fix: timezone issue read_chemstation_ms

Author: ethanbass

NEWS.md

@@ -8,6 +8,7 @@
 * Enabled `data.table` format in `read_shimadzu_ascii`.
 * Enabled automatic recognition of 'Agilent OpenLab' `.dx` file by `read_chroms`.
 * Fixed long format output for `read_shimadzu` ('Shimadzu' ASCII files).
+* Fixed timezone issue in some 'Agilent ChemStation' files.
 
 ## chromConverter 0.7.5
 

R/attach_metadata.R

@@ -384,7 +384,8 @@ attach_metadata <- function(x, meta, format_in, format_out, data_format,
   }, "chemstation" = {
     meta$date <- convert_timestamp(meta$date, datetime_formats =
                         c("%d-%b-%y, %H:%M:%S", "%m/%d/%Y %I:%M:%S %p",
-                          "%d/%m/%Y %I:%M:%S %p"))
+                          "%d/%m/%Y %I:%M:%S %p", "%d %b %y %I:%M %p %z",
+                          "%d %b %y %I:%M %p"))
     structure(x, sample_name = iconv(meta$sample_name, sub = ""),
               sample_id = meta$vial,
               file_version = meta$version,

R/read_chemstation_ms.R

@@ -100,8 +100,6 @@ read_chemstation_ms <- function(path, what = c("MS1", "BPC", "TIC"),
       seek(f, where = offset, origin = "start")
       read_cs_string(f, type = 1)
     })
-    meta$date <- as.POSIXct(strptime(meta$date, format="%d %b %y %I:%M %p %z"),
-                            tz="UTC")
     meta$detector <- "MS"
     dat <- lapply(dat, function(x){
       attach_metadata(x, meta, format_in = metadata_format,

tests/testthat/test-extra-agilent.R

@@ -39,7 +39,8 @@ test_that("read_chroms can read 'Agilent' MS files", {
   expect_equal(attr(x1,"sample_name"), attr(x,"sample_name"))
   expect_equal(attr(x1,"source_sha1"), attr(x,"source_sha1"))
   expect_equal(attr(x1,"time_unit"), attr(x,"time_unit"))
-  expect_equal(attr(x1,"run_datetime"), attr(x,"run_datetime"))
+  # expect_equal(as.numeric(attr(x1,"run_datetime")),
+  #              as.numeric(attr(x,"run_datetime"))) #timezone is wrong on entab
   expect_equal(attr(x1,"operator"), attr(x,"operator"))
   expect_equal(attr(x1,"method"), attr(x,"method"))
   expect_equal(attr(x1,"detector"), attr(x,"detector"))
@@ -50,7 +51,7 @@ test_that("read_chroms can read 'Agilent' MS files", {
                     progress_bar = FALSE, precision = 0)[[1]]
   expect_equal(class(x2)[1], "matrix")
   expect_equal(dim(x2), c(2534, 841))
-  # expect_equal(attr(x2,"run_datetime"), attr(x,"run_datetime")) # date time is wrong in rainbow
+  expect_equal(attr(x2,"run_datetime"), attr(x1,"run_datetime"))
   expect_equal(attr(x2, "method"), attr(x1, "method"))
   expect_equal(attr(x2, "detector"), attr(x1, "detector"))
   expect_equal(attr(x2, "data_format"), "wide")