Merge pull request #81 from ldecicco-USGS/master

New testing

.travis.yml

@@ -12,6 +12,7 @@ env:
      - R_BUILD_ARGS="--no-build-vignettes --no-manual"
      - R_CHECK_ARGS="--no-build-vignettes --no-manual --as-cran"
      - BOOTSTRAP_LATEX=""
+     - NOT_CRAN="true" 
 
 script: "./travis-tool.sh run_tests"
 
@@ -19,7 +20,8 @@ before_script:
   - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
   - chmod 755 ./travis-tool.sh
   - "./travis-tool.sh bootstrap"
-  - "./travis-tool.sh install_deps - ./travis-tool.sh install_r XML RCurl plyr reshape2 lubridate httr knitr xtable"
+  - "./travis-tool.sh install_deps - ./travis-tool.sh install_r XML RCurl plyr reshape2 lubridate httr knitr xtable testthat"
+
 
 on_failure:
   - "./travis-tool.sh dump_logs"

DESCRIPTION

 Package: dataRetrieval
 Type: Package
 Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
-Version: 2.1.1
+Version: 2.1.2
 Date: 2015-02-01
 Authors@R: c( person("Robert", "Hirsch", role = c("aut"),
     email = "rhirsch@usgs.gov"),

R/getWebServiceData.R

@@ -20,7 +20,7 @@
 getWebServiceData <- function(obs_url){
   possibleError <- tryCatch({
     h <- basicHeaderGatherer()
-    returnedDoc <- getURI(obs_url, headerfunction = h$update)      
+    returnedDoc <- getURI(obs_url, headerfunction = h$update, encoding='gzip')      
   }, warning = function(w) {
     warning(w, "with url:", obs_url)
   }, error = function(e) {

