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Improving error handling.

Merged Improving error handling.
ldecicco-USGS:master into master
Merged Laura A DeCicco requested to merge ldecicco-USGS:master into master
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6
R/importWQP.R
+ 94
− 85
@@ -28,107 +28,116 @@
#' }
importWQP <- function(url, zip=FALSE, tz=""){
h <- basicHeaderGatherer()
if(zip){
headerInfo <- HEAD(url)$headers
temp <- tempfile()
options(timeout = 120)
possibleError <- tryCatch(
download.file(url,temp, quiet=TRUE, mode='wb'),
error = function(e) e
)
} else {
h <- basicHeaderGatherer()
possibleError <- tryCatch(
doc <- getURL(url, headerfunction = h$update),
error = function(e) e
)
}
tryCatch({
if(!inherits(possibleError, "error")){
if(zip){
headerInfo <- HEAD(url)$headers
temp <- tempfile()
options(timeout = 120)
download.file(url,temp, quiet=TRUE, mode='wb')
doc <- unzip(temp)
unlink(temp)
} else {
doc <- getURL(url, headerfunction = h$update)
headerInfo <- h$value()
}
if(tz != ""){
tz <- match.arg(tz, c("America/New_York","America/Chicago",
"America/Denver","America/Los_Angeles",
"America/Anchorage","America/Honolulu",
"America/Jamaica","America/Managua",
"America/Phoenix","America/Metlakatla"))
}
}, warning = function(w) {
message(paste("URL caused a warning:", url))
message(w)
}, error = function(e) {
message(paste("URL does not seem to exist:", url))
message(e)
return(NA)
})
if(tz != ""){
tz <- match.arg(tz, c("America/New_York","America/Chicago",
"America/Denver","America/Los_Angeles",
"America/Anchorage","America/Honolulu",
"America/Jamaica","America/Managua",
"America/Phoenix","America/Metlakatla"))
}
numToBeReturned <- as.numeric(headerInfo["Total-Result-Count"])
numToBeReturned <- as.numeric(headerInfo["Total-Result-Count"])
if (!is.na(numToBeReturned) & numToBeReturned != 0){
if (!is.na(numToBeReturned) | numToBeReturned != 0){
suppressWarnings(namesData <- read.delim(if(zip) doc else textConnection(doc) , header = TRUE, quote="\"",
dec=".", sep='\t',
colClasses='character',
fill = TRUE,nrow=1))
classColumns <- setNames(rep('character',ncol(namesData)),names(namesData))
classColumns[grep("MeasureValue",names(classColumns))] <- NA
suppressWarnings(retval <- read.delim(if(zip) doc else textConnection(doc), header = TRUE, quote="\"",
dec=".", sep='\t',
colClasses=as.character(classColumns),
fill = TRUE))
actualNumReturned <- nrow(retval)
retval[,names(which(sapply(retval[,grep("MeasureValue",names(retval))], function(x)all(is.na(x)))))] <- ""
if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
offsetLibrary <- setNames(c(5, 4, 6, 5, 7, 6, 8, 7, 9, 8, 10, 10),
c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
timeZoneStart <- offsetLibrary[retval$ActivityStartTime.TimeZoneCode]
timeZoneEnd <- offsetLibrary[retval$ActivityEndTime.TimeZoneCode]
timeZoneStart[is.na(timeZoneStart)] <- 0
timeZoneEnd[is.na(timeZoneEnd)] <- 0
if("ActivityStartDate" %in% names(retval)){
if(any(retval$ActivityStartDate != "")){
suppressWarnings(retval$ActivityStartDate <- as.Date(parse_date_time(retval$ActivityStartDate, c("Ymd", "mdY"))))
suppressWarnings(namesData <- read.delim(if(zip) doc else 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
suppressWarnings(retval <- read.delim(if(zip) doc else 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")
offsetLibrary <- setNames(c(5, 4, 6, 5, 7, 6, 8, 7, 9, 8, 10, 10),
c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
timeZoneStart <- offsetLibrary[retval$ActivityStartTime.TimeZoneCode]
timeZoneEnd <- offsetLibrary[retval$ActivityEndTime.TimeZoneCode]
timeZoneStart[is.na(timeZoneStart)] <- 0
timeZoneEnd[is.na(timeZoneEnd)] <- 0
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))){
retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),format="%Y-%m-%d %H:%M:%S", tz = "UTC"))
retval$ActivityStartDateTime <- retval$ActivityStartDateTime + timeZoneStart*60*60
retval$ActivityStartDateTime <- as.POSIXct(retval$ActivityStartDateTime)
attr(retval$ActivityStartDateTime, "tzone") <- "UTC"
}
}
if("ActivityEndDate" %in% names(retval)){
if(any(retval$ActivityEndDate != "")){
suppressWarnings(retval$ActivityEndDate <- as.Date(parse_date_time(retval$ActivityEndDate, c("Ymd", "mdY"))))
}
}
if(any(!is.na(timeZoneStart))){
retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),format="%Y-%m-%d %H:%M:%S", tz = "UTC"))
retval$ActivityStartDateTime <- retval$ActivityStartDateTime + timeZoneStart*60*60
retval$ActivityStartDateTime <- as.POSIXct(retval$ActivityStartDateTime)
attr(retval$ActivityStartDateTime, "tzone") <- "UTC"
if(any(!is.na(timeZoneEnd))){
retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time),format="%Y-%m-%d %H:%M:%S", tz = "UTC"))
retval$ActivityEndDateTime <- retval$ActivityEndDateTime + timeZoneEnd*60*60
retval$ActivityEndDateTime <- as.POSIXct(retval$ActivityEndDateTime)
attr(retval$ActivityEndDateTime, "tzone") <- "UTC"
}
}
if(any(!is.na(timeZoneEnd))){
retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time),format="%Y-%m-%d %H:%M:%S", tz = "UTC"))
retval$ActivityEndDateTime <- retval$ActivityEndDateTime + timeZoneEnd*60*60
retval$ActivityEndDateTime <- as.POSIXct(retval$ActivityEndDateTime)
attr(retval$ActivityEndDateTime, "tzone") <- "UTC"
}
if(all(is.na(retval$ActivityEndDateTime))){
retval$ActivityEndDateTime <- NULL
}
return(retval)
if(all(is.na(retval$ActivityEndDateTime))){
retval$ActivityEndDateTime <- NULL
} else {
warning("No data to retrieve")
return(NA)
}
return(retval)
} else {
warning("No data to retrieve")
return(NA)
if(zip){
unlink(temp)
}
message(e)
}
}
\ No newline at end of file