update MS term for MsQuality and adjust tests

tnaake · Aug 17, 2023 · 6c98d83 · 6c98d83
1 parent 60fa9fd
commit 6c98d83
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Showing 2 changed files with 10 additions and 11 deletions.
diff --git a/R/function_calculateMetrics_from_Spectra.R b/R/function_calculateMetrics_from_Spectra.R
@@ -331,7 +331,7 @@ transformIntoMzQC <- function(spectra_metrics) {
         file_format <- getCVTemplate(accession = filenameToCV(raw_file))
 
         ## obtain information on the MsQuality package
-        software <- toAnalysisSoftware(id = "MS:1003162",#### has to be "MS:4000151", 
+        software <- toAnalysisSoftware(id = "MS:4000151",
             version = packageDescription("MsQuality")$Version)
 
         ## obtain information on the run qualities

diff --git a/tests/testthat/test_function_calculateMetrics_from_Spectra.R b/tests/testthat/test_function_calculateMetrics_from_Spectra.R
@@ -630,8 +630,7 @@ test_that("calculateMetricsFromSpectra, format = 'mzQC'.", {
         ".environment", "refClass", "environment", "refObject"))
     expect_equal(metrics_spectra[[1]]$contactAddress, as.character(NA))
     expect_equal(metrics_spectra[[2]]$contactAddress, as.character(NA))
-
-
+
     ## controlled vocabularies and description
     expect_equal(metrics_spectra[[1]]$controlledVocabularies[[1]]$name, 
         "Proteomics Standards Initiative Mass Spectrometry Ontology")
@@ -643,18 +642,18 @@ test_that("calculateMetricsFromSpectra, format = 'mzQC'.", {
         "A mzQC document on the sample 20171016_POOL_POS_3_105-134.mzML")
 
     ## software
-    #expect_equal(metrics_spectra[[1]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$accession, "MS:4000151")
-    #expect_equal(metrics_spectra[[1]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$name, "MsQuality")
+    expect_equal(metrics_spectra[[1]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$accession, "MS:4000151")
+    expect_equal(metrics_spectra[[1]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$name, "MsQuality")
     expect_equal(metrics_spectra[[1]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$version, 
         packageDescription("MsQuality")$Version)
-    #expect_equal(metrics_spectra[[1]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$description, 
-    #    "")
-    #expect_equal(metrics_spectra[[2]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$accession, "MS:4000151")
-    #expect_equal(metrics_spectra[[2]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$name, "MsQuality")
+    expect_equal(metrics_spectra[[1]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$description, 
+        "\"MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.\" [DOI:10.1101/2023.05.12.540477, https://github.com/tnaake/MsQuality/]")
+    expect_equal(metrics_spectra[[2]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$accession, "MS:4000151")
+    expect_equal(metrics_spectra[[2]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$name, "MsQuality")
     expect_equal(metrics_spectra[[2]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$version, 
         packageDescription("MsQuality")$Version)
-    #expect_equal(metrics_spectra[[2]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$description, 
-    #    "")
+    expect_equal(metrics_spectra[[2]]$runQualities[[1]]$metadata$analysisSoftware[[1]]$description, 
+        "\"MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.\" [DOI:10.1101/2023.05.12.540477, https://github.com/tnaake/MsQuality/]")
 
     ## chromatographyDuration
     expect_equal(