Nothing
context("General functions")
test_that("General NWIS retrievals working", {
testthat::skip_on_cran()
multiSite <- readNWISdata(
sites = c("04025500", "040263491"), service = "iv",
parameterCd = "00060",
startDate = "2020-11-01", endDate = "2020-11-02"
)
expect_is(multiSite$dateTime, "POSIXct")
recent_uv <- readNWISdata(
siteNumber = "04025500", parameterCd = "00060",
service = "uv",
startDate = as.Date(Sys.Date() - 10),
endDate = Sys.Date()
)
expect_equal(grep(
x = attr(recent_uv, "url"),
pattern = "https://waterservices.usgs.gov/nwis/iv/"
), 1)
older_uv <- readNWISdata(
siteNumber = "04025500",
parameterCd = "00060",
service = "uv",
startDate = "2016-01-01",
endDate = "2016-01-02"
)
expect_equal(grep(
x = attr(older_uv, "url"),
pattern = "https://nwis.waterservices.usgs.gov/nwis/iv/"
), 1)
expect_error(readNWISdata(), "No arguments supplied")
expect_error(readNWISdata(siteNumber = NA), "NA's are not allowed in query")
bBoxEx <- readNWISdata(bBox = c(-83, 36.5, -81, 38.5), parameterCd = "00010")
expect_true(length(unique(bBoxEx$site_no)) > 1)
startDate <- as.Date("2013-10-01")
endDate <- as.Date("2014-09-30")
waterYear <- readNWISdata(
bBox = c(-83, 36.5, -81, 38.5),
parameterCd = "00010",
service = "dv",
startDate = startDate,
endDate = endDate
)
expect_is(waterYear$dateTime, "POSIXct")
siteInfo <- readNWISdata(
stateCd = "WI",
parameterCd = "00010",
hasDataTypeCd = "iv",
service = "site"
)
expect_is(siteInfo$station_nm, "character")
gw_data <- readNWISdata(
stateCd = "AL",
service = "gwlevels",
startDate = "2024-05-01",
endDate = "2024-05-30")
expect_true(nrow(gw_data) > 0)
expect_equal(attr(gw_data, "url"),
"https://nwis.waterdata.usgs.gov/nwis/gwlevels?state_cd=AL&begin_date=2024-05-01&end_date=2024-05-30&date_format=YYYY-MM-DD&rdb_inventory_output=file&TZoutput=0&range_selection=date_range&list_of_search_criteria=state_cd&format=rdb")
gw_data2 <- readNWISdata(
state_cd = "AL",
service = "gwlevels",
startDate = "2024-05-01",
endDate = "2024-05-30")
expect_equal(nrow(gw_data), nrow(gw_data2))
# nolint start: line_length_linter
url <- "https://waterservices.usgs.gov/nwis/dv/?site=09037500&format=rdb&ParameterCd=00060&StatCd=00003&startDT=1985-10-02&endDT=2012-09-06"
dv <- importRDB1(url, asDateTime = FALSE)
# nolint end
dailyStat <- readNWISdata(
site = c("03112500", "03111520", "02319394"),
service = "stat", statReportType = "daily",
statType = c("p25", "p50", "p75", "min", "max"),
parameterCd = "00065",
convertType = FALSE
)
expect_true(length(dailyStat$min_va) > 1)
expect_is(dailyStat$p25_va, "character")
waterYearStat <- readNWISdata(
site = c("01646500"),
service = "stat", statReportType = "annual",
statYearType = "water", missingData = "on"
)
expect_is(waterYearStat$mean_va, "numeric")
expect_is(waterYearStat$parameter_cd, "character")
