
#' options = list()) {
#' dups <- sum(duplicated(paste0(selectedSamples$plateID, selectedSamples$wellPos)))
#' ifelse(dups != 0, stop("duplicated positions"), 1)
#'
#' types <- c("NMR",
#' "MS-TRY",
#' "MS-TRY-EVOQ",
#' "MS-BILE-EVOQ",
#' "MS-Q300",
#' "MS-BILE",
#' "MS-AA",
#' "MS-EICOS",
#' "MS-URPP",
#' "MS-LIPIDS",
#' "MS-MRMSP",
#' "MS-MRMSN",
#' "TIMS-LIPIDS-P",
#' "TIMS-LIPIDS-N",
#' "CYT")
#' choice <- which(type == types)
#'
#' cat(crayon::blue("request >> getRUN >> running: ", types[choice], "\n"))
#'
#' # qry <- getDevice(c(deviceName = deviceName,
#' # methodName = methodName,
#' # matrixName = matrixName))
#' # deviceName <- qry[[1]]
#' # methodName <- qry[[2]]
#' # matrixName <- qry[[3]]
#'
#'
#' runName <- paste(projectName,
#' cohortName,
#' matrixName,
#' methodName,
#' runID,
#' sep = "_")
#'
#' if (type == "NMR" && matrixName == "SER") {
#' LTR_NAME <- "LTR-PLA"
#' } else {
#' LTR_NAME <- paste0("LTR-", matrixName)
#' }
#'
#'
#' if ("date" %in% names(options)) {
#' date <- options$date
#' } else {
#' date <- format(Sys.time(), "%d%m%y")
#' }
#'
#' switch(choice,
#' runNMR(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_TRY(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_TRYE(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_BILEE(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_Q300(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_BILE(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_AA(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_EICOS(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_URPP(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_LIPIDS(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_MRMSP(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_MRMSN(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runTIMS_LIPIDS_P(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runTIMS_LIPIDS_N(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runCYT(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date))
#' return(runName)
#' }
#'
#' #' write run file for MS-TRY
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_TRY <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 8, "column" = 12, "sampleType" = "Blank"))
#' mixTest <- fillRequest(r, request = c(runParam, "sampleID" = "mix test", "row" = -1, "column" = 12, "sampleType" = "Analyte"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk, mixTest, doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Analyte",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MSWaters"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-TRY
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_TRYE <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 1, "column" = 10, "sampleType" = "Blank"))
#' mixTest <- fillRequest(r, request = c(runParam, "sampleID" = "mix test", "row" = 2, "column" = 10, "sampleType" = "Sample"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Sample"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Sample"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Sample"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Sample"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk, mixTest, doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MS-TRYE"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-BILE Evoq
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_BILEE <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#' blkPos <- getPlatePos(by = "col")
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName)
#' #"platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank", "platePosition" = 2))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#'
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[1 + (plateCounter * 7)])))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[2 + (plateCounter * 7)]),
#' QC4, QC3, QC2, QC1,
#' doubleBlk <- setPosition(doubleBlk, blkPos[3 + (plateCounter * 7)])))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[4 + (plateCounter * 7)]), LTR4))
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[5 + (plateCounter * 7)]), LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[6 + (plateCounter * 7)]),
#' doubleBlk <- setPosition(doubleBlk, blkPos[7 + (plateCounter * 7)])))
#'
#' run <- printRequest(rl, list("assay" = "MS-BILEE"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-TRY
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_Q300 <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 8, "column" = 12, "sampleType" = "Blank"))
#' mixTest <- fillRequest(r, request = c(runParam, "sampleID" = "mix test", "row" = -1, "column" = 12, "sampleType" = "Analyte"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 1, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 2, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 3, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 4, "column" = 12, "sampleType" = "Analyte"))
#' LTR5 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR6 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR7 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#'
#' rl <- addRequest(rl, list(doubleBlk, cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(LTR2, LTR3, LTR4, LTR5, LTR6)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Analyte",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(singleBlk, LTR7))
#' rl <- addRequest(rl, list(doubleBlk, LTR7))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MS-Q300"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#'
#' #' write run file for MS-BILE
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_BILE <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 2))
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, QC4, QC3, QC2, QC1, doubleBlk))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Analyte",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk))
#'
#'
#' run <- printRequest(rl, list("assay" = "MS-BILE"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS AA
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_AA <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 2))
#'
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 12, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 0, "column" = 12, "sampleType" = "Blank"))
#' cal9 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL09", "row" = 1, "column" = 12, "sampleType" = "Calibrant"))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Calibrant"))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Calibrant"))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Calibrant"))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Calibrant"))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Calibrant"))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Calibrant"))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Calibrant"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Calibrant"))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC"))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC"))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC"))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Sample"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Sample"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Sample"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Sample"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk, QC1, doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk))
