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emeScheme_extract.R
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emeScheme_extract.R
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#' Extract metadasta from one dataFile from an \code{emeScheme} object
#'
#' One \code{emeScheme} object can contain metadata for multiple dataFiles. For
#' archiving, these should be split into single \code{emeScheme} objects, one
#' for each \code{DataFileNameMetaData$dataFileName}. This function extracts the
#' metadasta from one dataFile in an \code{emeScheme} object and returns an
#' \code{emeScheme} object.
#'
#' The filtering is done as followed:
#' \describe{
#' \item{DataFileMetaDFata}{\code{DataFileMetaData$dataFileName == dataFile}}
#' \item{Treatment}{\code{Treatment$parameter \%in\% DataFileMetaData$mappingColumn}
#' and \code{DataFileMetaData$columnData == "Treatment"} }
#' \item{Measurement}{\code{Measurement$name \%in\% DataFileMetaData$mappingColumn}
#' and \code{DataFileMetaData$columnData == "Measurement"} }
#' }
#' @param dataFile name of dataFile whose metadata will be extracted from
#' \code{x}. Has to be an exact match, no wildcards are expanded.
#' @param x \code{emeScheme} object from which to extract the metadata
#'
#' @return An \code{emeScheme} object containing metadata for the data file \code{dataFileName}
#'
#' @importFrom magrittr %>% %<>%
#' @importFrom methods is
#' @export
#'
#' @examples
#' emeScheme_extract("smell.csv", dmdScheme_example())
#' ## returns the emeScheme data for the data file 'smell.csv'
#'
#' emeScheme_extract("DoesNotExist", dmdScheme_example())
#' ## returns an empty emeScheme
emeScheme_extract <- function(
dataFile,
x
) {
# Argument check ----------------------------------------------------------
if (!is(dataFile, "character")) {
stop("dataFile has to be a string")
}
if (length(dataFile) > 1) {
stop("dataFile has to be of length 1")
}
if (!is(x, "emeSchemeSet")) {
stop("x has to be an object of type emeSchemeSet")
}
# Get property name of x --------------------------------------------------
propertyName <- attr(x, "propertyName")
# DataFileMetaData: keep only rows in which dataFileName == dataFile ------
attrs <- attributes(x$DataFileMetaData)
x$DataFileMetaData <- subset(x$DataFileMetaData, x$DataFileMetaData == dataFile)
rownames(x$DataFileMetaData) <- NULL
if (nrow(x$DataFileMetaData) > 0) {
attrs[["row.names"]] <- 1:nrow(x$DataFileMetaData)
} else {
attrs[["row.names"]] <- NULL
}
attributes(x$DataFileMetaData) <- attrs
# Treatment: Only keep treatmentID which are still in DataFileMetaData ------
selTreatmentID <- subset(
x = x$DataFileMetaData$mappingColumn,
subset = (x$DataFileMetaData$columnData == "Treatment") | (x$DataFileMetaData$columnData == "Species")
)
attrs <- attributes(x$Treatment)
x$Treatment <- subset(x$Treatment, x$Treatment$treatmentID %in% selTreatmentID)
rownames(x$Treatment) <- NULL
if (nrow(x$Treatment) > 0) {
attrs[["row.names"]] <- 1:nrow(x$Treatment)
} else {
attrs[["row.names"]] <- NULL
}
attributes(x$Treatment) <- attrs
# Measurement: Only keep measurementID which are still in DataFileMetaData ---------
selMeasurementID <- subset(
x = x$DataFileMetaData$mappingColumn,
subset = (x$DataFileMetaData$columnData == "Measurement")
)
attrs <- attributes(x$Measurement)
x$Measurement <- subset(x$Measurement, x$Measurement$measurementID %in% selMeasurementID)
rownames(x$Measurement) <- NULL
if (nrow(x$Measurement) > 0) {
attrs[["row.names"]] <- 1:nrow(x$Measurement)
} else {
attrs[["row.names"]] <- NULL
}
attributes(x$Measurement) <- attrs
# ExtractionMethod: Only keep extractionMethodID which are still in DataFileMetaData --------
selDataExtractionID <- unique(x$Measurement$dataExtractionID)
attrs <- attributes(x$DataExtraction)
x$DataExtraction <- subset(x$DataExtraction, x$DataExtraction$dataExtractionID %in% selDataExtractionID)
rownames(x$DataExtraction) <- NULL
if (nrow(x$DataExtraction) > 0) {
attrs[["row.names"]] <- 1:nrow(x$DataExtraction)
} else {
attrs[["row.names"]] <- NULL
}
attributes(x$DataExtraction) <- attrs
# Species: Only keep speciesID which are still in treatmentID ----------------------------------
selTreatmentID <- subset(
x = x$DataFileMetaData$mappingColumn,
subset = (x$DataFileMetaData$columnData == "Species")
)
selSpeciesID <- subset( x$Treatment, subset = x$Treatment$treatmentID %in% selTreatmentID, select = "treatmentLevel") %>%
unlist() %>%
strsplit(",") %>%
unlist() %>%
trimws()
attrs <- attributes(x$Species)
x$Species <- subset(x$Species, x$Species$speciesID %in% selSpeciesID)
rownames(x$Species) <- NULL
if (nrow(x$Species) > 0) {
attrs[["row.names"]] <- 1:nrow(x$Species)
} else {
attrs[["row.names"]] <- NULL
}
attributes(x$Species) <- attrs
# Set property name -------------------------------------------------------
attr(x, "propertyName") <- paste(dataFile, propertyName, sep = "_")
# Return ------------------------------------------------------------------
return(x)
}