compress sample ODF files

R/odf.R

@@ -743,7 +743,7 @@ ODF2oce <- function(ODF, coerce=TRUE, debug=getOption("oceDebug"))
 #' # so we must alter the unit before converting to a CTD object. Note that
 #' # read.odf() on this data file produces a warning suggesting that the user
 #' # repair the unit, using the method outlined here.
-#' odf <- read.odf(system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF", package="oce"))
+#' odf <- read.odf(system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF.gz", package="oce"))
 #' ctd <- as.ctd(odf) ## so we can e.g. extract potential temperature
 #' ctd[["conductivityUnit"]] <- list(unit=expression(), scale="")
 #' #
@@ -1083,7 +1083,7 @@ read.odf <- function(file, columns=NULL, debug=getOption("oceDebug"))
     res@metadata$header <- NULL
 
     ## catch erroneous units on CRAT, which should be in a ratio, and hence have no units.
-    ## This is necessary for the sample file inst/extdata/CTD_BCD2014666_008_1_DN.ODF
+    ## This is necessary for the sample file inst/extdata/CTD_BCD2014666_008_1_DN.ODF.gz
     if (length(grep("CRAT", ODFnames))) {
         which <- grep("CRAT", ODFnames)
         for (w in which) {

create_data/odf/create_odf.R

@@ -1,5 +1,5 @@
 library(oce)
-odf <- read.oce("../../inst/extdata/CTD_BCD2014666_008_1_DN.ODF")
+odf <- read.oce("../../inst/extdata/CTD_BCD2014666_008_1_DN.ODF.gz")
 save(odf, file="odf.rda")
 tools::resaveRdaFiles("odf.rda")
 

tests/testthat/test_flags.R

@@ -175,7 +175,7 @@ test_that("ctd flag with subset() (issue 1410)", {
 })
 
 test_that("odf flag with subset() (issue 1410)", {
-          file <- system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF", package="oce")
+          file <- system.file("extdata", "CTD_BCD2014666_008_1_DN.ODF.gz", package="oce")
           odf <- expect_warning(read.odf(file), "should be unitless")
           ## # Find a region with interesting flags
           ## > which(odf[["sigmaThetaFlag"]]!=1)

tests/testthat/test_odf.R

@@ -7,8 +7,8 @@ context("ODF")
 ## of distinct NULL_VALUE entries, one per data item, and by having the
 ## first few data entries modified. This tests the ability to handle
 ## a different code for each data type.
-test_that("ODF file", {
-          expect_warning(d <- read.ctd.odf("CTD_BCD2014666_008_1_DN_altered.ODF"),
+test_that("ODF CTD file", {
+          expect_warning(d <- read.ctd.odf("CTD_BCD2014666_008_1_DN_altered.ODF.gz"),
                          "\"CRAT_01\" should be unitless")
           expect_equal(d[["temperatureUnit"]]$unit, expression(degree*C))
           expect_equal(d[["temperatureUnit"]]$scale, "IPTS-68")
@@ -68,10 +68,41 @@ test_that("ODF file", {
           expect_equal(17, which(is.na(d[["oxygenFlag"]])))
           ## Next will be NA for bad pressure, salinity, temperature, but NOT
           ## for the altered bad sigmaTheta. This is because oce *calculates*
-          ## sigmaTheta.
+          ## sigmaTheta for the CTD case ... but contrast this with the
+          ## next test.
           expect_equal(c(2, 4, 14), which(is.na(d[["sigmaTheta"]]))) # computed
           expect_equal(18, which(is.na(d[["SIGP_01"]]))) # original data
           expect_equal(19, which(is.na(d[["sigmaThetaFlag"]])))
 
 })
 
+test_that("ODF CTD file (not as CTD)", {
+          expect_warning(d <- read.odf("CTD_BCD2014666_008_1_DN_altered.ODF.gz"),
+                         "\"CRAT_01\" should be unitless")
+          ## First, check as in the previous test.
+          expect_equal( 1, which(is.na(d[["scan"]])))
+          expect_equal( 2, which(is.na(d[["pressure"]])))
+          expect_equal( 3, which(is.na(d[["pressureFlag"]])))
+          expect_equal( 4, which(is.na(d[["temperature"]])))
+          expect_equal( 5, which(is.na(d[["temperatureFlag"]])))
+          expect_equal( 6, which(is.na(d[["conductivity"]])))
+          expect_equal( 7, which(is.na(d[["conductivityFlag"]])))
+          expect_equal( 8, which(is.na(d[["oxygenVoltage"]])))
+          expect_equal( 9, which(is.na(d[["oxygenVoltageFlag"]])))
+          expect_equal(10, which(is.na(d[["fluorometer"]])))
+          expect_equal(11, which(is.na(d[["fluorometerFlag"]])))
+          expect_equal(12, which(is.na(d[["par"]])))
+          expect_equal(13, which(is.na(d[["parFlag"]])))
+          expect_equal(14, which(is.na(d[["salinity"]])))
+          expect_equal(15, which(is.na(d[["salinityFlag"]])))
+          expect_equal(16, which(is.na(d[["oxygen"]])))
+          expect_equal(17, which(is.na(d[["oxygenFlag"]])))
+          ## Now, for the part that's different: in the present case,
+          ## the sigmaTheta value will be AS READ IN, not calculated.
+          ## That calculation only works when it knows it is a CTD. Therefore,
+          ## the next tests are different from in the previous block.
+          expect_equal(18, which(is.na(d[["sigmaTheta"]]))) # computed
+          expect_equal(18, which(is.na(d[["SIGP_01"]]))) # original data
+          expect_equal(19, which(is.na(d[["sigmaThetaFlag"]])))
+
+})