#' rl <- addRequest(rl, list(QC4, QC3, QC2, QC1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MSBruker"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS MRMSP
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_MRMSP <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin1", "row" = 1, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc2 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin2", "row" = 2, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc3 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin3", "row" = 3, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc4 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin4", "row" = 4, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc5 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin5", "row" = 5, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc6 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin6", "row" = 6, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc7 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin7", "row" = 7, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc8 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin8", "row" = 8, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12))
#'
#' casib1 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin1", "row" = 5, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib2 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin2", "row" = 6, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib3 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin3", "row" = 7, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib4 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin4", "row" = 8, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' ### header
#' rl <- addRequest(rl, list(pqc1,
#' pqc2,
#' pqc3,
#' pqc4,
#' pqc5,
#' LTR <- setPosition(LTR, "A11"),
#' LTR <- setPosition(LTR, "B11"),
#' pqc6,
#' pqc7,
#' pqc8))
#'
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = ((i - 1) %/% 10) + 1, "column" = 12, "platePosition" =1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc,
#' LTR <- setPosition(LTR, "C11"),
#' LTR <- setPosition(LTR, "D11")))
#'
#' run <- printRequest(rl, list("assay" = "MS_MRMSP"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS MRMSN
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_MRMSN <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin1", "row" = 1, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc2 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin2", "row" = 2, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc3 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin3", "row" = 3, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc4 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin4", "row" = 4, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc5 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin5", "row" = 5, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc6 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin6", "row" = 6, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc7 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin7", "row" = 7, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc8 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin8", "row" = 8, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12))
#'
#' casib1 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin1", "row" = 5, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib2 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin2", "row" = 6, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib3 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin3", "row" = 7, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib4 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin4", "row" = 8, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' ### header
#' rl <- addRequest(rl, list(pqc1,
#' pqc2,
#' pqc3,
#' pqc4,
#' pqc5,
#' LTR <- setPosition(LTR, "A11"),
#' LTR <- setPosition(LTR, "B11"),
#' pqc6,
#' pqc7,
#' pqc8))
#'
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = ((i - 1) %/% 10) + 1, "column" = 12, "platePosition" =1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc,
#' LTR <- setPosition(LTR, "C11"),
#' LTR <- setPosition(LTR, "D11")))
#'
#' run <- printRequest(rl, list("assay" = "MS_MRMSN"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for TIMS EICOSANOIDS
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_EICOS <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = runName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 2))
#'
#' rl <- new("requestList")
#'
#' conc <- list("a" = 1)
#' CAL1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 1, "column" = 11, "sampleType" = "Standard"))
#' CAL2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 2, "column" = 11, "sampleType" = "Standard"))
#' CAL3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 3, "column" = 11, "sampleType" = "Standard"))
#' CAL4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 4, "column" = 11, "sampleType" = "Standard"))
#' CAL5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 5, "column" = 11, "sampleType" = "Standard"))
#' CAL6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 6, "column" = 11, "sampleType" = "Standard"))
#' CAL7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 7, "column" = 11, "sampleType" = "Standard"))
#' CAL8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 8, "column" = 11, "sampleType" = "Standard"))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 1, "column" = 12, "sampleType" = "Standard"))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 2, "column" = 12, "sampleType" = "Standard"))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 3, "column" = 12, "sampleType" = "Standard"))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 4, "column" = 12, "sampleType" = "Standard"))
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "DoubleBlank", "row" = 0, "column" = 11, "sampleType" = "Standard"))
#' LTR1 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12))
#' ### header
#' rl <- addRequest(rl, list(doubleBlk,
#' CAL8,
#' CAL7,
#' CAL6,
#' CAL5,
#' CAL4,
#' CAL3,
#' CAL2,
#' CAL1,
#' doubleBlk,
#' LTR1,
#' QC4,
#' QC3,
#' QC2,
#' QC1,
#' doubleBlk,
#' LTR1))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' # footer
#' rl <- addRequest(rl, list(LTR4, LTR4, doubleBlk))
#' run <- printRequest(rl, list("assay" = "MS_EICOS"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for TIMS LIPIDS Positive
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runTIMS_LIPIDS_P <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = 1, "column" = 12, "platePosition" = 1, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 3, "column" = 1, "platePosition" = 0))
#' sblk <- fillRequest(r, request = c(runParam, "sampleID" = "Blank", "row" = 2, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#' blk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 1, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#'
#' ### header
#' rl <- addRequest(rl, list(LTR,
#' LTR,
#' LTR,
#' LTR,
#' pqc1<- setPosition(pqc1, "A11"),
#' pqc1 <- setPosition(pqc1, "B11"),
#' pqc1 <- setPosition(pqc1, "C11")))
#'
#' pqcList <- c(1:8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = pqcList[((i - 1) %/% 10) + 1], "column" = 12, "platePosition" = 1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' if (length(rows) < 80){
