Merge pull request #30 from rformassspectrometry/jomain

Complete unit test coverage
rformassspectrometry · Nov 20, 2024 · fd2ce6e · fd2ce6e
2 parents f1bdb81 + 2596efa
commit fd2ce6e
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Showing 7 changed files with 43 additions and 11 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -6,7 +6,7 @@ root = true
 charset = utf-8
 end_of_line = lf
 trim_trailing_whitespace = true
-insert_final_newline = false
+insert_final_newline = true
 
 [*.R]
 indent_style = space
@@ -22,4 +22,4 @@ indent_style = tab
 
 [.travis.yml]
 indent_style = space
-indent_size = 2
+indent_size = 2
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -53,9 +53,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.19'}
-          - { os: windows-latest, r: 'devel', bioc: '3.19'}
+          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: MsBackendMgf
 Title: Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
-Version: 1.13.0
+Version: 1.15.1
 Authors@R:
     c(person(given = "RforMassSpectrometry Package Maintainer",
              email = "maintainer@rformassspectrometry.org",
@@ -55,7 +55,7 @@ BugReports: https://github.com/RforMassSpectrometry/MsBackendMgf/issues
 URL: https://github.com/RforMassSpectrometry/MsBackendMgf
 biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics, DataImport
 Roxygen: list(markdown=TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate:
     'hidden_aliases.R'
     'MsBackendMgf.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# MsBackendMgf 1.15
+
+## Changes in 1.15.1
+
+- Complete unit test coverage.
+
 # MsBackendMgf 1.11
 
 ## Changes in 1.11.2

diff --git a/R/functions-mgf.R b/R/functions-mgf.R
@@ -203,7 +203,7 @@ readMgfSplit <- function(f, msLevel = 2L,
             as.double(unlist(spec, use.names = FALSE, recursive = FALSE)),
             ncol = length(spec[[1L]]), byrow = TRUE)
 
-    if(nrow(ms) > 1 && is.unsorted(ms[, 1L]))
+    if(.is_unsorted(ms))
         ms <- ms[order(ms[, 1L]), , drop = FALSE]
 
     r <- regexpr("=", desc, fixed = TRUE)
@@ -220,6 +220,9 @@ readMgfSplit <- function(f, msLevel = 2L,
     res
 }
 
+.is_unsorted <- function(x) {
+    nrow(x) && is.unsorted(x[, 1L])
+}
 
 #' Format MGF charge string into an integer compatible format.
 #'
@@ -289,7 +292,8 @@ readMgfSplit <- function(f, msLevel = 2L,
         paste0(z, "=", spd[, z], "\n")
     })
     if (exportTitle && !any(colnames(spd) == "TITLE")) {
-        if (!is.null(spectraNames(x)))
+        sn <- spectraNames(x)
+        if (!is.null(sn) && any(sn != as.character(seq_along(x))))
             title <- paste0("TITLE=", spectraNames(x), "\n")
         else
             title <- paste0("TITLE=msLevel ", spd$msLevel, "; retentionTime ",

diff --git a/tests/testthat/test_MsBackendMgf.R b/tests/testthat/test_MsBackendMgf.R
@@ -99,6 +99,11 @@ test_that("export,MsBackendMgf works", {
     res <- readLines(fl)
     expect_true(length(grep("TITLE", res)) == 0)
 
+    spectraNames(sps) <- NULL
+    export(MsBackendMgf(), sps, file = fl, exportTitle = TRUE)
+    res <- readLines(fl)
+    expect_true(length(grep("TITLE=msLevel", res)) == 0)
+
     expect_error(export(MsBackendMgf(), file = fl), "missing")
     expect_error(export(MsBackendMgf(), x = spd, file = fl), "spectra data to")
 

diff --git a/tests/testthat/test_functions-mgf.R b/tests/testthat/test_functions-mgf.R
@@ -41,6 +41,8 @@ test_that("readMgfSplit works", {
                full.names = TRUE, pattern = "mgf$")
 
     expect_error(readMgfSplit(fls), "Please provide a single mgf file.")
+    expect_error(readMgfSplit(fls[1], n = -3), "has to be an integer")
+    expect_error(readMgfSplit(fls[1], n = 3), "Consider increasing the value")
 
     res1 <- readMgfSplit(fls[1])
     cns <- c("rtime", "acquisitionNum", "precursorMz", "precursorIntensity",
@@ -90,14 +92,19 @@ test_that(".extract_mgf_spectrum works", {
     end <- grep("END IONS", mgf) - 1L
     n <- length(begin)
 
-    res <- MsBackendMgf:::.extract_mgf_spectrum(mgf[begin[1]:end[1]])
+    res <- .extract_mgf_spectrum(mgf[begin[1]:end[1]])
     expect_true(is.data.frame(res))
     expect_equal(names(res), c("TITLE", "PEPMASS", "CHARGE",
                                "RTINSECONDS", "SCANS", "PEPMASSINT",
                                "mz", "intensity"))
     expect_true(is.na(res$PEPMASSINT))
 
-    res <- MsBackendMgf:::.extract_mgf_spectrum(mgf[begin[2]:end[2]])
+    with_mocked_bindings(
+        ".is_unsorted" = function(...) TRUE,
+        code = expect_equal(res, .extract_mgf_spectrum(mgf[begin[1]:end[1]]))
+    )
+
+    res <- .extract_mgf_spectrum(mgf[begin[2]:end[2]])
     expect_true(is.data.frame(res))
     expect_equal(names(res), c("TITLE", "PEPMASS", "CHARGE",
                                "RTINSECONDS", "SCANS", "PEPMASSINT",
@@ -109,3 +116,13 @@ test_that(".format_charge works", {
     res <- .format_charge(c("4+", "3-", NA, "45"))
     expect_equal(res, c("4", "-3", NA_character_, "45"))
 })
+
+test_that(".is_unsorted works", {
+    x <- cbind(1:3, 1:3)
+    expect_false(.is_unsorted(x))
+
+    x <- cbind(c(1, 43, 2), 1:3)
+    expect_true(.is_unsorted(x))
+
+    expect_false(.is_unsorted(x[integer(), , drop = FALSE]))
+})