Temporarily disabled importSNV.TCGA and tests for refactoring.

elijah-tai · Mar 30, 2017 · 7e0e1f7 · 7e0e1f7
1 parent 6e260a5
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diff --git a/R/importSNV.TCGA.R b/R/importSNV.TCGA.R
@@ -38,6 +38,11 @@ importSNV.TCGA <- function(  fMAF,
                              silent = FALSE,
                              writeLog = TRUE) {
 
+    # ToDo ...
+    print("Temporarily disabled for refactoring. Returning without activity.")
+    return()
+
+
     myNotes <- character()
     myCall <- character()
 

diff --git a/tests/testthat/testImportSNV.TCGA.R b/tests/testthat/testImportSNV.TCGA.R
@@ -1,137 +1,137 @@
-# testImportSNV.TCGA.R
-
-# ==== BEGIN SETUP AND PREPARE =================================================
-OLOG <- as.character(getOption("rete.logfile"))   # save original logfile name
-logFileName(fPath = tempdir(), setOption = TRUE)  # make tempdir() the log dir
-NL <- .PlatformLineBreak
-# ==== END SETUP AND PREPARE ===================================================
-
-#context("Tools for importing MAF files into a rSNV file")
-options(stringsAsFactors=FALSE)
-testIN <- "importSNV_input_test_file.maf"
-testOUT <- "importSNV_output_test_file"
-testINcorr <- "importSNV_input_corr_file.maf"
-
-test_that("parameter errors are correctly handled", {
-    testMAF <- tempfile()
-    tOut <- tempfile()
-    trueIn <- data.frame()
-    input0 <- c("Hugo_Symbol" , "Entrez_Gene_Id" , "Center" , "NCBI_Build" , "Chromosome" , "Start_Position" , "End_Position" , "Strand" , "Variant_Classification" , "Variant_Type" , "Reference_Allele" , "Tumor_Seq_Allele1" , "Tumor_Seq_Allele2" , "dbSNP_RS" , "dbSNP_Val_Status" , "Tumor_Sample_Barcode" , "Matched_Norm_Sample_Barcode" , "Match_Norm_Seq_Allele1" , "Match_Norm_Seq_Allele2" , "Tumor_Validation_Allele1" , "Tumor_Validation_Allele2" , "Match_Norm_Validation_Allele1" , "Match_Norm_Validation_Allele2" , "Verification_Status" , "Validation_Status" , "Mutation_Status" )
-    input1 <- c("TMEM201" , 199953 , "WUGSC" , "GRCh38" , "chr1" , 9607661 , 9607661 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09" , "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a", "c.1265C>T" , "p.Pro422Leu", "p.P422L" , "ENST00000340381")
-    input2 <- c("PTCHD2" , 57540 , "WUGSC" , "GRCh38" , "chr1" , 11516130 , 11516130 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09" , "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a" , "c.1718C>T" , "p.Ala573Val" , "p.A573V" , "ENST00000294484")
-    input3 <- c("VWA5B1" , 127731 , "WUGSC" , "GRCh38" , "chr1" , 20319393 , 20319393 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09", "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a" , "c.853C>T" , "p.Pro285Ser" , "p.P285S" , "ENST00000375079")
-
-    trueIn <- rbind(input0, input1, input2, input3)
-
-    write.table(trueIn,  file=testMAF, sep="\t", append=FALSE, row.names =
-                    FALSE, col.names = FALSE, quote = FALSE)
-    # fMAF is not provided
-    expect_error(importSNV.TCGA(), "argument \"fMAF\" is missing, with no default")
-    # fMAF is NULL/empty vector
-    expect_error(importSNV.TCGA(fMAF = NULL, tOut), ".checkArgs> \"fMAF\" mode error: argument has mode \"NULL\" but function expects mode \"character\".")
-    # fMAF input vector contains non-string values
-    expect_error(importSNV.TCGA(fMAF = 123, tOut), ".checkArgs> \"fMAF\" mode error: argument has mode \"numeric\" but function expects mode \"character\".")
-
-    # rSNV is missing
-    expect_error(importSNV.TCGA(fMAF = testMAF), "argument \"rSNV\" is missing, with no default")
-    # if rSNV parameter is provided, but is NULL
-    expect_error(importSNV.TCGA(fMAF = testMAF, rSNV = NULL), ".checkArgs> \"rSNV\" mode error: argument has mode \"NULL\" but function expects mode \"character\".")
-    # if rSNV parameter is provided, but is non-string value
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, rSNV = 123), ".checkArgs> \"rSNV\" mode error: argument has mode \"numeric\" but function expects mode \"character\".")
-    # if rSNV is given vector input
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, rSNV = c("abc", "xyz")), ".checkArgs> \"rSNV\" length error: argument has length 2 but function expects length 1.")
