|
0
|
1 c_strDir <- file.path(getwd( ),"..")
|
|
|
2
|
|
|
3 source(file.path(c_strDir,"lib","Constants.R"))
|
|
|
4 source(file.path(c_strDir,"lib","ValidateData.R"))
|
|
|
5 strTestingDirectory = file.path(c_strDir,c_strTestingDirectory)
|
|
|
6
|
|
|
7 expect_equal(funcParseIndexSlices("1",cNames),c(1))
|
|
|
8
|
|
|
9 cNames = c("One","Two","Three","Four","Five","Six","Seven","Eight","Nine","Ten","Eleven",
|
|
|
10 "Twelve","Thirteen","Fourteen","Fifteen")
|
|
|
11
|
|
|
12 test_that("Just Numerics are parsed",{
|
|
|
13 expect_equal(funcParseIndexSlices("1",cNames),c(1))
|
|
|
14 expect_equal(funcParseIndexSlices("8,10",cNames),c(8,10))
|
|
|
15 expect_equal(funcParseIndexSlices("2-6",cNames), c(2,3,4,5,6))
|
|
|
16 expect_equal(funcParseIndexSlices("3,7,10-12",cNames), c(3,7,10,11,12))
|
|
|
17 })
|
|
|
18
|
|
|
19 test_that("Missing numbers are parsed",{
|
|
|
20 expect_equal(funcParseIndexSlices("-",cNames), c(2:15))
|
|
|
21 expect_equal(funcParseIndexSlices("-4",cNames), c(2,3,4))
|
|
|
22 expect_equal(funcParseIndexSlices("3-",cNames), c(3:15))
|
|
|
23 })
|
|
|
24
|
|
|
25 test_that("Words are parsed correctly",{
|
|
|
26 expect_equal(funcParseIndexSlices("One",cNames), c(1))
|
|
|
27 expect_equal(funcParseIndexSlices("Eight,Ten",cNames), c(8,10))
|
|
|
28 expect_equal(funcParseIndexSlices("Two-Six",cNames), c(2,3,4,5,6))
|
|
|
29 expect_equal(funcParseIndexSlices("Three,Seven,Ten-Twelve",cNames), c(3,7,10,11,12))
|
|
|
30 })
|
|
|
31
|
|
|
32 test_that("Missing words are parsed",{
|
|
|
33 expect_equal(funcParseIndexSlices("-Four",cNames), c(2:4))
|
|
|
34 expect_equal(funcParseIndexSlices("Three-",cNames), c(3:15))
|
|
|
35 })
|
|
|
36
|
|
|
37 test_that("Words and numbers are parsed correctly",{
|
|
|
38 expect_equal(funcParseIndexSlices("Eight,10",cNames), c(8,10))
|
|
|
39 expect_equal(funcParseIndexSlices("2-Six",cNames), c(2,3,4,5,6))
|
|
|
40 expect_equal(funcParseIndexSlices("Three,7,10-Twelve",cNames), c(3,7,10,11,12))
|
|
|
41 })
|
|
|
42
|
|
|
43
|
|
|
44 context("Test funcWriteMatrixToReadConfigFile")
|
|
|
45 # File to temporarily write to
|
|
|
46 strWriteMatrixRCTestFile = file.path(strTestingDirectory,c_strTemporaryFiles,"FuncWriteMatrixToReadConfigFileTemp.read.config")
|
|
|
47 # Files that hold answers
|
|
|
48 strFileSimpleRCFileAnswer = file.path(strTestingDirectory,c_strCorrectAnswers,"FuncWriteMatrixToReadConfigFile_SimpleAnswer.read.config")
|
|
|
49 strFileUseAllRCFileAnswer = file.path(strTestingDirectory,c_strCorrectAnswers,"FuncWriteMatrixToReadConfigFile_AllAnswer.read.config")
|
|
|
50 strFileAppendTrueRCFileAnswer = file.path(strTestingDirectory,c_strCorrectAnswers,"FuncWriteMatrixToReadConfigFile_AppendAnswer.read.config")
|
|
|
51 #Input matrix file
|
|
|
52 strFileMatrix = file.path(strTestingDirectory,c_strTestingInput,"TestMatrix.tsv")
|
|
|
53
|
|
|
54 #Get read config files in different scenarios
|
|
|
55 funcWriteMatrixToReadConfigFile(strWriteMatrixRCTestFile,"SimpleMatrix")
|
|
|
56 strSimpleInterface = readLines(strWriteMatrixRCTestFile)
|
|
|
57 funcWriteMatrixToReadConfigFile(strWriteMatrixRCTestFile,"AllMatrix",strRowIndices="1,2,3,4,5", strColIndices="10,11,12",acharDelimiter=" ")
|
|
|
58 strUseAllParametersInterface = readLines(strWriteMatrixRCTestFile)