# Empty data
# note....not empty anymore!
# nolint start: line_length_linter
urlTest <- "https://nwis.waterservices.usgs.gov/nwis/iv/?site=11447650&format=waterml,1.1&ParameterCd=63680&startDT=2016-12-13&endDT=2016-12-13"
x <- importWaterML1(urlTest)
expect_true(all(c("agency_cd", "site_no", "dateTime", "tz_cd") %in% names(x)))
# nolint end
# Test list:
args <- list(
sites = "05114000", service = "iv",
parameterCd = "00060",
startDate = "2014-05-01T00:00Z",
endDate = "2014-05-01T12:00Z"
)
instData <- readNWISdata(args)
args <- list(
sites = "05114000", service = "dv",
parameterCd = "00060",
startDate = "2014-05-01",
endDate = "2014-05-01"
)
dailyData <- readNWISdata(args)
expect_lt(nrow(dailyData), nrow(instData))
args <- list(stateCd = "OH", parameterCd = "00665")
sites <- whatNWISsites(args)
expect_type(sites, "list")
# Test counties:
dailyStaffordVA <- readNWISdata(
stateCd = "Virginia",
countyCd = "Stafford",
parameterCd = "00060",
startDate = "2015-01-01",
endDate = "2015-01-30"
)
expect_gt(nrow(dailyStaffordVA), 1)
AS <- readNWISdata(stateCd = "AS", service = "site")
expect_gt(nrow(AS), 0)
site_id <- "01594440"
rating_curve <- readNWISdata(
service = "rating",
site_no = site_id,
file_type = "base"
)
rating_curve2 <- readNWISrating(
siteNumber = site_id,
type = "base"
)
expect_equal(
attr(rating_curve, "url"),
"https://waterdata.usgs.gov/nwisweb/get_ratings/?site_no=01594440&file_type=base"
)
expect_equal(rating_curve$INDEP, rating_curve2$INDEP)
state_rating_list <- readNWISdata(
service = "rating",
file_type = "base",
period = 24
)
expect_true(all(names(state_rating_list) %in% c(
"agency_cd",
"site_no",
"type",
"update_time",
"url"
)))
multi_hucs <- c("07130007", "07130011")
multi_huc <- dataRetrieval::readNWISdata(
huc = multi_hucs,
parameterCd = "63680",
startDate = "2015-06-18",
endDate = "2015-06-18",
service = "dv"
)
expect_equal(2, nrow(multi_huc))
peak_data <- readNWISdata(
service = "peak",
state_cd = "PA"
)
expect_lt(nrow(peak_data), 100000)
peak_data <- readNWISdata(
service = "peak",
huc2_cd = "20"
)
expect_lt(nrow(peak_data), 100000)
})
test_that("whatNWISdata", {
# no service specified:
availableData <- whatNWISdata(siteNumber = "05114000")
expect_equal(ncol(availableData), 24)
uvData <- whatNWISdata(siteNumber = "05114000", service = "uv")
expect_equal(unique(uvData$data_type_cd), "uv")
# multiple services
uvDataMulti <- whatNWISdata(
siteNumber = c("05114000", "09423350"),
service = c("uv", "dv")
)
expect_true(all(unique(uvDataMulti$data_type_cd) %in% c("uv", "dv")))
# state codes:
flowAndTemp <- whatNWISdata(
stateCd = "WI", service = c("uv", "dv"),
parameterCd = c("00060", "00010"),
statCd = "00003"
)
expect_true(all(unique(flowAndTemp$data_type_cd) %in% c("uv", "dv")))
expect_true(all(unique(flowAndTemp$parm_cd) %in% c("00060", "00010")))
expect_true(all(unique(flowAndTemp$stat_cd) %in% c("00003", NA)))
# site service
sites <- whatNWISdata(stateCd = "WI", service = "site")
expect_true(all(c("gw", "sv", "qw", "dv", "pk", "uv")
%in% unique(sites$data_type_cd)))
})
test_that("General WQP retrievals working", {
testthat::skip_on_cran()
nameToUse <- "pH"
