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%	0.033

de.isas.mztab2.io.validators

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MzTabVersionValidatorTest	1	0	0	0	100%	0.019
	RefiningValidatorTest	1	0	0	0	100%	0.002
	DatabaseValidatorTest	3	0	0	0	100%	0.057
	SmallMoleculeQuantificationUnitValidatorTest	1	0	0	0	100%	0.004
	SoftwareValidatorTest	1	0	0	0	100%	0.002
	QuantificationMethodValidatorTest	1	0	0	0	100%	0.001
	AssayValidatorTest	2	0	0	0	100%	0.042
	SmallMoleculeFeatureQuantificationUnitValidatorTest	1	0	0	0	100%	0.002
	SmallMoleculeIdConfidenceMeasureValidatorTest	1	0	0	0	100%	0.028
	CvValidatorTest	3	0	0	0	100%	0.05
	FieldValidatorTest	1	0	0	0	100%	0.034
	SpectraRefValidatorTest	11	0	0	0	100%	0.103
	StudyVariableValidatorTest	5	0	0	0	100%	0.051
	MzTabIdValidatorTest	1	0	0	0	100%	0.002
	MsRunValidatorTest	2	0	0	0	100%	0.004

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

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MTDLineParserTest	23	0	0	0	100%	0.11
	MTDLineValidateTest	6	0	0	0	100%	0.038

de.isas.mztab2.io.serialization

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SerializersTest	43	0	0	0	100%	0.122
	SmallMoleculeEvidenceSerializerTest	1	0	0	0	100%	0.009
	SoftwareSerializerTest	1	0	0	0	100%	0.356
	StudyVariableSerializerTest	1	0	0	0	100%	0.002
	SmallMoleculeFeatureSerializerTest	1	0	0	0	100%	0.038
	ParameterConverterTest	4	0	0	0	100%	0.032
	InstrumentSerializerTest	1	0	0	0	100%	0.014
	CvSerializerTest	1	0	0	0	100%	0.001
	SampleProcessingSerializerTest	1	0	0	0	100%	0.293
	DatabaseSerializerTest	1	0	0	0	100%	0.002
	UriConverterTest	1	0	0	0	100%	0
	MsRunSerializerTest	1	0	0	0	100%	0.001
	SmallMoleculeSummarySerializerTest	1	0	0	0	100%	0.302
	SampleSerializerTest	1	0	0	0	100%	0.004
	AssaySerializerTest	4	0	0	0	100%	0.071
	PublicationSerializerTest	1	0	0	0	100%	0.006
	ContactSerializerTest	1	0	0	0	100%	0.293
	MetadataSerializerTest	1	0	0	0	100%	0.002

de.isas.mztab2.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MzTabWriterTest	16	0	0	0	100%	46.955
	MzTabValidatingWriterTest	2	0	0	0	100%	0.147
	MZTabFileParserTest	12	0	0	0	100%	2.369

uk.ac.ebi.pride.jmztab2.model

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	IOptColumnMappingBuilderTest	1	0	0	0	100%	0.015
	SectionTest	11	0	0	0	100%	0.055
	OptColumnMappingBuilderTest	7	0	0	0	100%	0.003
	MZTabColumnFactoryTest	1	0	0	0	100%	3.684

Test Cases

[Summary] [Package List] [Test Cases]