inst/tests/After_build_tests.R

-#Unit tests for tabbedDataRetrivals.R
-
-expect_that(formatCheckSiteNumber('01594440'),prints_text('01594440'))
-expect_that(formatCheckParameterCd('00001'),prints_text('00001'))
-expect_that(formatCheckDate('1985-01-01', "startDate"),prints_text('1985-01-01'))
-expect_that(dateFormatCheck('1985-01-01'), is_true())
-expect_that(dateFormatCheck('01/01/1985'), is_false())
-expect_that(checkStartEndDate('1985-01-01', '1985-01-31'), equals(c('1985-01-01', '1985-01-31')))
-
-DecYear <- c(1,1,2,3,4,4,5)
-ConcHigh <- c(1,2,3,4,5,5,6)
-dataInputForRemoveDuplicates <- data.frame(DecYear, ConcHigh)
-DecYear <- c(1,1,2,3,4,5)
-ConcHigh <- c(1,2,3,4,5,6)
-dataReturnForRemoveDuplicates <- data.frame(DecYear, ConcHigh)
-
-# actualReturnFromRemoveDuplicates <- removeDuplicates(dataInputForRemoveDuplicates)
-# expect_that(actualReturnFromRemoveDuplicates$DecYear, equals(dataReturnForRemoveDuplicates$DecYear))
-# expect_that(actualReturnFromRemoveDuplicates$ConcHigh, equals(dataReturnForRemoveDuplicates$ConcHigh))
-
-value <- c(1,2,3)
-code <- c("","","")
-dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-Date <- dateTime
-Q <- c(0.5, 1.0, 1.5)
-Qualifier <- code
-Julian <- c(49308.25, 49309.25, 49310.25)
-Month <- c(1,1,1)
-Day <- c(1,2,3)
-DecYear <- c(1985.00136612022, 1985.00409836066, 1985.00683060109)
-MonthSeq <- c(1621, 1621, 1621)
-LogQ <- c(-0.693147180559945, 0.0000000, 0.405465108108164)
-i <- c(1,2,3)
-comment1 <- c("","","")
-comment2 <- c("","<","")
-value2 <- c(2,3,4)
-comment3 <- c("","","<")
-value3 <- c(3,4,5)
-ConcLow <- c(6,6,7)
-ConcHigh <- c(6,9,12)
-Uncen <- c(1,0,0)
-ConcAve <- c(6.0,7.5,9.5)
-SinDY <- c(0.00858348109043033,0.0257479136805711,0.0429047581805647)
-CosDY <- c(0.999963161247638, 0.999668467513654, 0.999079166895931)
-
-dataReturnForPopulateDateColumns <- data.frame(Date,Julian,Month,Day,DecYear,MonthSeq,stringsAsFactors=FALSE)
-expect_that(populateDateColumns(dateTime), equals(dataReturnForPopulateDateColumns))
-
-dataInputForPopulateDaily <- data.frame(dateTime, value, code, stringsAsFactors=FALSE)
-Date <- as.Date(Date)
-dataReturnForPopulateDaily <- data.frame(Date, Q, dataReturnForPopulateDateColumns[,-1], Qualifier, LogQ, i, stringsAsFactors=FALSE)
-expect_that(populateDaily(dataInputForPopulateDaily, 2, interactive=FALSE), equals(dataReturnForPopulateDaily))
-
-dataInputForCompressData <- data.frame(dateTime, comment1, value, comment2, value2, comment3, value3, stringsAsFactors=FALSE)
-dataReturnForCompressData <- data.frame(dateTime, ConcLow, ConcHigh, Uncen, stringsAsFactors=FALSE)
-expect_that(compressData(dataInputForCompressData), equals(dataReturnForCompressData))
-
-dataInputForPopulateSampleData <- compressData(dataInputForCompressData)
-Date <- as.character(Date)
-dataReturnForPopulateSampleColumns <- data.frame(Date, ConcLow, ConcHigh, Uncen, ConcAve, dataReturnForPopulateDateColumns[,-1], SinDY, CosDY, stringsAsFactors=FALSE)
-expect_that(populateSampleColumns(dataInputForPopulateSampleData), equals(dataReturnForPopulateSampleColumns))
-
-code <- comment2
-dataInputForPopulateConcentrations <- data.frame(value, code, stringsAsFactors=FALSE)
-
-ConcLow <- c(1,0,3)
-ConcHigh <- c(1,2,3)
-Uncen <- c(1,0,1)
-dataReturnForPopulateConcentrations <- data.frame(ConcLow, ConcHigh, Uncen, stringsAsFactors=FALSE)
-expect_that(populateConcentrations(dataInputForPopulateConcentrations), equals(dataReturnForPopulateConcentrations))
-
-data(susQ)
-Daily1 <- getPreLoadedDailyData(susQ, interactive=FALSE)
-
-expect_that(Daily1$Date[1], equals(as.Date("1977-10-01")))
-expect_that(Daily1$Q[1], equals(2123.76348))
-expect_that(Daily1$Julian[1], equals(46659))
-expect_that(Daily1$Month[1], equals(10))
-expect_that(Daily1$Day[1], equals(274))
-expect_that(Daily1$DecYear[1], equals(1977.747268))
-expect_that(Daily1$MonthSeq[1], equals(1534))
-expect_that(Daily1$LogQ[1], equals(7.660945))
-expect_that(Daily1$Q7[7], equals(1723.28236))
-expect_that(Daily1$Q30[30], equals(2156.32785))
-
-
-
-
-
-
-
-
-
-
-
-

inst/tests/test_1.R

-expect_that(1 ^ 1, equals(1))
-expect_that(2 ^ 2, equals(4)) 
-expect_that(2 + 2 == 4, is_true())
-expect_that(2 == 1, is_false()) 
-expect_that(1, is_a('numeric')) 
-expect_that(print('Hello World!'), prints_text('Hello World!')) 
-expect_that(log('a'), throws_error()) 
-expect_that(factorial(16), takes_less_than(1))
\ No newline at end of file