-
-    # if silent is not given logical input
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = 1), ".checkArgs> \"silent\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = NULL), ".checkArgs> \"silent\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = c(TRUE, TRUE)), ".checkArgs> \"silent\" length error: argument has length 2 but function expects length 1.")
-
-    # writeLog is not given logical input
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = 1), ".checkArgs> \"writeLog\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = NULL), ".checkArgs> \"writeLog\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = c(TRUE, TRUE)), ".checkArgs> \"writeLog\" length error: argument has length 2 but function expects length 1.")
-
-    # if na.rm is not given logical input
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = 1), ".checkArgs> \"na.rm\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = NULL), ".checkArgs> \"na.rm\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
-    expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = c(TRUE, TRUE)), ".checkArgs> \"na.rm\" length error: argument has length 2 but function expects length 1.")
-    # ToDo - confirm that no log file was written.
-    expect_true(file.remove(testMAF))
-})
-
-test_that("a sane input gives an expected output with different input parameters", {
-
-    tOut <- tempfile()
-    tOut1 <- tempfile()
-    tOut2 <- tempfile()
-    trueOut <- data.frame()
-
-    # MAKE SMALL OUTPUT (trueOut) --------------------------------------------------
-    trueOut <- read.table(testOUT, sep = "\t", stringsAsFactors = FALSE)
-
-    # run the module on only fMAF and rSNV as parameters (moduleOut)
-    importSNV.TCGA(testIN, tOut, writeLog = FALSE)
-    # check if manual output = module output
-    module <- read.table(tOut, sep = "\t", stringsAsFactors = FALSE)
-
-    # TEST fMAF parameter ==========================================================
-    expect_equal(trueOut, module)
-    #===============================================================================
-
-    # TEST fMAF, rSNV, silent parameters ============================================
-    # run the module on fMAF and rSNV and silent as parameters
-    importSNV.TCGA(testIN, tOut1, silent=TRUE, writeLog = FALSE)
-    modulePre2 <- read.table(tOut1, sep = "\t", stringsAsFactors = FALSE)
-    # add to prexisting rSNV file
-    expect_equal(trueOut, modulePre2)
-    #===============================================================================
-
-    # TEST fMAF, rSNV, silent, writeLog parameters =================================
-    # run the module on fMAF, rSNV, silent and writeLog as parameters
-    importSNV.TCGA(testIN, tOut2, silent=FALSE, writeLog=FALSE)
-    modulePre3 <- read.table(tOut2, sep = "\t", stringsAsFactors = FALSE)
-    # add to prexisting rSNV file
-    expect_equal(trueOut, modulePre3)
-    #===============================================================================
-
-    # test input with rSNV as input and NA values -------------------------------------------
-    tOut3 <- tempfile()
-
-    # TEST fMAF, rSNV, silent, writeLog parameters, na.rm ==========================
-    # run the module on fMAF, rSNV, silent, writeLog and na.rm as parameters
-    importSNV.TCGA(testIN, tOut3, silent=FALSE, writeLog=FALSE, na.rm=TRUE)
-    moduleNA <- read.table(tOut3, sep = "\t", stringsAsFactors = FALSE)
-    # add to prexisting rSNV file
-    expect_equal(trueOut, moduleNA)
-})
-
-
-test_that("a corrupt input does not lead to corrupted output", {
-    # checking for version is not necessary : can handle all versions (2.4.1(latest) and below)
-    # other forms of corrupted input tested for in importSNV.TCGA.R
-
-    # this is the test for corrupted final line
-    tOut <- tempfile()
-    expect_warning(importSNV.TCGA(testINcorr, tOut), "incomplete final line found by readTableHeader on 'importSNV_input_corr_file.maf'")
-})
-
-test_that("silent and writeLog work as intended", {
-    # if silent=TRUE, check if output to console is supressed
-    tOut <- tempfile()
-    testF <- tempfile()
-    capture.output(importSNV.TCGA(testIN, tOut, silent = TRUE, writeLog = FALSE), file = testF)
-    expect_equal(length(readLines(testF)), 0)
-    expect_true(file.remove(testF))
-
-    # check writeLog works as intended
-    importSNV.TCGA(testIN, tOut, writeLog = TRUE)
-    expect_equal(readLines(unlist(getOption("rete.logfile")))[1], "event | title  | importSNV.TCGA")
-})
-
