From f1c330d6a614e0cc26bbc3282ea7ff894f457184 Mon Sep 17 00:00:00 2001
From: unknown <ldecicco@usgs.gov>
Date: Fri, 10 Oct 2014 09:11:28 -0500
Subject: [PATCH] Removed WaterML2 until fixed.
---
R/getWaterML2Data.r | 75 ---------------------------------------------
1 file changed, 75 deletions(-)
delete mode 100644 R/getWaterML2Data.r
diff --git a/R/getWaterML2Data.r b/R/getWaterML2Data.r
deleted file mode 100644
index f0fee9c2..00000000
--- a/R/getWaterML2Data.r
+++ /dev/null
@@ -1,75 +0,0 @@
-#' Function to return data from the WaterML2 data
-#'
-#' This function accepts a url parameter for a WaterML2 getObservation
-#'
-#' @param obs_url string containing the url for the retrieval
-#' @return mergedDF a data frame containing columns agency, site, dateTime, values, and remark codes for all requested combinations
-#' @export
-#' @import XML
-#' @importFrom dplyr rbind_all
-#' @examples
-#' URL <- "http://waterservices.usgs.gov/nwis/dv/?format=waterml,2.0&sites=01646500&startDT=2014-09-01&endDT=2014-09-08&statCd=00003¶meterCd=00060"
-#' \dontrun{dataReturned3 <- getWaterML2Data(URL)}
-getWaterML2Data <- function(obs_url){
-
- h <- basicHeaderGatherer()
- doc = tryCatch({
- returnedDoc <- getURL(obs_url, headerfunction = h$update)
- if(h$value()["Content-Type"] == "text/xml;charset=UTF-8"){
- xmlTreeParse(returnedDoc, getDTD = FALSE, useInternalNodes = TRUE)
- } else {
- message(paste("URL caused an error:", obs_url))
- message("Content-Type=",h$value()["Content-Type"])
- return(NA)
- }
-
- }, warning = function(w) {
- message(paste("URL caused a warning:", obs_url))
- message(w)
- }, error = function(e) {
- message(paste("URL does not seem to exist:", obs_url))
- message(e)
- return(NA)
- })
-
- doc <- xmlRoot(doc)
-
- ns <- xmlNamespaceDefinitions(doc, simplify = TRUE)
-
- timeseries2 <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point", namespaces = ns)
-
- xp <- xpathApply(doc, "//wml2:MeasurementTimeseries/wml2:point/wml2:MeasurementTVP", xpathSApply, ".//*[not(*)]", function(x)
- setNames(ifelse(nzchar(xmlValue(x)), xmlValue(x),
- ifelse("qualifier" == xmlName(x),xpathSApply(x,"./@xlink:title",namespaces = ns),"")), #originally I had the "" as xmlAttr(x)
- xmlName(x)), namespaces = ns)
-
- DF2 <- do.call(rbind_all, lapply(xp, t))
- DF2 <- as.data.frame(DF2,stringsAsFactors=FALSE)
- DF2$time <- gsub(":","",DF2$time)
- DF2$time <- with(DF2, ifelse(nchar(time) > 18,as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S%z")),
- ifelse("Z" == substr(time,(nchar(time)),nchar(time)),as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S",tz="GMT")),
- as.POSIXct(strptime(time, format="%Y-%m-%dT%H%M%S",tz="")))))
-
- DF2$time <- with(DF2, as.POSIXct(time,origin=as.POSIXct(strptime("1970-01-01 00:00:00", "%Y-%m-%d %H:%M:%S", tz="UTC"))))
-
- DF2$value <- as.numeric(gsub("true","",DF2$value))
-
- # Very specific to USGS:
- defaultQualifier <- as.character(xpathApply(doc, "//wml2:defaultPointMetadata/wml2:DefaultTVPMeasurementMetadata/wml2:qualifier/@xlink:title",namespaces = ns))
-
- if (length(defaultQualifier) == 0 && (typeof(defaultQualifier) == "character")) {
- defaultQualifier <- "NA"
- }
-
- if("qualifier" %in% names(DF2)){
- DF2$qualifier <- ifelse(defaultQualifier != DF2$qualifier,DF2$qualifier,defaultQualifier)
- } else {
- DF2$qualifier <- rep(defaultQualifier,nrow(DF2))
- }
-
-
- DF2$qualifier <- ifelse("Provisional data subject to revision." == DF2$qualifier, "P",
- ifelse("Approved for publication. Processing and review completed." == DF2$qualifier, "A", DF2$qualifier))
-
- return (DF2)
-}
--
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