# pHData <- readWQPdata(siteid = "USGS-04024315",
# characteristicName = nameToUse,
# service = "ResultWQX3")
# expect_is(pHData$Activity_StartDateTime, "POSIXct")
#
# # testing lists:
# startDate <- as.Date("2022-01-01")
# secchi.names <- c("Depth, Secchi disk depth",
# "Secchi depth",
# "Water transparency, Secchi disc",
# "Depth, Secchi disk depth (choice list)")
# # "Transparency, Secchi tube with disk",
# # "Secchi Reading Condition (choice list)",
# # "Depth, Secchi disk visible at bottom (Y/N) (choice list)")
#
# args_2 <- list(
# "startDateLo" = startDate,
# "startDateHi" = "2024-01-01",
# statecode = "WI",
# characteristicName = secchi.names
# )
#
# # Testing multiple lists:
# arg_3 <- list(
# "startDateLo" = startDate,
# "startDateHi" = "2023-12-31"
# )
# arg_4 <- list(
# statecode = "WI",
# characteristicName = secchi.names
# )
#
# lakeData <- readWQPdata(args_2, ignore_attributes = TRUE)
# expect_true(nrow(lakeData) > 0)
# lakeSites <- whatWQPsites(args_2)
# expect_type(lakeSites, "list")
#
# wqp.summary_no_atts <- readWQPdata(
# siteid = "USGS-04024315",
# characteristicName = nameToUse,
# ignore_attributes = TRUE,
# service = "ResultWQX3"
# )
# expect_true(!all(c("siteInfo", "variableInfo") %in% names(attributes(wqp.summary_no_atts))))
#
# rawPcode <- readWQPqw("USGS-01594440", "01075", "", "", legacy = FALSE)
# expect_true(all(c("url", "queryTime", "siteInfo", "headerInfo") %in%
# names(attributes(rawPcode))))
#
# # This means wqp_check_status was called:
# expect_true("dataProviders" %in% names(attr(rawPcode, "headerInfo")))
rawPcode2 <- readWQPqw("USGS-01594440", "01075", "", "", ignore_attributes = TRUE)
expect_true(all(!c( "queryTime", "siteInfo") %in%
names(attributes(rawPcode2))))
# This means wqp_check_status wasn't called:
expect_false("dataProviders" %in% names(attr(rawPcode2, "headerInfo")))
# pHData <- readWQPdata(siteid = "USGS-04024315",
# characteristicName = "pH",
# service = "ResultWQX3")
# expect_true(all(c("url", "queryTime", "siteInfo", "headerInfo") %in%
# names(attributes(pHData))))
#
# # This means wqp_check_status was called:
# expect_true("dataProviders" %in% names(attr(pHData, "headerInfo")))
#
# pHData2 <- readWQPdata(siteid = "USGS-04024315",
# characteristicName = "pH",
# ignore_attributes = TRUE,
# service = "ResultWQX3")
# expect_true(all(!c("queryTime", "siteInfo") %in%
# names(attributes(pHData2))))
#
# # This means wqp_check_status was called:
# expect_false("dataProviders" %in% names(attr(pHData2, "headerInfo")))
#
# 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)
#
# expect_true("dataProviders" %in% names(count_info))
})
test_that("zeroPad handles NAs", {
toPad <- c(1, 5, 55, NA)
padded <- zeroPad(toPad, 3)
expect_true(identical(c("001", "005", "055", NA), padded))
})
test_that("Dates with no days can be handled", {
testthat::skip_on_cran()
empty_df <- readNWISgwl("425957088141001", startDate = "1980-01-01")
expect_true(nrow(empty_df) > 0)
})
context("whatWQPsamples")
test_that("whatWQPsamples working", {
testthat::skip_on_cran()
# The warning is caused by a confirmed bug in WQP
siteInfo <- whatWQPsamples(siteid = "USGS-01594440")
expect_true(nrow(siteInfo) > 0)
})
context("whatWQPmetrics")
test_that("whatWQPmetrics working", {
testthat::skip_on_cran()
type <- "Stream"
