New defaults

DESCRIPTION

@@ -1,29 +1,32 @@
 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
-Version: 2.7.16.1
+Version: 2.7.17
 Authors@R: c(
     person("Laura", "DeCicco", role = c("aut","cre"),
             email = "[email protected]",
             comment=c(ORCID="0000-0002-3915-9487")),
     person("Robert", "Hirsch", role = c("aut"),
-            comment=c(ORCID="0000-0002-4534-075X")),
+            comment=c(ORCID = "0000-0002-4534-075X")),
     person("David","Lorenz", role=c("aut")),
     person("Jordan", "Read", role = c("ctb")),
     person("Jordan", "Walker", role = c("ctb")),
     person("Lindsay","Platt", role=c("ctb")),
     person("David","Watkins", role=c("aut"),
             email = "[email protected]",
-            comment=c(ORCID="0000-0002-7544-0700")),
+            comment=c(ORCID = "0000-0002-7544-0700")),
     person("David", "Blodgett", role="aut",
-            comment=c(ORCID="0000-0001-9489-1710"),
+            comment=c(ORCID = "0000-0001-9489-1710"),
             email = "[email protected]"),
     person("Mike", "Johnson", role=c("aut"),
             email = "[email protected]",
-            comment=c(ORCID="0000-0002-5288-8350")),
+            comment=c(ORCID = "0000-0002-5288-8350")),
     person("Aliesha", "Krall", role="ctb",
             email = "[email protected]",
-            comment=c(ORCID="0000-0003-2521-5043")))
+            comment=c(ORCID = "0000-0003-2521-5043")),
+    person("Lee", "Stanish", role="ctb",
+            email = "[email protected]",
+            comment=c(ORCID = "0000-0002-9775-6861")))
 Description: Collection of functions to help retrieve U.S. Geological Survey
     and U.S. Environmental Protection Agency water quality and
     hydrology data from web services. Data are discovered from 

NEWS

@@ -1,10 +1,12 @@
-dataRetrieval 2.7.16.1
+dataRetrieval 2.7.17
 ===================
+* Fixed bug with server problems causing errors.
+* Added message of service URL.
 * Removed the forced "empty returns" for WQP, since the WQP now has properly formatted empty returns.
 * Moved the column parsing to a dedicated function for WQP.
 * Took out zip option for WQP calls, they are not allowed on WQP anymore.
-* Deprecated getQuerySummary. Users should use readWQPsummary instead.
-* Added WQX 3.0 profiles
+* Added deprecated message getQuerySummary. Users should use readWQPsummary instead.
+* Added WQX 3.0 profiles.
 * siteInfo attribute for WQP queries converted to a full station return.
 * Cleaned up date conversion in WQP
 * Updated source for groundwater level data from waterservices to waterdata. Note that waterdata services will ALSO need updating within the next year, but this change will allow for some time to make changes.

R/AAA.R

@@ -19,20 +19,13 @@ is_dataRetrieval_user <- function() {
     identical(Sys.getenv("NOT_CRAN"), "true")
 }
 
-
-wqp_message_only_legacy <- function(){
-  message("NEWS: Legacy profile requested, and no equivalent/similar WQX 3.0
-profile currently exists. Legacy profiles do not include USGS data newer
-than March 11, 2024. 
-More details: 
+wqp_message <- function(){
+  message("NEWS: Data does not include USGS data newer than March 11, 2024. More details:
 https://doi-usgs.github.io/dataRetrieval/articles/Status.html")
 }
 
-wqp_message <- function(){
-  message("NEWS: Legacy data profiles will be retired. Please begin converting
-workflows to the WQX 3.0 profiles. Also, data from legacy profiles do not
-include USGS data newer than March 11, 2024. More details:
-https://doi-usgs.github.io/dataRetrieval/articles/Status.html")
+wqp_message_beta <- function(){
+  message("WQX3 services are in-development, use with caution.")
 }
 
 only_legacy <- function(service){
@@ -52,14 +45,6 @@ is_legacy <- function(service){
   return(legacy)
 }
 
