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%	0.002
	RefiningValidatorTest	1	0	0	0	100%	0.023
	DatabaseValidatorTest	3	0	0	0	100%	0.015
	SmallMoleculeQuantificationUnitValidatorTest	1	0	0	0	100%	0.006
	SoftwareValidatorTest	1	0	0	0	100%	0.002
	QuantificationMethodValidatorTest	1	0	0	0	100%	0.002
	AssayValidatorTest	2	0	0	0	100%	0.002
	SmallMoleculeFeatureQuantificationUnitValidatorTest	1	0	0	0	100%	0.004
	SmallMoleculeIdConfidenceMeasureValidatorTest	1	0	0	0	100%	0.003
	CvValidatorTest	3	0	0	0	100%	0.029
	FieldValidatorTest	1	0	0	0	100%	0.002
	SpectraRefValidatorTest	11	0	0	0	100%	0.063
	StudyVariableValidatorTest	5	0	0	0	100%	0.049
	MzTabIdValidatorTest	1	0	0	0	100%	0.002
	MsRunValidatorTest	2	0	0	0	100%	0.005

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

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MTDLineParserTest	23	0	0	0	100%	0.037
	MTDLineValidateTest	6	0	0	0	100%	0.033

de.isas.mztab2.io.serialization

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	SerializersTest	43	0	0	0	100%	0.068
	SmallMoleculeEvidenceSerializerTest	1	0	0	0	100%	0.002
	SoftwareSerializerTest	1	0	0	0	100%	0.125
	StudyVariableSerializerTest	1	0	0	0	100%	0.34
	SmallMoleculeFeatureSerializerTest	1	0	0	0	100%	0.015
	ParameterConverterTest	4	0	0	0	100%	0.002
	InstrumentSerializerTest	1	0	0	0	100%	0.114
	CvSerializerTest	1	0	0	0	100%	0.094
	UriSerializerTest	1	0	0	0	100%	0.109
	SampleProcessingSerializerTest	1	0	0	0	100%	0.044
	DatabaseSerializerTest	1	0	0	0	100%	0.096
	UriConverterTest	1	0	0	0	100%	0.248
	MsRunSerializerTest	1	0	0	0	100%	0.198
	SmallMoleculeSummarySerializerTest	1	0	0	0	100%	0.042
	SampleSerializerTest	1	0	0	0	100%	0.376
	AssaySerializerTest	4	0	0	0	100%	0.216
	PublicationSerializerTest	1	0	0	0	100%	0.026
	ContactSerializerTest	1	0	0	0	100%	0.366
	MetadataSerializerTest	1	0	0	0	100%	0.117

de.isas.mztab2.io

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	MzTabWriterTest	16	0	0	0	100%	32.895
	MzTabValidatingWriterTest	2	0	0	0	100%	0.059
	MZTabFileParserExtTest	1	0	0	0	100%	0.012
	MZTabFileParserTest	13	0	0	0	100%	2.386

uk.ac.ebi.pride.jmztab2.model

	Class	Tests	Errors	Failures	Skipped	Success Rate	Time
	IOptColumnMappingBuilderTest	1	0	0	0	100%	0.002
	SectionTest	11	0	0	0	100%	0.015
	OptColumnMappingBuilderTest	7	0	0	0	100%	0.006
	MZTabColumnFactoryTest	1	0	0	0	100%	2.467

Test Cases

[Summary] [Package List] [Test Cases]

