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#' @name SDMXGenericData
#' @rdname SDMXGenericData
#' @aliases SDMXGenericData,SDMXGenericData-method
#'
#' @usage
#' SDMXGenericData(xmlObj, namespaces)
#'
#' @param xmlObj object of class "XMLInternalDocument derived from XML package
#' @param namespaces object of class "data.frame" given the list of namespace URIs
#' @return an object of class "SDMXGenericData"
#'
#' @seealso \link{readSDMX}
#'
SDMXGenericData <- function(xmlObj, namespaces){
new("SDMXGenericData",
SDMXData(xmlObj, namespaces)
)
}
#methods
as.data.frame.SDMXGenericData <- function(x, row.names=NULL, optional=FALSE,
labels = FALSE, ...){
xmlObj <- x@xmlObj;
dataset <- NULL
schema <- slot(x,"schema")
sdmxVersion <- slot(schema,"version")
VERSION.21 <- sdmxVersion == "2.1"
#namespace
nsDefs.df <- getNamespaces(x)
ns <- findNamespace(nsDefs.df, "generic")
#series
seriesXML <- getNodeSet(xmlObj, "//ns:Series", namespaces = ns)
if(length(seriesXML) == 0){
seriesXML <- getNodeSet(xmlObj, "//Series")
}
seriesNb <- length(seriesXML)
if(seriesNb == 0) return(NULL);
conceptId <- "concept"
if(VERSION.21) conceptId <- "id"
#serie keys
keysXML <- getNodeSet(xmlDoc(getNodeSet(xmlObj,
"//ns:SeriesKey",
namespaces = ns)[[1]]),
"//ns:Value",
namespaces = ns)
keysNames <- unique(sapply(keysXML, function(x) xmlGetAttr(x, conceptId)))
#serie attributes
serieAttrsNames <- NULL
serieAttrsXML <- getNodeSet(xmlObj,
"//ns:Series/ns:Attributes/ns:Value",
namespaces = ns)
if(length(serieAttrsXML) > 0){
serieAttrsNames <- unique(sapply(serieAttrsXML, function(x){
xmlGetAttr(x, conceptId)
}))
}
#serie observation attributes
obsAttrsNames <- NULL
obsAttrsXML <- getNodeSet(xmlObj,
"//ns:Obs/ns:Attributes/ns:Value",
namespaces = ns)
if(length(obsAttrsXML) > 0){
obsAttrsNames <- unique(sapply(obsAttrsXML,function(x){
xmlGetAttr(x, conceptId)
}))
}
#output structure
serieNames <- keysNames
if(!is.null(serieAttrsNames)) serieNames <- c(serieNames, serieAttrsNames)
serieNames <- c(serieNames, "obsTime", "obsValue")
if(!is.null(obsAttrsNames)) serieNames <- c(serieNames, obsAttrsNames)
#obs parser function
parseObs <- function(obs){
obsXML <- xmlDoc(obs)
#time
timeElement <- "Time"
if(VERSION.21) timeElement <- "ObsDimension"
obsTimeXML <- getNodeSet(obsXML,
paste("//ns:",timeElement,sep=""),
namespaces=ns)[[1]]
obsTime <- NA
if(!VERSION.21){
obsTime <- xmlValue(obsTimeXML)
} else {
obsTime <- xmlGetAttr(obsTimeXML,"value")
}
obsTime <- as.data.frame(obsTime)
#value
obsValue <- NA
obsValuesXML <- getNodeSet(obsXML,
"//ns:ObsValue",
namespaces = ns)
if(length(obsValuesXML) > 0){
obsValueXML <- obsValuesXML[[1]]
obsValue <- as.numeric(xmlGetAttr(obsValueXML, "value"))
}
obsValue <- as.data.frame(obsValue)
#attributes
obsAttrs.df <- NULL
if(!is.null(obsAttrsNames)){
obsAttrsXML <- getNodeSet(obsXML,
"//ns:Attributes/ns:Value",
namespaces = ns)
if(length(obsAttrsXML) > 0){
obsAttrsValues <- sapply(obsAttrsXML,
function(x){
as.character(xmlGetAttr(x, "value"))
})
obsAttrsNames <- sapply(obsAttrsXML,
function(x){
as.character(xmlGetAttr(x, conceptId))
})
obsAttrs.df <- structure(obsAttrsValues, .Names = obsAttrsNames)
obsAttrs.df <- as.data.frame(lapply(obsAttrs.df, as.character), stringsAsFactors=FALSE)