#' rl <- addRequest(rl, list(pqc))
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc1 <- setPosition(pqc1, "D11"),
#' pqc1 <- setPosition(pqc1, "E11"),
#' LTR,
#' LTR,
#' sblk, sblk,
#' blk, blk, blk))
#'
#' run <- printRequest(rl, list("assay" = "TIMS_LIPIDS_P"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for TIMS LIPIDS Negative
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runTIMS_LIPIDS_N <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = 1, "column" = 12, "platePosition" = 1, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 3, "column" = 1, "platePosition" = 0))
#' sblk <- fillRequest(r, request = c(runParam, "sampleID" = "Blank", "row" = 2, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#' blk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 1, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#'
#' ### header
#' rl <- addRequest(rl, list(LTR,
#' LTR,
#' LTR,
#' LTR,
#' pqc1<- setPosition(pqc1, "A11"),
#' pqc1 <- setPosition(pqc1, "B11"),
#' pqc1 <- setPosition(pqc1, "C11")))
#'
#' pqcList <- c(1:8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = pqcList[((i - 1) %/% 10) + 1], "column" = 12, "platePosition" = 1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' if (length(rows) < 80){
#' rl <- addRequest(rl, list(pqc))
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc1 <- setPosition(pqc1, "D11"),
#' pqc1 <- setPosition(pqc1, "E11"),
#' LTR,
#' LTR,
#' sblk, sblk,
#' blk, blk, blk))
#'
#' run <- printRequest(rl, list("assay" = "TIMS_LIPIDS_N"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-URPP
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_URPP <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 1
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = plateCounter,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 7, "column" = 12, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 6, "column" = 12, "sampleType" = "Blank"))
#' QC <- fillRequest(r, request = c(runParam, "sampleID" = "QC 1", "row" = 5, "column" = 12, "sampleType" = "QC"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 0, "column" = 0))
#' LTR_cond <- fillRequest(r, request = c(runParam, "sampleID" = "LTR cond", "row" = 8, "column" = 12, "sampleType" = "QC"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR))
#' LTR@column <- 3
#' rl <- addRequest(rl, list(LTR))
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if (i %% 8 == 0) {
#' LTR@column <- i %/% 8
#' rl <- addRequest(rl, list(rlist, LTR))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' if (length(rows) < 80){
#' rl <- addRequest(rl, list(LTR))
#' }
#'
#' run <- printRequest(rl, list("assay" = "MS_URPP"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-LIPIDS
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_LIPIDS <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 5))
#'
#' rl <- new("requestList")
#'
#' conc <- list("a" = 1)
#' COND1 <- fillRequest(r, request = c(runParam, "sampleID" = "COND01", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND2 <- fillRequest(r, request = c(runParam, "sampleID" = "COND02", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND3 <- fillRequest(r, request = c(runParam, "sampleID" = "COND03", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND4 <- fillRequest(r, request = c(runParam, "sampleID" = "COND04", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND5 <- fillRequest(r, request = c(runParam, "sampleID" = "COND05", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND6 <- fillRequest(r, request = c(runParam, "sampleID" = "COND06", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND7 <- fillRequest(r, request = c(runParam, "sampleID" = "COND07", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND8 <- fillRequest(r, request = c(runParam, "sampleID" = "COND08", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 1, "column" = 11, "sampleType" = "Unknown"))
#' posLTR <- c("A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11",
#' "A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12")
#' ### header
#' counter <- 1
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(COND1,
#' COND2,
#' COND3,
#' COND4,
#' COND5,
#' COND6,
#' COND7,
#' COND8,
#' LTR))
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleType" = "Unknown" ,"sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = as.numeric(rows[i]), "column" = as.numeric(columns[i])))
#'
#' if (i %% 8 == 0) {
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' #LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5 + counter %% 4, "column" = 12, "sampleType" = "Unknown"))
#' rl <- addRequest(rl, list(rlist, LTR))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' # footer
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(LTR))
#'
#' run <- printRequest(rl, list("assay" = "MSSciex"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-CYT
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runCYT <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 5))
#'
#' rl <- new("requestList")
#'
#' conc <- list("a" = 1)
#' COND1 <- fillRequest(r, request = c(runParam, "sampleID" = "COND01", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND2 <- fillRequest(r, request = c(runParam, "sampleID" = "COND02", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND3 <- fillRequest(r, request = c(runParam, "sampleID" = "COND03", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND4 <- fillRequest(r, request = c(runParam, "sampleID" = "COND04", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND5 <- fillRequest(r, request = c(runParam, "sampleID" = "COND05", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND6 <- fillRequest(r, request = c(runParam, "sampleID" = "COND06", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND7 <- fillRequest(r, request = c(runParam, "sampleID" = "COND07", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND8 <- fillRequest(r, request = c(runParam, "sampleID" = "COND08", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 1, "column" = 11, "sampleType" = "Unknown"))
#' posLTR <- c("A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11",
#' "A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12")
#' ### header
#' counter <- 1
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(COND1,
#' COND2,
#' COND3,
#' COND4,
#' COND5,
#' COND6,
#' COND7,
#' COND8,
#' LTR))
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleType" = "Unknown" ,"sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = as.numeric(rows[i]), "column" = as.numeric(columns[i])))
#'
#' if (i %% 8 == 0) {
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' #LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5 + counter %% 4, "column" = 12, "sampleType" = "Unknown"))
#' rl <- addRequest(rl, list(rlist, LTR))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' # footer
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(LTR))
#'
#' run <- printRequest(rl, list("assay" = "MSSciex"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for NMR
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param date - the date of the run
#' #' @return a list
#' runNMR <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' LTR <- 4
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' plateCounter <- 1
#' for (plate in plateList) {
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' plateLength <- length(positions)
#'