-
-# ==== BEGIN TEARDOWN AND RESTORE ==============================================
-logName <- unlist(getOption("rete.logfile"))
-if (file.exists(logName)) { file.remove(logName)}
-options("rete.logfile" = OLOG)
-# ==== END  TEARDOWN AND RESTORE ===============================================
-# [END]
+# # testImportSNV.TCGA.R
+#
+# # ==== BEGIN SETUP AND PREPARE =================================================
+# OLOG <- as.character(getOption("rete.logfile"))   # save original logfile name
+# logFileName(fPath = tempdir(), setOption = TRUE)  # make tempdir() the log dir
+# NL <- .PlatformLineBreak
+# # ==== END SETUP AND PREPARE ===================================================
+#
+# #context("Tools for importing MAF files into a rSNV file")
+# options(stringsAsFactors=FALSE)
+# testIN <- "importSNV_input_test_file.maf"
+# testOUT <- "importSNV_output_test_file"
+# testINcorr <- "importSNV_input_corr_file.maf"
+#
+# test_that("parameter errors are correctly handled", {
+#     testMAF <- tempfile()
+#     tOut <- tempfile()
+#     trueIn <- data.frame()
+#     input0 <- c("Hugo_Symbol" , "Entrez_Gene_Id" , "Center" , "NCBI_Build" , "Chromosome" , "Start_Position" , "End_Position" , "Strand" , "Variant_Classification" , "Variant_Type" , "Reference_Allele" , "Tumor_Seq_Allele1" , "Tumor_Seq_Allele2" , "dbSNP_RS" , "dbSNP_Val_Status" , "Tumor_Sample_Barcode" , "Matched_Norm_Sample_Barcode" , "Match_Norm_Seq_Allele1" , "Match_Norm_Seq_Allele2" , "Tumor_Validation_Allele1" , "Tumor_Validation_Allele2" , "Match_Norm_Validation_Allele1" , "Match_Norm_Validation_Allele2" , "Verification_Status" , "Validation_Status" , "Mutation_Status" )
+#     input1 <- c("TMEM201" , 199953 , "WUGSC" , "GRCh38" , "chr1" , 9607661 , 9607661 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09" , "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a", "c.1265C>T" , "p.Pro422Leu", "p.P422L" , "ENST00000340381")
+#     input2 <- c("PTCHD2" , 57540 , "WUGSC" , "GRCh38" , "chr1" , 11516130 , 11516130 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09" , "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a" , "c.1718C>T" , "p.Ala573Val" , "p.A573V" , "ENST00000294484")
+#     input3 <- c("VWA5B1" , 127731 , "WUGSC" , "GRCh38" , "chr1" , 20319393 , 20319393 , "+" , "Missense_Mutation" , "SNP" , "C" , "C" , "T" , "novel" , "TCGA-QQ-A8VF-01A-11D-A37C-09", "TCGA-QQ-A8VF-10A-01D-A37F-09" , "Somatic" , "Illumina" , "HiSeq" , "2000" , "2109690d-e8b1-4b5c-9a39-21af273324cf" , "fe2daf93-56f1-4236-9b58-bf18f0e47d3a" , "c.853C>T" , "p.Pro285Ser" , "p.P285S" , "ENST00000375079")
+#
+#     trueIn <- rbind(input0, input1, input2, input3)
+#
+#     write.table(trueIn,  file=testMAF, sep="\t", append=FALSE, row.names =
+#                     FALSE, col.names = FALSE, quote = FALSE)
+#     # fMAF is not provided
+#     expect_error(importSNV.TCGA(), "argument \"fMAF\" is missing, with no default")
+#     # fMAF is NULL/empty vector
+#     expect_error(importSNV.TCGA(fMAF = NULL, tOut), ".checkArgs> \"fMAF\" mode error: argument has mode \"NULL\" but function expects mode \"character\".")
+#     # fMAF input vector contains non-string values
+#     expect_error(importSNV.TCGA(fMAF = 123, tOut), ".checkArgs> \"fMAF\" mode error: argument has mode \"numeric\" but function expects mode \"character\".")
+#
+#     # rSNV is missing
+#     expect_error(importSNV.TCGA(fMAF = testMAF), "argument \"rSNV\" is missing, with no default")
+#     # if rSNV parameter is provided, but is NULL
+#     expect_error(importSNV.TCGA(fMAF = testMAF, rSNV = NULL), ".checkArgs> \"rSNV\" mode error: argument has mode \"NULL\" but function expects mode \"character\".")
+#     # if rSNV parameter is provided, but is non-string value
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, rSNV = 123), ".checkArgs> \"rSNV\" mode error: argument has mode \"numeric\" but function expects mode \"character\".")
+#     # if rSNV is given vector input
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, rSNV = c("abc", "xyz")), ".checkArgs> \"rSNV\" length error: argument has length 2 but function expects length 1.")
+#
+#     # if silent is not given logical input
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = 1), ".checkArgs> \"silent\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = NULL), ".checkArgs> \"silent\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, silent = c(TRUE, TRUE)), ".checkArgs> \"silent\" length error: argument has length 2 but function expects length 1.")
