ReadSpecClipboard extended to work also with connections (to facili…

…tate testing on non windows platforms).

Snapshot testing for main function `InterpretMSSpectrum` implemented.

R/ReadSpecClipboard.R

@@ -1,5 +1,6 @@
 #' @title ReadSpecClipboard.
 #' @description Read a mass spectrum from the windows clipboard.
+#' @param con A connection other than 'clipboard' can be provided.
 #' @return A spectrum as two-column matrix.
 #' @export
 #' @examples
@@ -10,21 +11,21 @@
 #'     InterpretMSSpectrum::ReadSpecClipboard()
 #'   }
 #' }
-ReadSpecClipboard <- function() {
-  stopifnot(length(grep("Windows", utils::sessionInfo()$running))==1)
+ReadSpecClipboard <- function(con = "clipboard") {
+  if (length(grep("Windows", utils::sessionInfo()$running))!=1 && con == "clipboard") return(NULL)
   # source could be Excel (German/English) or DA directly
-  spec <- readLines("clipboard")
+  spec <- readLines(con = con)
   spec <- gsub("\t", " ", spec) # replace Tabs
   if (length(grep("[^[:digit:],/. ]", spec[1])) == 1) spec <- spec[-1] # strip header if present
   spec <- gsub(",", ".", spec) # replace Colons
   spec <- gsub(" +$", "", spec) # trim white space end
   spec <- gsub("^ +", "", spec) # trim white space start
   # convert to numeric matrix
   spec <- as.matrix(
-      t(sapply(spec, function(x) {
-        as.numeric(strsplit(x, " ")[[1]])
-      }))
-    )
+    t(sapply(spec, function(x) {
+      as.numeric(strsplit(x, " ")[[1]])
+    }))
+  )
   if (ncol(spec) >= 3) spec <- spec[, 2:3]
   rownames(spec) <- 1:nrow(spec)
   colnames(spec) <- c("mz", "int")

tests/testthat/_snaps/InterpretMSSpectrum.md

@@ -0,0 +1,10 @@
+# InterpretMSSpectrum works
+
+    Code
+      InterpretMSSpectrum::InterpretMSSpectrum(spec = inp, correct_peak = cp, met_db = mdb,
+        formula_db = fdb, silent = FALSE)
+    Warning <simpleWarning>
+      [RemoveEmptyFragments] No Fragments left after step GetRdisopResult
+      no non-missing arguments to max; returning -Inf
+      [RemoveEmptyFragments] No Fragments left after step RemoveByScore
+

tests/testthat/test-InterpretMSSpectrum.R

@@ -18,5 +18,9 @@ testthat::test_that(
     inp <- InterpretMSSpectrum::esi_spectrum    
     out <- InterpretMSSpectrum::InterpretMSSpectrum(spec=inp, precursor = 263.0534, param = "ESIneg", dppm = 1, silent=TRUE)
     testthat::expect_length(out, 6)
+
+    # test the main output as snapshot test
+    testthat::expect_snapshot(InterpretMSSpectrum::InterpretMSSpectrum(spec=inp, correct_peak=cp, met_db=mdb, formula_db=fdb, silent=FALSE))
+
   }
 )

tests/testthat/test-ReadSpecClipboard.R

@@ -0,0 +1,10 @@
+testthat::test_that(
+	desc = "ReadSpecClipboard works as expected", 
+	code = {
+	  fn <- tempfile(fileext = ".txt")
+    x <- as.matrix(InterpretMSSpectrum::apci_spectrum)
+    rownames(x) <- 1:nrow(x)
+    write.table(x = x, file = fn, row.names = FALSE)
+    testthat::expect_equal(InterpretMSSpectrum::ReadSpecClipboard(con = fn), x)
+	}
+)