|
|
|
59 funcWriteMatrixToReadConfigFile(strWriteMatrixRCTestFile,"SimpleMatrix")
|
|
|
60 funcWriteMatrixToReadConfigFile(strWriteMatrixRCTestFile,"SimpleMatrix")
|
|
|
61 strAppendFalseInterface = readLines(strWriteMatrixRCTestFile)
|
|
|
62 funcWriteMatrixToReadConfigFile(strWriteMatrixRCTestFile,"SimpleMatrix")
|
|
|
63 funcWriteMatrixToReadConfigFile(strWriteMatrixRCTestFile,"SimpleMatrix",fAppend=TRUE)
|
|
|
64 strAppendTrueInterface = readLines(strWriteMatrixRCTestFile)
|
|
|
65
|
|
|
66 test_that("Correct config file is written",{
|
|
|
67 expect_equal(strSimpleInterface,readLines(strFileSimpleRCFileAnswer))
|
|
|
68 expect_equal(strUseAllParametersInterface,readLines(strFileUseAllRCFileAnswer))
|
|
|
69 expect_equal(strAppendFalseInterface,readLines(strFileSimpleRCFileAnswer))
|
|
|
70 expect_equal(strAppendTrueInterface,readLines(strFileAppendTrueRCFileAnswer))
|
|
|
71 })
|
|
|
72
|
|
|
73 context("Test funcReadConfigFile")
|
|
|
74 lsSimpleRC = funcReadConfigFile(strFileSimpleRCFileAnswer,strFileMatrix)
|
|
|
75 lsAllRC = funcReadConfigFile(strFileUseAllRCFileAnswer,strFileMatrix)
|
|
|
76
|
|
|
77 lsSimpleListAnswer = list()
|
|
|
78 lsSimpleListAnswer[[1]]=c("SimpleMatrix",strFileMatrix,"\t","-","-")
|
|
|
79 lsAllListAnswer = list()
|
|
|
80 lsAllListAnswer[[1]]=c("AllMatrix",strFileMatrix," ","1,2,3,4,5","10,11,12")
|
|
|
81
|
|
|
82 test_that("Test readConfigFile reads in files correctly.",{
|
|
|
83 expect_equal(lsSimpleRC,lsSimpleListAnswer)
|
|
|
84 expect_equal(lsAllRC,lsAllListAnswer)
|
|
|
85 })
|
|
|
86
|
|
|
87
|
|
|
88 context("Test funcReadMatrix")
|
|
|
89
|
|
|
90 #Read in config files
|
|
|
91 dfSimpleRead = funcReadMatrix("SimpleMatrix",strFileMatrix,"\t","2,4,5","7,3,5")
|
|
|
92 dfUseAllParametersRead = funcReadMatrix("AllMatrix",strFileMatrix,"\t","2,3,4","6,2,4")
|
|
|
93
|
|
|
94 dfSimpleReadCorrect = as.data.frame(as.matrix(rbind(c(21,23,24),c(41,43,44),c(61,63,64))))
|
|
|
95 rownames(dfSimpleReadCorrect) = c("Feature2", "Feature4", "Feature6")
|
|
|
96 colnames(dfSimpleReadCorrect) = c("Sample1", "Sample3", "Sample4")
|
|
|
97
|
|
|
98 dfUseAllReadCorrect = as.data.frame(as.matrix(rbind(c(11,12,13),c(31,32,33),c(51,52,53))))
|
|
|
99 rownames(dfUseAllReadCorrect) = c("Feature1", "Feature3", "Feature5")
|
|
|
100 colnames(dfUseAllReadCorrect) = c("Sample1", "Sample2", "Sample3")
|
|
|
101
|
|
|
102 test_that("Matrix file is read correctly.",{
|
|
|
103 expect_equal(dfSimpleRead,dfSimpleReadCorrect)
|
|
|
104 expect_equal(dfUseAllParametersRead,dfUseAllReadCorrect)
|
|
|
105 })
|
|
|
106
|
|
|
107 context("Test funcReadMatrices")
|
|
|
108
|
|
|
109 sConfigureFile1Matrix = file.path(strTestingDirectory,c_strTestingInput,"1Matrix.read.config")
|
|
|
110 mtxOne = as.data.frame(as.matrix(rbind(c(11,12,13,14,15),c(21,22,23,24,25),c(31,32,33,34,35),c(41,42,43,44,45),
|
|
|
111 c(51,52,53,54,55),c(61,62,63,64,65),c(71,72,73,74,75),c(81,82,83,84,85),
|
|
|
112 c(91,92,93,94,95),c(101,102,103,104,105),c(111,112,113,114,115),c(121,122,123,124,125),
|
|
|
113 c(131,132,133,134,135),c(141,142,143,144,145),c(151,152,153,154,155))))
|
|
|
114 rownames(mtxOne) = c("Feature1","Feature2","Feature3","Feature4","Feature5","Feature6","Feature7","Feature8","Feature9","Feature10",
