fix: read_agilent_amx, detect flow gradients, added t0

Author: ethanbass

R/call_openchrom.R

@@ -184,7 +184,7 @@ write_openchrom_batchfile <- function(files, path_out,
 #' indicating whether 'OpenChrom' is configured correctly. Otherwise, returns
 #' the path to OpenChrom command-line application.
 #' @author Ethan Bass
-#' @seealso [call_openchrom]
+#' @seealso [`call_openchrom`]
 #' @export
 
 configure_openchrom <- function(cli = c("null", "true", "false", "status"), path = NULL){

R/read_agilent_amx.R

@@ -165,7 +165,14 @@ parse_pump_method <- function(file_path, format_out = "data.frame",
 
   timetable_nodes <- xml2::xml_find_all(doc, ".//TimetableEntry")
 
-  gradient <- purrr::map_dfr(timetable_nodes, function(node) {
+  composition_nodes <- timetable_nodes[
+    xml2::xml_attr(timetable_nodes, "type") == "ChangeSolventCompositionType"
+  ]
+  flow_nodes <- timetable_nodes[
+    xml2::xml_attr(timetable_nodes, "type") == "ChangeFlowType"
+  ]
+
+  gradient <- purrr::map_dfr(composition_nodes, function(node) {
     data.frame(
       time_min = get_amx_num(node, ".//Time"),
       channel  = c("A", "B", "C", "D"),
@@ -177,22 +184,59 @@ parse_pump_method <- function(file_path, format_out = "data.frame",
       )
     )
   })
+
+  flow_gradient <- purrr::map_dfr(flow_nodes, function(node) {
+    data.frame(
+      time_min = get_amx_num(node, ".//Time"),
+      channel  = "flow",
+      percent  = get_amx_num(node, ".//Flow")
+    )
+  })
+
   if (nrow(gradient) != 0){
     gradient <- gradient[gradient$channel %in% active_channels, ]
 
-    if (gradient_format == "wide") {
-      gradient <- tidyr::pivot_wider(gradient, names_from = "channel",
-                                     values_from = "percent",
-                                     names_prefix = "pct_")
+    zero_row <- data.frame(
+      time_min = 0,
+      channel  = active_channels,
+      percent  = solvents$percentage
+    )
+
+    if (!any(gradient$time_min == 0)) {
+      gradient <- rbind(zero_row, gradient)
+    }
+  }
+  if (nrow(flow_gradient) != 0) {
+    flow_zero <- data.frame(
+      time_min = 0,
+      channel  = "flow",
+      percent  = get_amx_num(doc, "/PumpMethod/Flow")
+    )
+    if (!any(flow_gradient$time_min == 0)) {
+      flow_gradient <- rbind(flow_zero, flow_gradient)
     }
   }
+  if (nrow(gradient) != 0 || nrow(flow_gradient) != 0){
+    gradient <- rbind(gradient, flow_gradient)
+    gradient <- gradient[order(gradient$time_min), ]
+  }
+  if (nrow(gradient) != 0 && gradient_format == "wide") {
+    gradient <- tidyr::pivot_wider(gradient, names_from = "channel",
+                                   values_from = "percent",
+                                   names_prefix = "pct_")
+    if ("pct_flow" %in% names(gradient)) {
+      names(gradient)[names(gradient) == "pct_flow"] <- "flow_mL_min"
+      gradient <- tidyr::fill(gradient, "flow_mL_min", .direction = "down")
+    }
+  }
+
   gradient <- convert_format_out(gradient, format_out = format_out)
   list(
-    flow_mL_min       = get_amx_num(doc, ".//Flow"),
-    stop_time_min     = get_amx_num(doc, ".//StopTimeValue"),
-    post_time_min     = get_amx_num(doc, ".//PostTimeValue"),
-    pressure_low_bar  = get_amx_num(doc, ".//LowPressureLimit"),
-    pressure_high_bar = get_amx_num(doc, ".//HighPressureLimit"),
+    flow_mL_min       = get_amx_num(doc, "/PumpMethod/Flow"),
+    stop_time_min     = get_amx_num(doc, "/PumpMethod/StopTime/StopTimeValue"),
+    post_time_min     = get_amx_num(doc, "/PumpMethod/PostTime/PostTimeValue"),
+    pressure_low_bar  = get_amx_num(doc, "/PumpMethod/LowPressureLimit"),
+    pressure_high_bar = get_amx_num(doc, "/PumpMethod/HighPressureLimit"),
     solvents          = solvents,
     gradient          = gradient
   )

man/configure_openchrom.Rd

@@ -218,7 +218,7 @@ test_that("read_chroms can write 'Agilent ChemStation' version 81 files to CDF",
 
   xx <- read_chroms(fs::path(path_out, "5970_mix_10nG.cdf"),
                     progress_bar = FALSE)[[1]]
-  expect_equal(x, xx, ignore_attr=TRUE, tolerance=1e-7)
+  expect_equal(x, xx, ignore_attr = TRUE, tolerance = 1e-7)
   expect_equal(get_times(x), get_times(xx))
   fields <-c("sample_name", "detector", "detector_id", "detector_y_unit",
              "method", "operator", "time_interval", "time_unit", "run_datetime")
@@ -628,7 +628,7 @@ test_that("read_chroms can read 'Agilent ACAML' files", {
   expect_s3_class(x2, "tbl")
 })
 