#' if (plateLength < 51) {
#' LTR_positionList <- seq(1,4, by = 1)[1:LTR]
#' } else {
#' LTR_positionList <- seq(2 ,8, by = 2)[1:LTR]
#' # LTR_positionList <- seq(1 ,8, by = 1)[1:LTR] # LTR = 8
#' }
#'
#' if ("title" %in% colnames(selectedSamples)) {
#' title <- selectedSamples$title[plateNames == plate]
#' } else {
#' title <- rep("", plateLength)
#' }
#'
#' plate1S <- data.frame("_sampleID" = paste0(sampleID, "_", tubeLabel),
#' "_matrixName" = rep(matrixName, plateLength),
#' "_runName" = rep(currentRunName, plateLength),
#' "_sampleType" = rep("S", plateLength),
#' "_methodName" = rep(methodName, plateLength),
#' "_deviceName" = rep(deviceName, plateLength),
#' "_projectName" = rep(projectName, plateLength),
#' "_platePosition" = rep(1, plateLength),
#' "row" = rows,
#' "column" = columns,
#' "_title" = title, check.names = FALSE)
#'
#' plate1LTR <- data.frame("_sampleID" = rep(LTR_NAME, LTR),
#' "_matrixName" = rep(matrixName, LTR),
#' "_runName" = rep(currentRunName, LTR),
#' "_sampleType" = rep("LTR", LTR),
#' "_methodName" = rep(methodName, LTR),
#' "_deviceName" = rep(deviceName, LTR),
#' "_projectName" = rep(projectName, LTR),
#' "_platePosition" = rep(1, LTR),
#' "row" = LTR_positionList,
#' "column" = rep(c(12), LTR),
#' "_title" = rep("", LTR), check.names = FALSE)
#'
#' plate1 <- rbind(plate1S, plate1LTR)
#' # ordering plate by row
#' F <- sort(plate1$col, index.return = TRUE)$ix
#' plate1 <- plate1[F,]
#' F <- sort(plate1$row, index.return = TRUE)$ix
#' plate1 <- plate1[F,]
#' plate1 <- makeBruker(plate1, methodName, deviceName, plateCounter)
#' saveRun(plate1, currentRunName, methodName)
#' req <- c(req, list(requestList = NA, run = plate1))
#' plateCounter <- plateCounter + 1
#' }
#' return(req)
#' }
#'
#' makeBruker <- function(conf, methodName, deviceName, plateCounter) {
#' method <- dbGetQuery(con, paste0("select * from methods
#' where method_name = '", methodName, "'"))
#' method_request <- fromJSON(method$method_request)
#' device <- dbGetQuery(con, paste0("select * from devices
#' where dev_name = '", deviceName, "'"))
#' res <- list()
#' counter = 1
#' for (i in 1:nrow(conf)) {
#' for (j in 1:length(method_request$experiments)) {
#' holder <- RCToNum(conf$row[i], conf$column[i]) + (100 * plateCounter)
#' res[[counter]] <- data.frame(HOLDER = holder,
#' USER = method_request$user,
#' NAME = conf$`_runName`[i],
#' TITLE = paste(conf$`_projectName`[i],
#' method$method_name,
#' conf$`_matrixName`[i],
#' conf$`_sampleID`[i],
#' paste0("R", conf$row[i],
#' "C", conf$column[i],
#' "\\n"),
#' sep = "_"),
#' EXPNO = paste0(i, j - 1),
#' SOLVENT = method_request$solvent,
#' EXPERIMENT = method_request$experiments[j],
#' PARAMETERS = paste0("usera2,",
#' conf$`_sampleID`[i]),
#' DISK = device$dev_path
#' )
#' counter = counter + 1
#' }
#' }
#' p <- data.frame(do.call("rbind", res))
#' return(p)
#' }
#'
#' #' write run file
#' #' @param run - the selected samples for run
#' #' @param runName - the run name
#' #' @return write the file
#' #' @importFrom utils write.table
#' #' @importFrom DBI dbGetQuery dbDisconnect
#' #' @importFrom rolodex.samples openDb
#' saveRun <- function(run, runName, methodName){
#' con <- openDb()
#' method <- dbGetQuery(con, paste0("select * from methods
#' where method_name = '", methodName, "'"))
#' dbDisconnect(con)
#' fileFormat <- fromJSON(method$method_options)$fileFormat
#' fileExtension <- fromJSON(method$method_options)$fileExtension
#' if (fileFormat == "tsv") {
#' sep = "\t"
#' } else if (fileFormat == "csv") {
#' sep = ","
#' } else {
#' stop("request >> getRun: unknown file extension")
#' }
#'
#' file <- paste0("configurationFiles/",
#' runName, ".",
#' fileExtension)
#' write.table(run,
#' file = file,
#' sep = sep,
#' dec = ".",
#' row.names = FALSE,
#' quote = TRUE)
#' # if (grepl("_NMR-", runName)) {
#' # txt <- system(
#' # paste0(
#' # "~/git/cheminfo-js/getRunOrder/build/toNMR-macos -r configurationFiles/",
#' # runName,
#' # ".tsv"),
#' # intern = TRUE
#' # )
#' # fileConn <- file(paste0("configurationFiles/", runName, ".csv"))
#' # writeLines(txt, fileConn)
#' # close(fileConn)
#' # }
#' cat(crayon::green("request >> getRUN >> ", file, " written\n"))
#' }
jwist/request documentation built on Aug. 10, 2022, 4:11 p.m.
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#' #' create configuration files
#' #' @param selectedSamples - the selected samples for run
#' #' @param type - the type of run
#' #' @param matrixName - the id of the samples matrix
#' #' @param deviceName - the id of the device to run the experiments
#' #' @param methodName - the id of the method to be run
#' #' @param cohortName - the name of the cohort to run
#' #' @param projectName - the name of the project
#' #' @param runID - the name of the run
#' #' @param options - options
#' #' @return the name of the device
#' #' @export
#' getRun <- function(selectedSamples,
#' type,
#' matrixName,
#' deviceName,
#' methodName,
#' cohortName,
#' projectName,
#' runID,
#' options = list()) {
#' dups <- sum(duplicated(paste0(selectedSamples$plateID, selectedSamples$wellPos)))
#' ifelse(dups != 0, stop("duplicated positions"), 1)
#'
#' types <- c("NMR",
#' "MS-TRY",
#' "MS-TRY-EVOQ",
#' "MS-BILE-EVOQ",
#' "MS-Q300",
#' "MS-BILE",
#' "MS-AA",
#' "MS-EICOS",
#' "MS-URPP",
#' "MS-LIPIDS",
#' "MS-MRMSP",
#' "MS-MRMSN",
#' "TIMS-LIPIDS-P",
#' "TIMS-LIPIDS-N",
#' "CYT")
#' choice <- which(type == types)
#'
#' cat(crayon::blue("request >> getRUN >> running: ", types[choice], "\n"))
#'
#' # qry <- getDevice(c(deviceName = deviceName,
#' # methodName = methodName,
#' # matrixName = matrixName))
#' # deviceName <- qry[[1]]
#' # methodName <- qry[[2]]
#' # matrixName <- qry[[3]]
#'
#'
#' runName <- paste(projectName,
#' cohortName,
#' matrixName,
#' methodName,
#' runID,
#' sep = "_")
#'
#' if (type == "NMR" && matrixName == "SER") {
#' LTR_NAME <- "LTR-PLA"
#' } else {
#' LTR_NAME <- paste0("LTR-", matrixName)
#' }
#'
#'
#' if ("date" %in% names(options)) {
#' date <- options$date
#' } else {
#' date <- format(Sys.time(), "%d%m%y")
#' }
#'
#' switch(choice,
#' runNMR(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_TRY(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_TRYE(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_BILEE(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_Q300(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_BILE(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_AA(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_EICOS(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_URPP(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_LIPIDS(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_MRMSP(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runMS_MRMSN(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runTIMS_LIPIDS_P(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runTIMS_LIPIDS_N(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date),
#' runCYT(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date))
#' return(runName)
#' }
#'
#' #' write run file for MS-TRY
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_TRY <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 8, "column" = 12, "sampleType" = "Blank"))
#' mixTest <- fillRequest(r, request = c(runParam, "sampleID" = "mix test", "row" = -1, "column" = 12, "sampleType" = "Analyte"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk, mixTest, doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Analyte",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MSWaters"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-TRY
