basic getObservation parsing working

NAMESPACE

@@ -7,6 +7,7 @@ export(constructWQPURL)
 export(countyCd)
 export(countyCdLookup)
 export(getWebServiceData)
+export(importNGMWN_wml2)
 export(importRDB1)
 export(importWQP)
 export(importWaterML1)

R/importNGWMN_wml2.R

+#' Function to return data from the WaterML2 data
+#'
+#' This function accepts a url parameter for a WaterML2 getObservation. This function is still under development,
+#' but the general functionality is correct.
+#'
+#' @param input character or raw, containing the url for the retrieval or a path to the data file, or raw XML.
+#' @param asDateTime logical, if \code{TRUE} returns date and time as POSIXct, if \code{FALSE}, character
+#' @param tz character to set timezone attribute of datetime. Default is an empty quote, which converts the 
+#' datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column).
+#' Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
+#' "America/Anchorage","America/Honolulu","America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla"
+#' @return mergedDF a data frame time, value, description, qualifier, and identifier
+#' @export
+#' @importFrom xml2 read_xml
+#' @importFrom xml2 xml_find_all
+#' @importFrom xml2 xml_text
+#' @importFrom xml2 xml_attr
+#' @importFrom lubridate parse_date_time
+#' @examples
+#' 
+importNGMWN_wml2 <- function(input, asDateTime=FALSE, tz=""){
+  
+  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"))
+  }else{tz = "UTC"}
+  
+  raw <- FALSE
+  if(class(input) == "character" && file.exists(input)){
+    returnedDoc <- read_xml(input)
+  }else if(class(input) == 'raw'){
+    returnedDoc <- read_xml(input)
+    raw <- TRUE
+  } else {
+    returnedDoc <- xml_root(getWebServiceData(input, encoding='gzip'))
+  }
+  
+  
+  
+  timeSeries <- xml_find_all(returnedDoc, "//wml2:MeasurementTimeseries") #each parameter/site combo
+  
+  if(0 == length(timeSeries)){
+    df <- data.frame()
+    if(!raw){
+      attr(df, "url") <- input
+    }
+    return(df)
+  }
+  
+  mergedDF <- NULL
+  
+  for(t in timeSeries){
+    gmlID <- xml_attr(t,"id")
+    uomTitle <- xml_attr(xml_find_all(t, ".//wml2:uom"), "title")
+    TVP <- xml_find_all(t, ".//wml2:MeasurementTVP")#time-value pairs
+    time <- xml_text(xml_find_all(TVP,".//wml2:time"))
+    if(asDateTime){
+      time <- parse_date_time(time, c("%Y","%Y-%m-%d","%Y-%m-%dT%H:%M","%Y-%m-%dT%H:%M:%S",
+                                      "%Y-%m-%dT%H:%M:%OS","%Y-%m-%dT%H:%M:%OS%z"), exact = TRUE)
+      #^^setting tz in as.POSIXct just sets the attribute, does not convert the time!
+      attr(time, 'tzone') <- tz 
+    }
+    valueNodes <- xml_find_all(TVP,".//wml2:value")
+    values <- as.numeric(xml_text(valueNodes))
+    nVals <- length(values)
+    gmlID <- rep(gmlID, nVals)
+    uomTitle <- rep(uomTitle, nVals)
+    
+    uom <- removeBlanks(xml_attr(valueNodes, "uom", default = NA))
+    source <- xml_attr(xml_find_all(TVP, ".//wml2:source"), "title")
+    comment <- removeBlanks(xml_text(xml_find_all(TVP, ".//wml2:comment")))
+    
+    df <- cbind.data.frame(source, time, value=values, uom, uomTitle, comment, gmlID,
+                           stringsAsFactors=FALSE)
+    if (is.null(mergedDF)){
+      mergedDF <- df
+    } else {
+      similarNames <- intersect(colnames(mergedDF), colnames(df))
+      mergedDF <- full_join(mergedDF, df, by=similarNames)
+    }
+  }
+  
+  if(!raw){
+    url <- input
+    attr(mergedDF, "url") <- url
+  }
+  attr(mergedDF, "gml:identifier") <- xml_text(xml_find_all(returnedDoc, ".//gml:identifier")) 
+  attr(mergedDF, "generationDate") <- xml_text(xml_find_all(returnedDoc, ".//wml2:generationDate")) 
+  
+  return(mergedDF)
+  
+}
+
+
+#replace blank cells with NAs
+removeBlanks <- function(input){
+  input <- sapply(input, function(f){is.na(f)<-which(f == '');f})
+  return(input)
+}
+
+

R/readNGWMNdata.R

+#' import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
+#' Only water level data and site metadata is currently available through the web service.  
+#' @param asDateTime
+#' @param sites
+#' @param request
+#' 
+
+readNGWMNdata <- function(sites, request = "observation", asDateTime = TRUE){
+  
+}
+  
\ No newline at end of file

man/importNGMWN_wml2.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/importNGWMN_wml2.R
+\name{importNGMWN_wml2}
+\alias{importNGMWN_wml2}
+\title{Function to return data from the WaterML2 data}
+\usage{
+importNGMWN_wml2(input, asDateTime = FALSE, tz = "")
+}
+\arguments{
+\item{input}{character or raw, containing the url for the retrieval or a path to the data file, or raw XML.}
+
+\item{asDateTime}{logical, if \code{TRUE} returns date and time as POSIXct, if \code{FALSE}, character}
+
+\item{tz}{character to set timezone attribute of datetime. Default is an empty quote, which converts the 
+datetimes to UTC (properly accounting for daylight savings times based on the data's provided tz_cd column).
+Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
+"America/Anchorage","America/Honolulu","America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla"}
+}
+\value{
+mergedDF a data frame time, value, description, qualifier, and identifier
+}
+\description{
+This function accepts a url parameter for a WaterML2 getObservation. This function is still under development,
+but the general functionality is correct.
+}
+\examples{
+
+}
+

man/readNGWMNdata.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/readNGWMNdata.R
+\name{readNGWMNdata}
+\alias{readNGWMNdata}
+\title{import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}}
+\usage{
+readNGWMNdata(sites, request = "observation", asDateTime = TRUE)
+}
+\arguments{
+\item{request}{}
+}
+\description{
+import data from the National Groundwater Monitoring Network \link{http://cida.usgs.gov/ngwmn/}
+}
+