Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Exceptions
• Deprecated Methods

Deprecated Interfaces

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

Deprecated Classes

Class and Description
ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignParser
ubic.gemma.core.apps.ArrayDesignProbeRenamerCli renaming probes is not a good idea in general
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.web.util.upload.CommonsMultipartFile
ubic.gemma.model.association.phenotype.DataAnalysisEvidence
ubic.gemma.model.association.phenotype.DifferentialExpressionEvidence
ubic.gemma.model.association.phenotype.DifferentialExpressionEvidenceImpl
ubic.gemma.model.association.phenotype.ExperimentalEvidence
ubic.gemma.web.services.rest.util.args.FactorValueValueArg
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.web.controller.common.GemmaClassicHomePageController
ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject
ubic.gemma.model.association.phenotype.GenericEvidence
ubic.gemma.model.association.phenotype.GenericExperiment
ubic.gemma.model.association.phenotype.LiteratureEvidence
ubic.gemma.core.apps.MeshTermFetcherCli should not be part of Gemma main code
ubic.gemma.model.common.auditAndSecurity.Person not needed
ubic.gemma.persistence.service.common.auditAndSecurity.PersonDaoImpl as Person is deprecated
ubic.gemma.model.association.phenotype.PhenotypeAssociation
ubic.gemma.core.association.phenotype.PhenotypeAssociationConstants
ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerServiceImpl
ubic.gemma.model.association.phenotype.PhenotypeAssociationPublication
ubic.gemma.model.association.phenotype.PhenotypeAssociationPublicationImpl
ubic.gemma.core.association.phenotype.PhenotypeAssoManagerServiceHelperImpl
ubic.gemma.core.association.phenotype.PhenotypeAssoOntologyHelperImpl
ubic.gemma.model.association.phenotype.PhenotypeMappingType
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.web.taglib.SimplePageContext

Deprecated Exceptions

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

Deprecated Methods

Method and Description
ubic.gemma.persistence.util.Slice.add(O)
ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController.addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject>, Boolean)
ubic.gemma.web.controller.genome.gene.GeneSetController.addSessionGroups(Collection<SessionBoundGeneSetValueObject>, Boolean)
ubic.gemma.persistence.service.genome.GeneDao.findByPhysicalLocation(PhysicalLocation)
ubic.gemma.persistence.service.expression.experiment.FactorValueService.findByValue(String)
ubic.gemma.persistence.service.expression.experiment.FactorValueDao.findByValue(String)
ubic.gemma.persistence.util.SpringContextUtil.getApplicationContext(boolean, boolean, String[]) this method does not support producing Gemma Web contexts, please migrate existing code to use SpringContextUtil.getApplicationContext(boolean, String...) instead.
ubic.gemma.persistence.util.Settings.getBaseUrl()
ubic.gemma.core.util.AbstractSpringAwareCLI.getBean(Class<T>)
ubic.gemma.core.util.AbstractSpringAwareCLI.getBean(String, Class<T>) Use Autowired to specify your dependencies, this is just a wrapper around the current BeanFactory.
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getBioAssayCount() use #getNumberOfBioAssays() instead.
ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject.getCurrentGroup() use UserValueObject.getGroups() instead
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getDownregulatedCount() use DiffExResultSetSummaryValueObject.getNumberOfDownregulatedProbes() instead.
ubic.gemma.web.taglib.SimplePageContext.getExpressionEvaluator()
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getExpressionExperimentCount() use ArrayDesignValueObject.getNumberOfExpressionExperiments() instead.
ubic.gemma.model.expression.biomaterial.BioMaterialValueObject.getFactorValueObjects() use BioMaterialValueObject.getFactorValues()
ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject.getFactorValuesUsed() This was renamed for clarity.
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.quantitationtype.QuantitationType.getIsMaskedPreferred()
ubic.gemma.model.genome.gene.GeneProductValueObject.getNucleotideEnd()
ubic.gemma.core.util.AbstractSpringAwareCLI.getPersisterHelper()
ubic.gemma.web.controller.common.auditAndSecurity.UserValueObject.getRole() use UserValueObject.getGroups() instead
ubic.gemma.persistence.util.Settings.getRootContext()
ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject.getTaxonId() use #getTaxonObject() instead
ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject.getTaxonID() use #getTaxonObject() instead
ubic.gemma.model.common.search.SearchSettings.getTermUri() use SearchSettings.getQuery() and SearchSettings.isTermQuery() instead.
ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.getUpregulatedCount() use DiffExResultSetSummaryValueObject.getNumberOfUpregulatedProbes() instead.
ubic.gemma.model.expression.experiment.FactorValue.getValue() use FactorValue.getCharacteristics() instead.
ubic.gemma.web.taglib.SimplePageContext.getVariableResolver()
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.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl.loadValueObjects(Collection<ExpressionExperimentSet>) extremely inefficient for EESets, use ExpressionExperimentSetDaoImpl.loadValueObjects(Collection, boolean) if possible.
ubic.gemma.persistence.util.Slice.remove(Object)
ubic.gemma.web.controller.genome.gene.GeneSetController.removeSessionGroups(Collection<SessionBoundGeneSetValueObject>)
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.SearchService.searchExpressionExperiments(String, Long) use SearchService.search(SearchSettings, Class) with Object.getClass() instead.
ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisSummaryValueObject.setEditable(boolean)
ubic.gemma.model.common.quantitationtype.QuantitationType.setIsMaskedPreferred(boolean)
ubic.gemma.model.genome.gene.GeneProductValueObject.setNucleotideEnd(Long)
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.search.SearchSettings.setTermUri(String) URI can be set with #setQuery(String) instead.
ubic.gemma.model.expression.experiment.FactorValue.setValue(String) use FactorValue.setCharacteristics(Set) ()} instead.
ubic.gemma.web.controller.GeneralSearchControllerImpl.showForm(HttpServletRequest, HttpServletResponse, BindException)
ubic.gemma.core.analysis.expression.coexpression.CoexpressionMetaValueObject.trim() because this is too ad hoc and messy
ubic.gemma.web.controller.genome.gene.GeneSetController.updateSessionGroups(Collection<SessionBoundGeneSetValueObject>)