tests/testthat/tests_imports.R

In usgs/dataRetrieval: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data

context("importRDB_noCRAN")

test_that("External importRDB1 tests", {
  testthat::skip_on_cran()
  
  siteNumber <- "02177000"
  startDate <- "2012-09-01"
  endDate <- "2012-10-01"
  offering <- "00003"
  property <- "00060"
   
  obs_url <- constructNWISURL(siteNumber,property,
            startDate,endDate,"dv",format="tsv")
  data <- importRDB1(obs_url)
  expect_is(data$datetime, 'Date') 
  
  urlMultiPcodes <- constructNWISURL("04085427",c("00060","00010"),
          startDate,endDate,"dv",statCd=c("00003","00001"),"tsv")
  multiData <- importRDB1(urlMultiPcodes)
  pCodeCols <- grep("X", colnames(multiData))
  expect_true(length(pCodeCols)/2 > 2)
  
  unitDataURL <- constructNWISURL(siteNumber,property,
          "2013-11-03","2013-11-03","uv",format="tsv") #includes timezone switch
  unitData <- importRDB1(unitDataURL, asDateTime=TRUE)
  
  # Need to think of a way to automatically check timezone conversion:
#   expect_that(as.numeric(unitData[which(unitData$tz_cd == "EST")[1],"datetime"]),
#               equals(as.numeric(as.POSIXct("2013-11-03 01:00:00", tz="UTC")+60*60*5)))
  
  
  qwURL <- constructNWISURL(c('04024430','04024000'),
           c('34247','30234','32104','34220'),
          "2010-11-03","","qw",format="rdb") 
  qwData <- importRDB1(qwURL, tz="America/Chicago")
  expect_is(qwData$sample_dt, 'Date')
  expect_is(qwData$startDateTime, 'POSIXct')
  
 
  site <- "05427850"

  url <- constructNWISURL(site,"00060","2015-01-01", "","dv",
                          format="tsv",
                          statCd = "laksjd")
  # And....now there's data there:
  expect_error(importRDB1(url))
})

context("importRDB")
test_that("CRAN-friendly importRDB test", {
  filePath <- system.file("extdata", package="dataRetrieval")
  fileName <- "RDB1Example.txt"
  fullPath <- file.path(filePath, fileName)
  importUserRDB <- importRDB1(fullPath)
  
  # default is to turn dates to characters
  expect_is(importUserRDB$datetime, 'Date')
  
})

context("importWaterML1")
test_that("CRAN-friendly importWaterML1 test", {
  filePath <- system.file("extdata", package="dataRetrieval")
  fileName <- "WaterML1Example.xml"
  fullPath <- file.path(filePath, fileName)
  importUserWML1 <- importWaterML1(fullPath, asDateTime = TRUE)
  # default is to turn dates to characters
  expect_is(importUserWML1$dateTime, 'POSIXct')
  
})

test_that("External importWaterML1 test", {
  testthat::skip_on_cran()

  siteNumber <- "02177000"
  startDate <- "2012-09-01"
  endDate <- "2012-10-01"
  offering <- '00003'
  property <- '00060'
  obs_url <- constructNWISURL(siteNumber,property,startDate,endDate,'dv')

  data <- importWaterML1(obs_url,TRUE)
  expect_is(data$dateTime, 'POSIXct')

  groundWaterSite <- "431049071324301"
  startGW <- "2013-10-01"
  endGW <- "2014-06-30"
  groundwaterExampleURL <- constructNWISURL(groundWaterSite, NA,
           startGW,endGW, service="gwlevels")
  groundWater <- importWaterML1(groundwaterExampleURL)

  expect_is(groundWater$dateTime, 'character')

  unitDataURL <- constructNWISURL(siteNumber,property,
          "2020-10-30","2020-11-01",'uv')
  unitData <- importWaterML1(unitDataURL,TRUE)
  expect_is(unitData$dateTime, 'POSIXct')

  # Two sites, two pcodes, one site has two data descriptors
  siteNumber <- c('01480015',"04085427") #one site seems to have lost it's 2nd dd
  obs_url <- constructNWISURL(siteNumber,c("00060","00010"),startDate,endDate,'dv')
  data <- importWaterML1(obs_url)
  
  expect_true(length(unique(data$site_no)) == 2)
  expect_true(ncol(data) == 8) # 3 data, 3 remark codes, and 4 (agency, site, dateTime, tz)

  inactiveSite <- "05212700"
  inactiveSite <- constructNWISURL(inactiveSite, "00060", "2014-01-01", "2014-01-10",'dv')
  inactiveSite <- importWaterML1(inactiveSite)
  expect_true(nrow(inactiveSite) == 0)

  inactiveAndActive <- c("07334200","05212700")
  inactiveAndActive <- constructNWISURL(inactiveAndActive, "00060", 
                                        "2014-01-01", "2014-12-31",'dv')
  inactiveAndActive <- importWaterML1(inactiveAndActive)
  # 
  # The inactive site became active, need a new test.
  # expect_true(length(unique(inactiveAndActive$site_no)) < 2)
  
