SomaLogic · stufield · Apr 24, 2024 · Apr 18, 2024 · Apr 23, 2024 · Apr 23, 2024
diff --git a/R/adat2eSet.R b/R/adat2eSet.R
@@ -32,10 +32,12 @@
 adat2eSet <- function(adat) {
 
   if ( !requireNamespace("Biobase", quietly = TRUE) ) {
+    # nocov start
     stop(
       "The `Biobase` package is required to use this function.\n",
       "See ?adat2eSet for installation instructions.", call. = FALSE
     )
+    # nocov end
   }
 
   stopifnot("`adat` must have intact attributes." = is_intact_attr(adat))

diff --git a/R/groupGenerics.R b/R/groupGenerics.R
@@ -166,10 +166,23 @@ Summary.soma_adat <- function(..., na.rm = FALSE) {
   args <- lapply(list(...), function(x) {
     if ( is.soma_adat(x) ) {
       data.matrix(x[, getAnalytes(x)])
+      .apts <- getAnalytes(x)
+      rfu <- x[, .apts]
+      mode_ok <- vapply(rfu, function(.x) {
+        is.numeric(.x) || is.complex(.x) || is.logical(.x)
+      }, NA)
+      if ( !all(mode_ok) ) {
+        warning(
+          "Non-numeric variable(s) detected in `soma_adat` object ",
+          "where RFU values should be. Removing: ",
+          .value(names(rfu[, .apts])[!mode_ok]), ".", call. = FALSE
+        )
+      }
+      data.matrix(rfu[, mode_ok])
     } else if ( !is.numeric(x) && !is.logical(x) && !is.complex(x) ) {
-      stop(deparse(.Generic),
-        " is only defined on a `soma_adat` with all numeric-alike variables.",
-        call. = FALSE
+      stop("`", .Generic, "()`",
+         " is only defined on a `soma_adat` with all numeric-alike variables.",
+         call. = FALSE
       )
     } else {
       x
@@ -197,11 +210,11 @@ Summary.soma_adat <- function(..., na.rm = FALSE) {
 #' @export
 Math.soma.adat <- function(x, ...) {
   .msg <- paste(
-    "The", .value("soma.adat"), "class is now", .value("soma_adat"),
-    "\nPlease either:\n",
+    "The", .value("soma.adat"), "class is now", .value("soma_adat"), ".\n",
+    "Please either:\n",
     "  1) Re-class with x <- addClass(x, 'soma_adat')\n",
     "  2) Re-call 'x <- read_adat(file)' to pick up the new 'soma_adat' class.\n"
   )
   cat(.msg)
-  deprecate_stop("2019-01-31", "SomaDataIO::Math.soma.adat()")
+  deprecate_stop("(2019-01-31)", "SomaDataIO::Math.soma.adat()")
 }
diff --git a/R/pivotExpressionSet.R b/R/pivotExpressionSet.R
@@ -25,10 +25,12 @@
 pivotExpressionSet <- function(eSet) {
 
   if ( !requireNamespace("Biobase", quietly = TRUE) ) {
+    # nocov start
     stop(
       "The `Biobase` package is required to use this function.\n",
       "See ?adat2eSet for installation instructions.", call. = FALSE
     )
+    # nocov end
   }
 
   # samples (rows) x features (cols); move rn -> 1st column

diff --git a/R/read-annotations.R b/R/read-annotations.R
@@ -10,7 +10,7 @@
 #' @examples
 #' \dontrun{
 #'   # for example
-#'   file <- "~/Desktop/SomaScan_V4.1_7K_Annotated_Content_20210616.xlsx"
+#'   file <- "~/Downloads/SomaScan_11K_Annotated_Content.xlsx"
 #'   anno_tbl <- read_annotations(file)
 #' }
 #' @importFrom readxl read_xlsx
@@ -48,7 +48,7 @@ read_annotations <- function(file) {
   # file modified
   if ( !identical(md5_file, md5_true) ) {
     warning(
-      "Checksum mismatch.", .value(basename(file)), " may have been modified.",
+      "Checksum mismatch. ", .value(basename(file)), " may have been modified.",
       call. = FALSE
     )
   }

