inst/tests/test_various.R

In RObsDat: Store your observations: R-Package to the Observations Data Model from CUAHSI

context("various")

if(FALSE){

test_that("NA data does not produce an error", {
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	example(addDataValues)
	example.data <- xts(c(5,6,NA), seq(as.POSIXct("2012-01-01", tz="UTC"), as.POSIXct("2013-01-01", tz="UTC"), length.out=3))
	addDataValues(example.data, Site="test", Variable="test_dist",  Source="Madeup", QualityControlLevel="ok")
	})


test_that("multicolumn import works correctly with timeseries", {
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	example(addDataValues)
	example.data <- xts(data.frame(a=1:3, b=4:6), seq(as.POSIXct("2012-01-01", tz="UTC"), as.POSIXct("2013-01-01", tz="UTC"), length.out=3))
	
	addVariable(Name="Distance", Unit="cm", ValueType="Field Observation", GeneralCategory="Instrumentation", Code="test_dist_2")
	addVariable(Name="Distance", Unit="cm", ValueType="Field Observation", GeneralCategory="Instrumentation", Code="test_dist_3")

	addDataValues(example.data, Site="test", Variable=c("test_dist_2", "test_dist_3"),  Source="Madeup", QualityControlLevel="ok")

	inDB <- getDataMatrix(variables=c("test_dist_2", "test_dist_3"), select.time=index(example.data))
	expect_that(inDB$data[1,1,], is_equivalent_to(coredata(example.data)[,1]))
	expect_that(inDB$data[1,2,], is_equivalent_to(coredata(example.data)[,2]))

	})

test_that("multicolumn import works correctly with multi variable, multi site data", {
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	example(addDataValues)
	example.data <- data.frame(a=1:3, b=4:6)

	
	addVariable(Code="test_dist_2", Name="Distance", Unit="cm", ValueType="Field Observation", GeneralCategory="Instrumentation")
	addVariable(Name="Distance", Unit="cm", ValueType="Field Observation", GeneralCategory="Instrumentation", Code="test_dist_3")

	addSite(Code="test_2", Name="Virtual test site 2", x=-5, y=46, LatLongDatum="WGS84", Elevation=1500, State="Germany")
	addSite(Code="test_3", Name="Virtual test site 3", x=-5, y=46, LatLongDatum="WGS84", Elevation=1500, State="Germany")

	addDataValues(Date=as.POSIXct("2012-01-01", tz="UTC"), Value=example.data, Site=c("test","test_2","test_3"), Variable=c("test_dist_2", "test_dist_3"),  Source="Madeup", QualityControlLevel="ok")


	#let's fail if too many entries in database
	options(warn=2)
	inDB <- getDataMatrix(variables=c("test_dist_2", "test_dist_3"), select.time=as.POSIXct("2012-01-01", tz="UTC"))
	options(warn=1)
	expect_that(inDB[,1], equals(example.data[,1]))
	expect_that(inDB[,2], equals(example.data[,2]))

	})


test_that("no duplicates are generated from multiple calls", {
	#Setup
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	example(addDataValues)
	  #count records
	c.variable <- NROW(getMetadata("Variable"))
	c.site <- NROW(getMetadata("Site"))
	c.meta <- NROW(getMetadata("ISOMetadata"))
	c.source <- NROW(getMetadata("Source"))
	c.data <- NROW(getDataValues()@values)
	  #second call
	exampleCommands()
	#example(addDataValues)
	#Confirmations
	expect_that(c.variable, equals(NROW(getMetadata("Variable"))))
	expect_that(c.site, equals(NROW(getMetadata("Site"))))
	expect_that(c.meta, equals(NROW(getMetadata("ISOMetadata"))))
	expect_that(c.source, equals(NROW(getMetadata("Source"))))
	#ToDo: check why one is missing.
	expect_that(c.data, equals(NROW(getDataValues()@values)))
		})

test_that("Duplicates in dataset to import are detected", {
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	example(addDataValues)
	example.data4 <- cbind(101:109)
	addVariable(Name="Water depth", Unit="cm", ValueType="Field Observation", GeneralCategory="Instrumentation", Code="test_height")

	date.data4 <- seq(as.POSIXct("2011-02-02", tz="UTC"), as.POSIXct("2012-01-01", tz="UTC"), length.out=3)
	expect_error(addDataValues(Value=example.data4, Date=rep(date.data4, 3), Site="test", Variable=rep(c("test_height", "test_dist", "test_height"), each=3),  Source="Madeup", QualityControlLevel="ok"))


		})

test_that("Multicolumn-Data can be imported", {
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	example(addDataValues)
	addVariable(Name="Water depth", Unit="cm", ValueType="Field Observation", GeneralCategory="Instrumentation", Code="test_height")
	example.data2 <- xts(2001:2366, seq(as.POSIXct("2010-01-01", tz="UTC"), as.POSIXct("2011-01-01", tz="UTC"), length.out=366))
	addDataValues(example.data2, Site="test", Variable="test_height",  Source="Madeup", QualityControlLevel="ok")

	example.data3 <- xts(cbind(1:10,11:20), seq(as.POSIXct("2011-01-02", tz="UTC"), as.POSIXct("2012-01-01", tz="UTC"), length.out=10))
	addDataValues(example.data3, Site="test", Variable=c("test_height", "test_dist"),  Source="Madeup", QualityControlLevel="ok")


	#Worldbank example
	example.data4 <- cbind(101:120)
	date.data4 <- seq(as.POSIXct("2011-02-02", tz="UTC"), as.POSIXct("2012-01-01", tz="UTC"), length.out=10)
	addDataValues(Value=example.data4, Date=c(date.data4, date.data4), Site="test", Variable=rep(c("test_height", "test_dist"), each=10),  Source="Madeup", QualityControlLevel="ok")


		})
test_that("Download of QUASHI vocabulary works", {
	#Setup
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	try(getMetadata("Site"))
	getMetadata("Site")
	unit.meta <- getMetadata("Units")
	

	#Confirmations
	expect_that(NROW(unit.meta)>200, equals(TRUE))
		})

test_that("CV table not working correctly with wrong arguments", {
	on.exit( { cat("Exiting and deleting RODM.db\n")
				unlink("RODM.db")})
	getDefaultDB()
	#Setup
	#oldwarn <- getOption("warn")
	#options(warn=2)
        expect_that(
		getMetadata(table = "VariableName", EXACT = TRUE, ID = 0),
		throws_error("Multiple datasets")
		)
	#must produce an error, not a warning
	#options(warn=oldwarn)

	#Confirmations
	#expect_that(1, equals(1))
	#expect_that(1:10, is_equivalent_to(1:10))
		})

test_that("", {
	#Setup

	#Confirmations
	expect_that(1, equals(1))
	expect_that(1:10, is_equivalent_to(1:10))
		})
}