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_TRYE <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 1, "column" = 10, "sampleType" = "Blank"))
#' mixTest <- fillRequest(r, request = c(runParam, "sampleID" = "mix test", "row" = 2, "column" = 10, "sampleType" = "Sample"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Calibration sample", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "Qualitycontrol sample", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Sample"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Sample"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Sample"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Sample"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk, mixTest, doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MS-TRYE"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-BILE Evoq
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_BILEE <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#' blkPos <- getPlatePos(by = "col")
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName)
#' #"platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank", "platePosition" = 2))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#'
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[1 + (plateCounter * 7)])))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[2 + (plateCounter * 7)]),
#' QC4, QC3, QC2, QC1,
#' doubleBlk <- setPosition(doubleBlk, blkPos[3 + (plateCounter * 7)])))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[4 + (plateCounter * 7)]), LTR4))
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[5 + (plateCounter * 7)]), LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk <- setPosition(doubleBlk, blkPos[6 + (plateCounter * 7)]),
#' doubleBlk <- setPosition(doubleBlk, blkPos[7 + (plateCounter * 7)])))
#'
#' run <- printRequest(rl, list("assay" = "MS-BILEE"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-TRY
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_Q300 <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + plateCounter %% 2)
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 8, "column" = 12, "sampleType" = "Blank"))
#' mixTest <- fillRequest(r, request = c(runParam, "sampleID" = "mix test", "row" = -1, "column" = 12, "sampleType" = "Analyte"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 1, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 2, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 3, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 4, "column" = 12, "sampleType" = "Analyte"))
#' LTR5 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR6 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR7 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#'
#' rl <- addRequest(rl, list(doubleBlk, cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(LTR2, LTR3, LTR4, LTR5, LTR6)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Analyte",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(singleBlk, LTR7))
#' rl <- addRequest(rl, list(doubleBlk, LTR7))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MS-Q300"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#'
#' #' write run file for MS-BILE
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_BILE <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 2))
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 0, "sampleType" = "Blank"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(10, 20, 40, 50, 100, 200, 1000, 5000, 10000)))))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(5, 10, 20, 25, 50, 100, 500, 2500, 5000)))))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(3, 6, 12, 15, 30, 60, 300, 1500, 3000)))))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.8, 1.6, 3.2, 4, 8, 16, 80, 400, 800)))))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.4, 0.8, 1.6, 2, 4, 8, 40, 200, 400)))))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Standard", "options" = list(list("conc" = c(0.2, 0.4, 0.8, 1, 2, 4, 20, 100, 200)))))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(2, 4, 8, 10, 20, 40, 200, 1000, 2000)))))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(8, 16, 32, 40, 80, 160, 800, 4000, 8000)))))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(16, 32, 64, 80, 160, 320, 1600, 8000, 16000)))))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC", "options" = list(list("conc" = c(20, 40, 80, 100, 200, 400, 2000, 10000, 20000)))))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Analyte"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Analyte"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Analyte"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Analyte"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, QC4, QC3, QC2, QC1, doubleBlk))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Analyte",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk))
#'
#'
#' run <- printRequest(rl, list("assay" = "MS-BILE"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS AA
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_AA <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 2))
#'
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 0, "column" = 12, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 0, "column" = 12, "sampleType" = "Blank"))
#' cal9 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL09", "row" = 1, "column" = 12, "sampleType" = "Calibrant"))
#' cal8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 1, "column" = 11, "sampleType" = "Calibrant"))
#' cal7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 2, "column" = 11, "sampleType" = "Calibrant"))
#' cal6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 3, "column" = 11, "sampleType" = "Calibrant"))
#' cal5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 4, "column" = 11, "sampleType" = "Calibrant"))
#' cal4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 5, "column" = 11, "sampleType" = "Calibrant"))
#' cal3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 6, "column" = 11, "sampleType" = "Calibrant"))
#' cal2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 7, "column" = 11, "sampleType" = "Calibrant"))
#' cal1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 8, "column" = 11, "sampleType" = "Calibrant"))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 1, "column" = 12, "sampleType" = "QC"))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 2, "column" = 12, "sampleType" = "QC"))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 3, "column" = 12, "sampleType" = "QC"))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 4, "column" = 12, "sampleType" = "QC"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12, "sampleType" = "Sample"))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12, "sampleType" = "Sample"))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12, "sampleType" = "Sample"))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12, "sampleType" = "Sample"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk, QC1, doubleBlk))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk))
#' rl <- addRequest(rl, list(QC4, QC3, QC2, QC1))
#' rl <- addRequest(rl, list(LTR, doubleBlk, LTR))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' ### footer
