cleaned up TODOs

R/importNGWMN_wml2.R

@@ -117,7 +117,9 @@ importNGWMN_wml2 <- function(input, asDateTime=FALSE, tz=""){
       url <- input
       attr(mergedDF, "url") <- url
     }
-    mergedDF$date <- as.Date(mergedDF$date)
+    if(asDateTime){
+      mergedDF$date <- as.Date(mergedDF$date)
+    }
     nonDateCols <- grep("date",names(mergedDF), value=TRUE, invert = TRUE)
     
     mergedDF[nonDateCols][mergedDF[nonDateCols] == "" | mergedDF[nonDateCols]== -999999.0] <- NA
@@ -140,7 +142,6 @@ importNGWMN_wml2 <- function(input, asDateTime=FALSE, tz=""){
     siteLocs <- data.frame(matrix(unlist(siteLocs), nrow=length(siteLocs), byrow=TRUE), stringsAsFactors = FALSE)
     names(siteLocs) <- c("dec_lat_va", "dec_lon_va")
     siteLocs <- mutate(siteLocs, dec_lat_va=as.numeric(dec_lat_va), dec_lon_va=as.numeric(dec_lon_va))
-    #siteLocs <- data.frame(dec_lat_va=as.numeric(siteLocs[[1]][1]), dec_lon_va=as.numeric(siteLocs[[1]][2]), stringsAsFactors = FALSE)
     mergedDF <- cbind.data.frame(site, description = siteDesc, siteLocs, stringsAsFactors = FALSE) 
   }
   else{

R/importWaterML2.r

@@ -79,7 +79,6 @@ importWaterML2 <- function(obs_url, asDateTime=FALSE, tz=""){
   for(t in timeSeries){
     TVP <- xml_find_all(t, ".//wml2:MeasurementTVP")#time-value pairs
     time <- xml_text(xml_find_all(TVP,".//wml2:time"))
-    #TODO: if asDateTime....
     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)

R/readNGWMNdata.R

@@ -5,8 +5,8 @@
 #' \code{FALSE} since time zone information is not included.  
 #' @param featureID character Vector of feature IDs in the formatted with agency code and site number 
 #' separated by a period, e.g. \code{USGS.404159100494601}.
-#' @param service character Identifies which web service to access.  Only \code{observation} is currently 
-#' supported, which retrieves all water level for each site.   
+#' @param service character Identifies which web service to access.  \code{observation} retrieves all water level for each site,
+#' and \code{featureOfInterest} retrieves a data frame of site information, including description, latitude, and longitude.   
 #' @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 time zone offset).
 #' Possible values to provide are "America/New_York","America/Chicago", "America/Denver","America/Los_Angeles",
@@ -26,10 +26,11 @@
 #' #multiple sites
 #' sites <- c("USGS.272838082142201","USGS.404159100494601", "USGS.401216080362703")
 #' multiSiteData <- readNGWMNdata(sites)
-#' 
+#' attributes(multiSiteData)
 #' 
 #' #non-USGS site
-#' site <- "MBMG.892195"
+#' #accepts colon or period between agency and ID
+#' site <- "MBMG:892195"
 #' data <- readNGWMNdata(featureID = site)
 #' 
 #' #site with no data returns empty data frame
@@ -37,8 +38,6 @@
 #' noDataSite <- readNGWMNdata(featureID = noDataSite, service = "observation")
 #' }
 #' 
-#TODO: accept colon or period! change examples
-#TODO: deal with NA fIDs
 readNGWMNdata <- function(..., service = "observation", asDateTime = TRUE, tz = ""){
   message("          ********************************************************
           DISCLAIMER: NGWMN retrieval functions are still in flux, 
@@ -56,10 +55,6 @@ readNGWMNdata <- function(..., service = "observation", asDateTime = TRUE, tz =
     attrs <- c("url","gml:identifier","generationDate","responsibleParty", "contact")
     featureID <- na.omit(gsub(":",".",dots[['featureID']]))
     
-    #featureID <- na.omit(featureID)
-    #featureID <- featureID[!is.na(featureID)]
-    #featureID <- gsub(":",".",featureID) #getFeatureOfInterest returns with colons
-    #TODO: call featureOfInterest outside loop
     for(f in featureID){
       obsFID <- retrieveObservation(featureID = f, asDateTime, attrs)
       obsFIDattr <- saveAttrs(attrs, obsFID)
@@ -76,7 +71,6 @@ readNGWMNdata <- function(..., service = "observation", asDateTime = TRUE, tz =
   }else if(service == "featureOfInterest"){
     if("featureID" %in% names(dots)){
       featureID <- na.omit(gsub(":",".",dots[['featureID']]))
-      #TODO: can do multi site calls with encoded comma
       allSites <- retrieveFeatureOfInterest(featureID = featureID)
     }
     if("bbox" %in% names(dots)){
@@ -94,6 +88,9 @@ readNGWMNdata <- function(..., service = "observation", asDateTime = TRUE, tz =
 #'
 #' @param featureID character Vector of feature IDs in the formatted with agency code and site number 
 #' separated by a period, e.g. \code{USGS.404159100494601}.
+#' @param asDateTime logical Should dates and times be converted to date/time objects,
+#' or returned as character?  Defaults to \code{TRUE}.  Must be set to \code{FALSE} if a site 
+#' contains non-standard dates.
 #' 
 #' @export
 #' 
@@ -116,8 +113,9 @@ readNGWMNdata <- function(..., service = "observation", asDateTime = TRUE, tz =
 #' noDataSite <- readNGWMNlevels(featureID = noDataSite)
 #' }
 