MzTabVersionValidatorTest

testValidateRefine

0.002

SerializersTest

	testWriteIndexedDoubles	0
	testAddLineWithParameters	0
	testUpperCaseCamelCaseMadnessToUnderscore	0
	testWriteAsStringArray_JsonGenerator_List	0
	testAddLine	0
	testPrintOptColumnMappingGlobal	0.01
	testWriteString_3args_1	0
	testWriteString_3args_2	0
	testGetElementName	0.001
	testAsMap	0
	testWriteNumber_3args_1	0
	testWriteNumber_3args_2	0
	testWriteNumber_3args_3	0
	testWriteNumber_3args_4	0
	testPrintAbundanceCoeffVarStudyVar	0
	testPrintOptColumnMappingIndexedElementCvParameter	0.027
	testAddSubElementParameter	0.003
	testWriteOptColumnMappings	0.002
	testCapitalCamelCaseToUnderscore	0
	testWriteNumber_JsonGenerator_Double	0
	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	0.001
	testCheckForNull	0
	testCamelCaseToUnderscoreLowerCase	0
	testAddLineWithProperty	0
	testAddSubElementStrings	0
	testGetPropertyNames	0
	testAddLineWithPropertyParameters	0
	testPrintAbundanceStudyVar	0
	testAddLineWithMetadataProperty	0.001
	testPrintAbundanceAssay	0
	testAddIndexedLine_5args_1	0
	testAddIndexedLine_5args_2	0.006
	testPrintOptColumnMappingIndexedElement	0
	testMixedCamelCaseToUnderscore	0.001
	testWriteAsNumberArray_3args_1	0
	testWriteAsNumberArray_3args_2	0

MzTabWriterTest

	testSmlNullEmptyHandling	0.067
	testWriteSmallMoleculeSummaryWithNullToTsvWithJackson	0.001
	testReadWriteRoundtripWithJacksonLipidomicsExample	0.364
	testWriteMzTabToTsvWithJacksonInvalidEncoding	0.001
	testUserParameterToString	0.001
	testLargeNumberOfFeaturesFromMTBLS263	12.844
	testWriteJsonMapper	0.011
	testWriteDefaultToString	0.002
	testReadWriteRoundtripWithJacksonLda2MouseLiver	17.054
	testWriteMetadataToTsvWithJackson	0.003
	testCvParameterToString	0
	testWriteMzTabToTsvWithJacksonForPath	0.007
	testReadWriteRoundtripWithJacksonLda2StdMix	2.438
	testWriteMzTabToTsvWithJackson	0.003
	testWriteSmallMoleculeFeaturesToTsvWithJackson	0
	testReadWriteRoundtripWithJacksonMTBLS263	0.097

MTDLineParserTest

	testQuantMethod	0.005
	testDatabase	0
	testPublication	0
	testMsRunWithInstrumentRef	0
	testMsRunLocationNull	0.001
	testUri	0.021
	testMzTabFileInfo	0.001
	testAssay	0
	testMsRun	0.001
	testIdConfidenceMeasure	0
	testCv	0
	testCreateMetadata	0.003
	testSmQuantUnit	0
	testContact	0.001
	testDerivatizationAgent	0
	testInstrument	0.001
	testSampleProcessing	0
	testCustom	0
	testStudyVariable	0.001
	testSample	0
	testSmFeatureQuantUnit	0.001
	testSmIdReliability	0
	testSoftware	0

SmallMoleculeEvidenceSerializerTest

testSerialize

0.002

RefiningValidatorTest

testValidateRefine

0.023

DatabaseValidatorTest

	testValidateRefineCustomDatabase	0.013
	testValidateRefineNullDatabase	0.001
	testValidateRefineNoDatabase	0.001

IOptColumnMappingBuilderTest

testBuild

0.002

SmallMoleculeQuantificationUnitValidatorTest

testValidateRefine

0.006

SoftwareSerializerTest

testSerialize

0.125

StudyVariableSerializerTest

testSerialize

0.34

SmallMoleculeFeatureSerializerTest

testSerialize

0.015

SectionTest

	testIsMetadata	0.013
	testGetLevel	0
	testIsHeader	0
	testFindSection_String	0
	testToHeaderSection	0
	testIsComment	0
	testGetPrefix	0
	testIsData	0
	testToDataSection	0
	testFindSection_int	0.001
	testValues	0

ParameterConverterTest

	testConvertUserParam	0.001
	testEscapeStringHandling	0
	testConvertWithValue	0.001
	testConvert	0