|
|
|
115 "Feature11","Feature12","Feature13","Feature14","Feature15")
|
|
|
116 colnames(mtxOne) = c("Sample1","Sample2","Sample3","Sample4","Sample5")
|
|
|
117 sConfigureFile2Matrix = file.path(strTestingDirectory,c_strTestingInput,"2Matrix.read.config")
|
|
|
118 mtxTwo = as.data.frame(as.matrix(rbind(c(11,12,13),c(21,22,23),c(31,32,33))))
|
|
|
119 rownames(mtxTwo) = c("Feature1","Feature2","Feature3")
|
|
|
120 colnames(mtxTwo) = c("Sample1","Sample2","Sample3")
|
|
|
121
|
|
|
122 sConfigureFile3Matrix = file.path(strTestingDirectory,c_strTestingInput,"3Matrix.read.config")
|
|
|
123 mtxThree = as.data.frame(as.matrix(rbind(c(11,12,14),c(21,22,24),c(31,32,34),c(41,42,44),
|
|
|
124 c(51,52,54),c(61,62,64),c(71,72,74),c(81,82,84),c(91,92,94))))
|
|
|
125 rownames(mtxThree) = c("Feature1","Feature2","Feature3","Feature4","Feature5","Feature6","Feature7","Feature8","Feature9")
|
|
|
126 colnames(mtxThree) = c("Sample1","Sample2","Sample4")
|
|
|
127
|
|
|
128 #Read one matrix
|
|
|
129 ldfRet1 = funcReadMatrices(configureFile=sConfigureFile1Matrix,strFileMatrix)
|
|
|
130 ldfRet1Answer = list( "Matrix1" = mtxOne)
|
|
|
131
|
|
|
132 #Read two matrices
|
|
|
133 ldfRet2 = funcReadMatrices(configureFile=sConfigureFile2Matrix,strFileMatrix)
|
|
|
134 ldfRet2Answer = list( "Matrix1" = mtxOne,
|
|
|
135 "Matrix2" = mtxTwo)
|
|
|
136
|
|
|
137 #Read three matrices from two different files
|
|
|
138 ldfRet3 = funcReadMatrices(configureFile=sConfigureFile3Matrix,strFileMatrix)
|
|
|
139 ldfRet3Answer = list( "Matrix1" = mtxOne,
|
|
|
140 "Matrix2" = mtxTwo,
|
|
|
141 "Matrix3" = mtxThree)
|
|
|
142
|
|
|
143 test_that("Test funcReadMatrices read in the correct matrices not matter the number or source",{
|
|
|
144 expect_equal(ldfRet1,ldfRet1Answer)
|
|
|
145 expect_equal(ldfRet2,ldfRet2Answer)
|
|
|
146 expect_equal(ldfRet3,ldfRet3Answer)
|
|
|
147 })
|
|
|
148
|
|
|
149 context("Test funcWriteMatrices")
|
|
|
150 strFuncWriteMatricesMatrix1 = file.path(strTestingDirectory,c_strTemporaryFiles,"FuncWriteMatrices1.tsv")
|
|
|
151 strFuncWriteMatricesMatrix2 = file.path(strTestingDirectory,c_strTemporaryFiles,"FuncWriteMatrices2.tsv")
|
|
|
152 strFuncWriteMatricesMatrix1Answer = file.path(strTestingDirectory, c_strCorrectAnswers,"FuncWriteMatrices1.tsv")
|
|
|
153 strFuncWriteMatricesMatrix2Answer = file.path(strTestingDirectory, c_strCorrectAnswers,"FuncWriteMatrices2.tsv")
|
|
|
154 strFuncWriteMatricesRCFile = file.path(strTestingDirectory,c_strTemporaryFiles,"FuncWriteMatrices.read.config")
|
|
|
155 strFuncWriteMatricesRCFileAnswer = file.path(strTestingDirectory, c_strCorrectAnswers,"FuncWriteMatrices.read.config")
|
|
|
156 funcWriteMatrices(list("1"=mtxOne, "2"=mtxThree),c(strFuncWriteMatricesMatrix1, strFuncWriteMatricesMatrix2), strFuncWriteMatricesRCFile)
|
|
|
157
|
|
|
158 test_that("Test that writing to a file occurs correctly, for both matrix and configure file.",{
|
|
|
159 expect_equal(readLines(strFuncWriteMatricesMatrix1Answer),readLines(strFuncWriteMatricesMatrix1))
|
|
|
160 expect_equal(readLines(strFuncWriteMatricesMatrix2Answer),readLines(strFuncWriteMatricesMatrix2))
|
|
|
161 expect_equal(readLines(strFuncWriteMatricesRCFileAnswer),readLines(strFuncWriteMatricesRCFile))
|
|
|
162 })
|
