Deprecated API

Contents

• Interfaces
• Classes
• Exceptions
• Fields
• Methods

Interfaces

Interface	Description
ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService
ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelper
ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelper
ubic.gemma.persistence.service.common.auditAndSecurity.PersonDao	as Person is deprecated

Classes

Class	Description
ubic.gemma.core.apps.ArrayDesignProbeRenamerCli	renaming probes is not a good idea in general
ubic.gemma.core.apps.FactorValueMigratorCLI	this will be removed as soon as all the old-style characteristics are migrated
ubic.gemma.core.apps.MeshTermFetcherCli	should not be part of Gemma main code
ubic.gemma.core.apps.RNASeqBatchInfoCli	this should not be necessary and the regular batch population tool can be used instead.
ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARIIntermediateFileParser
ubic.gemma.core.association.phenotype.fileUpload.literatureEvidence.SFARILineInfo
ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants
ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl
ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelperImpl
ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl
ubic.gemma.core.config.PropertySourcesConfiguration	This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
ubic.gemma.core.config.Settings	This has been replaced with Spring-based configuration SettingsConfig and usage of Value to inject configurations. You can use @Value("${property}") as replacement.
ubic.gemma.core.loader.association.phenotype.CtdDatabaseImporterCli
ubic.gemma.core.loader.association.phenotype.DgaDatabaseImporterCli
ubic.gemma.core.loader.association.phenotype.EvidenceImporterAbstractCLI
ubic.gemma.core.loader.association.phenotype.ExternalDatabaseEvidenceImporterAbstractCLI
ubic.gemma.core.loader.association.phenotype.GwasDatabaseImporterCli
ubic.gemma.core.loader.association.phenotype.OmimDatabaseImporterCli
ubic.gemma.core.loader.association.phenotype.RgdDatabaseImporterCli
ubic.gemma.core.loader.association.phenotype.SfariDatabaseImporterCli
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser
ubic.gemma.model.association.phenotype.DataAnalysisEvidence
ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence
ubic.gemma.model.association.phenotype.ExperimentalEvidence
ubic.gemma.model.association.phenotype.GenericEvidence
ubic.gemma.model.association.phenotype.GenericExperiment
ubic.gemma.model.association.phenotype.LiteratureEvidence
ubic.gemma.model.association.phenotype.PhenotypeAssociation
ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication
ubic.gemma.model.association.phenotype.PhenotypeMappingType
ubic.gemma.model.common.auditAndSecurity.eventType.AutomatedAnnotationEvent	this event type was used by the auto-tagger, which has been removed. This event type has been kept so that the audit-trails can still properly display these events, but creation new events of this type should not occur.
ubic.gemma.model.common.auditAndSecurity.eventType.FailedBatchInformationMissingEvent	use BatchInformationMissingEvent
ubic.gemma.model.common.auditAndSecurity.Person	not needed
ubic.gemma.model.expression.experiment.FactorValueValueObject	aim towards using the FactorValueBasicValueObject. This one is confusing. Once usage of this type has been completely phased out, revise the BioMaterialValueObject and relevant DAOs and Services.
ubic.gemma.model.genome.gene.phenotype.valueObject.ExperimentalEvidenceValueObject
ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject
ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl	as Person is deprecated
ubic.gemma.persistence.service.expression.experiment.FactorValueMigratorServiceImpl
ubic.gemma.rest.PhenotypeWebService
ubic.gemma.rest.providers.EntityNotFoundExceptionMapper	Phenocarta is scheduled for removal
ubic.gemma.rest.serializers.FactorValueValueObjectSerializer
ubic.gemma.rest.util.args.FactorValueValueArg
ubic.gemma.web.controller.BaseFormController	SimpleFormController is deprecated, use annotations-based GET/POST mapping instead.
ubic.gemma.web.controller.common.GemmaClassicHomePageController
ubic.gemma.web.taglib.SimplePageContext
ubic.gemma.web.util.upload.CommonsMultipartFile

Exceptions

Exceptions	Description
ubic.gemma.core.association.phenotype.EntityNotFoundException

Fields

Field	Description
ubic.gemma.rest.util.args.FilterArgLexer.tokenNames	Use FilterArgLexer.VOCABULARY instead.
ubic.gemma.rest.util.args.FilterArgParser.tokenNames	Use FilterArgParser.VOCABULARY instead.

