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Merge pull request DOI-USGS#866 from ldecicco-USGS/develop
Add wildcard CQL
2 parents df7edad + 7cdbe0c commit 12fe6c8

25 files changed

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‎.gitignore‎

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@@ -17,3 +17,5 @@ vignettes/*.R
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/.quarto/
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**/*.quarto_ipynb

‎DESCRIPTION‎

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Package: dataRetrieval
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Type: Package
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Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality Data
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Version: 2.7.22.9001
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Version: 2.7.23
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Authors@R: c(
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person("Laura", "DeCicco", role = c("aut","cre"),
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email = "ldecicco@usgs.gov",

‎NEWS‎

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dataRetrieval 2.7.22.9000
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dataRetrieval 2.7.23
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===================
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* Added data.table to Imports
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* Added read_waterdata_stats_por and read_waterdata_stats_daterange to access USGS daily data statistics.
@@ -16,6 +16,9 @@ the request attribute
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* Added read_waterdata_field_meta, read_waterdata_combine_meta,
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and read_waterdata_channel
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* Removed readNWISgwl and readNWISmeas as services have been turned off
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* Updated CQL2 templates to allow HUC queries specifically to use a wildcard
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to get multiple inclusive HUCs.
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* Add deprecation message to readNGWMN functions. read_ngwmn will be coming soon.
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dataRetrieval 2.7.22

‎R/citations.R‎

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@@ -13,7 +13,9 @@
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#'
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#' @examples
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#' \donttest{
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#' nwisData <- readNWISdv("04085427", "00060", "2012-01-01", "2012-06-30")
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#' nwisData <- read_waterdata_daily(monitoring_location_id = "USGS-04085427",
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#' parameter_code = "00060",
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#' time = c("2012-01-01", "2012-06-30"))
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#' nwis_citation <- create_NWIS_bib(nwisData)
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#' nwis_citation
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#'
@@ -24,16 +26,14 @@ create_NWIS_bib <- function(x){
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textVersion <- paste0("U.S. Geological Survey, ",
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format(attr(x, "queryTime"), "%Y"),
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", National Water Information System data available on the World Wide Web (USGS Water Data for the Nation), accessed ",
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", USGS Water Data for the Nation: U.S. Geological Survey National Water Information System database, accessed ",
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format(attr(x, "queryTime"), "%b %d, %Y"),
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", at ",
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attr(x, "url"),
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", https://dx.doi.org/10.5066/F7P55KJN")
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", at https://dx.doi.org/10.5066/F7P55KJN")
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ref <- utils::bibentry(
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bibtype = "Manual",
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textVersion = textVersion,
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title = "National Water Information System data available on the World Wide Web (USGS Water Data for the Nation)",
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title = "USGS Water Data for the Nation: U.S. Geological Survey National Water Information System database",
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author = utils::person("U.S. Geological Survey"),
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doi = "10.5066/F7P55KJN",
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note = paste("Accessed", format(attr(x, "queryTime"), "%b %d, %Y")),

‎R/construct_api_requests.R‎

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@@ -54,7 +54,9 @@ construct_api_requests <- function(service,
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"computation_identifier")
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if(service %in% c("monitoring-locations", "parameter-codes",
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"time-series-metadata")){
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"time-series-metadata",
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"field-measurements-metadata",
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"combined-metadata")){
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comma_params <- c(comma_params, "id")
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}
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@@ -138,14 +140,19 @@ construct_api_requests <- function(service,
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baseURL <- baseURL |>
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httr2::req_headers(`Content-Type` = "application/query-cql-json")
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post_params <- list(
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"params" = unname(post_params)
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)
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template_path_post <- system.file("templates/post.CQL2", package = "dataRetrieval")
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template_post <- readChar(template_path_post, file.info(template_path_post)$size)
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if(length(post_params) > 1){
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post_params <- list(
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"params" = unname(post_params)
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)
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template_path_post <- system.file("templates/post.CQL2", package = "dataRetrieval")
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template_post <- readChar(template_path_post, file.info(template_path_post)$size)
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x <- whisker::whisker.render(template_post, post_params)
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} else {
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x <- post_params[[1]]
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}
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x <- whisker::whisker.render(template_post, post_params)
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baseURL <- httr2::req_body_raw(baseURL, x)
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} else {
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#' dataRetrieval:::cql2_param(parameter)
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#'
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cql2_param <- function(parameter){
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template_path <- system.file("templates/param.CQL2", package = "dataRetrieval")
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template <- readChar(template_path, file.info(template_path)$size)
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parameters <- paste0(unlist(parameter), collapse = '", "')
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parameters <- paste0('"', parameters, '"')
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parameter_list <- list("property" = names(parameter),
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"parameter" = parameters)
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return(whisker::whisker.render(template, parameter_list))
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# Wildcards:
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if(names(parameter) %in% c("hydrologic_unit_code")){
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template_path <- system.file("templates/param.CQL2.like", package = "dataRetrieval")
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template <- readChar(template_path, file.info(template_path)$size)
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params <- c()
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for(i in parameter[[1]]){
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parameter_list <- list("property" = names(parameter),
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"parameter" = i)
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params <- c(params,
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whisker::whisker.render(template, parameter_list))
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}
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template_path_or <- system.file("templates/post.CQL2.or", package = "dataRetrieval")
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template_or <- readChar(template_path_or, file.info(template_path_or)$size)
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post_params <- list(
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"params" = paste0(params, collapse = ", ")
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)
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cql_text <- whisker::whisker.render(template_or, post_params)
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} else { # INs
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parameters <- paste0(unlist(parameter), collapse = '", "')
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parameters <- paste0('"', parameters, '"')
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parameter_list <- list("property" = names(parameter),
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"parameter" = parameters)
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template_path <- system.file("templates/param.CQL2", package = "dataRetrieval")
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template <- readChar(template_path, file.info(template_path)$size)
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cql_text <- whisker::whisker.render(template, parameter_list)
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}
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return(cql_text)
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}
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‎R/get_ogc_data.R‎