siteInfo <- whatWQPmetrics(countycode = "US:55:025", siteType = type)
expect_true(ncol(siteInfo) >= 21)
})
context("whatWQPdata")
test_that("whatWQPdata working", {
testthat::skip_on_cran()
site1 <- whatWQPdata(siteid = "USGS-01594440")
expect_is(site1, "data.frame")
expect_equal(1, nrow(site1))
type <- "Stream"
sites <- whatWQPdata(countycode = "US:55:025", siteType = type)
expect_gt(nrow(sites), 1)
lakeSites <- whatWQPdata(siteType = "Lake, Reservoir, Impoundment", statecode = "US:55")
expect_is(lakeSites$activityCount, "numeric")
})
context("whatNWISsites")
test_that("whatNWISsites working", {
testthat::skip_on_cran()
siteListPhos <- whatNWISsites(stateCd = "OH", parameterCd = "00665")
expect_true(nrow(siteListPhos) > 0)
expect_true(is.numeric(siteListPhos$dec_lat_va))
bboxSites <- whatNWISsites(bbox = c(-92.5, 45.4, -87, 47), parameterCd = "00060")
expect_true(nrow(bboxSites) > 0)
expect_true(is.numeric(bboxSites$dec_lat_va))
#gwlevels:
info <- whatNWISsites(stateCd = "NY", service="gwlevels")
expect_true(nrow(info) > 0)
expect_equal(attr(info, "url"), "https://waterservices.usgs.gov/nwis/site/?stateCd=NY&format=mapper&hasDataTypeCd=gw")
})
context("readWQPdots")
test_that("readWQPdots working", {
testthat::skip_on_cran()
# bbox vector turned into single string with coords separated by semicolons
formArgs_bbox <- dataRetrieval:::readWQPdots(bbox = c(-92.5, 45.4, -87, 47))
expect_true(length(formArgs_bbox) == 2)
expect_true(length(gregexpr(",", formArgs_bbox)[[1]]) == 3)
# NWIS names (siteNumber) converted to WQP expected names (siteid)
formArgs_site <- dataRetrieval:::readWQPdots(siteNumber = "04010301")
expect_true(length(formArgs_site) == 2)
expect_true("siteid" %in% names(formArgs_site$values))
expect_false("siteNumber" %in% names(formArgs_site$values))
# NWIS names (stateCd) converted to WQP expected names (statecode)
formArgs <- dataRetrieval:::readWQPdots(stateCd = "OH", parameterCd = "00665")
expect_true(length(formArgs$values) == 2)
expect_true("statecode" %in% names(formArgs$values))
expect_false("stateCd" %in% names(formArgs$values))
bbox <- c(-86.97361, 34.48827, -86.61349, 34.65623)
what_bbox <- whatWQPdata(bBox = bbox)
expect_true(nrow(what_bbox) > 0)
x <- whatWQPsites(bBox = bbox)
expect_true(nrow(x) > 0)
df <- readWQPdata(bBox = bbox,
characteristicName = "Total Coliform",
startDateLo = "2023-01-01",
startDateHi = "2023-12-31",
service = "ResultWQX3",
dataProfile = "narrow")
expect_true(nrow(df) > 0)
df_legacy <- readWQPdata(bBox = bbox,
characteristicName = "Total Coliform",
startDateLo = "2023-01-01",
startDateHi = "2023-12-31",
service = "Result",
dataProfile = "narrowResult")
expect_true(nrow(df_legacy) > 0)
})
context("getWebServiceData")
test_that("long urls use POST", {
testthat::skip_on_cran()
baseURL <- dataRetrieval:::drURL("Result")
url <- paste0(baseURL,
rep("reallylongurl", 200),
collapse = ""
)
with_mock(
RETRY = function(method, ...) {
return(method == "POST")
},
status_code = function(resp) 200,
headers = function(resp) list(`content-type` = "logical"),
content = function(resp, encoding) resp,
expect_true(getWebServiceData(url)),
.env = "httr"
)
})
test_that("ngwmn urls don't use post", {
testthat::skip_on_cran()