-wqp_message_now <- function(service){
-  if(only_legacy(service)){
-    return(wqp_message_only_legacy())
-  } else if (service %in% c("Result", "Station", "Activity")){
-    return(wqp_message())
-  }
-}
-
 nwis_message <- function(){
   return("WARNING: NWIS does not deliver
 discrete water quality data newer than March 11, 2024

R/constructNWISURL.R

@@ -319,7 +319,8 @@ constructNWISURL <- function(siteNumbers,
 #' retrieval for the earliest possible record.
 #' @param endDate character ending date for data retrieval in the form YYYY-MM-DD. Default is "" which indicates
 #' retrieval for the latest possible record.
-#' @param legacy Logical. If TRUE, uses legacy WQP services. Default is FALSE.
+#' @param legacy Logical. If TRUE, uses legacy WQP services. Default is TRUE.
+#' Setting legacy = FALSE uses WQX3.0 WQP services, which are in-development, use with caution.
 #' @keywords data import WQP web service
 #' @return url string
 #' @export

R/getWebServiceData.R

@@ -173,7 +173,7 @@ has_internet_2 <- function(obs_url) {
 #'
 #' @param url the query url
 getQuerySummary <- function(url) {
-  wqp_message_only_legacy()
+  wqp_message()
   queryHEAD <- httr::HEAD(url)
   retquery <- httr::headers(queryHEAD)
 

