ci: indexing, test csv output first

Author: ethanbass

tests/testthat/test-read_chroms.R

@@ -5,6 +5,15 @@ path_uv <- "testdata/dad1.uv" #chemstation 131
 
 x <- read_chroms(path_csv, format_in = "chemstation_csv", progress_bar = FALSE)[[1]]
 
+test_that("chromconverter can read `Agilent Chemstation` csv file", {
+  expect_equal(dim(x), c(1944, 1))
+  expect_equal(head(x[,1], n = 3), c(-4.086018, -4.113674, -4.142761),
+               tolerance = .0001, ignore_attr = TRUE)
+  expect_equal(head(rownames(x), n = 3), c("0.002", "0.0086666666667",
+                                         "0.0153333333333"))
+
+})
+
 test_that("Aston parser can read `Agilent Chemstation` 131 files", {
   skip_if_missing_dependencies()
   skip_if_not(file.exists(path_csv))
@@ -26,14 +35,13 @@ test_that("Aston parser can read `Agilent Chemstation` 131 files", {
 
 x1 <- read_chroms(path_uv, format_in = "chemstation_uv", parser = "chromconverter",
                   find_files = FALSE,
-                  read_metadata = TRUE, progress_bar = FALSE)
+                  read_metadata = TRUE, progress_bar = FALSE)[[1]]
 
 test_that("read_chemstation_uv parser can read chemstation 131 files", {
-  expect_equal(as.numeric(x[[1]][,1]), as.numeric(x1[[1]][,"220"]))
-  expect_equal(as.numeric(rownames(x[[1]])), as.numeric(rownames(x1[[1]])))
-  expect_equal(length(x1), length(path_uv))
-  expect_equal(class(x1[[1]])[1], "matrix")
-  expect_equal(attr(x1[[1]], "data_format"), "wide")
+  expect_equal(as.numeric(x[,1]), as.numeric(x1[,"220"]))
+  expect_equal(as.numeric(rownames(x)), as.numeric(rownames(x1)))
+  expect_equal(class(x1)[1], "matrix")
+  expect_equal(attr(x1, "data_format"), "wide")
 })
 
 test_that("extract_metadata function works", {
@@ -51,13 +59,13 @@ test_that("entab parser can read `Agilent Chemstation` 131 files", {
 
   x1 <- read_chroms(file, format_in = "chemstation_uv", parser = "entab",
                     find_files = FALSE,
-                    read_metadata = TRUE, progress_bar = FALSE)
+                    read_metadata = TRUE, progress_bar = FALSE)[[1]]
 
-  expect_equal(as.numeric(x[[1]][,1]), as.numeric(x1[[1]][,"220"]))
-  expect_equal(as.numeric(rownames(x[[1]])), as.numeric(rownames(x1[[1]])))
-  expect_equal(class(x1[[1]])[1], "matrix")
-  expect_equal(attr(x1[[1]], "parser"), "entab")
-  expect_equal(attr(x1[[1]], "data_format"), "wide")
+  expect_equal(as.numeric(x[,1]), as.numeric(x1[,"220"]))
+  expect_equal(as.numeric(rownames(x)), as.numeric(rownames(x1)))
+  expect_equal(class(x1)[1], "matrix")
+  expect_equal(attr(x1, "parser"), "entab")
+  expect_equal(attr(x1, "data_format"), "wide")
 })
 
 test_that("Shimadzu ascii parser works", {