SoftwareValidatorTest

testValidateRefine

0.002

MzTabValidatingWriterTest

	testWrite_OutputStreamWriter_MzTab	0.044
	testWrite_Path_MzTab	0.015

InstrumentSerializerTest

testInstrument

0.114

ParsingPrimitivesTest

	testVersionRegexp	0.001
	testParserVersionRegexp	0.001
	testAdductRegexp	0
	testIntegerParsing	0
	testIdentificationReliability	0

QuantificationMethodValidatorTest

testValidateRefine

0.002

AssayValidatorTest

	testValidateRefineAssayHasMsRun	0.002
	testValidateRefineNullAssay	0

MTDLineValidateTest

	testPublication	0.03
	testInvalidColUnitLabel	0.001
	testMZTabDescription	0
	testIndexElement	0.001
	testDuplicationID	0.001
	testNullMsRun	0

SmallMoleculeFeatureQuantificationUnitValidatorTest

testValidateRefine

0.004

OptColumnMappingBuilderTest

	testForIndexedElement	0.001
	testWithCvParameterWithoutParamName	0.004
	testWithCvParameterWithoutCvAccession	0
	testWithParameterGlobal	0.001
	testWithCvParameterWithoutCvLabel	0
	testForGlobal	0
	testWithParameterIndexedElement	0

SmallMoleculeIdConfidenceMeasureValidatorTest

testValidateRefine

0.003

CvSerializerTest

testSerialize

0.094

MZTabFileParserExtTest

testStudyVariableAssayRefs

0.012

UriSerializerTest

testSerialize

0.109

CvValidatorTest

	testValidateCvWithEmptyElements	0.027
	testValidateCvWithNullElements	0
	testValidateRefineNullCv	0.001

SampleProcessingSerializerTest

testSerialize

0.044

MZTabColumnFactoryTest

testOptionalColumnsAndManyRows

2.467

DatabaseSerializerTest

testSerialize

0.096

FieldValidatorTest

testValidateLine

0.002

SpectraRefValidatorTest

	testValidateOfNullRunLocation	0.006
	testValidateOfEmptyRefList	0.001
	testValidatePatternSpectraRefIndex	0.003
	testValidateLineWithUnsupportedRefIdFormat	0.013
	testValidateLineWithOneSpectraRefThermo	0.001
	testValidatePatternSpectraRefScan	0.017
	testValidatePatternWiff	0
	testValidateLineWithOneSpectraRef	0
	testValidatePatternThermo	0.001
	testValidatePatternSpectraRefSpectrum	0
	testValidatePatternWaters	0.011

StudyVariableValidatorTest

	testValidateRefine	0.002
	testStudyVariableAssayRefs	0.001
	testTwoStudyVariableMultipleAssaysMissingNamesAndMissingDescription	0.039
	testTwoStudyVariableMultipleAssaysMultipleUndefinedStudyVariables	0.005
	testSingleStudyVariableNoNameMultipleAssays	0.002

UriConverterTest

testConvert

0.248

MsRunSerializerTest

testSerialize

0.198

MZTabFileParserTest

	testExamples[3: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.24
	testExamples[8: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	0.291
	testExamples[7: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.125
	testExamples[6: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.258
	testExamples[5: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.251
	testExamples[2: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	2.378
	testExamples[1: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	2.385
	testExamples[9: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.128
	testExamples[0: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.13
	testExamples[4: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.216
	testExamples[10: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.107
	testExamples[12: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.107
	testExamples[11: semantic validation of {0} on level {1} expecting {2} structural/logical errors and MzTab to be null: {3}]	1.107

SmallMoleculeSummarySerializerTest

testSerialize

0.042

MzTabIdValidatorTest

testValidateRefine

0.002

SampleSerializerTest

testSerialize

0.376

AssaySerializerTest

	testAssay	0.028
	testAssayWithCustom	0.087
	testAssayWithSampleRef	0.013
	testAssayWithMsRunRef	0.088

PublicationSerializerTest

testSerialize

0.026

ContactSerializerTest

testSerialize

0.366

MsRunValidatorTest

	testValidateRefineMissingLocation	0.002
	testValidateRefineMissingScanPolarity	0.003

MetadataSerializerTest

testSerialize

0.117