tests/testthat/test_local_odf.R

In dankelley/oce: Analysis of Oceanographic Data

# vim:textwidth=80:expandtab:shiftwidth=4:softtabstop=4

# INSTRUCTIONS: Any time a new file is added to local_data, add
# some tests here.

library(oce)
CRATwarning <- "\"conductivity\" \\(code name \"CRAT_01\"\\)" # portion of the warning

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Flemish Cap adcp file (with malformed CODEs and units)", {
        # some CODE values lack ' characters (like EWCT_01, line 252
        d <- read.oce("local_data/flemish_cap/MADCPS_hud2013021_1840_12556-106_3600.ODF")
        expect_equal(names(d[["data"]]), c("u", "v", "w", "errorVelocity", "a", "unknown", "time"))
        orig <-  list(u="EWCT_01", v="NSCT_01", w="VCSP_01", errorVelocity="ERRV_01",
            a="BEAM_01", unknown="UNKN_01", time="SYTM_01")
        expect_equal(d[["dataNamesOriginal"]], orig)
        # units (erroneously, 'M/s' in file, instead of 'm/s')
        expect_equal(d[["uUnit"]]$unit, expression(m/s))
        expect_equal(d[["vUnit"]]$unit, expression(m/s))
        expect_equal(d[["wUnit"]]$unit, expression(m/s))
        expect_equal(d[["errorVelocityUnit"]]$unit, expression(m/s))
    })}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Flemish Cap microcat file (with malformed CODE tokens that lack ' characters)", {
        expect_silent(d <- read.oce("local_data/flemish_cap/MCM_HUD2013021_1840_2305_300.ODF"))
        # oce names
        expect_equal(names(d[["data"]]), c("temperature", "pressure", "time", "conductivity", "salinity", "theta", "sigmaTheta"))
        # original names
        orig <- list(temperature="TEMP_01", pressure="PRES_01",
            time="SYTM_01", conductivity="CRAT_01",
            salinity="PSAL_01", theta="POTM_01", sigmaTheta="SIGP_01")
        expect_equal(d[["dataNamesOriginal"]], orig)
        # units
        expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["pressureUnit"]]$unit, expression(dbar))
        expect_equal(d[["conductivityUnit"]]$unit, expression())
        expect_equal(d[["salinityUnit"]]$unit, expression())
        expect_equal(d[["thetaUnit"]]$unit, expression(degree*C))
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression(kg/m^3))
})}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Bedford Basin CTD profile 1 (with proper CODE tokens)", {
        expect_silent(d <- read.oce("local_data/bedford_basin/CTD_BCD2010667_001_01_DN.ODF"))
        expect_equal(d[["startTime"]], as.POSIXct("2010-01-05 13:23:29", tz="UTC"))
        # oce names
        expect_equal(names(d[["data"]]),
            c("scan", "pressure", "temperature", "conductivity", "oxygenCurrent", "oxygenTemperature", "unknown",
                "fluorescence", "PSAR", "salinity", "oxygen", "sigmaTheta"))
        # original names
        orig <- list(scan="CNTR_01", pressure="PRES_01", temperature="TEMP_01",
            conductivity="CRAT_01", oxygenCurrent="OCUR_01",
            oxygenTemperature="OTMP_01", unknown="UNKN_01",
            fluorescence="FLOR_01", PSAR="PSAR_01",
            salinity="PSAL_01", oxygen="DOXY_01", sigmaTheta="SIGP_01")
        expect_equal(d[["dataNamesOriginal"]], orig)
        # units
        expect_equal(d[["pressureUnit"]]$unit, expression(dbar))
        expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["conductivityUnit"]]$unit, expression())
        expect_equal(d[["oxygenCurrentUnit"]]$unit, expression(mu*a))
        expect_equal(d[["oxygenTemperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["fluorescenceUnit"]]$unit, expression(mg/m^3))
        expect_equal(d[["PSARUnit"]]$unit, expression(mu*mol/m^2/s))
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression(kg/m^3))
})}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Bedford Basin CTD profile 2 (with proper CODE tokens)", {
        expect_silent(d <- read.oce("local_data/bedford_basin/CTD_BCD2011667_001_01_DN.ODF"))
        expect_equal(d[["startTime"]], as.POSIXct("2011-01-05 09:10:36", tz="UTC"))
        # oce names
        expect_equal(names(d[["data"]]),
            c("scan", "pressure", "temperature", "conductivity", "oxygenCurrent", "oxygenTemperature", "unknown",
                "fluorescence", "PSAR", "salinity", "oxygen", "sigmaTheta"))
        # original names
        orig <- list(scan="CNTR_01", pressure="PRES_01", temperature="TEMP_01",
            conductivity="CRAT_01", oxygenCurrent="OCUR_01",
            oxygenTemperature="OTMP_01", unknown="UNKN_01",
            fluorescence="FLOR_01", PSAR="PSAR_01",
            salinity="PSAL_01", oxygen="DOXY_01", sigmaTheta="SIGP_01")
        expect_identical(d[["dataNamesOriginal"]], orig)
        # units
        expect_equal(d[["pressureUnit"]]$unit, expression(dbar))
        expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["conductivityUnit"]]$unit, expression())
        expect_equal(d[["oxygenCurrentUnit"]]$unit, expression(mu*a))
        expect_equal(d[["oxygenTemperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["fluorescenceUnit"]]$unit, expression(mg/m^3))
        expect_equal(d[["PSARUnit"]]$unit, expression(mu*mol/m^2/s))
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression(kg/m^3))
})}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Bedford Basin CTD profile 3 (with proper CODE tokens)", {
        expect_silent(d <- read.oce("local_data/bedford_basin/CTD_BCD2012667_01_01_DN.ODF"))
        expect_equal(d[["startTime"]], as.POSIXct("2012-01-04 12:53:38", tz="UTC"))
        # oce names
        expect_equal(names(d[["data"]]),
            c("scan", "pressure", "temperature", "conductivity", "oxygenCurrent", "oxygenTemperature", "unknown",