-readNGWMNlevels <- function(featureID){
-  data <- readNGWMNdata(featureID = featureID, service = "observation")
+readNGWMNlevels <- function(featureID, asDateTime = TRUE){
+  data <- readNGWMNdata(featureID = featureID, service = "observation",
+                        asDateTime = asDateTime)
   return(data)
 }
 
@@ -156,7 +154,6 @@ readNGWMNsites <- function(featureID){
 }
 
 
-
 retrieveObservation <- function(featureID, asDateTime, attrs){
   #will need to contruct this more piece by piece if other versions, properties are added
   baseURL <- "https://cida-test.er.usgs.gov/ngwmn_cache/sos?request=GetObservation&service=SOS&version=2.0.0&observedProperty=urn:ogc:def:property:OGC:GroundWaterLevel&responseFormat=text/xml&featureOfInterest=VW_GWDP_GEOSERVER."
@@ -185,17 +182,15 @@ retrieveObservation <- function(featureID, asDateTime, attrs){
 
 #' retrieve feature of interest
 #' 
-#' @export
-#TODO: can do multisite calls
-#TODO: allow pass through srsName  needs to be worked in higher-up in dots
+#could allow pass through srsName - needs to be worked in higher-up in dots
 retrieveFeatureOfInterest <- function(..., asDateTime, srsName="urn:ogc:def:crs:EPSG::4269"){
   baseURL <- "https://cida-test.er.usgs.gov/ngwmn_cache/sos?request=GetFeatureOfInterest&service=SOS&version=2.0.0"
   dots <- list(...)
-  values <- convertDots(dots)
+  values <- gsub(x = convertDots(dots), pattern = ",", replacement = "%2C")
   
   if("featureID" %in% names(values)){
     foiURL <- "&featureOfInterest="
-    fidURL <- paste("VW_GWDP_GEOSERVER", values[['featureID']], sep=".", collapse = "%2C")
+    fidURL <- paste0("VW_GWDP_GEOSERVER.", values[['featureID']])
     url <- paste0(baseURL, foiURL, fidURL)
     
   }else if("bbox" %in% names(values)){
@@ -205,6 +200,8 @@ retrieveFeatureOfInterest <- function(..., asDateTime, srsName="urn:ogc:def:crs:
     stop()
   }
   siteDF <- importNGWMN_wml2(url, asDateTime)
+  attr(siteDF, "url") <- url
+  attr(siteDF, "queryTime") <- Sys.time()
   return(siteDF)
 }
 

man/readNGWMNdata.Rd

@@ -7,8 +7,8 @@
 readNGWMNdata(..., service = "observation", asDateTime = TRUE, tz = "")
 }
 \arguments{
-\item{service}{character Identifies which web service to access.  Only \code{observation} is currently 
-supported, which retrieves all water level for each site.}
+\item{service}{character Identifies which web service to access.  \code{observation} retrieves all water level for each site,
+and \code{featureOfInterest} retrieves a data frame of site information, including description, latitude, and longitude.}
 
 \item{asDateTime}{logical if \code{TRUE}, will convert times to POSIXct format.  Currently defaults to 
 \code{FALSE} since time zone information is not included.}
@@ -33,10 +33,11 @@ oneSite <- readNGWMNdata(featureID = site)
 #multiple sites
 sites <- c("USGS.272838082142201","USGS.404159100494601", "USGS.401216080362703")
 multiSiteData <- readNGWMNdata(sites)
-
+attributes(multiSiteData)
 
 #non-USGS site
-site <- "MBMG.892195"
+#accepts colon or period between agency and ID
+site <- "MBMG:892195"
 data <- readNGWMNdata(featureID = site)
 
 #site with no data returns empty data frame

man/readNGWMNlevels.Rd

@@ -4,11 +4,15 @@
 \alias{readNGWMNlevels}
 \title{Retrieve groundwater levels from the National Ground Water Monitoring Network \url{http://cida.usgs.gov/ngwmn/}.}
 \usage{
-readNGWMNlevels(featureID)
+readNGWMNlevels(featureID, asDateTime = TRUE)
 }
 \arguments{
 \item{featureID}{character Vector of feature IDs in the formatted with agency code and site number 
 separated by a period, e.g. \code{USGS.404159100494601}.}
+
+\item{asDateTime}{logical Should dates and times be converted to date/time objects,
+or returned as character?  Defaults to \code{TRUE}.  Must be set to \code{FALSE} if a site 
+contains non-standard dates.}
 }
 \description{
 Retrieve groundwater levels from the National Ground Water Monitoring Network \url{http://cida.usgs.gov/ngwmn/}.

tests/testthat/tests_userFriendly_fxns.R

@@ -241,8 +241,16 @@ test_that("NGWMN functions working", {
   expect_true(nrow(data) > 1)
   expect_true(is.numeric(oneSite$value))
   
-  
-})
-
-
-
+  #sites with colons and NAs work
+  na_colons <- c(NA, bboxSites$site[200:205], NA, NA)
+  returnDF <- readNGWMNdata(service = "observation", featureID = na_colons)
+  expect_is(returnDF, "data.frame")
+  expect_true(nrow(returnDF) > 1)
+  expect_true(!is.null(attributes(returnDF)$siteInfo))
+  
+  sites <- c("USGS:424427089494701", NA)
+  siteInfo <- readNGWMNsites(sites)
+  expect_is(siteInfo, "data.frame")
+  expect_true(nrow(siteInfo) == 1)
+  
+})
\ No newline at end of file