diff --git a/R/utils-read-adat.R b/R/utils-read-adat.R
@@ -217,7 +217,7 @@ catchDims <- function(x, y) {
     cli_rule(cr_bold("Trailing 2 RFU features"), line_col = "magenta")
   )
   nc <- ncol(rfu)
-  print(rfu[1:6, (nc - 1):nc])
+  print(head(as_tibble(rfu[, (nc - 1L):nc])))
   writeLines(cli_rule(line_col = "green", line = 2))
   invisible(NULL)
 }
diff --git a/R/zzz.R b/R/zzz.R
@@ -4,6 +4,7 @@
 .onLoad <- function(libname, pkgname) {
   # this is to make the active binding switch between
   # UTF-8 and ASCII symbol encodings
+  # nocov start
   `%enc%` <- function(utf, ascii) {
     if ( getOption("cli.unicode", TRUE) && l10n_info()$`UTF-8` ) {
       utf
@@ -17,6 +18,7 @@
   makeActiveBinding("symb_warn", function() "\u26A0" %enc% "!", pkgenv)
   makeActiveBinding("symb_point", function() "\u276F" %enc% ">", pkgenv)
   makeActiveBinding("symb_info", function() "\u2139" %enc% "i", pkgenv)
+  # nocov end
 }
 
 .onAttach <- function(libname, pkgname) {

diff --git a/man/read_annotations.Rd b/man/read_annotations.Rd
diff --git a/tests/testthat/_snaps/S3-print.md b/tests/testthat/_snaps/S3-print.md
@@ -1,4 +1,4 @@
-# `soma_adat` S3 print method returns known output
+# `soma_adat` S3 print method returns expected default output
 
     == SomaScan Data ===============================================================
          SomaScan version     V4 (5k)
@@ -35,7 +35,7 @@
     #   SampleDescription <chr>, ...
     ================================================================================
 
----
+# `soma_adat` S3 print method returns expected head output
 
     == SomaScan Data ===============================================================
          SomaScan version     V4 (5k)
@@ -67,7 +67,7 @@
     #   SampleDescription <chr>, ...
     ================================================================================
 
----
+# `soma_adat` S3 print method returns expected `show_header = TRUE` output
 
     == SomaScan Data ===============================================================
          SomaScan version     V4 (5k)
@@ -105,7 +105,7 @@
     # i 20 more rows
     ================================================================================
 
----
+# `soma_adat` S3 print method returns expected `grouped_df` output
 
     == SomaScan Data ===============================================================
          SomaScan version     V4 (5k)
@@ -143,7 +143,7 @@
     #   AssayNotes <lgl>, ...
     ================================================================================
 
----
+# `soma_adat` S3 print method returns expected broken attributes output
 
     == SomaScan Data ===============================================================
          SomaScan version     unknown (NA)

diff --git a/tests/testthat/_snaps/groupGenerics.md b/tests/testthat/_snaps/groupGenerics.md
@@ -19,3 +19,13 @@
     Output
       ================================================================================
 