                "fluorescence", "PSAR", "salinity", "oxygen", "sigmaTheta", "oxygenSaturation"))
        # original names
        orig <- list(scan="CNTR_01", pressure="PRES_01", temperature="TEMP_01",
            conductivity="CRAT_01", oxygenCurrent="OCUR_01",
            oxygenTemperature="OTMP_01", unknown="UNKN_01",
            fluorescence="FLOR_01", PSAR="PSAR_01",
            salinity="PSAL_01", oxygen="DOXY_01", sigmaTheta="SIGP_01",
            oxygenSaturation="OSAT_01")
        expect_identical(d[["dataNamesOriginal"]], orig)
        # units
        expect_equal(d[["pressureUnit"]]$unit, expression(dbar))
        expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["conductivityUnit"]]$unit, expression())
        expect_equal(d[["oxygenCurrentUnit"]]$unit, expression(mu*a))
        expect_equal(d[["oxygenTemperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["fluorescenceUnit"]]$unit, expression(mg/m^3))
        expect_equal(d[["PSARUnit"]]$unit, expression(mu*mol/m^2/s))
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression(kg/m^3))
})}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Bedford Basin CTD profile 4 (no units for OCUR_01, OTMP_01, CRAT_01, FLOR_01, PSAR_01, PSAL_01, DOXY_01, or SIGP_01)", {
        expect_silent(d <- read.oce("local_data/bedford_basin/CTD_BCD2013667_001_01_DN.ODF"))
        expect_equal(d[["startTime"]], as.POSIXct("2013-01-02 15:04:39", tz="UTC"))
        # oce names
        expect_equal(names(d[["data"]]),
            c("scan", "pressure", "temperature", "conductivity", "oxygenCurrent", "oxygenTemperature", "unknown",
                "fluorescence", "PSAR", "salinity", "oxygen", "sigmaTheta"))
        # original names
        orig <- list(scan="CNTR_01", pressure="PRES_01", temperature="TEMP_01",
            conductivity="CRAT_01", oxygenCurrent="OCUR_01",
            oxygenTemperature="OTMP_01", unknown="UNKN_01",
            fluorescence="FLOR_01", PSAR="PSAR_01",
            salinity="PSAL_01", oxygen="DOXY_01", sigmaTheta="SIGP_01")
        expect_identical(d[["dataNamesOriginal"]], orig)
        # This is a weird file, with missing units, but we check
        # anyway (comparing against manual inspection of the file) to be sure that
        # things are at least read correctly.
        expect_equal(d[["pressureUnit"]]$unit, expression())
        expect_equal(d[["temperatureUnit"]]$unit, expression())
        expect_equal(d[["conductivityUnit"]]$unit, expression())
        expect_equal(d[["oxygenCurrentUnit"]]$unit, expression())
        expect_equal(d[["oxygenTemperatureUnit"]]$unit, expression())
        expect_equal(d[["fluorescenceUnit"]]$unit, expression())
        expect_equal(d[["PSARUnit"]]$unit, expression())
        expect_equal(d[["oxygenUnit"]]$unit, expression())
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression())
})}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Bedford Basin CTD profile 5 (with proper CODE tokens but no unit for PSAR_01)", {
        expect_warning(d <- read.oce("local_data/bedford_basin/CTD_BCD2014667_001_01_DN.ODF"), CRATwarning)
        expect_equal(d[["startTime"]], as.POSIXct("2014-01-08 13:37:15", tz="UTC"))
        # oce names
        expect_equal(names(d[["data"]]),
            c("scan", "pressure", "temperature", "conductivity", "oxygenVoltage", "unknown",
                "fluorescence", "PSAR", "salinity", "oxygen", "sigmaTheta"))
        # original names
        orig <- list(scan="CNTR_01", pressure="PRES_01", temperature="TEMP_01",
            conductivity="CRAT_01", oxygenVoltage="OXYV_01",
            unknown="UNKN_01", fluorescence="FLOR_01", PSAR="PSAR_01",
            salinity="PSAL_01", oxygen="DOXY_01", sigmaTheta="SIGP_01")
        expect_identical(d[["dataNamesOriginal"]], orig)
        # units
        expect_equal(d[["pressureUnit"]]$unit, expression(dbar))
        expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["conductivityUnit"]]$unit, expression(S/m))
        expect_equal(d[["oxygenVoltageUnit"]]$unit, expression(V))
        expect_equal(d[["fluorescenceUnit"]]$unit, expression(mg/m^3))
        expect_equal(d[["PSARUnit"]]$unit, expression())
        expect_equal(d[["oxygenUnit"]]$unit, expression(ml/l))
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression(kg/m^3))
})}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Bedford Basin CTD profile 6 (with proper CODE tokens)", {
        expect_warning(d <- read.oce("local_data/bedford_basin/CTD_BCD2015667_001_01_DN.ODF"), CRATwarning)
        expect_equal(d[["startTime"]], as.POSIXct("2015-01-07 13:28:34", tz="UTC"))
        # oce names
        expect_equal(names(d[["data"]]),
            c("scan", "pressure", "temperature", "conductivity", "oxygenVoltage", "fluorescence",
                "PSAR", "salinity", "oxygen", "sigmaTheta"))
        # original names
        orig <- list(scan="CNTR_01", pressure="PRES_01", temperature="TEMP_01",
            conductivity="CRAT_01", oxygenVoltage="OXYV_01",
            fluorescence="FLOR_01", PSAR="PSAR_01",
            salinity="PSAL_01", oxygen="DOXY_01", sigmaTheta="SIGP_01")
        expect_identical(d[["dataNamesOriginal"]], orig)
        # units
        expect_equal(d[["pressureUnit"]]$unit, expression(dbar))
        expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["conductivityUnit"]]$unit, expression(S/m))
        expect_equal(d[["oxygenVoltageUnit"]]$unit, expression(V))
        expect_equal(d[["fluorescenceUnit"]]$unit, expression(mg/m^3))
        expect_equal(d[["PSARUnit"]]$unit, expression())
        expect_equal(d[["salinityUnit"]]$unit, expression())
        expect_equal(d[["oxygenUnit"]]$unit, expression(ml/l))
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression(kg/m^3))
})}