inst/tests/test_2.R

-#Unit tests for tabbedDataRetrivals.R
-
-# dateFormatCheck:
-expect_that(dateFormatCheck('1985-01-01'), is_true())
-expect_that(dateFormatCheck('01/01/1985'), is_false())
-# formatCheckSiteNumber:
-# formatCheckDate:
-expect_that(formatCheckDate('1985-01-01', "startDate"),prints_text('1985-01-01'))
-# checkStartEndDate:
-expect_that(checkStartEndDate('1985-01-01', '1985-01-31'), equals(c('1985-01-01', '1985-01-31')))
-
-value <- c(1,2,3)
-code <- c("","","")
-dateTime <- c('1985-01-01', '1985-01-02', '1985-01-03')
-Date <- as.Date(dateTime)
-Q <- c(0.5, 1.0, 1.5)
-Qualifier <- code
-Julian <- c(49308, 49309, 49310)
-Month <- c(1,1,1)
-Day <- c(1,2,3)
-DecYear <- c(1985.00136612022, 1985.00409836066, 1985.00683060109)
-MonthSeq <- c(1621, 1621, 1621)
-LogQ <- c(-0.693147180559945, 0.0000000, 0.405465108108164)
-i <- c(1,2,3)
-comment1 <- c("","","")
-comment2 <- c("","<","")
-value2 <- c(2,3,4)
-comment3 <- c("","","<")
-value3 <- c(3,4,5)
-ConcLow <- c(6,6,7)
-ConcHigh <- c(6,9,12)
-Uncen <- c(1,0,0)
-ConcAve <- c(6.0,7.5,9.5)
-SinDY <- c(0.00858348109043033,0.0257479136805711,0.0429047581805647)
-CosDY <- c(0.999963161247638, 0.999668467513654, 0.999079166895931)
-
-dataReturnForPopulateDateColumns <- data.frame(Date,Julian,Month,Day,DecYear,MonthSeq,stringsAsFactors=FALSE)
-# populateDateColumns:
-dateTime <- as.Date(dateTime)
-expect_that(populateDateColumns(dateTime), equals(dataReturnForPopulateDateColumns))
-
-dataInputForPopulateDaily <- data.frame(dateTime, value, code, stringsAsFactors=FALSE)
-Date <- as.Date(Date)
-
-dataReturnForPopulateDaily <- data.frame(Date, Q, dataReturnForPopulateDateColumns[,-1], Qualifier, LogQ, i, stringsAsFactors=FALSE)
-# populateDaily:
-expect_that(populateDaily(dataInputForPopulateDaily, 2, interactive=FALSE), gives_warning())
-# expect_that(populateDaily(dataInputForPopulateDaily, 2, interactive=FALSE), equals(dataReturnForPopulateDaily))
-
-dataInputForCompressData <- data.frame(dateTime, comment1, value, comment2, value2, comment3, value3, stringsAsFactors=FALSE)
-dataReturnForCompressData <- data.frame(dateTime, ConcLow, ConcHigh, Uncen, stringsAsFactors=FALSE)
-# compressData:
-
-expect_that(compressData(dataInputForCompressData), equals(dataReturnForCompressData))
-
-dataInputForPopulateSampleData <- compressData(dataInputForCompressData)
-# Date <- as.character(Date)
-dataReturnForPopulateSampleColumns <- data.frame(Date, ConcLow, ConcHigh, Uncen, ConcAve, dataReturnForPopulateDateColumns[,-1], SinDY, CosDY, stringsAsFactors=FALSE)
-# populateSampleColumns
-
-code <- comment2
-dataInputForPopulateConcentrations <- data.frame(value, code, stringsAsFactors=FALSE)
-ConcLow <- c(1,0,3)
-ConcHigh <- c(1,2,3)
-Uncen <- c(1,0,1)
-dataReturnForPopulateConcentrations <- data.frame(ConcLow, ConcHigh, Uncen, stringsAsFactors=FALSE)
-# populateConcentrations:
-expect_that(populateConcentrations(dataInputForPopulateConcentrations), equals(dataReturnForPopulateConcentrations))
-
-# removeDuplicates:
-DecYear <- c(1,1,2,3,4,4,5)
-ConcHigh <- c(1,2,3,4,5,5,6)
-dataInputForRemoveDuplicates <- data.frame(DecYear, ConcHigh)
-DecYear <- c(1,1,2,3,4,5)
-ConcHigh <- c(1,2,3,4,5,6)
-dataReturnForRemoveDuplicates <- data.frame(DecYear, ConcHigh)
-actualReturnFromRemoveDuplicates <- removeDuplicates(dataInputForRemoveDuplicates)
-expect_that(actualReturnFromRemoveDuplicates$DecYear, equals(dataReturnForRemoveDuplicates$DecYear))
-expect_that(actualReturnFromRemoveDuplicates$ConcHigh, equals(dataReturnForRemoveDuplicates$ConcHigh))
-
-
-# retrieveNWISData:
-Daily2 <- getNWISdvData('01594440','00060', '1985-01-01', '1985-01-31')
-expect_that(Daily2$agency[1], equals("USGS"))
-expect_that(Daily2$site[1], equals("01594440"))
-
-# getNWISSiteInfo:
-INFO1 <- getNWISSiteInfo('01594440')
-expect_that(INFO1$station.nm, equals("PATUXENT RIVER NEAR BOWIE, MD"))
-
-# getNWISPcodeInfo:
-INFO2 <- getNWISPcodeInfo('01075')
-expect_that(INFO2$parameter_nm, equals("Silver, water, filtered, micrograms per liter"))
-
-# populateSiteINFO:
-INFO1 <- populateSiteINFO(INFO1, '01594440', interactive=FALSE)
-expect_that(INFO1$drainSqKm, equals(901.3158588))
-
-# populateParameterINFO:
-INFO2$param.nm <- INFO2$parameter_nm
-INFO2$param.units <- INFO2$parameter_units
-INFO2$paramShortName <- INFO2$srsname
-INFO2$paramNumber <- INFO2$parameter_cd
-
-# getDVData:
-Daily <- getNWISDaily('01594440','00060', '1985-01-01', '1985-03-31', interactive=FALSE)
-expect_that(Daily$Date[1], equals(as.Date("1985-01-01")))
-expect_that(Daily$Q[1], equals(4.44574488))
-expect_that(Daily$Julian[1], equals(49308))
-expect_that(Daily$Month[1], equals(1))
-expect_that(Daily$Day[1], equals(1))
-expect_that(Daily$DecYear[1], equals(1985.001366))
-expect_that(Daily$MonthSeq[1], equals(1621))
-expect_that(Daily$LogQ[1], equals(1.49194743))
-expect_that(Daily$Q7[7], equals(8.725634))
-
-# getSampleData:
-Sample <- getNWISSample('01594440','01075', '1985-01-01', '1985-03-31', interactive=FALSE)
-expect_that(Sample$Date, equals(as.Date("1985-03-13")))
-expect_that(Sample$ConcLow, equals(NA))
-expect_that(Sample$ConcHigh, equals(1))
-expect_that(Sample$Uncen, equals(0))
-expect_that(Sample$ConcAve, equals(0.5))
-expect_that(Sample$Julian, equals(49379))
-expect_that(Sample$Month, equals(3))
-

