Surefire Report

Summary

[Summary] [Package List] [Test Cases]

Note: failures are anticipated and checked for with assertions while errors are unanticipated.

Package List

[Summary] [Package List] [Test Cases]

Note: package statistics are not computed recursively, they only sum up all of its testsuites numbers.

de.isas.mztab2

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	ParsingPrimitivesTest	5	0	0	0	100%	0.002

de.isas.mztab2.io.validators

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MzTabVersionValidatorTest	1	0	0	0	100%	0
	DatabaseValidatorTest	3	0	0	0	100%	0.001
	SmallMoleculeQuantificationUnitValidatorTest	1	0	0	0	100%	0
	SoftwareValidatorTest	1	0	0	0	100%	0.007
	QuantificationMethodValidatorTest	1	0	0	0	100%	0.001
	AssayValidatorTest	2	0	0	0	100%	0.001
	SmallMoleculeFeatureQuantificationUnitValidatorTest	1	0	0	0	100%	0.03
	SmallMoleculeIdConfidenceMeasureValidatorTest	1	0	0	0	100%	0.001
	CvValidatorTest	3	0	0	0	100%	0.003
	StudyVariableValidatorTest	5	0	0	0	100%	0.005
	MzTabIdValidatorTest	1	0	0	0	100%	0.001
	MsRunValidatorTest	2	0	0	0	100%	0.001

uk.ac.ebi.pride.jmztab2.utils.parser

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MTDLineParserTest	23	0	0	0	100%	0.055
	MTDLineValidateTest	6	0	0	0	100%	0.009

de.isas.mztab2.io.serialization

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SerializersTest	43	0	0	0	100%	0.035
	SmallMoleculeEvidenceSerializerTest	1	0	0	0	100%	0.048
	SoftwareSerializerTest	1	0	0	0	100%	0.001
	StudyVariableSerializerTest	1	0	0	0	100%	0.003
	SmallMoleculeFeatureSerializerTest	1	0	0	0	100%	0.048
	ParameterConverterTest	4	0	0	0	100%	0.001
	InstrumentSerializerTest	1	0	0	0	100%	0.005
	CvSerializerTest	1	0	0	0	100%	0.006
	SampleProcessingSerializerTest	1	0	0	0	100%	0.089
	DatabaseSerializerTest	1	0	0	0	100%	0.013
	UriConverterTest	1	0	0	0	100%	0
	MsRunSerializerTest	1	0	0	0	100%	0.019
	SmallMoleculeSummarySerializerTest	1	0	0	0	100%	0.041
	SampleSerializerTest	1	0	0	0	100%	0.016
	AssaySerializerTest	4	0	0	0	100%	0.012
	PublicationSerializerTest	1	0	0	0	100%	0.071
	ContactSerializerTest	1	0	0	0	100%	0.038
	MetadataSerializerTest	1	0	0	0	100%	0.012

de.isas.mztab2.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MzTabWriterTest	16	0	0	0	100%	28.937
	MzTabValidatingWriterTest	2	0	0	0	100%	0.134
	MZTabFileParserTest	12	0	0	0	100%	1.605

uk.ac.ebi.pride.jmztab2.model

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SectionTest	11	0	0	0	100%	0.013
	OptColumnMappingBuilderTest	7	0	0	0	100%	0.002
	MZTabColumnFactoryTest	1	0	0	0	100%	2.267

Test Cases

[Summary] [Package List] [Test Cases]

MzTabVersionValidatorTest

testValidateRefine

0

SerializersTest

	testWriteIndexedDoubles	0.012
	testAddLineWithParameters	0
	testUpperCaseCamelCaseMadnessToUnderscore	0
	testWriteAsStringArray_JsonGenerator_List	0
	testAddLine	0
	testPrintOptColumnMappingGlobal	0
	testWriteString_3args_1	0
	testWriteString_3args_2	0
	testGetElementName	0
	testAsMap	0
	testWriteNumber_3args_1	0
	testWriteNumber_3args_2	0
	testWriteNumber_3args_3	0
	testWriteNumber_3args_4	0
	testPrintAbundanceCoeffVarStudyVar	0
	testPrintOptColumnMappingIndexedElementCvParameter	0.003
	testAddSubElementParameter	0.001
	testWriteOptColumnMappings	0
	testCapitalCamelCaseToUnderscore	0
	testWriteNumber_JsonGenerator_Double	0
	testAddSubElementParameters	0
	testWriteAsStringArray_3args_1	0.001
	testWriteAsStringArray_3args_2	0
	testPrintOptColumnMappingGlobalCvParameter	0
	testWriteNumber_JsonGenerator_Integer	0
	testGetReference	0
	testWriteObject_4args_1	0.001
	testWriteObject_4args_2	0
	testCheckForNull	0
	testCamelCaseToUnderscoreLowerCase	0
	testAddLineWithProperty	0
	testAddSubElementStrings	0
	testGetPropertyNames	0.001
	testAddLineWithPropertyParameters	0
	testPrintAbundanceStudyVar	0
	testAddLineWithMetadataProperty	0
	testPrintAbundanceAssay	0
	testAddIndexedLine_5args_1	0
	testAddIndexedLine_5args_2	0.001
	testPrintOptColumnMappingIndexedElement	0
	testMixedCamelCaseToUnderscore	0
	testWriteAsNumberArray_3args_1	0
	testWriteAsNumberArray_3args_2	0