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(doubleBlk, LTR4))
#' rl <- addRequest(rl, list(cal8, cal7, cal6, cal5, cal4, cal3, cal2, cal1))
#' rl <- addRequest(rl, list(doubleBlk, doubleBlk))
#'
#' run <- printRequest(rl, list("assay" = "MSBruker"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS MRMSP
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_MRMSP <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin1", "row" = 1, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc2 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin2", "row" = 2, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc3 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin3", "row" = 3, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc4 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin4", "row" = 4, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc5 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin5", "row" = 5, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc6 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin6", "row" = 6, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc7 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin7", "row" = 7, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc8 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin8", "row" = 8, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12))
#'
#' casib1 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin1", "row" = 5, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib2 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin2", "row" = 6, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib3 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin3", "row" = 7, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib4 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin4", "row" = 8, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' ### header
#' rl <- addRequest(rl, list(pqc1,
#' pqc2,
#' pqc3,
#' pqc4,
#' pqc5,
#' LTR <- setPosition(LTR, "A11"),
#' LTR <- setPosition(LTR, "B11"),
#' pqc6,
#' pqc7,
#' pqc8))
#'
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = ((i - 1) %/% 10) + 1, "column" = 12, "platePosition" =1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc,
#' LTR <- setPosition(LTR, "C11"),
#' LTR <- setPosition(LTR, "D11")))
#'
#' run <- printRequest(rl, list("assay" = "MS_MRMSP"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS MRMSN
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_MRMSN <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin1", "row" = 1, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc2 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin2", "row" = 2, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc3 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin3", "row" = 3, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc4 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin4", "row" = 4, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc5 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin5", "row" = 5, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc6 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin6", "row" = 6, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc7 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin7", "row" = 7, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' pqc8 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC_Burnin8", "row" = 8, "column" = 1, "platePosition" =2, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12))
#'
#' casib1 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin1", "row" = 5, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib2 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin2", "row" = 6, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib3 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin3", "row" = 7, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' casib4 <- fillRequest(r, request = c(runParam, "sampleID" = "CASI_Burnin4", "row" = 8, "column" = 4, "platePosition" =2, "sampleType" = "standard"))
#' ### header
#' rl <- addRequest(rl, list(pqc1,
#' pqc2,
#' pqc3,
#' pqc4,
#' pqc5,
#' LTR <- setPosition(LTR, "A11"),
#' LTR <- setPosition(LTR, "B11"),
#' pqc6,
#' pqc7,
#' pqc8))
#'
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = ((i - 1) %/% 10) + 1, "column" = 12, "platePosition" =1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc,
#' LTR <- setPosition(LTR, "C11"),
#' LTR <- setPosition(LTR, "D11")))
#'
#' run <- printRequest(rl, list("assay" = "MS_MRMSN"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for TIMS EICOSANOIDS
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_EICOS <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = runName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 2))
#'
#' rl <- new("requestList")
#'
#' conc <- list("a" = 1)
#' CAL1 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL01", "row" = 1, "column" = 11, "sampleType" = "Standard"))
#' CAL2 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL02", "row" = 2, "column" = 11, "sampleType" = "Standard"))
#' CAL3 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL03", "row" = 3, "column" = 11, "sampleType" = "Standard"))
#' CAL4 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL04", "row" = 4, "column" = 11, "sampleType" = "Standard"))
#' CAL5 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL05", "row" = 5, "column" = 11, "sampleType" = "Standard"))
#' CAL6 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL06", "row" = 6, "column" = 11, "sampleType" = "Standard"))
#' CAL7 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL07", "row" = 7, "column" = 11, "sampleType" = "Standard"))
#' CAL8 <- fillRequest(r, request = c(runParam, "sampleID" = "CAL08", "row" = 8, "column" = 11, "sampleType" = "Standard"))
#' QC1 <- fillRequest(r, request = c(runParam, "sampleID" = "QC01", "row" = 1, "column" = 12, "sampleType" = "Standard"))
#' QC2 <- fillRequest(r, request = c(runParam, "sampleID" = "QC02", "row" = 2, "column" = 12, "sampleType" = "Standard"))
#' QC3 <- fillRequest(r, request = c(runParam, "sampleID" = "QC03", "row" = 3, "column" = 12, "sampleType" = "Standard"))
#' QC4 <- fillRequest(r, request = c(runParam, "sampleID" = "QC04", "row" = 4, "column" = 12, "sampleType" = "Standard"))
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "DoubleBlank", "row" = 0, "column" = 11, "sampleType" = "Standard"))
#' LTR1 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5, "column" = 12))
#' LTR2 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 6, "column" = 12))
#' LTR3 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 7, "column" = 12))
#' LTR4 <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 8, "column" = 12))
#' ### header
#' rl <- addRequest(rl, list(doubleBlk,
#' CAL8,
#' CAL7,
#' CAL6,
#' CAL5,
#' CAL4,
#' CAL3,
#' CAL2,
#' CAL1,
#' doubleBlk,
#' LTR1,
#' QC4,
#' QC3,
#' QC2,
#' QC1,
#' doubleBlk,
#' LTR1))
#'
#' qcList <- list(QC4, LTR2, QC1, LTR2, QC3, LTR3, LTR3, QC2)
#' chunkSize <- floor(length(rows)/8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam,
#' "sampleType" = "Sample",
#' "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]),
#' "row" = as.numeric(rows[i]),
#' "column" = as.numeric(columns[i])))
#' if (i %% chunkSize == 0) {
#' rl <- addRequest(rl,
#' list(rlist,
