Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
#' 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
#' @examples
#' # These examples require an internet connection to run
#' rawSampleURL <- constructNWISURL('USGS-01594440','01075', '1985-01-01', '1985-03-31',"wqp")
#' rawSample <- basicWQPData(rawSampleURL)
basicWQPData <- function(url){
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$value()["Total-Result-Count"])
if (!is.na(numToBeReturned) | numToBeReturned != 0){
namesData <- read.delim(textConnection(doc), header = TRUE, quote="\"",
dec=".", sep='\t',
colClasses='character',
fill = TRUE,nrow=1)
classColumns <- setNames(rep('character',ncol(namesData)),names(namesData))
classColumns["ActivityStartDate"] <- "Date"
classColumns[grep("MeasureValue",names(classColumns))] <- NA
retval <- read.delim(textConnection(doc), header = TRUE, quote="\"",
dec=".", sep='\t',
colClasses=as.character(classColumns),
fill = TRUE)
actualNumReturned <- nrow(retval)
retval[,names(which(sapply(retval[,grep("MeasureValue",names(retval))], function(x)all(is.na(x)))))] <- ""
if(actualNumReturned != numToBeReturned) warning(numToBeReturned, " sample results were expected, ", actualNumReturned, " were returned")
timeZoneLibrary <- setNames(c("America/New_York","America/New_York","America/Chicago","America/Chicago",
"America/Denver","America/Denver","America/Los_Angeles","America/Los_Angeles",
"America/Anchorage","America/Anchorage","America/Honolulu","America/Honolulu"),
c("EST","EDT","CST","CDT","MST","MDT","PST","PDT","AKST","AKDT","HAST","HST"))
timeZoneStart <- as.character(timeZoneLibrary[retval$ActivityStartTime.TimeZoneCode])
timeZoneEnd <- as.character(timeZoneLibrary[retval$ActivityEndTime.TimeZoneCode])
if(any(!is.na(timeZoneStart))){
if(length(unique(timeZoneStart)) == 1){
retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time),format="%Y-%m-%d %H:%M:%S", tz=unique(timeZoneStart)))
} else {
# warning("Mixed time zone information")
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
if(any(is.na(timeZoneStart))){
warning("Missing time zone information, all dateTimes default to user's local time")
retval$ActivityStartDateTime <- with(retval, as.POSIXct(paste(ActivityStartDate, ActivityStartTime.Time), format="%Y-%m-%d %H:%M:%S"),tz=Sys.timezone())
} else {
for(i in seq_along(row.names(retval))){
timeZone <- timeZoneStart[i]
retval$ActivityStartDateTime[i] <- with(retval, as.POSIXct(paste(ActivityStartDate[i], ActivityStartTime.Time[i]), format="%Y-%m-%d %H:%M:%S",tz=timeZone))
}
}
}
}
if(any(!is.na(timeZoneEnd))){
if(length(unique(timeZoneEnd)) == 1){
retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time), format="%Y-%m-%d %H:%M:%S",tz=unique(timeZoneEnd)))
} else {
warning("Mixed time zone information")
if(any(is.na(timeZoneEnd))){
warning("Missing time zone information, all dateTimes default to user's local time")
retval$ActivityEndDateTime <- with(retval, as.POSIXct(paste(ActivityEndDate, ActivityEndTime.Time), format="%Y-%m-%d %H:%M:%S"), tz=Sys.timezone())
} else {
for(i in seq_along(row.names(retval))){
retval$ActivityEndDateTime[i] <- with(retval, as.POSIXct(paste(ActivityEndDate[i], ActivityEndTime.Time[i]), format="%Y-%m-%d %H:%M:%S",tz=timeZoneEnd[i]))
}
}
}
}
if(any(retval$ActivityEndDate != "")){
retval$ActivityEndDate <- as.Date(retval$ActivityEndDate)
}
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)
}
}