Methods

Method	Description
ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject.trim()	because this is too ad hoc and messy
ubic.gemma.core.context.SpringContextUtils.getApplicationContext(boolean, boolean, String[])	this method does not support producing Gemma Web contexts, please migrate existing code to use SpringContextUtils.getApplicationContext(String[], String...) instead.
ubic.gemma.core.ontology.OntologyService.findExperimentsCharacteristicTags(String, int, boolean)
ubic.gemma.core.search.SearchSource.searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>)	use SearchSource.searchBioSequence(SearchSettings) (SearchSettings)} instead
ubic.gemma.core.search.SearchSource.searchCompositeSequenceAndGene(SearchSettings)	use SearchSource.searchCompositeSequence(SearchSettings) instead
ubic.gemma.core.search.source.CompositeSearchSource.searchBioSequenceAndGene(SearchSettings, Collection<SearchResult<Gene>>)
ubic.gemma.core.search.source.CompositeSearchSource.searchCompositeSequenceAndGene(SearchSettings)
ubic.gemma.core.util.AbstractCLI.getBean(String, Class<T>)	Use Autowired to specify your dependencies, this is just a wrapper around the current BeanFactory.
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getBioAssaySetId()	use #getExperimentAnalyzedId() instead
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getFactorValuesUsed()	This was renamed for clarity.
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getSourceExperiment()	use #getSourceExperimentId() instead
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getDownregulatedCount()	use DiffExResultSetSummaryValueObject.getNumberOfDownregulatedProbes() instead.
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getUpregulatedCount()	use DiffExResultSetSummaryValueObject.getNumberOfUpregulatedProbes() instead.
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isEditable()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isOwnedByCurrentUser()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isPublic()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.isShared()
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setEditable(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setOwnedByCurrentUser(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setPublic(boolean)
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setShared(boolean)
ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject.getActionName()
ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType.getId()	you should never use this property, rely instead on the actual type via Object.getClass().
ubic.gemma.model.common.description.BibliographicReference.getAnnotatedAbstract()
ubic.gemma.model.common.description.BibliographicReference.getAnnotations()
ubic.gemma.model.common.description.BibliographicReference.setAnnotatedAbstract(String)
ubic.gemma.model.common.description.BibliographicReference.setAnnotations(Set<Characteristic>)
ubic.gemma.model.common.description.Characteristic.isMigratedToStatement()
ubic.gemma.model.common.description.Characteristic.setMigratedToStatement(boolean)
ubic.gemma.model.common.description.DatabaseEntry.getUri()
ubic.gemma.model.common.description.DatabaseEntry.setUri(String)
ubic.gemma.model.common.quantitationtype.QuantitationType.getIsMaskedPreferred()
ubic.gemma.model.common.quantitationtype.QuantitationType.setIsMaskedPreferred(boolean)
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getExpressionExperimentCount()	use ArrayDesignValueObject.getNumberOfExpressionExperiments() instead.
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getTaxonID()	use #getTaxonObject() instead
ubic.gemma.model.expression.biomaterial.BioMaterialValueObject.getFactorValueObjects()	use BioMaterialValueObject.getFactorValues()
ubic.gemma.model.expression.experiment.ExperimentalFactor.getAnnotations()
ubic.gemma.model.expression.experiment.ExperimentalFactor.setAnnotations(Set<Characteristic>)
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getBioAssayCount()	use #getNumberOfBioAssays() instead.
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getTaxonId()	use #getTaxonObject() instead
ubic.gemma.model.expression.experiment.FactorValue.getOldStyleCharacteristics()
ubic.gemma.model.expression.experiment.FactorValue.getValue()	use FactorValue.getMeasurement() or FactorValue.getCharacteristics() to retrieve the value.
ubic.gemma.model.expression.experiment.FactorValue.setOldStyleCharacteristics(Set<Characteristic>)