baseURL <- dataRetrieval:::drURL("NGWMN")
url <- paste0(baseURL,
rep("urlwithngwmn", 200),
collapse = ""
)
with_mock(
RETRY = function(method, ...) {
return(method == "POST")
},
status_code = function(resp) 200,
headers = function(resp) list(`content-type` = "logical"),
content = function(resp, encoding) resp,
expect_false(getWebServiceData(url)),
.env = "httr"
)
})
test_that("400 errors return a verbose error", {
testthat::skip_on_cran()
# nolint start: line_length_linter
url <- "https://waterservices.usgs.gov/nwis/site/?stateCd=IA&bBox=-92.821445,42.303044,-92.167168,42.646524&format=mapper"
# nolint end
expect_message(getWebServiceData(url))
})
test_that("internal functions", {
# get empty_col type
expect_equal(dataRetrieval:::empty_col("numeric"), numeric())
expect_equal(dataRetrieval:::empty_col("character"), character())
expect_equal(dataRetrieval:::empty_col("Date"), as.Date(numeric(), origin = "1970-01-01"))
# add empty columns
df1 <- data.frame(
a = 1:2,
b = c("a", "b"),
c = as.Date(c("2010-01-01", "2010-01-02")),
stringsAsFactors = FALSE
)
df2 <- data.frame(
d = 1:2,
b = c("a", "b"),
e = factor(c("c", "d")),
stringsAsFactors = FALSE
)
df2_ret <- dataRetrieval:::add_empty_col(df2, df1, c("a", "c"))
df1_ret <- dataRetrieval:::add_empty_col(df1, df2, c("d", "e"))
expect_true(ncol(df2_ret) == 5)
expect_true(ncol(df1_ret) == 5)
expect_true(all(is.na(df2_ret[, c("a", "c")])))
expect_true(all(is.na(df1_ret[, c("d", "e")])))
bound_df <- dataRetrieval:::r_bind_dr(df1, df2)
expect_true(nrow(bound_df) == 4)
expect_true(class(bound_df$c) == "Date")
expect_true(class(bound_df$a) == "integer")
expect_true(class(bound_df$b) == "character")
})
test_that("profiles", {
testthat::skip_on_cran()
# Data profiles: "Organization Data"
org_data <- readWQPdata(
statecode = "WI",
countycode = "Dane",
service = "Organization"
)
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName"
) %in% names(org_data)))
# Data profiles: "Site Data Only"
site_data <- readWQPdata(
statecode = "WI",
countycode = "Dane",
service = "StationWQX"
)
expect_true(all(c("ProviderName", "Location_Identifier") %in% names(site_data)))
# Data profiles: "Project Data"
project_data <- readWQPdata(
statecode = "WI",
countycode = "Dane",
service = "Project"
)
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName"
) %in% names(project_data)))
# Data profiles: "Project Monitoring Location Weighting Data"
proj_mlwd <- readWQPdata(
statecode = "WI",
countycode = "Dane",
service = "ProjectMonitoringLocationWeighting"
)
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName"
) %in% names(proj_mlwd)))
# Data profiles: "narrow":
# samp_data <- readWQPdata(
# siteid = "USGS-04024315",
# service = "ResultWQX3",
# dataProfile = "narrow"
# )
#
# expect_true(all(c(
# "Activity_StartDateTime",
# "LastChangeDate"
# ) %in% names(samp_data)))
# Data profiles: "Sample Results (biological metadata)"
samp_bio <- readWQPdata(
siteid = "USGS-04024315",
dataProfile = "biological",
service = "Result"
)
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName"
) %in% names(samp_bio)))
# Data profiles: "Sample Results (narrow)"
samp_narrow <- readWQPdata(
siteid = "USGS-04024315",
dataProfile = "narrowResult",
