R/readWQPdata.R

In dataRetrieval: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data

#' General Data Import from Water Quality Portal
#'
#' Imports data from Water Quality Portal web service. This function gets the data from here:
#' <https://www.waterqualitydata.us>.
#'
#' This function uses \dots as a query input, which can be very flexible, but also
#' has a steeper learning curve. For a quick overview, scroll down to the Examples
#' in this help file to see many query options.
#'
#' @details
#'
#' There are currently 10 legacy options
#' for data provided by the Water Quality Portal:
#'
#'
#' Legacy:
#' \tabular{lll}{
#' WQP Radio Button \tab service argument \tab Base URL  \cr
#' Sample Results \tab Result \tab /data/Result/search \cr
#' Site Data Only \tab Station \tab /data/Station/search \cr
#' Sampling Activity \tab Activity \tab /data/Activity/search \cr
#' Sampling Activity Metrics \tab ActivityMetric \tab /data/ActivityMetric/search \cr
#' Site Summary (not advertised on WQP)  \tab SiteSummary \tab /data/summary/monitoringLocation/search \cr
#' Project Data \tab Project \tab /data/Project/search \cr
#' Project Monitoring Location Weighting Data \tab ProjectMonitoringLocationWeighting \tab /data/ProjectMonitoringLocationWeighting/search \cr
#' Result Detection Quantitation Limit Data \tab ResultDetectionQuantitationLimit \tab /data/ResultDetectionQuantitationLimit/search \cr
#' Biological Habitat Metrics \tab BiologicalMetric \tab /data/BiologicalMetric/search \cr
#' 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 <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
#' description for this help file. One way to figure out how to construct a WQP query is to go to the "Advanced"
#' form in the Water Quality Portal. Use the form to discover what parameters are available. Once the query is
#' set in the form, scroll down to the "Query URL". You will see the parameters
#' after "https://www.waterqualitydata.us/#". For example, if you chose "Nutrient"
#' in the Characteristic Group dropdown, you will see characteristicType=Nutrient
#' in the Query URL. The corresponding argument for dataRetrieval is
#' characteristicType = "Nutrient". dataRetrieval users do not need to include
#' mimeType, and providers is optional (these arguments are picked automatically).
#' @param service character. See Details for more information.
#' @param querySummary logical to only return the number of records and unique sites that
#' will be returned from this query. Choosing TRUE is deprecated, readWQPsummary
#' is recommended instead.
#' @param tz character to set timezone attribute of dateTime. Default is "UTC", and converts the
#' date times 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", as well as the following which do not use daylight savings
#' time: "America/Honolulu",
#' "America/Jamaica","America/Managua","America/Phoenix", and "America/Metlakatla".
#' See also  `OlsonNames()`
#' for more information on time zones.
#' @param ignore_attributes logical to choose to ignore fetching site and status
#' attributes. Default is `FALSE`.
#' @param convertType logical, defaults to `TRUE`. If `TRUE`, the function
#' will convert the data to dates, datetimes,
#' numerics based on a standard algorithm. If false, everything is returned as a character.
#' @keywords data import WQP web service
#' @return A data frame, the specific columns will depend on the "service" and/or "dataProfile".
#'
#' There are also several useful attributes attached to the data frame:
#' \tabular{lll}{
#' Name \tab Type \tab Description \cr
#' url \tab character \tab The url used to generate the data \cr
#' siteInfo \tab data.frame \tab A data frame containing information on the requested sites \cr
#' headerInfo \tab data.frame \tab A data frame returned from the WQP status service \cr
#' queryTime \tab POSIXct \tab The time the data was returned \cr
#' }
#' @export
#' @examplesIf is_dataRetrieval_user()
#' \donttest{
#'
#' # Legacy:
#' nameToUse <- "pH"
#' pHData <- readWQPdata(siteid = "USGS-04024315",
#'                       characteristicName = nameToUse)
#' ncol(pHData)
#' attr(pHData, "siteInfo")
#' attr(pHData, "queryTime")
#' attr(pHData, "url")
#'
#' # WQX3:
#' pHData_wqx3 <- readWQPdata(siteid = "USGS-04024315",
#'                            characteristicName = nameToUse,
#'                            service = "ResultWQX3",
#'                            dataProfile = "basicPhysChem")
#' attr(pHData_wqx3, "url")
#'
#' # More examples:
#' # querying by county
#' DeWitt <- readWQPdata(
#'   statecode = "Illinois",
#'   countycode = "DeWitt",
#'   characteristicName = "Nitrogen"
#' )
#'
#' attr(DeWitt, "url")
#'
#' DeWitt_wqx3 <- readWQPdata(
#'    statecode = "Illinois",
#'    countycode = "DeWitt",
#'    characteristicName = "Nitrogen",
#'    service = "ResultWQX3",
#'    dataProfile = "basicPhysChem",
#'    ignore_attributes = TRUE)
#'
#' attr(DeWitt_wqx3, "url")
#'
#' # Data profile: "Sampling Activity"
#' activity <- readWQPdata(
#'   siteid = "USGS-04024315",
#'   service = "Activity"
#' )
#' attr(activity, "url")
#'
#' # activity_wqx3 <- readWQPdata(
#' #   siteid = "USGS-04024315",
#' #   service = "ActivityWQX3"
#' # )
#' # attr(activity_wqx3, "url")
#'
#' Dane_activity <- readWQPdata(
#'   statecode = "Wisconsin",
#'   countycode = "Dane",
#'   startDateLo = "2023-01-01",
#'   startDateHi = "2023-12-31",
#'   service = "Activity"
#' )
#' attr(Dane_activity, "url")
#'
#' # Dane_activity_wqx3 <- readWQPdata(
#' #   statecode = "Wisconsin",
#' #   countycode = "Dane",
#' #   startDateLo = "2023-01-01",
#' #   startDateHi = "2023-12-31",
#' #   service = "ActivityWQX3"
#' # )
#' # attr(Dane_activity_wqx3, "url")
#'
#' ########################################################
#' # Additional examples:
#'
#'
#' # Data profiles: "Organization Data"
#' org_data <- readWQPdata(
#'   statecode = "WI",
#'   countycode = "Dane",
#'   service = "Organization"
#' )
#'
#' # Data profiles: "Project Data"
#' project_data <- readWQPdata(
#'   statecode = "WI",
#'   countycode = "Dane",
#'   service = "Project"
#' )
#'
#' # Data profiles: "Project Monitoring Location Weighting Data"
#' proj_mlwd <- readWQPdata(
#'   statecode = "WI",
#'   countycode = "Dane",
#'   service = "ProjectMonitoringLocationWeighting"
#' )
#'
#' # Data profiles: "Sample Results (physical/chemical metadata)"
#' samp_data <- readWQPdata(
#'   siteid = "USGS-04024315",
#'   dataProfile = "resultPhysChem",
#'   service = "Result"
#' )
#'
#' # Data profiles: "Sample Results (biological metadata)"
#' samp_bio <- readWQPdata(
#'   siteid = "USGS-04024315",
#'   dataProfile = "biological",
#'   service = "Result"
#' )
#'
#'
#' # Data profiles: "Sample Results (narrow)"
#' samp_narrow <- readWQPdata(
#'   siteid = "USGS-04024315",
#'   service = "Result",
#'   dataProfile = "narrowResult"
#' )
#'
#' # samp_narrow_wqx3 <- readWQPdata(
#' #   siteid = "USGS-04024315",
#' #   service = "ResultWQX3",
#' #   dataProfile = "narrow"
#' # )
#'
#'
#' # Data profiles: "Sampling Activity"
#' samp_activity <- readWQPdata(
#'   siteid = "USGS-04024315",
#'   dataProfile = "activityAll",
#'   service = "Activity"
#' )
#'
#' # Data profile: "Sampling Activity Metrics"
#' act_metrics <- readWQPdata(
#'   statecode = "WI",
#'   countycode = "Dane",
#'   service = "ActivityMetric"
#' )
#'
#' # Data profile: "Result Detection Quantitation Limit Data"
#' dl_data <- readWQPdata(
#'   siteid = "USGS-04024315",
#'   service = "ResultDetectionQuantitationLimit"
#' )
#'
#' # other options:
#' Phosphorus <- readWQPdata(
#'   statecode = "WI", countycode = "Dane",
#'   characteristicName = "Phosphorus",
#'   startDateLo = "2023-01-01",
#'   ignore_attributes = TRUE,
#'   convertType = FALSE
#' )
#'
#' rawPHsites_legacy <- readWQPdata(siteid = c("USGS-05406450", "USGS-05427949", "WIDNR_WQX-133040"),
#'                         characteristicName = "pH",
#'                         service = "Result",
#'                         dataProfile = "narrowResult" )
#'
#' # rawPHsites <- readWQPdata(siteid = c("USGS-05406450", "USGS-05427949", "WIDNR_WQX-133040"),
#' #                           characteristicName = "pH",
#' #                           service = "ResultWQX3",
#' #                           dataProfile = "narrow" )
#'
#' }
readWQPdata <- function(
  ...,
  service = "Result",
  querySummary = FALSE,
  tz = "UTC",
  ignore_attributes = FALSE,
  convertType = TRUE
) {
  tz <- match.arg(tz, OlsonNames())