  
  #raw XML
  url <- constructNWISURL(service = 'dv', siteNumber = '02319300', parameterCd = "00060", 
                          startDate = "2014-01-01", endDate = "2014-01-01")
  raw <- httr::content(httr::GET(url), as = 'raw')
  rawParsed <- importWaterML1(raw)
  expect_true(nrow(rawParsed) > 0)
  expect_true(data.class(rawParsed$X_00060_00003) == "numeric")
  
  #no data
  url <- constructNWISURL("05212700", "00060", "2014-01-01", "2014-01-10",'dv', statCd = "00001")
  noData <- importWaterML1(url) 
  expect_true(class(attr(noData,"url"))=="character")
  expect_true(all(dim(noData)==0))
  
  url <- constructNWISURL(service = 'iv', site = c('02319300','02171500'), 
                          startDate = "2015-04-04", endDate = "2015-04-05")
  data <- importWaterML1(url, tz = "America/New_York", asDateTime = TRUE)
  expect_true(data.class(data$dateTime) == "POSIXct")
  expect_true(nrow(data) > 0)
  
  expect_error(readNWISdata(sites="05114000", 
                              service="iv",
                              parameterCd="00060",
                              startDate="2014-05-01T00:00",
                              endDate="2014-05-01T12:00",
                              tz="blah"))

  arg.list <- list(sites="05114000", 
                   parameterCd="00060",
                   startDate="2014-05-01T00:00",
                   endDate="2014-05-01T12:00")
  
  chi_iv <- readNWISdata(arg.list, 
                         service="iv",
                         tz="America/Chicago")
  
  expect_true(all(chi_iv$tz_cd == "America/Chicago"))
  expect_equal(chi_iv$dateTime[1], as.POSIXct("2014-05-01T00:00", format = "%Y-%m-%dT%H:%M", tz="America/Chicago"))
  expect_equal(chi_iv$dateTime[nrow(chi_iv)], as.POSIXct("2014-05-01T12:00", format = "%Y-%m-%dT%H:%M", tz="America/Chicago"))
  
})

# test_that("no data val replacement works", {
  #may need to change dates and/or site if this data is estimated
  #run this test when changing anything with ML1 parser!
  # iceSite <- "04024430"
  # naData <- readNWISuv(siteNumbers = iceSite, parameterCd = "00060",
  #                      startDate = "2017-12-17", endDate = "2017-12-18")
  # expect_gt(sum(is.na(naData$X_00060_00000)), 0)
  # expect_false(any(na.omit(naData$X_00060_00000 < -99)))
# })

context("importWaterML2")

test_that("importWaterML2 internal test", {
  filePath <- system.file("extdata", package="dataRetrieval")
  fileName <- "WaterML2Example.xml"
  xml_full <- xml2::read_xml(file.path(filePath, fileName))
  measurementTS <- xml2::xml_find_all(xml_full, "//wml2:MeasurementTimeseries")
  UserData <- importWaterML2(measurementTS)
  expect_is(UserData$value, 'numeric')
  # expect_is(UserData$qualifier, 'character')
  
})

test_that("importWaterML2 external test", {
  testthat::skip_on_cran()
  url <- "https://waterservices.usgs.gov/nwis/iv/?format=waterml,2.0&sites=01646500&parameterCd=00060,00065"
  xml <- getWebServiceData(url)
  measurementTS2 <- xml2::xml_find_all(xml, "//wml2:MeasurementTimeseries")
  exData <- importWaterML2(measurementTS2)
  expect_is(exData$value, 'numeric')
  expect_gt(nrow(exData),0)
})
  

context("importWQP_noCRAN")

test_that("External WQP tests", {
  testthat::skip_on_cran()
 
  rawSampleURL <- constructWQPURL('USGS-01594440','01075', '', '')
  rawSample <- importWQP(rawSampleURL)
  expect_is(rawSample$ActivityStartDateTime, 'POSIXct')
  
  url2 <- constructWQPURL('USGS-01594440','01075', '', '', zip = FALSE)
  rawSample2 <- suppressWarnings(importWQP(url2, FALSE))
  expect_is(rawSample2$ActivityStartDateTime, 'POSIXct')
  
  STORETex <- constructWQPURL('WIDNR_WQX-10032762','Specific conductance', '', '')
  STORETdata <- importWQP(STORETex)
  expect_is(STORETdata$ActivityStartDateTime, 'POSIXct')
})