-test_that("read_agilent_amx works correctly", {
+test_that("read_agilent_amx works correctly, part 1", {
   skip_on_cran()
   skip_if_not_installed("chromConverterExtraTests")
   path <- system.file("column_storage_ACN100.amx",
@@ -644,7 +644,11 @@ test_that("read_agilent_amx works correctly", {
   expect_equal(method1$dad$peakwidth_nm, 4)
   expect_equal(nrow(method1$pump$gradient), 0)
   expect_equal(as.numeric(method1$metadata$created), 1767977263.0)
+})
 
+test_that("read_agilent_amx works correctly, part 2", {
+  skip_on_cran()
+  skip_if_not_installed("chromConverterExtraTests")
   path <- system.file("Glucosinolates-XDB5.amx",
                       package = "chromConverterExtraTests")
   skip_if_not(file.exists(path))
@@ -658,7 +662,7 @@ test_that("read_agilent_amx works correctly", {
   expect_equal(method2$dad$peakwidth_nm, 4)
   expect_equal(c(method2$dad$spectra_from_nm, method2$dad$spectra_to_nm),
                c(190,400))
-  expect_shape(method2$pump$gradient, dim = c(8,3))
+  expect_shape(method2$pump$gradient, dim = c(9,3))
   expect_equal(method2$column$post_time_min, 6)
   expect_equal(method2$column$temp_controls$temperature_C, c(40, 40))
   expect_equal(method2$autosampler$injection_volume_uL, 5)
@@ -668,10 +672,34 @@ test_that("read_agilent_amx works correctly", {
                                 gradient_format = "long")
   expect_s3_class(method_dt$dad$signals, "data.table")
   expect_s3_class(method_dt$pump$gradient, "data.table")
-  expect_shape(method_dt$pump$gradient, dim = c(16,3))
+  expect_shape(method_dt$pump$gradient, dim = c(18, 3))
 
   method_tibble <- read_agilent_amx(path, format_out = "tibble")
   expect_s3_class(method_tibble$dad$signals, "tbl")
   expect_s3_class(method_tibble$pump$gradient, "tbl")
-  expect_shape(method_tibble$pump$gradient, dim = c(8,3))
+  expect_shape(method_tibble$pump$gradient, dim = c(9, 3))
+})
+
+
+test_that("read_agilent_amx works correctly, part 3", {
+  skip_on_cran()
+  skip_if_not_installed("chromConverterExtraTests")
+  path <- system.file("flow_rate_example.amx",
+                      package = "chromConverterExtraTests")
+  skip_if_not(file.exists(path))
+  method3 <- read_agilent_amx(path)
+  expect_equal(names(method3$metadata),
+               c("method_name", "version", "status", "created", "created_by",
+                 "modified", "modified_by")
+  )
+  expect_equal(method3$dad$peakwidth_nm, 4)
+  expect_equal(c(method3$dad$spectra_from_nm, method3$dad$spectra_to_nm),
+               c(190,400))
+  expect_shape(method3$pump$gradient, dim = c(10,4))
+  expect_equal(method3$column$post_time_min, 2.5)
+  expect_equal(method3$column$temp_controls$temperature_C, c(25, 25))
+  expect_equal(method3$autosampler$injection_volume_uL, 1)
+  expect_equal(as.numeric(method3$metadata$created), 1779656802.0)
+  expect_equal(method3$pump$gradient$flow_mL_min,
+               c(0.4,0.5,0.5,0.5,0.55,0.55,0.6,0.6,0.7,0.7))
 })

tests/testthat/test-extra-agilent.R

@@ -89,8 +89,10 @@ test_that("extract_metadata function works", {
   meta <- extract_metadata(x1, what = c("sample_name"))
   expect_named(meta, c("name", "sample_name"))
 
-  x2 <- read_chroms(rep(path_uv, 2), parser = "chromConverter",
+  expect_warning({
+    x2 <- read_chroms(rep(path_uv, 2), parser = "chromConverter",
                     progress_bar = FALSE)
+  })
   attr(x2[[1]],"detector") <- NULL
   meta2 <- extract_metadata(x2)
   expect_equal(nrow(meta2), length(x2))