ubic.gemma.model.expression.experiment.FactorValue.setValue(String)
ubic.gemma.model.expression.experiment.FactorValueValueObject.getDescription()
ubic.gemma.model.expression.experiment.FactorValueValueObject.getFactorValue()
ubic.gemma.model.expression.experiment.FactorValueValueObject.getMeasurementObject()	use #getMeasurement() instead, this is only named like this for the Gemma Web frontend.
ubic.gemma.model.expression.experiment.Statement.getValue()	use Statement.getSubject() instead
ubic.gemma.model.expression.experiment.Statement.getValueUri()	use Statement.getSubjectUri() instead
ubic.gemma.model.expression.experiment.Statement.setValue(String)	use Statement.setSubject(String) instead
ubic.gemma.model.expression.experiment.Statement.setValueUri(String)	use Statement.setSubjectUri(String) instead
ubic.gemma.model.genome.gene.GeneProductValueObject.getNucleotideEnd()
ubic.gemma.model.genome.gene.GeneProductValueObject.setNucleotideEnd(Long)
ubic.gemma.model.genome.Gene.getPhenotypeAssociations()
ubic.gemma.model.genome.Gene.setPhenotypeAssociations(Set<PhenotypeAssociation>)
ubic.gemma.persistence.hibernate.TypedResultTransformer.transformList(List)	Use TypedResultTransformer.transformListTyped(List) instead.
ubic.gemma.persistence.service.AbstractService.ensureInSession(O)	avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate session
ubic.gemma.persistence.service.expression.bioAssayData.RawAndProcessedExpressionDataVectorServiceImpl.thaw(Collection<DesignElementDataVector>)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.loadWithOldStyleCharacteristics(Long, boolean)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.updateIgnoreAcl(FactorValue)	do not use this, it is only a workaround to make FV migration faster
ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)
ubic.gemma.persistence.service.expression.experiment.FactorValueDaoImpl.loadWithOldStyleCharacteristics(Long, boolean)
ubic.gemma.persistence.service.expression.experiment.FactorValueService.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueService.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)	do not use, this is only for migrating old-style characteristics to statements and will be removed
ubic.gemma.persistence.service.expression.experiment.FactorValueService.loadWithOldStyleCharacteristics(Long, boolean)	do not use this, it is only meant for the purpose of migrating old-style characteristics to statements
ubic.gemma.persistence.service.expression.experiment.FactorValueService.saveStatementIgnoreAcl(FactorValue, Statement)	do not use this, it is meant for FactorValue migration only
ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl.loadIdsWithNumberOfOldStyleCharacteristics(Set<Long>)
ubic.gemma.persistence.service.expression.experiment.FactorValueServiceImpl.loadWithOldStyleCharacteristics(Long, boolean)
ubic.gemma.persistence.service.genome.GeneDao.findByPhysicalLocation(PhysicalLocation)
ubic.gemma.persistence.util.Slice.add(O)
ubic.gemma.persistence.util.Slice.remove(Object)
ubic.gemma.rest.GeneWebService.getGeneEvidence(GeneArg<?>)
ubic.gemma.rest.RootWebService.ApiInfoValueObject.getDocs()
ubic.gemma.rest.TaxaWebService.findCandidateGenesInTaxon(TaxonArg<?>, StringArrayArg, Boolean)
ubic.gemma.rest.TaxaWebService.getGenesEvidenceInTaxon(TaxonArg<?>, GeneArg<?>)
ubic.gemma.rest.util.args.FilterArgLexer.getTokenNames()
ubic.gemma.rest.util.args.FilterArgParser.getTokenNames()
ubic.gemma.rest.util.args.GeneArgService.getGeneEvidence(GeneArg<?>, Taxon)
ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject.getCurrentGroup()	use UserValueObject.getGroups() instead
ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject.getRole()	use UserValueObject.getGroups() instead
ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController.addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>, Boolean)
ubic.gemma.web.controller.GeneralSearchControllerImpl.showForm(HttpServletRequest, HttpServletResponse, BindException)
ubic.gemma.web.controller.genome.gene.GeneSetController.addSessionGroups(Collection<SessionBoundGeneSetValueObject>, Boolean)
ubic.gemma.web.controller.genome.gene.GeneSetController.removeSessionGroups(Collection<SessionBoundGeneSetValueObject>)
ubic.gemma.web.controller.genome.gene.GeneSetController.updateSessionGroups(Collection<SessionBoundGeneSetValueObject>)
ubic.gemma.web.taglib.SimplePageContext.getExpressionEvaluator()
ubic.gemma.web.taglib.SimplePageContext.getVariableResolver()