MzTabWriterTest

	testSmlNullEmptyHandling	0.057
	testWriteSmallMoleculeSummaryWithNullToTsvWithJackson	0.002
	testReadWriteRoundtripWithJacksonLipidomicsExample	0.4
	testWriteMzTabToTsvWithJacksonInvalidEncoding	0.001
	testUserParameterToString	0
	testLargeNumberOfFeaturesFromMTBLS263	9.839
	testWriteJsonMapper	0.016
	testWriteDefaultToString	0.005
	testReadWriteRoundtripWithJacksonLda2MouseLiver	15.872
	testWriteMetadataToTsvWithJackson	0.002
	testCvParameterToString	0
	testWriteMzTabToTsvWithJacksonForPath	0.011
	testReadWriteRoundtripWithJacksonLda2StdMix	2.656
	testWriteMzTabToTsvWithJackson	0.002
	testWriteSmallMoleculeFeaturesToTsvWithJackson	0
	testReadWriteRoundtripWithJacksonMTBLS263	0.074

MTDLineParserTest

	testQuantMethod	0.009
	testDatabase	0.001
	testPublication	0.001
	testMsRunWithInstrumentRef	0.002
	testMsRunLocationNull	0.001
	testUri	0
	testMzTabFileInfo	0.001
	testAssay	0.004
	testMsRun	0.001
	testIdConfidenceMeasure	0
	testCv	0.004
	testCreateMetadata	0.008
	testSmQuantUnit	0.001
	testContact	0.006
	testDerivatizationAgent	0.005
	testInstrument	0.001
	testSampleProcessing	0.001
	testCustom	0
	testStudyVariable	0.001
	testSample	0.002
	testSmFeatureQuantUnit	0
	testSmIdReliability	0.001
	testSoftware	0.001

SmallMoleculeEvidenceSerializerTest

testSerialize

0.048

DatabaseValidatorTest

	testValidateRefineCustomDatabase	0.001
	testValidateRefineNullDatabase	0
	testValidateRefineNoDatabase	0

SmallMoleculeQuantificationUnitValidatorTest

testValidateRefine

0

SoftwareSerializerTest

testSerialize

0.001

StudyVariableSerializerTest

testSerialize

0.003

SmallMoleculeFeatureSerializerTest

testSerialize

0.048

SectionTest

	testIsMetadata	0.004
	testGetLevel	0.001
	testIsHeader	0
	testFindSection_String	0
	testToHeaderSection	0.001
	testIsComment	0
	testGetPrefix	0
	testIsData	0
	testToDataSection	0
	testFindSection_int	0
	testValues	0

ParameterConverterTest

	testConvertUserParam	0.001
	testEscapeStringHandling	0
	testConvertWithValue	0
	testConvert	0

SoftwareValidatorTest

testValidateRefine

0.007

MzTabValidatingWriterTest

	testWrite_OutputStreamWriter_MzTab	0.078
	testWrite_Path_MzTab	0.056

InstrumentSerializerTest

testInstrument

0.005

ParsingPrimitivesTest

	testVersionRegexp	0.001
	testParserVersionRegexp	0
	testAdductRegexp	0
	testIntegerParsing	0.001
	testIdentificationReliability	0

QuantificationMethodValidatorTest

testValidateRefine

0.001

AssayValidatorTest

	testValidateRefineAssayHasMsRun	0.001
	testValidateRefineNullAssay	0

MTDLineValidateTest

	testPublication	0.006
	testInvalidColUnitLabel	0
	testMZTabDescription	0.001
	testIndexElement	0.001
	testDuplicationID	0
	testNullMsRun	0.001

SmallMoleculeFeatureQuantificationUnitValidatorTest

testValidateRefine

0.03

OptColumnMappingBuilderTest

	testForIndexedElement	0
	testWithCvParameterWithoutParamName	0
	testWithCvParameterWithoutCvAccession	0
	testWithParameterGlobal	0
	testWithCvParameterWithoutCvLabel	0
	testForGlobal	0.001
	testWithParameterIndexedElement	0

SmallMoleculeIdConfidenceMeasureValidatorTest

testValidateRefine

0.001

CvSerializerTest

testSerialize

0.006

CvValidatorTest

	testValidateCvWithEmptyElements	0.003
	testValidateCvWithNullElements	0
	testValidateRefineNullCv	0

SampleProcessingSerializerTest

testSerialize

0.089

MZTabColumnFactoryTest

testOptionalColumnsAndManyRows

2.267

DatabaseSerializerTest

testSerialize

0.013

StudyVariableValidatorTest

	testValidateRefine	0.001
	testStudyVariableAssayRefs	0
	testTwoStudyVariableMultipleAssaysMissingNamesAndMissingDescription	0.003
	testTwoStudyVariableMultipleAssaysMultipleUndefinedStudyVariables	0.001
	testSingleStudyVariableNoNameMultipleAssays	0

UriConverterTest

testConvert

0

MsRunSerializerTest

testSerialize

0.019

MZTabFileParserTest

	testExamples[2: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.551
	testExamples[6: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.042
	testExamples[1: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.604
	testExamples[7: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	0.99
	testExamples[11: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	0.986
	testExamples[10: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	0.997
	testExamples[3: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.034
	testExamples[5: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.04
	testExamples[8: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1
	testExamples[9: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	0.999
	testExamples[0: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	0.987
	testExamples[4: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.038

SmallMoleculeSummarySerializerTest

testSerialize

0.041

MzTabIdValidatorTest

testValidateRefine

0.001

SampleSerializerTest

testSerialize

0.016

AssaySerializerTest

	testAssay	0.008
	testAssayWithCustom	0.002
	testAssayWithSampleRef	0.001
	testAssayWithMsRunRef	0.001

PublicationSerializerTest

testSerialize

0.071

ContactSerializerTest

testSerialize

0.038

MsRunValidatorTest

	testValidateRefineMissingLocation	0.001
	testValidateRefineMissingScanPolarity	0

MetadataSerializerTest

testSerialize

0.012