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#' Basic Water Quality Portal Data grabber
#'
#' Imports data from the Water Quality Portal based on a specified url.
#'
#' @param url string URL to Water Quality Portal#' @keywords data import USGS web service
#' @return retval dataframe raw data returned from the Water Quality Portal. Additionally, a POSIXct dateTime column is supplied for
#' start and end times.
#' @export
#' @import RCurl
#' @importFrom lubridate parse_date_time
#' @examples
#' # These examples require an internet connection to run
#'
#' ## Examples take longer than 5 seconds:
#' rawSampleURL <- constructWQPURL('USGS-01594440','01075', '1985-01-01', '1985-03-31')
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h <- basicHeaderGatherer()
retval = tryCatch({
doc <- getURL(url, headerfunction = h$update)
}, warning = function(w) {
message(paste("URL caused a warning:", url))
message(w)
}, error = function(e) {
message(paste("URL does not seem to exist:", url))
message(e)
return(NA)
})
if(h$value()["Content-Type"] == "text/tab-separated-values;charset=UTF-8"){
numToBeReturned <- as.numeric(h$value()["Total-Result-Count"])
if (!is.na(numToBeReturned) | numToBeReturned != 0){
namesData <- read.delim(textConnection(doc), header = TRUE, quote="\"",
dec=".", sep='\t',
colClasses='character',
fill = TRUE,nrow=1)
classColumns <- setNames(rep('character',ncol(namesData)),names(namesData))
classColumns[grep("MeasureValue",names(classColumns))] <- NA
retval <- read.delim(textConnection(doc), header = TRUE, quote="\"",
dec=".", sep='\t',
colClasses=as.character(classColumns),
fill = TRUE)
actualNumReturned <- nrow(retval)
retval[,names(which(sapply(retval[,grep("MeasureValue",names(retval))], function(x)all(is.na(x)))))] <- ""
if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
"America/Denver","America/Denver","America/Los_Angeles","America/Los_Angeles",
"America/Anchorage","America/Anchorage","America/Honolulu","America/Honolulu"),
c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
timeZoneStart <- as.character(timeZoneLibrary[retval$ActivityStartTime.TimeZoneCode])
timeZoneEnd <- as.character(timeZoneLibrary[retval$ActivityEndTime.TimeZoneCode])
timeZoneStart[is.na(timeZoneStart)] <- ""
timeZoneEnd[is.na(timeZoneEnd)] <- ""
if("ActivityStartDate" %in% names(retval)){
if(any(retval$ActivityStartDate != "")){
suppressWarnings(retval$ActivityStartDate <- as.Date(parse_date_time(retval$ActivityStartDate, c("Ymd", "mdY"))))
}
}
if("ActivityEndDate" %in% names(retval)){
if(any(retval$ActivityEndDate != "")){
suppressWarnings(retval$ActivityEndDate <- as.Date(parse_date_time(retval$ActivityEndDate, c("Ymd", "mdY"))))
}
}
if(any(!is.na(timeZoneStart))){
if(length(unique(timeZoneStart)) == 1){
retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),format="%Y-%m-%d %H:%M:%S", tz=unique(timeZoneStart)))
} else {
mostCommonTZ <- names(sort(summary(as.factor(timeZoneStart)),decreasing = TRUE)[1])
retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),
format="%Y-%m-%d %H:%M:%S",
tz=mostCommonTZ))
additionalTZs <- names(sort(summary(as.factor(timeZoneStart)),decreasing = TRUE)[-1])
for(i in additionalTZs){
retval$ActivityStartDateTime[timeZoneStart == i] <- with(retval[timeZoneStart == i,],
as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),
format="%Y-%m-%d %H:%M:%S",
tz=i))
}
}
}
if(any(!is.na(timeZoneEnd))){
if(length(unique(timeZoneEnd)) == 1){
retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time), format="%Y-%m-%d %H:%M:%S",tz=unique(timeZoneEnd)))
} else {
mostCommonTZ <- names(sort(summary(as.factor(timeZoneEnd)),decreasing = TRUE)[1])
retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time),
format="%Y-%m-%d %H:%M:%S",
tz=mostCommonTZ))
additionalTZs <- names(sort(summary(as.factor(timeZoneEnd)),decreasing = TRUE)[-1])
for(i in additionalTZs){
retval$ActivityEndDateTime[timeZoneEnd == i] <- with(retval[timeZoneEnd == i,],
as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time),
format="%Y-%m-%d %H:%M:%S",
tz=i))
}
}
}
return(retval)
} else {
warning("No data to retrieve")
return(NA)
}
} else {
message(paste("URL caused an error:", url))
message("Content-Type=",h$value()["Content-Type"])
return(NA)
}
}