Align tests with latest code base

wincowgerDEV · Aug 9, 2023 · cd50169 · cd50169
1 parent 845ffd9
commit cd50169
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Showing 13 changed files with 61 additions and 86 deletions.
diff --git a/data/raman_hdpe.RData b/data/raman_hdpe.RData
diff --git a/inst/extdata/raman_hdpe.rds b/inst/extdata/raman_hdpe.rds
diff --git a/tests/testthat/test-adj_intens.R b/tests/testthat/test-adj_intens.R
@@ -21,3 +21,4 @@ test_that("adj_intens() runs without error", {
   expect_no_error(adj_intens(raman_hdpe, type = "transmittance"))
   expect_no_error(adj_intens(raman_hdpe))
 })
+
diff --git a/tests/testthat/test-adj_range.R b/tests/testthat/test-adj_range.R
@@ -1,4 +1,4 @@
-test_that("restric range provides correct range", {
+test_that("restrict_range() provides correct range", {
   test_noise = as_OpenSpecy(x = seq(400,4000, by = 10), spectra = data.table(intensity = rnorm(361)))
   expect_silent(single_range <- restrict_range(test_noise, min_range = 1000, max_range = 2000))
   expect_silent(double_range <- restrict_range(test_noise, min_range = c(1000, 2000) , max_range = c(1500, 2500)))
@@ -8,17 +8,18 @@ test_that("restric range provides correct range", {
   expect_identical(double_range$wavenumber, c(seq(1000,1500, by = 10), seq(2000,2500, by = 10)))
 })
 
-test_that("flatten_range.OpenSpecy() function test", {
+test_that("flatten_range() function test", {
     #spectrum <- read_any(read_extdata(file = "ftir_ps.0"))
     test <- as_OpenSpecy(x = 1:10, spectra = data.table(V1 = 1:10))
-    flattened_data <- flatten_range(object = test, min_range = c(4, 7), max_range = c(5, 10), make_rel = F)
+    flattened_data <- flatten_range(test, min_range = c(4, 7), max_range = c(5, 10), make_rel = F)
     expect_equal(flattened_data$spectra$V1[4:5], c(4.5, 4.5))
     expect_equal(flattened_data$spectra$V1[7:10], c(8.5, 8.5, 8.5, 8.5))
 })
 
 
 test_that("flatten_range() error handling", {
-    expect_error(flatten_range(test_data), "You need to specify a min and max range to flatten.")
-    expect_error(flatten_range(test_data, min_range = c(1000), max_range = c(2000, 3000)), "min_range and max_range need to be the same length.")
-    expect_error(flatten_range(test_data, min_range = c(2000), max_range = c(1000)), "all min_range values must be lower than corresponding max_range")
+  test <- as_OpenSpecy(x = 1:10, spectra = data.table(V1 = 1:10))
+    expect_error(flatten_range(test), "You need to specify a min and max range to flatten.")
+    expect_error(flatten_range(test, min_range = c(1000), max_range = c(2000, 3000)), "min_range and max_range need to be the same length.")
+    expect_error(flatten_range(test, min_range = c(2000), max_range = c(1000)), "all min_range values must be lower than corresponding max_range")
 })
diff --git a/tests/testthat/test-as_OpenSpecy.R b/tests/testthat/test-as_OpenSpecy.R
@@ -77,6 +77,5 @@ test_that("OpenSpecy objects are transcribed to and from hyperSpec objects", {
     expect_true(is_OpenSpecy(OpenHyper))
     expect_equal(OpenHyper$wavenumber,hyperOpenSpecy@wavelength)
     expect_equal(unlist(OpenHyper$spectra$V1),unname(t(hyperOpenSpecy$spc)[,1]))
-
-})
 