#' qcList[[(((i - 1)/(chunkSize)) %% length(qcList)) + 1]]))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' # footer
#' rl <- addRequest(rl, list(LTR4, LTR4, doubleBlk))
#' run <- printRequest(rl, list("assay" = "MS_EICOS"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for TIMS LIPIDS Positive
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runTIMS_LIPIDS_P <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = 1, "column" = 12, "platePosition" = 1, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 3, "column" = 1, "platePosition" = 0))
#' sblk <- fillRequest(r, request = c(runParam, "sampleID" = "Blank", "row" = 2, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#' blk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 1, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#'
#' ### header
#' rl <- addRequest(rl, list(LTR,
#' LTR,
#' LTR,
#' LTR,
#' pqc1<- setPosition(pqc1, "A11"),
#' pqc1 <- setPosition(pqc1, "B11"),
#' pqc1 <- setPosition(pqc1, "C11")))
#'
#' pqcList <- c(1:8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = pqcList[((i - 1) %/% 10) + 1], "column" = 12, "platePosition" = 1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' if (length(rows) < 80){
#' rl <- addRequest(rl, list(pqc))
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc1 <- setPosition(pqc1, "D11"),
#' pqc1 <- setPosition(pqc1, "E11"),
#' LTR,
#' LTR,
#' sblk, sblk,
#' blk, blk, blk))
#'
#' run <- printRequest(rl, list("assay" = "TIMS_LIPIDS_P"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for TIMS LIPIDS Negative
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runTIMS_LIPIDS_N <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' pqc1 <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = 1, "column" = 12, "platePosition" = 1, "sampleType" = "standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 3, "column" = 1, "platePosition" = 0))
#' sblk <- fillRequest(r, request = c(runParam, "sampleID" = "Blank", "row" = 2, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#' blk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 1, "column" = 1, "platePosition" = 0, "sampleType" = "standard"))
#'
#' ### header
#' rl <- addRequest(rl, list(LTR,
#' LTR,
#' LTR,
#' LTR,
#' pqc1<- setPosition(pqc1, "A11"),
#' pqc1 <- setPosition(pqc1, "B11"),
#' pqc1 <- setPosition(pqc1, "C11")))
#'
#' pqcList <- c(1:8)
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if ((i - 1) %% 10 == 0) {
#' pqc <- fillRequest(r, request = c(runParam, "sampleID" = "PQC", "row" = pqcList[((i - 1) %/% 10) + 1], "column" = 12, "platePosition" = 1, "sampleType" = "pqc"))
#' rl <- addRequest(rl, list(pqc, rlist))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' if (length(rows) < 80){
#' rl <- addRequest(rl, list(pqc))
#' }
#' ### footer
#' rl <- addRequest(rl, list(pqc1 <- setPosition(pqc1, "D11"),
#' pqc1 <- setPosition(pqc1, "E11"),
#' LTR,
#' LTR,
#' sblk, sblk,
#' blk, blk, blk))
#'
#' run <- printRequest(rl, list("assay" = "TIMS_LIPIDS_N"))
#' saveRun(run, currentRunName, methodName)
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-URPP
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_URPP <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 1
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "projectName" = projectName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = plateCounter,
#' "sampleType" = "Sample")
#'
#' rl <- new("requestList")
#'
#' doubleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Double Blank", "row" = 7, "column" = 12, "sampleType" = "Blank"))
#' singleBlk <- fillRequest(r, request = c(runParam, "sampleID" = "Single Blank", "row" = 6, "column" = 12, "sampleType" = "Blank"))
#' QC <- fillRequest(r, request = c(runParam, "sampleID" = "QC 1", "row" = 5, "column" = 12, "sampleType" = "QC"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 0, "column" = 0))
#' LTR_cond <- fillRequest(r, request = c(runParam, "sampleID" = "LTR cond", "row" = 8, "column" = 12, "sampleType" = "QC"))
#'
#' ### header
#' rl <- addRequest(rl, list(doubleBlk,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR_cond,
#' LTR))
#' LTR@column <- 3
#' rl <- addRequest(rl, list(LTR))
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = rows[i], "column" = columns[i]))
#'
#' if (i %% 8 == 0) {
#' LTR@column <- i %/% 8
#' rl <- addRequest(rl, list(rlist, LTR))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#' if (length(rows) < 80){
#' rl <- addRequest(rl, list(LTR))
#' }
#'
#' run <- printRequest(rl, list("assay" = "MS_URPP"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-LIPIDS
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runMS_LIPIDS <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 5))
#'
#' rl <- new("requestList")
#'
#' conc <- list("a" = 1)
#' COND1 <- fillRequest(r, request = c(runParam, "sampleID" = "COND01", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND2 <- fillRequest(r, request = c(runParam, "sampleID" = "COND02", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND3 <- fillRequest(r, request = c(runParam, "sampleID" = "COND03", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND4 <- fillRequest(r, request = c(runParam, "sampleID" = "COND04", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND5 <- fillRequest(r, request = c(runParam, "sampleID" = "COND05", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND6 <- fillRequest(r, request = c(runParam, "sampleID" = "COND06", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND7 <- fillRequest(r, request = c(runParam, "sampleID" = "COND07", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND8 <- fillRequest(r, request = c(runParam, "sampleID" = "COND08", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 1, "column" = 11, "sampleType" = "Unknown"))
#' posLTR <- c("A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11",
#' "A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12")
#' ### header
#' counter <- 1
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(COND1,
#' COND2,
#' COND3,
#' COND4,
#' COND5,
#' COND6,
#' COND7,
#' COND8,
#' LTR))
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleType" = "Unknown" ,"sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = as.numeric(rows[i]), "column" = as.numeric(columns[i])))
#'
#' if (i %% 8 == 0) {
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' #LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5 + counter %% 4, "column" = 12, "sampleType" = "Unknown"))
#' rl <- addRequest(rl, list(rlist, LTR))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' # footer
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(LTR))
#'
#' run <- printRequest(rl, list("assay" = "MSSciex"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for MS-CYT
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param LTR_NAME - the name of LTR sample
#' #' @param date - the date of the run
#' #' @return void
#' runCYT <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#'
#' plateCounter <- 0
#' req <- list()
#' for (plate in plateList) {
#'
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' r <- new("request")
#' runParam <- list("runName" = currentRunName,
#' "methodName" = methodName,
#' "deviceName" = deviceName,
#' "matrixName" = matrixName,
#' "platePosition" = 1 + (plateCounter %% 5))
#'
#' rl <- new("requestList")
#'
#' conc <- list("a" = 1)