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@@ -53,6 +53,8 @@ get_ogc_data <- function(args,
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# Mostly drop the id column except ts-meta, monitoring location:
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if(!service %in% c("monitoring-locations",
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"time-series-metadata",
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"field-measurements-metadata",
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"combined-metadata",
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"parameter-codes")){
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return_list <- return_list[, names(return_list)[names(return_list)!= output_id]]
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}
@@ -88,9 +90,9 @@ move_id_col <- function(df, output_id){
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"time_series_id")]
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}
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91-
if("field_visit_id" %in% names(df)){
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df <- df[, c(names(df)[names(df)!= "field_visit_id"],
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"field_visit_id")]
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if("field_series_id" %in% names(df)){
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df <- df[, c(names(df)[names(df)!= "field_series_id"],
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"field_series_id")]
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}
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return(df)

‎R/importWQP.R‎

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@@ -62,14 +62,12 @@ importWQP <- function(obs_url, tz = "UTC",
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}
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last_chars <- as.character(substr(doc, nchar(doc)-1, nchar(doc)))
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if(last_chars != c("\n")){
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doc <- paste0(doc, "\n")
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}
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retval <- suppressWarnings(readr::read_delim(doc,
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col_types = readr::cols(.default = "c"),
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quote = ifelse(csv, '\"', ""),
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delim = ifelse(csv, ",", "\t")))
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retval <- data.table::fread(text = doc, data.table = FALSE,
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sep = ifelse(csv, ",", "\t"),
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fill = TRUE,
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quote = ifelse(csv, '\"', ""))
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attr(retval, 'spec') <- NULL
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‎R/readNGWMNdata.R‎

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#' }
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#'
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readNGWMNdata <- function(service, ..., asDateTime = TRUE, tz = "UTC") {
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message("DISCLAIMER: NGWMN retrieval functions are still in flux,
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and no future behavior or output is guaranteed")
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.Deprecated("",
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msg = "read_ngwmn_data coming soon. Check back at
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https://doi-usgs.github.io/dataRetrieval/articles/Status.html
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for more information")
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dots <- convertLists(...)
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‎R/read_waterdata_combined_meta.R‎

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#' monitoring_location_id = c("USGS-07069000",
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#' "USGS-07064000",
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#' "USGS-07068000"),
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#' #end = c("2024-07-01T00:00:00Z", NA),
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#' end = "P1M",
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#' parameter_code = "00060")
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#'
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#'
127+
#' hucs <- read_waterdata_combined_meta(
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#' hydrologic_unit_code = c("11010008", "11010009"),
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#' site_type = c("Stream", "Spring")
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#' )
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#' }
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read_waterdata_combined_meta <- function(monitoring_location_id = NA_character_,
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parameter_code = NA_character_,

‎R/read_waterdata_field_measurements.R‎

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#' @param field_visit_id `r get_ogc_params("field-measurements")$field_visit_id`
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#' @param vertical_datum `r get_ogc_params("field-measurements")$vertical_datum`
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#' @param measuring_agency `r get_ogc_params("field-measurements")$measuring_agency`
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#' @param control_condition `r get_ogc_params("field-measurements")$control_condition`
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#' What and where the control of flow is for the gage pool.
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#' @param measurement_rated `r get_ogc_params("field-measurements")$measurement_rated`
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#' Rated measurement based on the hydrologic/hydraulic conditions in which the measurement was made
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#' (excellent (2 percent), good (5 percent), fair (8 percent), or poor (more than 8 percent). percent)
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#' @param properties A vector of requested columns to be returned from the query.
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#' Available options are:
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#' `r dataRetrieval:::get_properties_for_docs("field-measurements", "field_measurement_id")`.
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observing_procedure = NA_character_,
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vertical_datum = NA_character_,
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measuring_agency = NA_character_,
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control_condition = NA_character_,
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measurement_rated = NA_character_,
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skipGeometry = NA,
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time = NA_character_,
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bbox = NA,

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