if (1 == length(list.files(path=".", pattern="local_data"))) {
    skip_on_cran()
    test_that("Bedford Basin CTD profile 7 (with proper CODE tokens but no PSAR_01 unit)", {
        expect_warning(d <- read.oce("local_data/bedford_basin/D16667001.ODF"), CRATwarning)
        expect_equal(d[["startTime"]], as.POSIXct("2016-01-06 13:17:37", tz="UTC"))
        # oce names
        expect_equal(names(d[["data"]]),
            c("scan", "pressure", "temperature", "conductivity", "oxygenVoltage", "unknown",
                "fluorescence", "PSAR", "salinity", "oxygen", "sigmaTheta"))
        # original names
        orig <- list(scan="CNTR_01", pressure="PRES_01", temperature="TEMP_01",
            conductivity="CRAT_01", oxygenVoltage="OXYV_01",
            unknown="UNKN", fluorescence="FLOR_01", PSAR="PSAR_01",
            salinity="PSAL_01", oxygen="DOXY_01", sigmaTheta="SIGP_01")
        expect_identical(d[["dataNamesOriginal"]], orig)
        # units
        expect_equal(d[["pressureUnit"]]$unit, expression(dbar))
        expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
        expect_equal(d[["conductivityUnit"]]$unit, expression(S/m))
        expect_equal(d[["oxygenVoltageUnit"]]$unit, expression(V))
        expect_equal(d[["fluorescenceUnit"]]$unit, expression(mg/m^3))
        expect_equal(d[["PSARUnit"]]$unit, expression())
        expect_equal(d[["salinityUnit"]]$unit, expression())
        expect_equal(d[["oxygenUnit"]]$unit, expression(ml/l))
        expect_equal(d[["sigmaThetaUnit"]]$unit, expression(kg/m^3))
})}