tests/testthat/test-readXmlFile.R

In RstoxData: Tools to Read and Manipulate Fisheries Data

# NMD Biotic v3.1
example <- system.file("testresources","biotic3.1_example.xml", package="RstoxData")

context("test-readXmlFile: DOM parse NMD Biotic v3.1")
defaultParseBiotic <- readXmlFile(example, stream = F)
expect_true(all(c("mission", "fishstation", "catchsample", "individual", "agedetermination") %in% names(defaultParseBiotic)))
expect_equal(nrow(defaultParseBiotic$fishstation), 2)
expect_equal(defaultParseBiotic$fishstation$fishingbait[[1]], "1")

context("test-readXmlFile: stream parse NMD Biotic v3.1")
streamParseBiotic <- readXmlFile(example, stream = T)
expect_true(all(c("mission", "fishstation", "catchsample", "individual", "agedetermination") %in% names(streamParseBiotic)))
expect_equal(nrow(streamParseBiotic$fishstation), 2)
expect_equal(streamParseBiotic$fishstation$fishingbait[[1]], "1")

# NMD Biotic v3
example <- system.file("testresources","biotic_v3_example.xml", package="RstoxData")

context("test-readXmlFile: DOM parse NMD biotic v3")
defaultParseBiotic <- readXmlFile(example, stream = F)
expect_true(all(c("mission", "fishstation", "catchsample", "individual", "agedetermination") %in% names(defaultParseBiotic)))
expect_equal(nrow(defaultParseBiotic$fishstation), 2)

context("test-readXmlFile: stream parse NMD biotic v3")
streamParseBiotic <- readXmlFile(example, stream = T)
expect_true(all(c("mission", "fishstation", "catchsample", "individual", "agedetermination") %in% names(streamParseBiotic)))
expect_equal(nrow(streamParseBiotic$fishstation), 2)

# NMD Echosounder
example <- system.file("testresources","libas_ListUserFile20__L40.0-2259.9_small.xml", package="RstoxData")

context("test-readXmlFile: DOM echosounder")
defaultParseEchosounder <- readXmlFile(example, stream = F)
expect_equal(nrow(defaultParseEchosounder$distance), 2)

context("test-readXmlFile: stream parse echosounder")
streamParseEchosounder <- readXmlFile(example, stream = T)
expect_equal(nrow(streamParseEchosounder$distance), 2)

# NMD Landing
example <- system.file("testresources","landing.xml", package="RstoxData")

context("test-readXmlFile: stream parse landing")
streamParse <- readXmlFile(example, stream = T)
expect_true(all(c("Art", "Dellanding", "Fangstdata", "Landingsdata", "Seddellinje") %in% names(streamParse)))
expect_false(any(is.na(streamParse$Produkt$Rundvekt)))
expect_false(all(is.na(streamParse$Produkt$Registreringsmerke_seddel)))

# Encodings
example <- system.file("testresources","biotic_v3_example.xml", package="RstoxData")

context("test-readXmlFile: Data text encoding")
encParse <- readXmlFile(example, stream = F)
expect_true(encParse$mission$missiontypename[1] == "Prøvebåt")
encParse <- readXmlFile(example, stream = T)
expect_true(encParse$mission$missiontypename[1] == "Prøvebåt")

context("test-readXmlFile: Path encoding")
testing <- paste0(tempfile(pattern=""), "_bio_å_prøve.xml")
file.copy(example, testing)
encParse <- readXmlFile(testing, stream = F)
expect_true(encParse$mission$missiontypename[1] == "Prøvebåt")
encParse <- readXmlFile(testing, stream = T)
expect_true(encParse$mission$missiontypename[1] == "Prøvebåt")
unlink(testing)

# ICES data
context("test-readXmlFile: ICES acoustic and biotic data reading")
icesFiles <- c("ICES_Acoustic_1.xml", "ICES_Biotic_1.xml", "ICES_Acoustic_2.xml", "ICES_Biotic_2.xml")
exampleDir <- system.file("testresources","", package="RstoxData")
print(paste0(exampleDir, "/", icesFiles))

for(item in icesFiles) {
	icesDataA <- readXmlFile(paste0(exampleDir, "/", item), stream = T)
	icesDataB <- readXmlFile(paste0(exampleDir, "/", item), stream = F)
	# There should be minimal differences (in the Survey table only)
	expect_true(length(all.equal(icesDataA, icesDataB)) <= 1)
}

# Zipped files:
context("test-readXmlFile: Zipped acoustic file")
example <- system.file("testresources", "echosounder_2020821.zip", package="RstoxData")
parsedAcousticZip <- readXmlFile(example)
expect_equal(parsedAcousticZip$sa$sa[1], 67.7185200)

context("test-readXmlFile: Zipped biotic file")
example <- system.file("testresources", "biotic_2020821.zip", package="RstoxData")
parsedBioticZip <- readXmlFile(example)
expect_equal(parsedBioticZip$individual$individualweight[1], 0.022)