#' COND1 <- fillRequest(r, request = c(runParam, "sampleID" = "COND01", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND2 <- fillRequest(r, request = c(runParam, "sampleID" = "COND02", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND3 <- fillRequest(r, request = c(runParam, "sampleID" = "COND03", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND4 <- fillRequest(r, request = c(runParam, "sampleID" = "COND04", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND5 <- fillRequest(r, request = c(runParam, "sampleID" = "COND05", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND6 <- fillRequest(r, request = c(runParam, "sampleID" = "COND06", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND7 <- fillRequest(r, request = c(runParam, "sampleID" = "COND07", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' COND8 <- fillRequest(r, request = c(runParam, "sampleID" = "COND08", "row" = -1, "column" = 11, "sampleType" = "Standard"))
#' LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 1, "column" = 11, "sampleType" = "Unknown"))
#' posLTR <- c("A11", "B11", "C11", "D11", "E11", "F11", "G11", "H11",
#' "A12", "B12", "C12", "D12", "E12", "F12", "G12", "H12")
#' ### header
#' counter <- 1
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(COND1,
#' COND2,
#' COND3,
#' COND4,
#' COND5,
#' COND6,
#' COND7,
#' COND8,
#' LTR))
#'
#' for (i in 1:length(rows)) {
#' rlist <- fillRequest(r, request = c(runParam, "sampleType" = "Unknown" ,"sampleID" = paste0(sampleID[i], "_", tubeLabel[i]), "row" = as.numeric(rows[i]), "column" = as.numeric(columns[i])))
#'
#' if (i %% 8 == 0) {
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' #LTR <- fillRequest(r, request = c(runParam, "sampleID" = LTR_NAME, "row" = 5 + counter %% 4, "column" = 12, "sampleType" = "Unknown"))
#' rl <- addRequest(rl, list(rlist, LTR))
#' } else {
#' rl <- addRequest(rl, list(rlist))
#' }
#' }
#'
#' # footer
#' LTR <- setPosition(LTR, posLTR[counter])
#' counter <- counter + 1
#' rl <- addRequest(rl, list(LTR))
#'
#' run <- printRequest(rl, list("assay" = "MSSciex"))
#' saveRun(run, currentRunName, methodName)
#' plateCounter <- plateCounter + 1
#' req <- c(req, list(requestList = rl, run = run))
#' }
#' return(req)
#' }
#'
#' #' write run file for NMR
#' #' @param selectedSamples - the selected samples for run
#' #' @param runName - the name of the run
#' #' @param projectName - the name of the project
#' #' @param matrixName - the id of the sample matrix
#' #' @param deviceName - the id of the device
#' #' @param methodName - the id of the method
#' #' @param date - the date of the run
#' #' @return a list
#' runNMR <- function(selectedSamples, runName, projectName, matrixName, deviceName, methodName, LTR_NAME, date) {
#' LTR <- 4
#'
#' plateList <- levels(factor(selectedSamples$plateID))
#' req <- list()
#' plateCounter <- 1
#' for (plate in plateList) {
#' currentRunName <- paste(runName,
#' plate,
#' sep = "_")
#'
#' plateNames <- selectedSamples$plateID
#'
#' sampleID <- selectedSamples$sampleID[plateNames == plate]
#' tubeLabel <- selectedSamples$tubeLabel[plateNames == plate]
#' positions <- selectedSamples$wellPos[plateNames == plate]
#' RC <- posToRC(positions)
#' columns <- RC$col
#' rows <- RC$row
#'
#' plateLength <- length(positions)
#'
#' if (plateLength < 51) {
#' LTR_positionList <- seq(1,4, by = 1)[1:LTR]
#' } else {
#' LTR_positionList <- seq(2 ,8, by = 2)[1:LTR]
#' # LTR_positionList <- seq(1 ,8, by = 1)[1:LTR] # LTR = 8
#' }
#'
#' if ("title" %in% colnames(selectedSamples)) {
#' title <- selectedSamples$title[plateNames == plate]
#' } else {
#' title <- rep("", plateLength)
#' }
#'
#' plate1S <- data.frame("_sampleID" = paste0(sampleID, "_", tubeLabel),
#' "_matrixName" = rep(matrixName, plateLength),
#' "_runName" = rep(currentRunName, plateLength),
#' "_sampleType" = rep("S", plateLength),
#' "_methodName" = rep(methodName, plateLength),
#' "_deviceName" = rep(deviceName, plateLength),
#' "_projectName" = rep(projectName, plateLength),
#' "_platePosition" = rep(1, plateLength),
#' "row" = rows,
#' "column" = columns,
#' "_title" = title, check.names = FALSE)
#'
#' plate1LTR <- data.frame("_sampleID" = rep(LTR_NAME, LTR),
#' "_matrixName" = rep(matrixName, LTR),
#' "_runName" = rep(currentRunName, LTR),
#' "_sampleType" = rep("LTR", LTR),
#' "_methodName" = rep(methodName, LTR),
#' "_deviceName" = rep(deviceName, LTR),
#' "_projectName" = rep(projectName, LTR),
#' "_platePosition" = rep(1, LTR),
#' "row" = LTR_positionList,
#' "column" = rep(c(12), LTR),
#' "_title" = rep("", LTR), check.names = FALSE)
#'
#' plate1 <- rbind(plate1S, plate1LTR)
#' # ordering plate by row
#' F <- sort(plate1$col, index.return = TRUE)$ix
#' plate1 <- plate1[F,]
#' F <- sort(plate1$row, index.return = TRUE)$ix
#' plate1 <- plate1[F,]
#' plate1 <- makeBruker(plate1, methodName, deviceName, plateCounter)
#' saveRun(plate1, currentRunName, methodName)
#' req <- c(req, list(requestList = NA, run = plate1))
#' plateCounter <- plateCounter + 1
#' }
#' return(req)
#' }
#'
#' makeBruker <- function(conf, methodName, deviceName, plateCounter) {
#' method <- dbGetQuery(con, paste0("select * from methods
#' where method_name = '", methodName, "'"))
#' method_request <- fromJSON(method$method_request)
#' device <- dbGetQuery(con, paste0("select * from devices
#' where dev_name = '", deviceName, "'"))
#' res <- list()
#' counter = 1
#' for (i in 1:nrow(conf)) {
#' for (j in 1:length(method_request$experiments)) {
#' holder <- RCToNum(conf$row[i], conf$column[i]) + (100 * plateCounter)
#' res[[counter]] <- data.frame(HOLDER = holder,
#' USER = method_request$user,
#' NAME = conf$`_runName`[i],
#' TITLE = paste(conf$`_projectName`[i],
#' method$method_name,
#' conf$`_matrixName`[i],
#' conf$`_sampleID`[i],
#' paste0("R", conf$row[i],
#' "C", conf$column[i],
#' "\\n"),
#' sep = "_"),
#' EXPNO = paste0(i, j - 1),
#' SOLVENT = method_request$solvent,
#' EXPERIMENT = method_request$experiments[j],
#' PARAMETERS = paste0("usera2,",
#' conf$`_sampleID`[i]),
#' DISK = device$dev_path
#' )
#' counter = counter + 1
#' }
#' }
#' p <- data.frame(do.call("rbind", res))
#' return(p)
#' }
#'
#' #' write run file
#' #' @param run - the selected samples for run
#' #' @param runName - the run name
#' #' @return write the file
#' #' @importFrom utils write.table
#' #' @importFrom DBI dbGetQuery dbDisconnect
#' #' @importFrom rolodex.samples openDb
#' saveRun <- function(run, runName, methodName){
#' con <- openDb()
#' method <- dbGetQuery(con, paste0("select * from methods
#' where method_name = '", methodName, "'"))
#' dbDisconnect(con)
#' fileFormat <- fromJSON(method$method_options)$fileFormat
#' fileExtension <- fromJSON(method$method_options)$fileExtension
#' if (fileFormat == "tsv") {
#' sep = "\t"
#' } else if (fileFormat == "csv") {
#' sep = ","
#' } else {
#' stop("request >> getRun: unknown file extension")
#' }
#'
#' file <- paste0("configurationFiles/",
#' runName, ".",
#' fileExtension)
#' write.table(run,
#' file = file,
#' sep = sep,
#' dec = ".",
#' row.names = FALSE,
#' quote = TRUE)
#' # if (grepl("_NMR-", runName)) {
#' # txt <- system(
#' # paste0(
#' # "~/git/cheminfo-js/getRunOrder/build/toNMR-macos -r configurationFiles/",
#' # runName,
#' # ".tsv"),
#' # intern = TRUE
#' # )
#' # fileConn <- file(paste0("configurationFiles/", runName, ".csv"))
#' # writeLines(txt, fileConn)
#' # close(fileConn)
#' # }
#' cat(crayon::green("request >> getRUN >> ", file, " written\n"))
#' }
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