R/readWQPdata.R

@@ -9,18 +9,9 @@
 #' 
 #' @details
 #'  
-#' There are currently 10 legacy and 4 modern WQX options
+#' There are currently 10 legacy options
 #' for data provided by the Water Quality Portal:
 #'  
-#' WQX:
-#' \tabular{llll}{
-#' WQP Radio Button \tab service argument \tab Base URL \tab dataProfile \cr 
-#' Monitoring Locations \tab StationWQX3 \tab /wqx3/Station/search \tab \cr
-#' Full Physical Chemical \tab ResultWQX3 \tab /wqx3/Result/search \tab fullPhysChem \cr
-#' Narrow \tab ResultWQX3 \tab /wqx3/Result/search \tab narrow \cr
-#' Basic Physical Chemical \tab ResultWQX3 \tab /wqx3/Result/search \tab basicPhysChem \cr
-#' Sampling Activity \tab ActivityWQX3 \tab /wqx3/Activity/search \cr
-#' }
 #' 
 #' Legacy:
 #' \tabular{lll}{
@@ -37,6 +28,18 @@
 #' Organization Data \tab Organization \tab /data/Organization/search \cr
 #' }
 #' 
+#' There are 4 WQX3 options. These are still in-development,
+#' and should be used with caution.
+#'  
+#' \tabular{llll}{
+#' WQP Radio Button \tab service argument \tab Base URL \tab dataProfile \cr 
+#' Monitoring Locations \tab StationWQX3 \tab /wqx3/Station/search \tab \cr
+#' Full Physical Chemical \tab ResultWQX3 \tab /wqx3/Result/search \tab fullPhysChem \cr
+#' Narrow \tab ResultWQX3 \tab /wqx3/Result/search \tab narrow \cr
+#' Basic Physical Chemical \tab ResultWQX3 \tab /wqx3/Result/search \tab basicPhysChem \cr
+#' Sampling Activity \tab ActivityWQX3 \tab /wqx3/Activity/search \cr
+#' }
+#' 
 #'
 #' @param \dots see \url{https://www.waterqualitydata.us/webservices_documentation} for a complete list of options.
 #' A list of arguments can also be supplied. For more information see the above 
@@ -82,36 +85,14 @@
 #' @export
 #' @examplesIf is_dataRetrieval_user()
 #' \donttest{
+#' 
 #' nameToUse <- "pH"
 #' pHData <- readWQPdata(siteid = "USGS-04024315", 
 #'                       characteristicName = nameToUse)
 #' ncol(pHData)
-#' attr(pHData, "url")
 #' attr(pHData, "siteInfo")
-#' attr(pHData, "headerInfo")[["dataProviders"]]
 #' attr(pHData, "queryTime")
 #'
-#' # dataProfile = Basic Physical Chemical
-#' pHData_basic <- readWQPdata(siteid = "USGS-04024315", 
-#'                       characteristicName = nameToUse,
-#'                       dataProfile = "basicPhysChem")
-#' attr(pHData_basic, "url") 
-#' ncol(pHData_basic)
-#'
-#' # dataProfile = Narrow
-#' pHData_narrow <- readWQPdata(siteid = "USGS-04024315", 
-#'                       characteristicName = nameToUse,
-#'                       dataProfile = "narrow")
-#' attr(pHData_narrow, "url") 
-#' ncol(pHData_narrow)
-#' 
-#' # Data profiles: "Site Data Only"
-#' site_data <- readWQPdata(
-#'   statecode = "WI",
-#'   countycode = "Dane",
-#'   service = "StationWQX3"
-#' )
-#'
 #' # More examples:
 #' # querying by county
 #' DeWitt <- readWQPdata(
@@ -123,83 +104,82 @@
 #' # Data profile: "Sampling Activity"
 #' activity <- readWQPdata(
 #'   siteid = "USGS-04024315",
-#'   service = "ActivityWQX3"
+#'   service = "Activity"
 #' )
 #' 
 #' Dane_activity <- readWQPdata(
 #'   statecode = "Wisconsin",
 #'   countycode = "Dane",
 #'   startDateLo = "2023-01-01",
 #'   startDateHi = "2023-12-31",
-#'   service = "ActivityWQX3"
+#'   service = "Activity"
 #' )
 #' 
 #' ########################################################
-#' # Legacy examples:
+#' # Additional examples:
 #'
 #' pHData_legacy <- readWQPdata(siteid = "USGS-04024315", 
 #'                       characteristicName = nameToUse,
 #'                       service = "Result",
 #'                       dataProfile = "narrowResult")
-#' attr(pHData_legacy, "url")
-#' 
-#' # Data profiles: "Organization Data" (legacy)
+#'  
+#' # Data profiles: "Organization Data" 
 #' org_data <- readWQPdata(
 #'   statecode = "WI",
 #'   countycode = "Dane",
 #'   service = "Organization"
 #' )
 #'
-#' # Data profiles: "Project Data"  (legacy)
+#' # Data profiles: "Project Data"  
 #' project_data <- readWQPdata(
 #'   statecode = "WI",
 #'   countycode = "Dane",
 #'   service = "Project"
 #' )
 #'
-#' # Data profiles: "Project Monitoring Location Weighting Data"  (legacy)
+#' # Data profiles: "Project Monitoring Location Weighting Data"
 #' proj_mlwd <- readWQPdata(
 #'   statecode = "WI",
 #'   countycode = "Dane",
 #'   service = "ProjectMonitoringLocationWeighting"
 #' )
 #'
-#' # Data profiles: "Sample Results (physical/chemical metadata)"  (legacy)
+#' # Data profiles: "Sample Results (physical/chemical metadata)" 
 #' samp_data <- readWQPdata(
 #'   siteid = "USGS-04024315",
 #'   dataProfile = "resultPhysChem",
 #'   service = "Result"
 #' )
 #'
-#' # Data profiles: "Sample Results (biological metadata)"  (legacy)
+#' # Data profiles: "Sample Results (biological metadata)"
 #' samp_bio <- readWQPdata(
 #'   siteid = "USGS-04024315",
 #'   dataProfile = "biological",
 #'   service = "Result"
 #' )
 #'
-#' # Data profiles: "Sample Results (narrow)" (legacy)
+#' # Data profiles: "Sample Results (narrow)" 
 #' samp_narrow <- readWQPdata(
 #'   siteid = "USGS-04024315",
 #'   service = "Result",
 #'   dataProfile = "narrowResult"
 #' )
 #'
-#' # Data profiles: "Sampling Activity"  (legacy)
+#' # Data profiles: "Sampling Activity"  
 #' samp_activity <- readWQPdata(
 #'   siteid = "USGS-04024315",
 #'   dataProfile = "activityAll",
 #'   service = "Activity"
 #' )
 #'
-#' # Data profile: "Sampling Activity Metrics"  (legacy)
+#' # Data profile: "Sampling Activity Metrics"
 #' act_metrics <- readWQPdata(
 #'   statecode = "WI",
 #'   countycode = "Dane",
 #'   service = "ActivityMetric"
 #' )
 #'
-#' # Data profile: "Result Detection Quantitation Limit Data"  (legacy)
+#' # Data profile: "Result Detection Quantitation Limit Data"  
 #' dl_data <- readWQPdata(
 #'   siteid = "USGS-04024315",
 #'   service = "ResultDetectionQuantitationLimit"
@@ -215,7 +195,7 @@
 #' )
 #' }
 readWQPdata <- function(...,
-                        service = "ResultWQX3",
+                        service = "Result",
                         querySummary = FALSE,
                         tz = "UTC",
                         ignore_attributes = FALSE,
@@ -240,9 +220,7 @@ readWQPdata <- function(...,
   baseURL <- drURL(service, arg.list = values)
 