+})
diff --git a/tests/testthat/test-conform_spec.R b/tests/testthat/test-conform_spec.R
@@ -12,7 +12,7 @@ test_that("conform_spec.default throws an error for non-OpenSpecy objects", {
   # Create a non-OpenSpecy object
   non_open_specy_object <- data.frame(wavenumber = c(1000, 1100, 1200),
                                       intensity = c(0.1, 0.2, 0.3))
-  
+
   # Test if the function throws an error for non-OpenSpecy object
   expect_error(conform_spec(non_open_specy_object, c(1000, 2000)))
 })
@@ -22,17 +22,15 @@ test_that("conform_spec.OpenSpecy conforms wavenumbers correctly", {
   wavenumber <- seq(1000, 2000, 5)
   intensity <- rnorm(length(wavenumber))
   open_specy_object <- as_OpenSpecy(wavenumber, data.table(intensity = intensity))
-  
+
   # Conform the wavenumbers to a new range
   new_wavenumbers <- c(1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900)
   conform_result <- conform_spec(open_specy_object, new_wavenumbers)
-  
+
   # Test if the wavenumber and intensity vectors have the same length after conforming
   expect_equal(length(conform_result$wavenumber), length(conform_result$spectra[[1]]))
-  
+
   # Test if the wavenumber range matches the new_wavenumbers vector
   expect_equal(min(conform_result$wavenumber), min(new_wavenumbers))
   expect_equal(max(conform_result$wavenumber), max(new_wavenumbers))
 })
-
-
diff --git a/tests/testthat/test-collapse_particles.R → tests/testthat/test-def_features.R b/tests/testthat/test-collapse_particles.R → tests/testthat/test-def_features.R
@@ -22,17 +22,16 @@ test_that("check that particles are identified when given character", {
 
 test_that("check that an error is thrown for invalid 'particles' input", {
     map <- read_extdata("CA_tiny_map.zip") |> read_any()
-    expect_error(def_features(map, map$metadata), 
-                 "Particles needs to be a character or logical vector.")
+    expect_error(def_features(map, map$metadata))
 })
 
 test_that("check that particles are identified with all TRUE or FALSE logical vectors", {
     map <- read_extdata("CA_tiny_map.zip") |> read_any()
-    
+
     # All TRUE case
     map$metadata$particles <- rep(TRUE, nrow(map$metadata))
     expect_error(identified_map <- def_features(map, map$metadata$particles))
-    
+
     # All FALSE case
     map$metadata$particles <- rep("test_FALSE", nrow(map$metadata))
     expect_error(identified_map <- def_features(map, map$metadata$particles))
@@ -44,25 +43,26 @@ test_that("check that the original OpenSpecy object remains unmodified", {
 
     particles <- ifelse(map$metadata$x == 1, "particle", "not_particle")
     identified_map <- def_features(map, particles)
-    
+
     expect_equal(map, map2)
 })
 
 test_that("check that collapse particles returns expected values", {
-map <- read_extdata("CA_tiny_map.zip") |> read_any()
-particles <- ifelse(map$metadata$x == 1, "particleA", "particleB")
-identified_map <- def_features(map, particles)
-test_collapsed <- collapse_spec(identified_map)
-expect_true(is_OpenSpecy(test_collapsed))
-
-map <- read_extdata("CA_tiny_map.zip") |> read_any()
-particles <- map$metadata$x == 1
-identified_map <- def_features(map, particles)
-test_collapsed <- collapse_spec(identified_map)
-expect_true(is_OpenSpecy(test_collapsed))
+  map <- read_extdata("CA_tiny_map.zip") |> read_any()
+  particles <- ifelse(map$metadata$x == 1, "particleA", "particleB")
+  identified_map <- def_features(map, particles)
+  test_collapsed <- collapse_spec(identified_map)
+  expect_true(is_OpenSpecy(test_collapsed))
 
-expect_equal(c("particle_id", "area", "feret_max", "centroid_y", "centroid_x"), names(test_collapsed$metadata))
+  map <- read_extdata("CA_tiny_map.zip") |> read_any()
+  particles <- map$metadata$x == 1
+  identified_map <- def_features(map, particles)
+  test_collapsed <- collapse_spec(identified_map)
+  expect_true(is_OpenSpecy(test_collapsed))
 
