Merge pull request #42 from ethanbass/master

fix: wrong time zones returned by strptime - needs followup
wkumler · Sep 17, 2024 · 158892b · 158892b
2 parents 5c35c7b + ae64a95
commit 158892b
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/R/grabMzmlFunctions.R b/R/grabMzmlFunctions.R
@@ -283,7 +283,8 @@ grabMzmlMetadata <- function(xml_data){
   time_node <- xml2::xml_find_first(xml_data, xpath = "//d1:run")
   time_val <- xml2::xml_attr(time_node, "startTimeStamp")
   if(!is.na(time_val)){
-    time_stamp <- as.POSIXct(strptime(time_val, "%Y-%m-%dT%H:%M:%SZ"))
+    time_val <- sub("Z$", "+0000", time_val)
+    time_stamp <- as.POSIXct(strptime(time_val, "%Y-%m-%dT%H:%M:%S%z", tz="UTC"))
   } else {
     time_stamp <- as.POSIXct(NA)
   }

diff --git a/tests/testthat/test_chroms.R b/tests/testthat/test_chroms.R
@@ -21,3 +21,8 @@ test_that("warning thrown when requesting chroms from mzXML", {
   expect_warning(grabMSdata(mzXML_filenames[2], grab_what = "chroms"),
                  regexp = "grab_what = 'chroms' not available for mzXML documents")
 })
+
+test_that("time stamp is correct", {
+  expect_identical(msdata_MRM_everything$metadata$timestamp,
+                   as.POSIXct("2022-08-11 12:34:56",tz="UTC"))
+})