inst/tests/run-all.R → tests/testthat.R

 library(testthat)
 library(dataRetrieval)
-
-test_package("dataRetrieval")
\ No newline at end of file
+test_check("dataRetrieval")
\ No newline at end of file

tests/testthat/tests_userFriendly_fxns.R

+context("Unit values")
+
+test_that("Unit value data returns correct types", {
+  testthat::skip_on_cran()
+  
+  siteNumber <- '05114000'
+  parameterCd <- '00060'
+  startDate <- "2014-10-10"
+  endDate <- "2014-10-10"
+
+  rawData <- readNWISuv(siteNumber,parameterCd,startDate,endDate)
+  rawData <- renameNWISColumns(rawData)
+  timeZoneChange <- readNWISuv(c('04024430','04024000'),parameterCd,
+                               "2013-11-03","2013-11-03", 
+                               tz="America/Chicago")
+  
+  
+  timeZoneChange <- renameNWISColumns(timeZoneChange)
+  expect_is(rawData$dateTime, 'POSIXct')
+  expect_is(rawData$Flow_Inst, 'numeric')
+  expect_that(attr(rawData, "url"), equals(
+      "http://nwis.waterservices.usgs.gov/nwis/iv/?site=05114000&format=waterml,1.1&ParameterCd=00060&startDT=2014-10-10&endDT=2014-10-10")
+  )
+  #First switchover to standard time:
+  expect_that(as.numeric(timeZoneChange[which(timeZoneChange$tz_cd == "CST")[1],"dateTime"]),
+              equals(as.numeric(as.POSIXct("2013-11-03 01:00:00", tz="UTC")+60*60*6)))
+  
+})
+
+context("importRDB")
+test_that("CRAN-friendly importRDB test", {
+  filePath <- system.file("extdata", package="dataRetrieval")
+  fileName <- "RDB1Example.txt"
+  fullPath <- file.path(filePath, fileName)
+  importUserRDB <- importRDB1(fullPath)
+  
+  # default is to turn dates to characters
+  expect_is(importUserRDB$datetime, 'character')
+  
+})
+
+context("Peak, rating, meas")
+test_that("peak, rating curves, surface-water measurements", {
+  testthat::skip_on_cran()
+  
+  siteNumbers <- c('01594440','040851325')
+  data <- readNWISpeak(siteNumbers)
+  expect_is(data$agency_cd, 'character')
+  
+  #Rating curvs:
+  siteNumber <- '01594440'
+  data <- readNWISrating(siteNumber, "base")
+  expect_that(length(attr(data, "RATING")),equals(7))
+  
+  #Surface meas:
+  siteNumbers <- c('01594440','040851325')
+  data <- readNWISmeas(siteNumbers)
+  expect_is(data$agency_cd, 'character')
+})
+