+  expect_contains(names(test_collapsed$metadata),
+                  c("particle_id", "area", "feret_max",
+                    "centroid_y", "centroid_x"))
 })
 
 
diff --git a/tests/testthat/test-io_spec.R b/tests/testthat/test-io_spec.R
@@ -1,4 +1,3 @@
-
 # Loading test data
 data(raman_hdpe)
 
@@ -7,21 +6,21 @@ test_that("Test read_spec and write_spec functions", {
     temp_file_yml <- tempfile(fileext = ".yml")
     temp_file_json <- tempfile(fileext = ".json")
     temp_file_rds <- tempfile(fileext = ".rds")
-    
+
     write_spec(raman_hdpe, temp_file_yml)
     write_spec(raman_hdpe, temp_file_json)
     write_spec(raman_hdpe, temp_file_rds)
-    
+
     # Now read the data back in and test equality
     spec_yml <- read_spec(temp_file_yml)
     spec_json <- read_spec(temp_file_json)
     spec_rds <- read_spec(temp_file_rds)
-    
+
     # Verify the equality of the original and the read data
-    expect_equal(raman_hdpe, spec_yml)
-    expect_equal(raman_hdpe, spec_json)
-    expect_equal(raman_hdpe, spec_rds)
-    
+    expect_equal(spec_yml, raman_hdpe)
+    expect_equal(spec_json, raman_hdpe)
+    expect_equal(spec_rds, raman_hdpe)
+
     # Clean up temporary files
     file.remove(temp_file_yml)
     file.remove(temp_file_json)
@@ -30,10 +29,10 @@ test_that("Test read_spec and write_spec functions", {
 
 test_that("Test to_hyperspec function", {
     hyperspec_object <- to_hyperSpec(raman_hdpe)
-    
+
     # Verify the class of the output
     expect_s4_class(hyperspec_object, "hyperSpec")
-    
+
     # Verify the equality of the content
     expect_equal(hyperspec_object@wavelength, raman_hdpe$wavenumber)
     expect_equal(c(hyperspec_object$spc), raman_hdpe$spectra$intensity)

diff --git a/tests/testthat/test-match_spec.R b/tests/testthat/test-match_spec.R
@@ -9,17 +9,17 @@ test_lib_extract <- filter_spec(test_lib, logic = test_lib$metadata$polymer_clas
 
 # Write the tests for cor_spec function
 test_that("cor_spec returns a data.table with correct columns", {
-    matches <- cor_spec(object = unknown,library =  test_lib)
+    matches <- cor_spec(unknown,library =  test_lib)
     expect_true(inherits(matches, "matrix"))
-    expect_identical(dim(matches), c(ncol(test_lib$spectra), ncol(unknown$spectra))) 
+    expect_identical(dim(matches), c(ncol(test_lib$spectra), ncol(unknown$spectra)))
     top_matches <- max_cor_named(cor_matrix = matches, na.rm = T)
     expect_true(length(top_matches) == 1)
     expect_true(ncol(filter_spec(test_lib, logic = names(top_matches))$spectra) == 1)
     test_lib$metadata$test <- NA
-    test_metadata <- get_metadata(object = test_lib, logic = names(top_matches), remove_empty = T)
+    test_metadata <- get_metadata(test_lib, logic = names(top_matches), remove_empty = T)
     expect_true(nrow(test_metadata) == 1)
     expect_true(!"test" %in% names(test_metadata))
-    full_test <- ident_spec(cor_matrix = matches, object = unknown, library = test_lib, top_n = 5, add_library_metadata = "sample_name")
+    full_test <- ident_spec(matches, unknown, library = test_lib, top_n = 5, add_library_metadata = "sample_name")
     expect_true(nrow(full_test) == 5)
 })
 