  service <- match.arg(
    service,
    c(
      "Result",
      "Station",
      "Activity",
      "ActivityMetric",
      "SiteSummary",
      "Project",
      "ProjectMonitoringLocationWeighting",
      "ResultDetectionQuantitationLimit",
      "BiologicalMetric",
      "Organization",
      "ResultWQX3",
      "StationWQX3",
      "ActivityWQX3"
    ),
    several.ok = FALSE
  )

  legacy <- is_legacy(service)

  valuesList <- readWQPdots(..., legacy = legacy)
  values <- valuesList[["values"]]

  baseURL <- httr2::request(pkg.env[[service]])
  POST <- FALSE

  if (!legacy) {
    if (service == "ResultWQX3" & !"dataProfile" %in% names(values)) {
      baseURL <- httr2::req_url_query(baseURL, dataProfile = "fullPhysChem")
    }
    baseURL <- httr2::req_url_query(baseURL, !!!values, .multi = "explode")
  } else {
    if ("siteid" %in% names(values)) {
      if (length(values[["siteid"]]) > 1) {
        sites <- values[["siteid"]]
        POST <- nchar(paste0(sites, collapse = "")) > 2048

        baseURL <- get_or_post(
          baseURL,
          POST = POST,
          siteid = sites,
          .multi = function(x) paste0(x, collapse = ";")
        )
        values <- values[names(values) != "siteid"]
      }
    }
    baseURL <- get_or_post(baseURL, POST = POST, !!!values, .multi = "explode")
  }

  if (querySummary) {
    retquery <- getQuerySummary(baseURL)
    return(retquery)
  } else {
    retval <- importWQP(baseURL, tz = tz, convertType = convertType)

    if (is.null(retval)) {
      return(NULL)
    }

    attr(retval, "legacy") <- legacy

    if (
      !all(is.na(retval)) &&
        !ignore_attributes &&
        !service %in% c("Station", "StationWQX")
    ) {
      params <- convertLists(...)
      params <- params[!names(params) %in% c("dataProfile", "service")]
      retval <- create_WQP_attributes(retval, params)
    }

    attr(retval, "url") <- baseURL$url

    if (legacy) {
      wqp_message()
    } else {
      wqp_message_beta()
      attr(retval, "wqp-request-id") <- attr(
        retval,
        "headerInfo"
      )$`wqp-request-id`
    }

    return(retval)
  }
}


create_WQP_attributes <- function(retval, ...) {
  col_legacy <- c(
    "CharacteristicName", #legacy
    "ResultMeasure.MeasureUnitCode",
    "ResultSampleFractionText"
  )
  col_wqx3 <- c(
    "Result_Characteristic", #wqx3
    "Result_MeasureUnit",
    "Result_SampleFraction"
  )
  if (all(col_legacy %in% names(retval))) {
    retvalVariableInfo <- retval[, col_legacy]
    retvalVariableInfo <- unique(retvalVariableInfo)
    names(retvalVariableInfo) <- c(
      "characteristicName",
      "param_units",
      "valueType"
    )

    attr(retval, "variableInfo") <- retvalVariableInfo
  } else if (all(col_wqx3 %in% names(retval))) {
    retvalVariableInfo <- retval[, col_wqx3]
    retvalVariableInfo <- unique(retvalVariableInfo)
    names(retvalVariableInfo) <- c(
      "characteristicName",
      "param_units",
      "valueType"
    )

    attr(retval, "variableInfo") <- retvalVariableInfo
  }

  siteInfo <- suppressWarnings(whatWQPsites(
    ...,
    legacy = attr(retval, "legacy")
  ))
  attr(retval, "siteInfo") <- siteInfo

  if (!attr(retval, "legacy")) {
    attr(retval, "headerInfo") <- wqp_check_status(
      attr(retval, "headerInfo")$`wqp-request-id`
    )
    attr(retval, "queryTime") <- as.POSIXct(
      attr(retval, "headerInfo")[["requestStartTime"]],
      format = "%Y-%m-%dT%H:%M:%OS",
      tz = "UTC"
    )
  } else {
    attr(retval, "queryTime") <- Sys.time()
  }

  return(retval)
}

#' Get WQP service metadata
#'
#' The information from this request is only available for a
#' limited time after the original query from the WQP. In the
#' readWQPdata and readWQPqw functions, the results from this
#' function will be attached as an attribute to the data.
#'
#' @param wqp_request_id A character returned from the header
#' of a WQP request.
#' @return a list generated from the WQP describing what data
#' was returned.
#' @export
#'
#' @examplesIf is_dataRetrieval_user()
#' \donttest{
#' rawPcode <- readWQPqw("USGS-01594440", "01075",
#'                       ignore_attributes = TRUE, legacy = FALSE)
#' headerInfo <- attr(rawPcode, "headerInfo")
#' wqp_request_id <- headerInfo$`wqp-request-id`
#' count_info <- wqp_check_status(wqp_request_id)
#' count_info[["dataProviders"]]
#' }
wqp_check_status <- function(wqp_request_id) {
  id_url <- paste0(pkg.env[["status"]], wqp_request_id)
  counts_list <- get_nldi_sources(id_url)
  return(counts_list)
}