--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/test-SummarizeMaaslin/test-SummarizeMaaslin.R	Mon Feb 09 12:17:40 2015 -0500
@@ -0,0 +1,72 @@
+c_strDir <- file.path(getwd( ),"..")
+
+source(file.path(c_strDir,"lib","Constants.R"))
+source(file.path(c_strDir,"lib","SummarizeMaaslin.R"))
+source(file.path(c_strDir,"lib","Utility.R"))
+
+context("Test funcSummarizeDirectory")
+strDirectoryNone = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","None")
+strDirectory1 = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","1")
+strDirectory3 = file.path(c_strDir,c_strTestingDirectory,c_strTestingInput,"funcSummarizeDirectory","3")
+strFileBase1 = "FileBase1.txt"
+strFileBase2 = "FileBase2.txt"
+
+sKeyword = "Q.value"
+sAltKeyword = "P.value"
+sAltSignificance = "0.35"
+
+sBaseName = "FuncSummarizeDirectory"
+
+#Output and answer files
+sNoFileResult = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileResult.txt")
+sNoFileResultAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileAltKeyResult.txt")
+sNoFileResultAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-NoFileAltSigResult.txt")
+sNoFileResultAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAnswer.txt")
+sNoFileResultAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAltKeyAnswer.txt")
+sNoFileResultAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-NoFileAltSigAnswer.txt")
+unlink(sNoFileResult)
+sCorrectResults1File = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileResult.txt")
+sCorrectResults1FileAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileAltKeyResult.txt")
+sCorrectResults1FileAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-1FileAltSigResult.txt")
+sCorrectResults1FileAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileResult.txt")
+sCorrectResults1FileAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileAltKeyResult.txt")
+sCorrectResults1FileAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-1FileAltSigResult.txt")
+unlink(sCorrectResults1File)
+sCorrectResults3Files = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileResult.txt")
+sCorrectResults3FilesAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileAltKeyResult.txt")
+sCorrectResults3FilesAltSig = file.path(c_strDir,c_strTestingDirectory,c_strTemporaryFiles,"FuncSummarizeDirectory-3FileAltSigResult.txt")
+sCorrectResults3FilesAnswer = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileResult.txt")
+sCorrectResults3FilesAnswerAltKeyword = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileAltKeyResult.txt")
+sCorrectResults3FilesAnswerAltSig = file.path(c_strDir,c_strTestingDirectory,c_strCorrectAnswers,"FuncSummarizeDirectory-3FileAltSigResult.txt")
+unlink(sCorrectResults3Files)
+
+#Run tests
+funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResult, astrKeyword=sKeyword, afSignificanceLevel="0.25")
+funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1File, astrKeyword=sKeyword, afSignificanceLevel="0.25")
+funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3Files, astrKeyword=sKeyword, afSignificanceLevel="0.25")
+
+funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResultAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25")
+funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1FileAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25")
+funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3FilesAltKeyword, astrKeyword=sAltKeyword, afSignificanceLevel="0.25")
+
+funcSummarizeDirectory(astrOutputDirectory=strDirectoryNone, strBaseName=sBaseName, astrSummaryFileName=sNoFileResultAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance)
+funcSummarizeDirectory(astrOutputDirectory=strDirectory1, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults1FileAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance)
+funcSummarizeDirectory(astrOutputDirectory=strDirectory3, strBaseName=sBaseName, astrSummaryFileName=sCorrectResults3FilesAltSig, astrKeyword= sKeyword, afSignificanceLevel=sAltSignificance)
+
+test_that("Check the cases where no, and real summary files exist.",{
+  expect_equal(readLines(sNoFileResult),readLines(sNoFileResultAnswer))
+  expect_equal(readLines(sCorrectResults1File),readLines(sCorrectResults1FileAnswer))
+  expect_equal(readLines(sCorrectResults3Files),readLines(sCorrectResults3FilesAnswer))
+})
+
+test_that("Check changing the keyword.",{
+  expect_equal(readLines(sNoFileResultAltKeyword),readLines(sNoFileResultAnswerAltKeyword))
+  expect_equal(readLines(sCorrectResults1FileAltKeyword),readLines(sCorrectResults1FileAnswerAltKeyword))
+  expect_equal(readLines(sCorrectResults3FilesAltKeyword),readLines(sCorrectResults3FilesAnswerAltKeyword))
+})
+
+test_that("Check that changing the significance threshold effects inclusion.",{
+  expect_equal(readLines(sNoFileResultAltSig),readLines(sNoFileResultAnswerAltSig))
+  expect_equal(readLines(sCorrectResults1FileAltSig),readLines(sCorrectResults1FileAnswerAltSig))
+  expect_equal(readLines(sCorrectResults3FilesAltSig),readLines(sCorrectResults3FilesAnswerAltSig))
+})