void CdfExportTest::exportCdf() { string command = "./apt-cdf-export -c ../../../rawq/test/data/Test3.CDF -ps Pae_16SrRNA_s_at -ps AFFX-Athal-Actin_5_r_at > " + testDir + "/export.Test3.txt"; vector<RegressionCheck *> checks; RegressionTest exportTest ("exportCdf", command.c_str(), checks); Verbose::out (1, "\nDoing exportCdf()"); if (!exportTest.run()) { Verbose::out (1, "Error in CdfExportTest::exportCdf(): " + exportTest.getErrorMsg()); numFailed++; } else { TextFileCheck exportCheck (testDir + "/export.Test3.txt", "data/export.Test3.txt", 0); if (exportCheck.check (errorMsg)) { numPassed++; } else { Verbose::out (1, "Error in CdfExportTest::exportCdf(): " + errorMsg); numFailed++; } } }
void MD5CheckTest::testFileNotFound() { string command = md5app + " -v 2 -i file_does_not_exist"; vector<RegressionCheck *> checks; RegressionTest differencesTest ("testFileNotFound", command.c_str(), checks); Verbose::out (1, "\nDoing testFileNotFound()"); if (differencesTest.run() == false) ++numPassed; else { Verbose::out (1, "Error in MD5CheckTest::testFileNotFound(): " + differencesTest.getErrorMsg()); ++numFailed; } }
void MD5CheckTest::testFailure() { string command = md5app + " -v 2 -i data/translations_md5.rpt"; vector<RegressionCheck *> checks; RegressionTest differencesTest ("testFailure", command.c_str(), checks); Verbose::out (1, "\nDoing testFailure()"); if (differencesTest.run() == false) ++numPassed; else { Verbose::out (1, "Error in MD5CheckTest::testFailure(): " + differencesTest.getErrorMsg()); ++numFailed; } }
// allowable differences only in checked datasets and header parameters void File5EquivalentTest::testDifferencesPositive() { string command = "./apt-file5-equivalent --epsilon 0.005 --correlation 1.1 --datasets-file ./data/datasets_similar.txt ./data/demean_false_diff1.ref.a5 ./data/demean_false_diff2.ref.a5"; vector<RegressionCheck *> checks; RegressionTest differencesTest ("testDifferencesPositive", command, checks); Verbose::out (1, "\nDoing testDifferencesPositive()"); if (differencesTest.run()) { ++numPassed; } else { Verbose::out (1, "Error in File5EquivalentTest::testDifferencesPositive(): " + differencesTest.getErrorMsg()); ++numFailed; } }
// ignore column with integer differences Cyto2.AntigenomicProbes.ProbeID void File5EquivalentTest::testIgnoreListPositive() { string command = "./apt-file5-equivalent -e 0.005 -c 1.1 -d ./data/datasets_integer_diff.txt -i ./data/ignore_columns.txt ./data/demean_false_diff1.ref.a5 ./data/demean_false_diff2.ref.a5"; vector<RegressionCheck *> checks; RegressionTest differencesTest ("testIgnoreListPositive", command, checks); Verbose::out (1, "\nDoing testIgnoreListPositive()"); if (differencesTest.run()) { ++numPassed; } else { Verbose::out (1, "Error in File5EquivalentTest::testIgnoreListPositive(): " + differencesTest.getErrorMsg()); ++numFailed; } }
void CelExtractTest::doExtractIntensitiesSubset() { string command = "./apt-cel-extract --probeset-ids=../../../regression-data/data/idata/cel-extract/HG-U133_Plus_2/ps.txt -o " + testDir + "/qt.extract.intensities.sub.txt -s ../../../regression-data/data/idata/lib/HG-U133_Plus_2/HG-U133_Plus_2.spf " + tissueCels; vector<RegressionCheck *> checks; checks.push_back(new MixedFileCheck(testDir + "/qt.extract.intensities.sub.txt", "../../../regression-data/data/idata/cel-extract/HG-U133_Plus_2/qt.extract.intensities.sub.txt", 0.1, 0,0)); RegressionTest extractTest ("qt-doExtractIntensitiesSubset", command.c_str(), checks); Verbose::out (1, "Doing qt-doExtractIntensitiesSubset()"); if (!extractTest.pass()) { Verbose::out(1, "Error in qt-doExtractIntensitiesSubset():" + extractTest.getErrorMsg()); numFailed++; } else { numPassed++; } }
// ddemean_true_diff3.ref.a5 WaveCorrection datasets X7,X8 have NaN values, verify that it ignores differences if the -n option is false void File5EquivalentTest::testIgnoreNanNumDifferences() { string command = "./apt-file5-equivalent -n false -e 0.00001 -c 0.999999 -d ./data/datasets_correlation.txt -i ./data/ignore_columns_wc-except-x7-x8.txt ./data/demean_true_diff2.ref.a5 ./data/demean_true_diff3.ref.a5"; vector<RegressionCheck *> checks; RegressionTest differencesTest ("testIgnoreNanNumDifferences", command, checks); Verbose::out (1, "\nDoing testIgnoreNanNumDifferences()"); if (differencesTest.run()) { ++numPassed; } else { Verbose::out (1, "Error in File5EquivalentTest::testIgnoreNanNumDifferences(): " + differencesTest.getErrorMsg()); ++numFailed; } }
// datasets WaveCorrection X1,X2 have all same values with changed sign, X3,X4,X5,X6 have only some values with changed sign void File5EquivalentTest::testSignAllowNegationPositive1() { string command = "./apt-file5-equivalent -s -e 0.0001 -c 0.9999 -d ./data/datasets_correlation.txt ./data/demean_true_diff2.ref.a5 ./data/demean_true_diff3.ref.a5"; vector<RegressionCheck *> checks; RegressionTest differencesTest ("testSignAllowNegationPositive1", command, checks); Verbose::out (1, "\nDoing testSignAllowNegationPositive1()"); if (differencesTest.run()) { ++numPassed; } else { Verbose::out (1, "Error in File5EquivalentTest::testSignAllowNegationPositive1(): " + differencesTest.getErrorMsg()); ++numFailed; } }