MzTabVersionValidatorTest

testValidateRefine

0.019

SerializersTest

	testWriteIndexedDoubles	0
	testAddLineWithParameters	0.078
	testUpperCaseCamelCaseMadnessToUnderscore	0
	testWriteAsStringArray_JsonGenerator_List	0.001
	testAddLine	0
	testPrintOptColumnMappingGlobal	0
	testWriteString_3args_1	0
	testWriteString_3args_2	0
	testGetElementName	0.001
	testAsMap	0
	testWriteNumber_3args_1	0
	testWriteNumber_3args_2	0.001
	testWriteNumber_3args_3	0
	testWriteNumber_3args_4	0.013
	testPrintAbundanceCoeffVarStudyVar	0.001
	testPrintOptColumnMappingIndexedElementCvParameter	0.001
	testAddSubElementParameter	0
	testWriteOptColumnMappings	0
	testCapitalCamelCaseToUnderscore	0
	testWriteNumber_JsonGenerator_Double	0.001
	testAddSubElementParameters	0
	testWriteAsStringArray_3args_1	0
	testWriteAsStringArray_3args_2	0.001
	testPrintOptColumnMappingGlobalCvParameter	0
	testWriteNumber_JsonGenerator_Integer	0
	testGetReference	0
	testWriteObject_4args_1	0
	testWriteObject_4args_2	0
	testCheckForNull	0
	testCamelCaseToUnderscoreLowerCase	0
	testAddLineWithProperty	0.001
	testAddSubElementStrings	0
	testGetPropertyNames	0
	testAddLineWithPropertyParameters	0
	testPrintAbundanceStudyVar	0
	testAddLineWithMetadataProperty	0
	testPrintAbundanceAssay	0
	testAddIndexedLine_5args_1	0.001
	testAddIndexedLine_5args_2	0
	testPrintOptColumnMappingIndexedElement	0
	testMixedCamelCaseToUnderscore	0.001
	testWriteAsNumberArray_3args_1	0
	testWriteAsNumberArray_3args_2	0

MzTabWriterTest

	testSmlNullEmptyHandling	0.059
	testWriteSmallMoleculeSummaryWithNullToTsvWithJackson	0.019
	testReadWriteRoundtripWithJacksonLipidomicsExample	0.559
	testWriteMzTabToTsvWithJacksonInvalidEncoding	0.001
	testUserParameterToString	0.001
	testLargeNumberOfFeaturesFromMTBLS263	11.847
	testWriteJsonMapper	0.01
	testWriteDefaultToString	0.003
	testReadWriteRoundtripWithJacksonLda2MouseLiver	30.62
	testWriteMetadataToTsvWithJackson	0.004
	testCvParameterToString	0.001
	testWriteMzTabToTsvWithJacksonForPath	0.009
	testReadWriteRoundtripWithJacksonLda2StdMix	3.728
	testWriteMzTabToTsvWithJackson	0.002
	testWriteSmallMoleculeFeaturesToTsvWithJackson	0
	testReadWriteRoundtripWithJacksonMTBLS263	0.09

MTDLineParserTest

	testQuantMethod	0.037
	testDatabase	0.001
	testPublication	0.001
	testMsRunWithInstrumentRef	0.002
	testMsRunLocationNull	0.001
	testUri	0
	testMzTabFileInfo	0.001
	testAssay	0.004
	testMsRun	0.002
	testIdConfidenceMeasure	0.001
	testCv	0.001
	testCreateMetadata	0.026
	testSmQuantUnit	0.001
	testContact	0.001
	testDerivatizationAgent	0
	testInstrument	0.001
	testSampleProcessing	0
	testCustom	0.001
	testStudyVariable	0
	testSample	0.001
	testSmFeatureQuantUnit	0
	testSmIdReliability	0
	testSoftware	0

SmallMoleculeEvidenceSerializerTest

testSerialize

0.009

RefiningValidatorTest

testValidateRefine

0.002

DatabaseValidatorTest

	testValidateRefineCustomDatabase	0.044
	testValidateRefineNullDatabase	0
	testValidateRefineNoDatabase	0.001

IOptColumnMappingBuilderTest

testBuild

0.015

SmallMoleculeQuantificationUnitValidatorTest

testValidateRefine

0.004

SoftwareSerializerTest

testSerialize

0.356

StudyVariableSerializerTest

testSerialize

0.002

SmallMoleculeFeatureSerializerTest

testSerialize

0.038

SectionTest

	testIsMetadata	0.007
	testGetLevel	0.001
	testIsHeader	0
	testFindSection_String	0.002
	testToHeaderSection	0
	testIsComment	0
	testGetPrefix	0.006
	testIsData	0
	testToDataSection	0
	testFindSection_int	0
	testValues	0.001