+#
+#     # writeLog is not given logical input
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = 1), ".checkArgs> \"writeLog\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = NULL), ".checkArgs> \"writeLog\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, writeLog = c(TRUE, TRUE)), ".checkArgs> \"writeLog\" length error: argument has length 2 but function expects length 1.")
+#
+#     # if na.rm is not given logical input
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = 1), ".checkArgs> \"na.rm\" mode error: argument has mode \"numeric\" but function expects mode \"logical\".")
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = NULL), ".checkArgs> \"na.rm\" mode error: argument has mode \"NULL\" but function expects mode \"logical\".")
+#     expect_error(importSNV.TCGA(fMAF = testMAF, tOut, na.rm = c(TRUE, TRUE)), ".checkArgs> \"na.rm\" length error: argument has length 2 but function expects length 1.")
+#     # ToDo - confirm that no log file was written.
+#     expect_true(file.remove(testMAF))
+# })
+#
+# test_that("a sane input gives an expected output with different input parameters", {
+#
+#     tOut <- tempfile()
+#     tOut1 <- tempfile()
+#     tOut2 <- tempfile()
+#     trueOut <- data.frame()
+#
+#     # MAKE SMALL OUTPUT (trueOut) --------------------------------------------------
+#     trueOut <- read.table(testOUT, sep = "\t", stringsAsFactors = FALSE)
+#
+#     # run the module on only fMAF and rSNV as parameters (moduleOut)
+#     importSNV.TCGA(testIN, tOut, writeLog = FALSE)
+#     # check if manual output = module output
+#     module <- read.table(tOut, sep = "\t", stringsAsFactors = FALSE)
+#
+#     # TEST fMAF parameter ==========================================================
+#     expect_equal(trueOut, module)
+#     #===============================================================================
+#
+#     # TEST fMAF, rSNV, silent parameters ============================================
+#     # run the module on fMAF and rSNV and silent as parameters
+#     importSNV.TCGA(testIN, tOut1, silent=TRUE, writeLog = FALSE)
+#     modulePre2 <- read.table(tOut1, sep = "\t", stringsAsFactors = FALSE)
+#     # add to prexisting rSNV file
+#     expect_equal(trueOut, modulePre2)
+#     #===============================================================================
+#
+#     # TEST fMAF, rSNV, silent, writeLog parameters =================================
+#     # run the module on fMAF, rSNV, silent and writeLog as parameters
+#     importSNV.TCGA(testIN, tOut2, silent=FALSE, writeLog=FALSE)
+#     modulePre3 <- read.table(tOut2, sep = "\t", stringsAsFactors = FALSE)
+#     # add to prexisting rSNV file
+#     expect_equal(trueOut, modulePre3)
+#     #===============================================================================
+#
+#     # test input with rSNV as input and NA values -------------------------------------------
+#     tOut3 <- tempfile()
+#
+#     # TEST fMAF, rSNV, silent, writeLog parameters, na.rm ==========================
+#     # run the module on fMAF, rSNV, silent, writeLog and na.rm as parameters
+#     importSNV.TCGA(testIN, tOut3, silent=FALSE, writeLog=FALSE, na.rm=TRUE)
+#     moduleNA <- read.table(tOut3, sep = "\t", stringsAsFactors = FALSE)
+#     # add to prexisting rSNV file
+#     expect_equal(trueOut, moduleNA)
+# })
+#
+#
+# test_that("a corrupt input does not lead to corrupted output", {
+#     # checking for version is not necessary : can handle all versions (2.4.1(latest) and below)
+#     # other forms of corrupted input tested for in importSNV.TCGA.R
+#
+#     # this is the test for corrupted final line
+#     tOut <- tempfile()
+#     expect_warning(importSNV.TCGA(testINcorr, tOut), "incomplete final line found by readTableHeader on 'importSNV_input_corr_file.maf'")
+# })
+#
+# test_that("silent and writeLog work as intended", {
+#     # if silent=TRUE, check if output to console is supressed
+#     tOut <- tempfile()
+#     testF <- tempfile()
+#     capture.output(importSNV.TCGA(testIN, tOut, silent = TRUE, writeLog = FALSE), file = testF)
+#     expect_equal(length(readLines(testF)), 0)
+#     expect_true(file.remove(testF))
+#
+#     # check writeLog works as intended
+#     importSNV.TCGA(testIN, tOut, writeLog = TRUE)
+#     expect_equal(readLines(unlist(getOption("rete.logfile")))[1], "event | title  | importSNV.TCGA")
+# })
+#
+#
+# # ==== BEGIN TEARDOWN AND RESTORE ==============================================
+# logName <- unlist(getOption("rete.logfile"))
+# if (file.exists(logName)) { file.remove(logName)}
+# options("rete.logfile" = OLOG)
+# # ==== END  TEARDOWN AND RESTORE ===============================================
+# # [END]