+# error conditions generate the expected output for deprecated `soma.adat`
+
+    Code
+      readLines(catfile)
+    Output
+      [1] "The 'soma.adat' class is now 'soma_adat' ."                                
+      [2] " Please either:"                                                           
+      [3] "   1) Re-class with x <- addClass(x, 'soma_adat')"                         
+      [4] "   2) Re-call 'x <- read_adat(file)' to pick up the new 'soma_adat' class."
+
diff --git a/tests/testthat/_snaps/parseCheck.md b/tests/testthat/_snaps/parseCheck.md
@@ -0,0 +1,28 @@
+# `parseCheck()` prints expected output
+
+    Code
+      specs
+    Output
+       [1] "== Parsing Specs ==============================================================="                                                                  
+       [2] "• Table Begin               '45'"                                                                                                                  
+       [3] "• Col.Meta Start            '46'"                                                                                                                  
+       [4] "• Col.Meta Shift            '35'"                                                                                                                  
+       [5] "• Header Row                '66'"                                                                                                                  
+       [6] "• Rows of the Col Meta      '46', '47', '48', '49', '50', '51', '52', '53', '54', '55', '56', '57', '58', '59', '60', '61', '62', '63', '64', '65'"
+       [7] "-- Col Meta -------------------------------------------------------------- 20 --"                                                                  
+       [8] "i SeqId, SeqIdVersion, SomaId, TargetFullName, Target, UniProt, EntrezGeneID,"                                                                     
+       [9] "i EntrezGeneSymbol, Organism, Units, Type, Dilution, PlateScale_Reference,"                                                                        
+      [10] "i CalReference, Cal_Example_Adat_Set001, ColCheck,"                                                                                                
+      [11] "i CalQcRatio_Example_Adat_Set001_170255, QcReference_170255,"                                                                                      
+      [12] "i Cal_Example_Adat_Set002, CalQcRatio_Example_Adat_Set002_170255"                                                                                  
+      [13] "-- Row Meta -------------------------------------------------------------- 34 --"                                                                  
+      [14] "i PlateId, PlateRunDate, ScannerID, PlatePosition, SlideId, Subarray, SampleId,"                                                                   
+      [15] "i SampleType, PercentDilution, SampleMatrix, Barcode, Barcode2d, SampleName,"                                                                      
+      [16] "i SampleNotes, AliquotingNotes, SampleDescription, AssayNotes, TimePoint,"                                                                         
+      [17] "i ExtIdentifier, SsfExtId, SampleGroup, SiteId, TubeUniqueID, CLI,"                                                                                
+      [18] "i HybControlNormScale, RowCheck, NormScale_20, NormScale_0_005, NormScale_0_5,"                                                                    
+      [19] "i ANMLFractionUsed_20, ANMLFractionUsed_0_005, ANMLFractionUsed_0_5, Age, Sex"                                                                     
+      [20] "-- Empty Strings Detected in Col.Meta ------------------------------------- ! --"                                                                  
+      [21] "i They may be missing in: [1] \"'Spuriomers', 'HybControls'\""                                                                                     
+      [22] "== Parse Diagnostic Complete ==================================================="                                                                  
+
diff --git a/tests/testthat/_snaps/utils-read-adat.md b/tests/testthat/_snaps/utils-read-adat.md
@@ -0,0 +1,47 @@
+# `checkHeader()` prints expected output
+
+    Code
+      checkHeader(header, verbose = TRUE)
+    Message
+      v Header passed checks and traps
+
+# .verbosity()` prints expected output
+
+    Code
+      .verbosity(adat, header)
+    Output
+      == Parsing Diagnostics =========================================================
+    Message
+      v ADAT version              > 1.2
+      v Header skip               > 41
+      v Table begin               > 20
+      v Col.Meta start            > 21
+      v Col.Meta shift            > 35
+      v Is old ADAT               > FALSE
+      v no. clinical variables    > 34
+      v no. RFU variables         > 5284
+      v Dim data matrix           > 1 x 5318
+      v Dim Col.Meta (annot.)     > 5284 x 20
+    Output
+      -- Head Col Meta ---------------------------------------------------------------
+      # A tibble: 6 x 20
+        SeqId    SeqIdVersion SomaId   TargetFullName      Target UniProt EntrezGeneID
+        <chr>    <chr>        <chr>    <chr>               <chr>  <chr>   <chr>       
+      1 10000-28 3            SL019233 Beta-crystallin B2  CRBB2  P43320  1415        
+      2 10001-7  3            SL002564 RAF proto-oncogene~ c-Raf  P04049  5894        
+      3 10003-15 3            SL019245 Zinc finger protei~ ZNF41  P51814  7592        
+      4 10006-25 3            SL019228 ETS domain-contain~ ELK1   P19419  2002        
+      5 10008-43 3            SL019234 Guanylyl cyclase-a~ GUC1A  P43080  2978        
+      6 10011-65 3            SL019246 Inositol polyphosp~ OCRL   Q01968  4952        
+      # i 13 more variables: EntrezGeneSymbol <chr>, Organism <chr>, Units <chr>,
+      #   Type <chr>, Dilution <chr>, PlateScale_Reference <chr>, CalReference <chr>,
+      #   Cal_Example_Adat_Set001 <chr>, ColCheck <chr>,
+      #   CalQcRatio_Example_Adat_Set001_170255 <chr>, QcReference_170255 <chr>,
+      #   Cal_Example_Adat_Set002 <chr>, CalQcRatio_Example_Adat_Set002_170255 <chr>
+      -- Trailing 2 RFU features -----------------------------------------------------
+      # A tibble: 1 x 2
+        seq.9997.12 seq.9999.1
+              <dbl>      <dbl>
+      1      11983.      1741.
+      ================================================================================
+