diff --git a/tests/testthat/test-process_spec.R b/tests/testthat/test-process_spec.R
@@ -8,6 +8,6 @@ test_that("process returns expected values",{
 test_that("sample_spec returns an OpenSpecy object with a subset of the spectra", {
   tiny_map <- read_any(read_extdata("CA_tiny_map.zip"))
   sampled <- sample_spec(tiny_map, size = 5)
-  expect_s3_class(result, "OpenSpecy")
-  expect_equal(ncol(result$spectra), 5)
+  expect_s3_class(sampled, "OpenSpecy")
+  expect_equal(ncol(sampled$spectra), 5)
 })
diff --git a/tests/testthat/test-read_opus.R b/tests/testthat/test-read_opus.R
@@ -1,13 +1,10 @@
 test_that("check that opus files are read", {
      expect_silent(data <- read_opus(read_extdata("ftir_ps.0")))
      expect_true(is_OpenSpecy(data))
-     expect_true(is_OpenSpecy(data2))
      expect_true(ncol(data$spectra) == 1)
-     expect_true(ncol(data2$spectra) == 1)
      expect_true(length(data$wavenumber) == 2126)
-     expect_true(length(data2$wavenumber) == 2126)
      expect_identical(names(data$metadata), c("x",
-                                              "y",               
+                                              "y",
                                               "unique_id",
                                               "sample_id",
                                               "date_time_sm",
@@ -19,33 +16,12 @@ test_that("check that opus files are read", {
                                               "beamspl",
                                               "laser_wn",
                                               "spc_in_file",
-                                              "zero_filling",    
+                                              "zero_filling",
                                               "temp_scanner_sm",
-                                              "temp_scanner_rf", 
+                                              "temp_scanner_rf",
                                               "hum_rel_sm",
-                                              "hum_rel_rf",      
+                                              "hum_rel_rf",
                                               "hum_abs_sm",
-                                              "hum_abs_rf",      
-                                              "file_id"))
-     expect_identical(names(data2$metadata), c("x",
-                                              "y",               
-                                              "unique_id",
-                                              "sample_id",
-                                              "date_time_sm",
-                                              "date_time_rf",
-                                              "sample_name",
-                                              "instr_name_range",
-                                              "resolution_wn",
-                                              "result_spc",
-                                              "beamspl",
-                                              "laser_wn",
-                                              "spc_in_file",
-                                              "zero_filling",    
-                                              "temp_scanner_sm",
-                                              "temp_scanner_rf", 
-                                              "hum_rel_sm",
-                                              "hum_rel_rf",      
-                                              "hum_abs_sm",
-                                              "hum_abs_rf",      
+                                              "hum_abs_rf",
                                               "file_id"))
 })
diff --git a/tests/testthat/test-share_spec.R b/tests/testthat/test-share_spec.R
@@ -14,12 +14,13 @@ test_that("share_text() gives expected output", {
   )
 })
 
-test_that("check that data will upload", {
-    skip_on_cran()
-    library(config)
-    conf <- config::get()
-    expect_no_error(share_spec(object = raman_hdpe, file = read_extdata("raman_hdpe.csv"), share = "cloud", s3_key_id = conf$s3_key_id, s3_secret_key = conf$s3_secret_key, s3_region = conf$s3_region, s3_bucket = conf$s3_bucket))
-})
+# TODO: Need to think about config file
+# test_that("check that data will upload", {
+#     skip_on_cran()
+#     library(config)
+#     conf <- config::get()
+#     expect_no_error(share_spec(object = raman_hdpe, file = read_extdata("raman_hdpe.csv"), share = "cloud", s3_key_id = conf$s3_key_id, s3_secret_key = conf$s3_secret_key, s3_region = conf$s3_region, s3_bucket = conf$s3_bucket))
+# })
 
 
 # Tidy up

diff --git a/tests/testthat/test-workflows.R b/tests/testthat/test-workflows.R
@@ -14,10 +14,10 @@ test_that("Zip folder Raman batch analysis", {
     expect_silent(matches <- cor_spec(batch3, library = lib))
     expect_silent(test_max_cor <- max_cor_named(matches))
     expect_silent(test_sn <- signal_noise(batch3, return = "run_signal_over_noise"))
-    
-    heatmap_spec(object = batch3, 
-                      sn = test_sn, 
-                      cor = test_max_cor, 
+
+    heatmap_spec(batch3,
+                      sn = test_sn,
+                      cor = test_max_cor,
                       min_sn = 4,
                       min_cor = 0.7,
                       selected_spectrum = 2,