if(any(obsAttrs.df == "NA")){
obsAttrs.df[obsAttrs.df == "NA"] <- NA
}
if(!is.na(obsAttrs.df) && ifelse(is.na(any(obsAttrs.df == "NULL")),FALSE,
any(obsAttrs.df == "NULL"))){
obsAttrs.df[obsAttrs.df == "NULL"] <- NA
}
}
}
#output
obsR <- cbind(obsTime, obsValue)
if(!is.null(obsAttrs.df)) obsR <- cbind(obsR, obsAttrs.df)
return(obsR)
}
#function to parse a Serie
parseSerie <- function(x){
# Single serie XMLInternalNode converted into a XMLInternalDocument
serieXML <- xmlDoc(x)
#parseobs
obssXML <- getNodeSet(serieXML, "//ns:Series/ns:Obs", namespaces = ns)
#apply obsParser
obsdf <- NULL
if(length(obssXML) > 0){
obsdf <- do.call("rbind.fill",lapply(obssXML, function(x) parseObs(x)))
}
#Key values
#SeriesKey (concept attributes/values) are duplicated according to the
#number of Time observations
keyValuesXML <- getNodeSet(serieXML,
"//ns:SeriesKey/ns:Value",
namespaces = ns)
keyValues <- sapply(keyValuesXML, function(x){
as.character(xmlGetAttr(x, "value"))
})
keyNames <- sapply(keyValuesXML, function(x){
as.character(xmlGetAttr(x, conceptId))
})
keydf <- structure(keyValues, .Names = keyNames)
keydf <- as.data.frame(lapply(keydf, as.character), stringsAsFactors=FALSE)
if(!is.null(obsdf)){
keydf <- keydf[rep(base::row.names(keydf), nrow(obsdf)),]
if(class(keydf) == "data.frame"){
base::row.names(keydf) <- 1:nrow(obsdf)
colnames(keydf) <- keyNames
}
}
#serie attributes
attrs.df <- NULL
serieAttrsXML <- getNodeSet(serieXML,
"//ns:Series/ns:Attributes/ns:Value",
namespaces = ns)
if(!is.null(serieAttrsXML)){
if(length(serieAttrsXML) > 0){
attrsValues <- sapply(serieAttrsXML, function(x){
as.character(xmlGetAttr(x, "value"))
})
attrsNames <- sapply(serieAttrsXML, function(x){
as.character(xmlGetAttr(x, conceptId))
})
attrs.df <- structure(attrsValues, .Names = attrsNames)
attrs.df <- as.data.frame(lapply(attrs.df, as.character),
stringsAsFactors=FALSE)
if(!is.null(obsdf)){
attrs.df <- attrs.df[rep(base::row.names(attrs.df), nrow(obsdf)),]
if(!is(attrs.df, "data.frame")){
attrs.df <- as.data.frame(attrs.df, stringsAsFactors = FALSE)
colnames(attrs.df) <- attrsNames
}
base::row.names(attrs.df) <- 1:nrow(obsdf)
}
}
}
#single Serie as DataFrame
serie <- keydf
if(!is.null(attrs.df)) serie <- cbind(serie, attrs.df)
if(!is.null(obsdf)) serie <- cbind(serie, obsdf)
#convert factor columns
if("obsTime" %in% colnames(serie)){
serie[,"obsTime"] <- as.character(serie[,"obsTime"])
}
if(!is.null(obsAttrsNames) & !is.null(obsdf)){
for(i in 1:length(colnames(obsdf))){
serie[,colnames(obsdf)[i]] <- as.character(serie[,colnames(obsdf)[i]])
}
}
return(serie)
}
#converting SDMX series to a DataFrame R object
dataset <- do.call("rbind.fill", lapply(seriesXML, function(x){
serie <- parseSerie(x)
}))
dataset <- dataset[,serieNames]
dataset$obsValue <- as.numeric(dataset$obsValue)
if(any(as.character(dataset$obsValue) == "NaN", na.rm = TRUE)){
dataset[as.character(dataset$obsValue) == "NaN",]$obsValue <- NA
}
if(!is.null(dataset)) base::row.names(dataset) <- 1:nrow(dataset)
#enrich with labels
if(labels){
dsd <- slot(x, "dsd")
if(!is.null(dsd)) dataset <- addLabels.SDMXData(dataset, dsd)
}
# output
return(encodeSDMXOutput(dataset))
}
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