service = "Result"
)
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName"
) %in% names(samp_narrow)))
# Data profiles: "Sampling Activity"
samp_activity <- readWQPdata(
siteid = "USGS-04024315",
dataProfile = "activityAll",
service = "Activity"
)
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName"
) %in% names(samp_activity)))
# # Data profile: "Sampling Activity Metrics"
# act_metrics <- readWQPdata(
# statecode = "WI",
# countycode = "Dane",
# service = "ActivityMetric"
# )
#
# expect_true(all(c(
# "OrganizationIdentifier",
# "OrganizationFormalName"
# ) %in% names(act_metrics)))
# Data profile: "Result Detection Quantitation Limit Data"
dl_data <- readWQPdata(
siteid = "USGS-04024315",
service = "ResultDetectionQuantitationLimit"
)
expect_true(all(c(
"OrganizationIdentifier",
"OrganizationFormalName"
) %in% names(dl_data)))
})
test_that("readWQPsummary", {
testthat::skip_on_cran()
dane_county_data <- readWQPsummary(
countycode = "US:55:025",
summaryYears = 5,
siteType = "Stream"
)
summary_names <- c(
"Provider",
"MonitoringLocationIdentifier",
"YearSummarized",
"CharacteristicType",
"CharacteristicName",
"ActivityCount",
"ResultCount",
"LastResultSubmittedDate",
"OrganizationIdentifier",
"OrganizationFormalName",
"MonitoringLocationName",
"MonitoringLocationTypeName",
"ResolvedMonitoringLocationTypeName",
"HUCEightDigitCode",
"MonitoringLocationUrl",
"CountyName",
"StateName",
"MonitoringLocationLatitude",
"MonitoringLocationLongitude"
)
expect_true(all(summary_names %in% names(dane_county_data)))
expect_true(diff(range(dane_county_data$YearSummarized)) <= 5)
lake_sites <- readWQPsummary(
siteType = "Lake, Reservoir, Impoundment",
CharacteristicName = "Temperature, water",
countycode = "US:55:025"
)
expect_true(all(summary_names %in% names(lake_sites)))
expect_true(diff(range(lake_sites$YearSummarized)) >= 5)
site1 <- readWQPsummary(
siteid = "USGS-07144100",
summaryYears = 5
)
expect_type(site1$ActivityCount, "double")
expect_type(site1$MonitoringLocationIdentifier, "character")
# nolint start: line_length_linter
expect_equal(
attr(site1, "url"),
"https://www.waterqualitydata.us/data/summary/monitoringLocation/search?siteid=USGS-07144100&summaryYears=5&dataProfile=periodOfRecord&mimeType=csv"
)
# nolint end
})
test_that("importWQP convertType", {
testthat::skip_on_cran()
# rawSampleURL_NoZip <- constructWQPURL("USGS-01594440", "01075", "", "")
# rawSampleURL_NoZip_char <- importWQP(rawSampleURL_NoZip, convertType = FALSE)
# expect_is(rawSampleURL_NoZip_char$Result_Measure, "character")
#
# Put back in when services get more robust.
# phos <- readWQPdata(statecode = "WI", countycode = "Dane",
# characteristicName = "Phosphorus",
# startDateLo = "2022-06-01",
# startDateHi = "2022-09-01",
# convertType = FALSE,
# service = "ResultWQX")
# expect_is(phos$Result_Measure, "character")
SC <- readWQPqw(siteNumbers = "USGS-05288705", parameterCd = "00300",
convertType = FALSE, legacy = FALSE)
expect_is(SC$Result_Measure, "character")
lakeSites_chars <- whatWQPdata(
siteType = "Lake, Reservoir, Impoundment",
statecode = "US:55", convertType = FALSE
)
expect_is(lakeSites_chars$lat, "character")
})
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