Reconfigure header info during collapseAdats()

- `collapseAdats()` now does a better job of maintaining useful information when combining ADATs during the collapse - `PlateScale*` and `Cal*` information is now merged, rather than concatenated, resulting in shorter set of attributes - new values in downstream ADATs are maintained, and no longer lost when written - the majority of HEADER information is still that of the first, initial ADAT in the list - the `stopifnot()` call gets more clear error message - closes #86
SomaLogic · Mar 18, 2024 · 0debb6c · 0debb6c
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diff --git a/NEWS.md b/NEWS.md
@@ -84,6 +84,14 @@
 
 ### Updates and Improvements :hammer:
 
+* `collapseAdats()` better combines `HEADER` information (#86)
+  - certain information, e.g. `PlateScale` and `Cal*`,
+    are better maintained in the final collapsed ADAT
+  - other entries are combined by pasting into a single string
+  - should result in less duplication of superfluous entries and 
+    retention of more "useful" `HEADER` information
+    in the resulting (collapsed) `soma_adat`
+
 * Update `read_annotations()` with `11k` content (#85)
 
 * Update `transform()` and `scaleAnalytes()`

diff --git a/R/loadAdatsAsList.R b/R/loadAdatsAsList.R
@@ -50,7 +50,7 @@
 #'
 #' # Alternatively use `collapse = TRUE`
 #' \donttest{
-#' loadAdatsAsList(files, collapse = TRUE)
+#'   loadAdatsAsList(files, collapse = TRUE)
 #' }
 #' @importFrom stats setNames
 #' @export
@@ -82,15 +82,47 @@ loadAdatsAsList <- function(files, collapse = FALSE, verbose = interactive(), ..
 #' @export
 collapseAdats <- function(x) {
   is_adat <- vapply(x, is.soma_adat, NA)
-  stopifnot(all(is_adat))
+  stopifnot("All entries in list `x` must be `soma_adat` class." = all(is_adat))
   common <- Reduce(intersect, lapply(x, names))   # common df names
   # rm names so rownames are re-constructed via `rbind()`
   new <- lapply(unname(x), function(.x) dplyr::select(.x, all_of(common)))
   new <- do.call(rbind, new)
   new_header <- lapply(x, attr, which = "Header.Meta") |>
-    lapply(`[[`, "HEADER")
-  attributes(new)$Header.Meta$HEADER <- Reduce(`c`, new_header)
-  nms <- names(attributes(x[[1L]]))         # attr order or 1st adat
+    lapply(`[[`, "HEADER") |>
+    Reduce(f = combine_header)
+  new_header$CollapsedAdats <- paste(names(x), collapse = ", ")
+  attributes(new)$Header.Meta$HEADER <- new_header
+  nms <- names(attributes(x[[1L]]))         # attr order of 1st adat
   attributes(new) <- attributes(new)[nms]   # orig order
   new
 }
+
+
+# helper to smartly combine header info
+# from multiple ADATs
+combine_header <- function(x, y) {
+  # intersecting entries: to be pasted/merged
+  keep <- c("AssayRobot", "CreatedDate", "Title", "ExpDate")
+  keep <- intersect(keep, intersect(names(x), names(y)))
+  # plate and cal entries: to be pasted/merged
+  plt <- intersect(grep("^Plate|^Cal", names(x), value = TRUE),
+                   grep("^Plate|^Cal", names(y), value = TRUE))
+  # new entries in 'y': to be added
+  set_yx <- setdiff(names(y), names(x))
+  for ( i in c(keep, plt, set_yx) ) {
+    if ( i %in% names(x) ) {
+      x[[i]] <- paste_xy(x[[i]], y[[i]]) # maintains attrs of 'x'
+    } else {
+      x[[i]] <- y[[i]] # new added entries
+    }
+  }
+  x
+}
+
+# pastes and maintains attrs
+paste_xy <- function(x, y, sep = ", ", ...) {
+  atts <- attributes(x)   # maintain attrs of 'x'
+  x <- paste(x, y, sep = sep, ...)
+  attributes(x) <- atts
+  x
+}
diff --git a/man/loadAdatsAsList.Rd b/man/loadAdatsAsList.Rd
diff --git a/tests/testthat/_snaps/loadAdatsAsList.md b/tests/testthat/_snaps/loadAdatsAsList.md
@@ -51,7 +51,7 @@
       [1] "!AssayVersion"
       
       $AssayRobot
-      [1] "Fluent 1 L-307"
+      [1] "Fluent 1 L-307, Fluent 1 L-307"
       attr(,"raw_key")
       [1] "!AssayRobot"
       
@@ -66,7 +66,7 @@
       [1] "!CreatedBy"
       
       $CreatedDate
-      [1] "2020-07-24"
+      [1] "2020-07-24, 2020-07-25"
       attr(,"raw_key")
       [1] "!CreatedDate"
       
@@ -121,7 +121,7 @@
       [1] "!StudyOrganism"
       
       $Title
-      [1] "Example Adat Set001, Example Adat Set002"
+      [1] "Example Adat Set001, Example Adat Set002, Example Adat Set001, Example Adat Set002"
       attr(,"raw_key")
       [1] "!Title"
       
@@ -215,64 +215,7 @@
       attr(,"raw_key")
       [1] "PlateTailTest_Example_Adat_Set002"
       
-      $AdatId
-      [1] "GID-1234-56-7890-abcdef"
-      attr(,"raw_key")
-      [1] "!AdatId"
-      
-      $Version
-      [1] "1.2"
-      attr(,"raw_key")
-      [1] "!Version"
-      
-      $AssayType
-      [1] "PharmaServices"
-      attr(,"raw_key")
-      [1] "!AssayType"
-      
-      $AssayVersion
-      [1] "V4"
-      attr(,"raw_key")
-      [1] "!AssayVersion"
-      
-      $AssayRobot
-      [1] "Fluent 1 L-307"
-      attr(,"raw_key")
-      [1] "!AssayRobot"
-      
-      $Legal
-      [1] "Experiment details and data have been processed to protect Personally Identifiable Information (PII) and comply with existing privacy laws."
-      attr(,"raw_key")
-      [1] "!Legal"
-      
-      $CreatedBy
-      [1] "PharmaServices"
-      attr(,"raw_key")
-      [1] "!CreatedBy"
-      
-      $CreatedDate
-      [1] "2020-07-25"
-      attr(,"raw_key")
-      [1] "!CreatedDate"
-      
-      $EnteredBy
-      [1] "Technician2"
-      attr(,"raw_key")
-      [1] "!EnteredBy"
-      
-      $GeneratedBy
-      [1] "Px (Build:  : ), Canopy_0.1.1"
-      attr(,"raw_key")
-      [1] "!GeneratedBy"
-      
-      $StudyMatrix
-      [1] "EDTA Plasma"
-      attr(,"raw_key")
-      [1] "!StudyMatrix"
-      
-      $Title
-      [1] "Example Adat Set001, Example Adat Set002"
-      attr(,"raw_key")
-      [1] "!Title"
+      $CollapsedAdats
+      [1] "example_data10.adat, single_sample.adat"