ParameterConverterTest

	testConvertUserParam	0.031
	testEscapeStringHandling	0
	testConvertWithValue	0
	testConvert	0

SoftwareValidatorTest

testValidateRefine

0.002

MzTabValidatingWriterTest

	testWrite_OutputStreamWriter_MzTab	0.125
	testWrite_Path_MzTab	0.022

InstrumentSerializerTest

testInstrument

0.014

ParsingPrimitivesTest

	testVersionRegexp	0.007
	testParserVersionRegexp	0.018
	testAdductRegexp	0
	testIntegerParsing	0
	testIdentificationReliability	0

QuantificationMethodValidatorTest

testValidateRefine

0.001

AssayValidatorTest

	testValidateRefineAssayHasMsRun	0.001
	testValidateRefineNullAssay	0.04

MTDLineValidateTest

	testPublication	0.002
	testInvalidColUnitLabel	0.007
	testMZTabDescription	0.001
	testIndexElement	0.002
	testDuplicationID	0.001
	testNullMsRun	0

SmallMoleculeFeatureQuantificationUnitValidatorTest

testValidateRefine

0.002

OptColumnMappingBuilderTest

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

SmallMoleculeIdConfidenceMeasureValidatorTest

testValidateRefine

0.028

CvSerializerTest

testSerialize

0.001

CvValidatorTest

	testValidateCvWithEmptyElements	0.042
	testValidateCvWithNullElements	0
	testValidateRefineNullCv	0.001

SampleProcessingSerializerTest

testSerialize

0.293

MZTabColumnFactoryTest

testOptionalColumnsAndManyRows

3.684

DatabaseSerializerTest

testSerialize

0.002

FieldValidatorTest

testValidateLine

0.034

SpectraRefValidatorTest

	testValidateOfNullRunLocation	0.002
	testValidateOfEmptyRefList	0.007
	testValidatePatternSpectraRefIndex	0.041
	testValidateLineWithUnsupportedRefIdFormat	0.009
	testValidateLineWithOneSpectraRefThermo	0.001
	testValidatePatternSpectraRefScan	0.001
	testValidatePatternWiff	0.001
	testValidateLineWithOneSpectraRef	0.001
	testValidatePatternThermo	0.001
	testValidatePatternSpectraRefSpectrum	0.001
	testValidatePatternWaters	0.017

StudyVariableValidatorTest

	testValidateRefine	0.01
	testStudyVariableAssayRefs	0.026
	testTwoStudyVariableMultipleAssaysMissingNamesAndMissingDescription	0.003
	testTwoStudyVariableMultipleAssaysMultipleUndefinedStudyVariables	0
	testSingleStudyVariableNoNameMultipleAssays	0

UriConverterTest

testConvert

0

MsRunSerializerTest

testSerialize

0.001

MZTabFileParserTest

	testExamples[3: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.536
	testExamples[6: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.529
	testExamples[0: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.431
	testExamples[5: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.543
	testExamples[1: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	2.303
	testExamples[7: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.433
	testExamples[9: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.429
	testExamples[4: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.536
	testExamples[11: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.432
	testExamples[8: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.431
	testExamples[10: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	1.429
	testExamples[2: semantic validation of {0} on level {1} expecting {2} structural/logical errors]	2.366

SmallMoleculeSummarySerializerTest

testSerialize

0.302

MzTabIdValidatorTest

testValidateRefine

0.002

SampleSerializerTest

testSerialize

0.004

AssaySerializerTest

	testAssay	0.001
	testAssayWithCustom	0.009
	testAssayWithSampleRef	0.033
	testAssayWithMsRunRef	0.001

PublicationSerializerTest

testSerialize

0.006

ContactSerializerTest

testSerialize

0.293

MsRunValidatorTest

	testValidateRefineMissingLocation	0.003
	testValidateRefineMissingScanPolarity	0

MetadataSerializerTest

testSerialize

0.002