   baseURL <- appendDrURL(baseURL, mimeType = "csv")
-
-  wqp_message_now(service)
-
+
   if(!legacy){
     if(service == "ResultWQX3" & !"dataProfile" %in% names(values)){
       baseURL <- appendDrURL(baseURL, dataProfile = "fullPhysChem")
@@ -264,19 +242,21 @@ readWQPdata <- function(...,
 
     attr(retval, "legacy") <- legacy
 
-    if(!legacy){
-      attr(retval, "wqp-request-id") <- attr(retval, "headerInfo")$`wqp-request-id`
-    }
-
     if (!all(is.na(retval)) && !ignore_attributes) {
       params <- list(...)
       params <- params[!names(params) %in% c("dataProfile", "service")]
       retval <- create_WQP_attributes(retval, params)
-
     } 
 
     attr(retval, "url") <- baseURL
-
+
+    if(legacy){
+      wqp_message()
+    } else {
+      wqp_message_beta()
+      attr(retval, "wqp-request-id") <- attr(retval, "headerInfo")$`wqp-request-id`
+    }
+
     return(retval)
   }
 }
@@ -296,7 +276,6 @@ create_WQP_attributes <- function(retval, ...){
     attr(retval, "queryTime") <- Sys.time()
   }
 
-  #If WQP adds a parameter metadata service/files, we could add that here.
   return(retval)
 }
 

R/readWQPqw.R

@@ -33,7 +33,8 @@
 #' numerics based on a standard algorithm. If false, everything is returned as a character.
 #' @param ignore_attributes logical to choose to ignore fetching site and parameter
 #' attributes. Default is \code{FALSE}.
-#' @param legacy Logical. If TRUE, use legacy WQP services. Default is FALSE.
+#' @param legacy Logical. If TRUE, uses legacy WQP services. Default is TRUE.
+#' Setting legacy = FALSE uses WQX3.0 WQP services, which are in-development, use with caution.
 #' @keywords data import USGS web service
 #' @return A data frame derived from the default data profile.
 #'
@@ -52,10 +53,9 @@
 #' \donttest{
 #' rawPcode <- readWQPqw("USGS-01594440", "01075", "", "")
 #' 
-#' attr(rawPcode, "url")
 #' attr(rawPcode, "siteInfo")
 #' attr(rawPcode, "queryTime")
-#' attr(rawPcode, "headerInfo")[["dataProviders"]]
+#' 
 #' 
 #' rawCharacteristicName <- readWQPqw("WIDNR_WQX-10032762", "Specific conductance", "", "")
 #' rawPHsites <- readWQPqw(c("USGS-05406450", "USGS-05427949", "WIDNR_WQX-133040"), "pH", "", "")
@@ -68,7 +68,7 @@ readWQPqw <- function(siteNumbers,
                       startDate = "",
                       endDate = "",
                       tz = "UTC",
-                      legacy = FALSE,
+                      legacy = TRUE,
                       querySummary = FALSE,
                       ignore_attributes = FALSE,
                       convertType = TRUE) {
@@ -88,7 +88,6 @@ readWQPqw <- function(siteNumbers,
 
     if(legacy){
       sites <- unique(retval$MonitoringLocationIdentifier)
-      wqp_message()
     } else {
       sites <- unique(retval$Location_Identifier)
     }
@@ -97,6 +96,11 @@ readWQPqw <- function(siteNumbers,
       retval <- create_WQP_attributes(retval, siteid = sites)
     } 
 
+    if(legacy){
+      wqp_message()
+    } else {
+      wqp_message_beta
+    }
     attr(retval, "url") <- url
 
     return(retval)